From the Curator-in-Chief's Desk
April 14, 2020
The pandemic of SARS-CoV-2 is unprecedented at many levels. Many scientists are trying to find ways to apply their expertise to tackle the overwhelming issues from fundamental research to applications in diagnostics and treatment. The "sound bites" touting "everything you need to know about coronavirus" are everywhere, but there are few places to find actual research publications with data. Keeping up with the most relevant research publications is challenging for any investigator, but when hundreds of publications and preprints are appearing every week, the task can be overwhelming.
The registry is an effort by ASM to provide aggregated access to vetted fundamental research on SARS-CoV-2, and other relevant viruses. The registry experts will highlight relevant preprints and publications that appear every week. The goal is to ensure maximum acceleration of fundamental discoveries which are essential to optimize our chances of defeating the pandemic.
The registry is a resource for all scientists working to address the current challenge and be ready for future epidemics. For those scientists with a strong desire to contribute, but with little or no experience with viruses in general and SARS-CoV-2 in particular, this registry will provide reliable and up-to-date scientific information in selected areas, vetted by experts.
We welcome your feedback and ideas to make the Registry a useful resource for the scientific community to fight against the pandemic.
Biweekly Commentary Letters
Oct. 7, 2022
By John J. Dennehy, Ph.D., professor at Queens College of the City University of New York, N.Y. Dennehy is a curator of the registry.
"Persistence of somatic symptoms after COVID-19 in the Netherlands: an observational cohort study" by Ballering, A., et al., published in The Lancet on Aug. 6, 2022.
The phenomenon of post-acute sequelae of COVID-19 (PASC, also known as long COVID-19) remains an enduring mystery to researchers and clinicians. While there is no formal definition of PASC, PASC most commonly refers to COVID-19 symptoms persisting 4 or more weeks after a primary SARS-CoV-2 infection has resolved. Unravelling the PASC enigma has been confounded by a lack of consensus on the symptoms attributable to PASC, the absence of an easily quantifiable disease biomarker and a lack of clarity regarding the number of individuals affected by PASC. As the study’s authors note, many of the symptoms of PASC, such as headaches, fatigue and muscle pain, were common in the general population before the COVID-19 pandemic and may have worsened during the pandemic due to anxiety-induced stress. Additionally, "some of the symptoms reported after COVID-19 might already have been present before COVID-19 and might even reflect a pre-existing susceptibility to COVID-19 itself, rather than being a consequence of SARS-CoV-2 infection."
To address these concerns, the Lifelines Corona Research Initiative was used to survey 76, 422 individuals in the north of Netherlands. From these participants, persistent symptoms in 4,231 individuals 90-150 days after COVID-19 diagnosis were matched to 8,462 controls. The study’s results showed that 381 (21.4%) of 1,782 COVID-19-positive participants versus 361 (8.7%) of 4,130 COVID-19-negative controls had at least 1 persistent symptom substantially increased to at least moderate severity at 90–150 days after COVID-19 diagnosis or matched timepoint. The survey results show that individuals infected with COVID-19 are significantly more likely to experience symptoms than individuals in the general population, and that these symptoms are attributable to prior COVID-19 infection. This outcome suggests that about 1 of 8 patients with COVID-19 will experience PASC after their COVID-19 infection has resolved. Additionally, this study will help define the core symptoms of PASC to assist researchers in identifying the biological causes of the phenomenon.
Sept. 9, 2022
By Tom Gallagher, Ph.D., professor of microbiology and immunology, Loyola University Chicago, Maywood, Il. Gallagher is a curator of the registry.
"Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-CoV-2 virus-like particles" by Syed, A., et al., published in The Proceedings of the National Academy of Sciences on July 19, 2022.
Noninfectious surrogates of SARS-CoV-2 offer ways to evaluate virus biology in biosafety level 2 (BSL2) laboratories. Amongst these mimics of the authentic virus are SARS-CoV-2 virus-like particles (SC2-VLPs). Syed, A., et al. developed a system to produce SC2-VLPs that can reflect aspects of authentic virus assembly and entry. The system produces secreted SC2-VLPs that include the 3 membrane proteins of the virus (S, E and M) along with an internal N-RNA ribonucleoprotein complex. The secreted SC2-VLPs transduce RNAs into target cells, with accumulation of RNA translation products serving to measure transduction efficiencies. The SC2-VLP system can be used to dissect SARS-CoV-2 assembly, egress and entry without requiring BSL3 research infrastructures.
SARS-CoV-2 evolution has introduced changes into the 4 structural proteins. To determine whether these alterations might be adaptive, facilitating assembly and/or entry, the authors compared ancestral (B.1) with more recent Delta and Omicron SC2-VLP systems. Changes in S and N proteins, but not E and M proteins, were associated with enhanced transduction. It is worth noting that the VLP system can systematically evaluate the functional impacts of adaptive mutations in all 4 CoV structural proteins. Other commonly used rhabdo- and lenti-viral transduction systems are limited to assessing the consequences of only the S protein variations.
The SC2-VLP transduction process offers a straightforward platform to assess neutralization by antibodies and other entry-blocking antivirals. Syed, A., et al. demonstrated that VLP neutralization titers matched those obtained through more cumbersome assays using authentic SARS-CoV-2, and then went on to demonstrate that both vaccinee sera and convalescent sera from COVID19 survivors showed significantly reduced neutralization of omicron VLPs. These findings align with several other reports that pressed the development of updated bivalent vaccines targeting both ancestral and current Omicron lineages.
The SC2-VLP system provides ways to assess the relative fitness of SARS-CoV-2 variants in the fundamental assembly and entry steps of virus infection. Concurrently, the VLP system readily reveals the virus variations conferring escape from antibody neutralization. Several selective pressures driving SARS-CoV-2 variations can be effectively dissected using the SC2-VLP system.
Aug. 26, 2022
By Linda Saif, Ph.D., distinguished university professor, Center for Food Animal Health, Ohio Agricultural Research and Development Center, Departments of Animal Sciences and Veterinary Preventive Medicine; co-director, Viruses and Emerging Pathogens Program, The Infectious Diseases Institute, The Ohio State University. Saif is a curator of the ASM registry.
"Antibody and Memory B-Cell Immunity in a Heterogeneously SARS-CoV-2-Infected and -Vaccinated Population" by Bednaski, E., et al., published in mBio on June 23, 2022.
Multiple SARS-CoV-2 vaccines are deployed globally, yet most studies have focused on single vaccines distributed in high-income countries. Consequently, there are few direct comparisons of B cell immunity to heterogenous vaccines in recipients with/without SARS-CoV-2 infections in the same population. This is an important study of antibody and memory B-cell immune responses in Mexico where 5 different SARS-CoV-2 vaccines [BNT162b2 mRNA vaccine (Pfizer), adenovirus-based vaccines-- ChAdOx1-S (AstraZeneca), Sputnik V (Gamaleya) and Ad5-nCoV (CanSino), and inactivated CoronaVac (Sinovac)] were used in the population and SARS-CoV-2 incidence is high. The authors measured spike-binding (stabilized prefusion S protein) and neutralizing antibody titers (nAb to original and emergent SARS-CoV-2 variants including Omicron) as well as the numbers of spike/RBD-specific memory B cells in 197 recipients of the 5 vaccines.
Notably each vaccine alone elicited variable levels of B cell immunity in individuals, with highest nAbs in BNT162b2 vaccinees and lowest in CoronaVac recipients against the variants tested; most had undetectable nAbs to Omicron. Importantly SARS-CoV-2 infections pre-vaccination across all 5 vaccine groups, potentiated and broadened B cell responses including nAbs to Omicron and SARS-CoV.
The authors concluded that the increased breadth of the heterogenous B cell responses in the infected/vaccinated groups may contribute to broader population immunity to SARS-CoV-2. Because they observed high correlations among the B cell/antibody assays, they further suggested that binding antibodies to the prefusion Spike could be a surrogate for nAb assays in resource poor countries to predict likelihood of infections in a population or in individuals, to target booster shots or treatments.
Limitations of this study include the relatively low numbers of vaccine recipients and convalescent sera (n=197 vaccinees distributed across the 5 vaccine groups), especially post-vaccine/infection cohorts (n=11) and no infected, unvaccinated cohort (if available). Also sera were collected at varying times post infection/vaccination. Future studies include characterization of cellular immunity that is more cross-reactive to the variants. This work underscores the need to examine the spectrum of immune responses to SARS-CoV-2 vaccines and variants in low/middle-income countries where infections are widespread and heterogeneous vaccines are used.
July 29, 2022
By Zhengli Shi, Ph.D., senior scientist, Wuhan Institute of Virology, Chinese Academy of Sciences. Shi is a curator of the registry.
"Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4, and BA.5" by Wang, Q., et al., published in Nature on July 5, 2022.
In the article first posted on bioRxiv and later published in Nature, Wang Q., et al. performed a systematic antigenic analysis of the recent surging stains derived from Omicron, BA.2.12.1 and BA.4/5. They assessed the sensitivity of each pseudovirus to neutralization by a panel of 21 monoclonal antibodies (mAbs) directed to known neutralizing epitopes on the viral spike receptor-binding domain (RBD) or N-terminal domain (NTD) and found that most of the mAbs lost neutralizing activity completely or partially against these subvariants. Similar results were observed when authors used the polyclonal sera from the persons who received three shots of mRNA vaccine, mRNA vaccine before or after non-Omicron infection, or either BA.1 or BA,2 breakthrough infection after vaccine. However, BA.4/5 is substantially more neutralization resistant and more likely to lead to vaccine breakthrough. By using point mutations, the authors confirmed that the substitutions at L452 confer largely to classes 2 and 3 mAbs targeting the RBD. F486V broadly impaired the neutralizing activity of several class 1 and 2 RBD mAbs. The authors also measured the binding affinity of spike proteins of the subvariants to dimeric human ACE2. In addition to the neutralization antibody escape, these subvariants gain a slightly higher affinity for the receptor than an ancestral strain carrying the D614G in spike. The results in the paper provide important information in understanding the key residues in spikes which affect the neutralization activity and vaccine efficacy and call sustainable surveillance on SARS-CoV-2 evolution in the future.
July 1, 2022
By Yi-Wei Tang, M.D., Ph.D., F(AAM), FIDSA, chief medical officer, Danaher Diagnostic Platform and Cepheid (China), Shanghai. Tang is a curator of the registry.
"A Single-Round Infection Fluorescent SARS-CoV-2 Neutralization Test for COVID-19 Serological Testing at a Biosafety Level-2 Laboratory" by Zou, J. et al., published in Viruses on June 2, 2022.
We are in the third year in the fight against the pandemic COVID-19. Multiple studies have shown that neutralizing antibodies, generated in our body following natural infection or vaccination, are correlated with protection against subsequent infection or reinfection with COVID-19. The gold standard assay for determining neutralizing antibodies is the conventional plaque reduction neutralization test (PRNT) which remains labor-intensive, time-consuming and, critically, requires infectious SARS-CoV-2 virus and biosafety level-3 (BSL-3) facilities. Numerous alternative methods have been explored to provide ideally quick, simple and safe neutralizing antibody detection methods.
A group of scientists from University of Texas Medical Branch developed a novel single-round infection ﬂuorescent SARS-CoV-2 virus (SFV) that can be safely used at the BSL-2 level for high-throughput neutralization and antiviral testing. In this study, the authors evaluated the performance characteristics of the SFV-based neutralization test (SFVNT) in comparison to the gold standard PRNT using 80 PRNT-positive and 92 PRNT-negative clinical serum or plasma specimens. The SFVNT exhibited 100% sensitivity and speciﬁcity compared to the PRNT. Furthermore, the neutralizing titers generated by the SFVNT and PRNT are highly correlated, with R2 of 0.903 (p < 0.0001). The linear regression lines ﬁt the titer values with R2 values within the ranges of 0.990 to 0.999 (p < 0.001), indicating a satisfactory titer linearity of the SFVNT assay. The differences in the neutralization titers performed on 4 negative and 4 positive samples in duplicate in 3 different assays by 2 different operators on different days were not statistically significant (p > 0.05) indicating that the SFVNT assay achieved high intra- and inter-assay precision.
In comparison to the other surrogate system, such as SARS-CoV-2 pseudovirus (that expresses and presents SARS-CoV-2 spike proteins on the surface of a non-coronavirus), to measure neutralizing antibodies at BSL-2 laboratories, the SFVNT assay developed and validated in the study had one unique advantage: SFV not only has the feature of being suitable for use at BSL-2 facilities but also likely reﬂects the "natural" status of spike proteins appearing on the authentic SARS-CoV-2 virus, because SFV virions are egressed and matured with all the structural components through an extract mechanism as an authentic SARS-CoV-2 infection. Therefore, the SFVNT may precisely mimic an authentic SARS-CoV-2 infection to measure neutralizing antibodies.
Compared with the conventional PRNT assay, the SFVNT shortened the turnaround time by several days. As the assay can be performed in 96-well or even 384-well microtiter plates, it has the potential to increase the testing capacity to high throughput. With implementation of automated workstations with a liquid handling robot, the SFVNT assay can become an automated, large-scale testing platform for COVID-19 patients or vaccinated people in general lab settings at a prompt manner.
June 17, 2022
By Vito Martella, D.V.M., Ph.D., professor of veterinary medicine, University Aldo Moro of Bari, Italy. Martella is a curator of the registry.
"Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages" by Tegally, H., et al., published on medRxiv on May 2, 2022.
Unprecedented efforts have been established worldwide to sequence SARS-CoV-2 strains, to monitor virus diversification. Following its emergence in Nov. 2019, a succession of SARS-CoV-2 variants have appeared, rapidly outcompeting the preceding strain and spreading globally. The most recent variant of concern, Omicron, appeared in late 2021. In a collaborative study from South Africa, the authors monitored the emergence of 2 lineages, BA.4 and BA.5, of the Omicron variant. Lineage BA.4 and BA.5 rapidly replaced the former lineages (BA.1, BA.2 and BA.3) and accounted for more than 50% of sequenced cases in South Africa from the first week of April 2022 onwards.
The spike proteins of BA.4 and BA.5 are identical, and comparable to BA.2 except for the addition of 69-70del, L452R, F486V and the wild type amino acid at Q493. Although BA.4 and BA.5 have identical mutational patterns in the 5’ genome region (from ORF1ab to Envelope), yet exhibit genetic divergence in the 3’ region, suggesting that BA.4 and BA.5 may be related by a recombination event. Recombination has been already observed for SARS-CoV-2 between Delta and Omicron variants or between Omicron lineages BA.1 and BA.2 and this phenomenon is able to increase dramatically virus diversity. Using a multinomial logistic regression model, BA.4 and BA.5 showed growth advantages of 0.08 (95% CI: 0.07 - 0.09) and 0.12 (95% CI: 0.09 - 0.15) per day respectively over BA.2 in South Africa population. Understanding if SARS-CoV-2 variants/lineages possess modified biological properties, in terms of antigenic profile, virulence and transmissibility, is pivotal to re-shape our response to COVID-19 pandemic.
May 27, 2022
By Catherine J. Pachuk, Ph.D., Chief Science Officer, Marizyme, Inc., Jupiter, Fla. Pachuk is a curator of the registry.
Early safety and efficacy results of an on-going Phase 3 trial for COVIFENZ were recently reported by Hager, K., et al. The study enrolled 24,141 participants from 85 centers across North/South America and the U.K. between March 15 and Sept. 2, 2021, during which time Delta and Gamma variants predominated. COVIFENZ was administered intramuscularly as 2 doses given 21 days apart. Primary vaccine efficacy (VE) was calculated after a median safety follow-up of at least 2 months. VE was 69.5% against any symptomatic infection and 78.8% against moderate-severe disease. No severe cases occurred in the vaccine group. Viral load at time of diagnosis was found to be more than 100-fold lower in the vaccine group compared to placebo suggesting an additional vaccine benefit of reducing infection transmission. No safety concerns were identified. While some COVID-19 vaccines tested earlier in the pandemic reported higher VE (>90%), comparisons to these effectiveness scores must be made with caution since VEs of earlier vaccines were measured against original strain virus while VE for COVIFENZ was measured primarily against more transmissible variant strains.
Given that COVIFENZ is a plant-based, non-mRNA vaccine containing an historically safe adjuvant, availability of COVIFENZ may lead to increased vaccination rates by providing an acceptable vaccine alternative for some percentage of the vaccine-hesitant group. Furthermore, with at least 6 months stability at 2-8 C, COVIFENZ is suitable for distribution within third-world countries. COVIFENZ is an important new COVID-19 vaccine that is also first in its class. While currently only available in Canada, based on its safety and efficacy, stability profile and unique characteristics, COVIFENZ has the potential to become a more significant vaccine globally.
May 13, 2022
By Jonathan D. Dinman, Ph.D., Professor of Cell Biology and Molecular Genetics, University of Maryland, College Park, Md. Dinman is a curator of the registry.
"Imatinib inhibits SARS-CoV-2 infection by an off-target-mechanism" by Strobelt et al., published in Scientific Reports on April 6, 2022.
COVID-19 is not going to "magically disappear," and indeed, the odds are that other coronaviruses will make the interspecies jump to humans. While effective vaccines were developed and deployed with remarkable alacrity, a variety of economic and sociological factors inhibit their widespread adoption. In contrast, people tend to be more receptive to the idea of taking a pill. Fortunately, the large investments made in fighting the HIV/AIDS epidemic defined critical chokepoints in viral lifecycles that are being used as foundational strategies for pharmacologic intervention. These include targeting the viral replication machinery with nucleoside analogs and protease inhibitors; both strategies have been successfully applied to SARS-CoV-2, e.g. Remdesivir, Molnupiravir and Paxlovid. Additional targets include, inhibiting viral entry and unpackaging, ribosomal frameshifting, viral assembly and exit from the cell.
Imatinib is benzamide whose inhibitory effect on the Ableson tyrosine-kinases Abl1 and Abl2 is exploited to treat a number of cancers. Prior studies showed that imatinib inhibited the early stages of SARS-CoV-1 and MERS-CoV infection. The current study showed that imatinib also inhibits SARS-CoV-2 infection, but only when administered before infection, suggesting that it inhibits viral entry. That it does so independently of Abl1 or Abl2 suggested that it directly targets the viral Spike protein, which was confirmed using a novel cellular thermal shift assay. These findings suggest that imatinib binds to Spike, preventing conformational rearrangements essential for viral entry into cells. With the caveats that antiviral activity was only demonstrated in cell culture, and viral inhibition was limited to approximately 2-orders of magnitude at micromolar concentrations, the importance of this work is that it demonstrates proof-of-principle for the idea that viral entry inhibitors can be developed to treat COVID-19. This is also consistent with HIV-1 viral entry inhibitors, including maraviroc (Selzentry), ibalizumab–uiyk (Trogarzo) and fostemavir (Rukobia). These findings give further support for targeting other critical viral lifecycle chokepoints for small molecule antiviral interventions. Given the effects of changes in climate and human migration on viral dissemination, it will be prudent to develop a broad arsenal of antiviral drugs that target multiple stages of virus lifecycles.
April 29, 2022
By Richard L. Hodinka, Ph.D., Professor Emeritus, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania. Hodinka is a curator of the registry.
"A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance," by Patchsung, M. et al., published as a preprint on medRxiv on March 18, 2022.
Advances in the development, validation, and availability of rapid and easy-to-use point-of-care (POC) molecular diagnostic assays for the detection of SARS-CoV-2 infection have impacted our ability to track and manage the current COVID-19 pandemic more effectively. Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic assays have shown promise in this regard. However, the technology is complex and there is a need for additional technical modifications to enhance sensitivity, incorporate multiplexed detection, and to further streamline and simplify the assay design for widespread use in a decentralized setting.
The article by Patchsung and colleagues describes the development and evaluation of a robust multiplexed CRISPR-based assay using isothermal reverse-transcription recombinase polymerase amplification (RT-RPA) of SARS-CoV-2 N and S genes and LwaCas13a and PsmCas13b enzymes from Leptotrichia wadei and Provotella spp., respectively, to simultaneously detect SARS-CoV-2 infection and identify the causative SARS-CoV-2 variants of concern (VOC), including Delta (B.1.617.2) and Omicron (B.1.1.529) VOCs. The authors extensively optimized assay components and reaction conditions to improve the efficiency of the multiplexed RT-RPA and CRISPR reactions to provide a test sensitivity and specificity comparable to RT-qPCR. The usability and portability of the platform was also enhanced allowing for convenient use and storage of premixed and lyophilized reagents; performance of the multiplexed RT-RPA and CAS13-based reactions in a single tube; results that can be directly read by eye with a low-cost light source and enzymes that can be locally manufactured, formulated, and distributed. The latter point was stressed by the authors as being of prime importance for low- and middle-income countries where disease detection and variant surveillance are critically needed, but commercial reagents, kits, and instruments are not always readily available.
The described platform may be of high practical value, particularly in settings where resources are limited. It has several key attributes suitable for POC use, including being sensitive and specific, user-friendly, rapid and robust, equipment-light, and readily deliverable to end-users. The assay also has the capacity to be expanded to detect other pathogens of significance and to accommodate built-in internal controls. Ultimately, time will tell whether the technology can be conveniently packaged and mass-produced as an affordable POC device. Additionally, independent clinical trials will be needed to further demonstrate its full diagnostic and surveillance potential.
April 8, 2022
By Sonia Navas-Martin, Ph.D., professor of microbiology and immunology, Drexel University College of Medicine, Philadelphia, Pa. Navas-Martin is a curator of the registry.
Developing broadly protective SARS-CoV-2 vaccines against variants of concern (VOCs) and potential new zoonotic coronaviruses is a top health priority. Glycosylation of viral entry proteins, including SARS-CoV-2 spike (S) protein, is an important posttranscriptional modification that influences protein integrity, viral infectivity, and immune responses. Of note, N-glycosite mutations have not been observed in any SARS-CoV-2 VOC. The impact of glycosylation of the SARS-CoV-2 spike in vaccine effectiveness remains largely unexplored.
In this study, Huang and colleagues investigate whether a glycoengineered Mono-GlcNAc-decorated S protein (SMG) elicits enhanced protective responses. Using a comprehensive experimental approach combining in vitro studies and animal models of SARS-CoV-2 infection, this study i) identifies the glycan profile of S protein in several cell types; ii) investigates the impact of glycosylation in SARS-CoV-2 pseudovirus infectivity; iii) isolates a novel broadly neutralizing antibody from mice immunized with SMG vaccine; and iv) demonstrates that a SMG vaccine provides superior humoral and cellular immune responses.
Limitations of this study include a lack of analysis on how S protein glycans may affect antigen presentation and B cell repertoires. It is promising that the SMG vaccine generated more S protein-specific B cells and more potent humoral and cellular immune responses.
In sum, this work demonstrates that removal of glycan shields from the SARS-CoV-2 Spike protein elicits enhanced immune protection against, Alpha, Gamma and Delta VOCs in hamster and mouse SARS-CoV-2 infection models. The significance of this discovery for vaccine optimization in humans needs to be confirmed in future clinical trials.
March 25, 2022
By John J. Dennehy, Ph.D., professor at Queens College of the City University of New York, N.Y. Dennehy is a curator of the registry.
"Rapid increase in Omicron infections in England during December 2021: REACT-1 study" published in Science on Feb. 8, 2022.
In Dec. 2021, the Omicron variant of concern rapidly replaced the previously dominant Delta variant of concern across the world. Because the REal-time Assessment of Community Transmission–1 (REACT-1) study was collecting self-administered throat and nose swabs from randomly selected English individuals ages 5 years and up, it was well-positioned to document this evolutionary transition. Between Nov. 23 to Dec. 14, 2021, 97,089 swabs were tested for the presence of SARS-CoV-2, with 1,192 testing positive. Large decreases in case incidence were reported for vaccinated older children (12-17 years) and adults aged 65 years or older, relative to unvaccinated younger children (5-11 years). Additionally, boosted adults were 3 to 4 times less likely to be infected than adults who had had 2 doses. These results illustrate the power of vaccination to reduce COVID-19 infections.
The first REact-1 sample positive for Omicron was collected on Dec. 3, 2021, and the proportion of samples positive for Omicron increased rapidly from Dec. 6, 2021 onwards. The authors estimated that Omicron increased from 10% to 90% of all daily infections in approximately 9 days. This increase was approximately 3.5 times faster than the 31 days needed for Delta to increase from 10% to 90% of all infections when it replaced variant of concern Alpha. Vaccine effectiveness was believed to be lower against Omicron than for Delta, consistent with other studies showing more breakthrough infections by Omicron than by other variants.
March 4, 2022
By Zhengli Shi, Ph.D., Senior Scientist, Wuhan Institute of Virology, Chinese Academy of Sciences. Shi is a curator of the registry.
"SARS-CoV-2 prolonged infection during advanced HIV disease evolves extensive immune escape" by Cele, S., et al., published in Cell Host & Microbe on Feb. 9 2022.
During the COVID-19 pandemic, multiple SARS-CoV-2 variants emerged, and some of them became more transmissible and show extensive escape from neutralizing immunity conferred by previous infections and vaccines developed with the ancestry strain. Although the biological features and immune escape mechanism of the mutations of the SARS-CoV-2 variants have been extensively analyzed, the driving force behind the mutations is not completely understood.
The article by Cele S., et al. examined a SARS-CoV-2 infection persisting over 6 months in a person with advanced HIV disease in South Africa, starting as ancestral lineage B.1.1.273. The authors longitudinally tracked the evolved virus up to day 190 post-diagnosis. Viral RNA was detected at high copy numbers, and virus was isolated throughout this period. The genome sequences showed that the SARS-CoV-2 virus continued evolving in the patient, particularly in the spike protein. Mutations were clustered in the N-terminal domain and the receptor binding domain of spike protein, including T95I, R190K, K417T, F490S, N501Y and D769Y in the day-190 viral isolate. These substitutions are shared with Beta, Gamma, Lambda or Omicron variant at the corresponding residues. Serum neutralization assay indicated that the evolved virus shows greatest escape from Beta-, Delta- and BNT162b2 vaccine-elicited antibodies. The results in this paper provide one explanation of SARS-CoV-2 variant emergence during the transmission, e.g. SARS-CoV-2 likely tends to evolve rapidly in immunocompromised persons. More work should be focused the SARS-CoV-2 surveillance in the immunocompromised patients, as well as the long-term, persistent-infection patients.
Feb. 18, 2022
By Yi-Wei Tang, M.D., Ph.D., F(AAM), FIDSA, Chief Medical Officer, Danaher Diagnostic Platform and Cepheid (China), Shanghai. Tang is a curator of the registry.
"Serological Markers of SARS-CoV-2 Reinfection" by Siddiqui, S., et al., published in mBio on Jan. 25, 2022.
Since the first case was identified, COVID-19 has been impacting public health and attracting attention from researchers worldwide. In 2020, the first observed cases of SARS-CoV-2 reinfection were reported in Hong Kong, and a recent meta-analysis showed that the pooled estimation of reinfection among recovered patients was 0.3% with a high heterogeneity among studies. To better define SARS-CoV-2 reinfection, the U.S. Centers for Disease Control and Prevention has proposed to use both (i) investigative criteria for identifying cases with a higher index of suspicion for reinfection and (ii) genomic testing of paired specimens.
On the other hand, determining the immunologic markers of authentic SARS-CoV-2 reinfection, with both novel and recirculating strains, as well as the immunologic mechanisms associated with disease attenuation, is necessary for informed public health decisions regarding social distancing, societal reopening, vaccine development, and vaccine deployment. In this study, Siddiqui and colleagues from the Massachusetts Institute of Technology identified a minimal set of SARS-CoV-2-specific markers of reinfection with robust discriminatory cross-validating power across both primates and humans. Using a nonhuman primate model of controlled SARS-CoV-2 reexposure, the authors deeply probed the humoral immune response following rechallenge with various doses of viral inocula. Several virus-specific humoral biomarkers of reinfection were observed, with significant increases in antibody titer and function upon rechallenge across a range of humoral features, including IgG1 to the receptor binding domain (RBD)of the spike protein (S) of SARS-CoV-2, IgG3 to the nucleocapsid protein (N), and FcγR2A receptor binding to anti-RBD antibodies. A striking evolution of S, RBD, S2, and N-specific immunity was observed across all animals, most dramatically in IgG1 titer to spike, RBD, and nucleocapsid and FcγR2A receptor binding to S1, spike, and RBD, with mean increases of 31.3-fold and 7.6-fold, respectively, upon reinfection. These features not only differentiated primary infection from reexposure and reinfection in monkeys but also were recapitulated in a sequencing-confirmed reinfection patient and in a cohort of putatively reinfected humans that evolved a PCR-positive test despite preexisting seropositivity. As such, this cross-species analysis using a controlled primate model and human cohorts reveals increases in antibody titers as promising cross-validated serological markers of reinfection and reexposure. Thus, simple serological analytes may support the identification of SARS-CoV-2 reinfections at a global level.
The serologic markers described in the study appeared to perform well in reinfections with different and dominant variants of concerns, e.g., Omicron reinfection following Delta SARS-CoV-2 infection. We look forward to seeing more data, both in primates and humans, on reinfection of genetically close related SARS-CoV-2 variants or "genotypes." A good example would be Omicron BA.2 reinfection following Omicron BA.1 infection or vice versa.
Feb. 4, 2022
By Tom Gallagher, Ph.D., professor of microbiology and immunology, Loyola University Chicago, Maywood, Il. Gallagher is a curator of the registry.
"The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism" by Willett, B. et al., published on medRxiv on Jan. 3, 2022.
Concomitant with the predictable findings that the amino acid substitutions and deletions in Omicron spikes alter antibody epitopes and allow for immune escape, Willett. B., et al. and other groups made separate discoveries relating to a distinctive omicron spike-directed cell entry process. While previously characterized SARS-CoV-2 spike proteins are rapidly-acting membrane fusogens, promptly directing protease-triggered virus entry at or near plasma membranes, Omicron spikes are less responsive to cell-surface serine proteases and therefore these viruses are first endocytosed and then proteolytically activated for fusion-entry by endosomal cathepsins. Consistently, the Omicron spikes are less potent than other VOC spikes in mediating the cell-surface fusions that generate pathological syncytia.
Jan. 21, 2022
By Shan-Lu Liu, M.D., Ph.D., professor, Department of Veterinary Biosciences, co-director, Viruses and Emerging Pathogens Program, The Infectious Diseases Institute, The Ohio State University; and Linda Saif, Ph.D., Distinguished University professor, Center for Food Animal Health, Ohio Agricultural Research and Development Center, Department of Animal Sciences and Department of Veterinary Preventive Medicine, co-director, Viruses and Emerging Pathogens Program, The Infectious Diseases Institute, The Ohio State University. Saif is a curator of the registry.
"Considerable escape of SARS-CoV-2 Omicron to antibody neutralization" by Planas, D., et al., published in Nature on Dec. 23, 2021.
The Omicron variant has caused significant public health concern worldwide, especially regarding current vaccine efficacy. Omicron contains over 55 mutations, with more than 32 in the spike and 15 in the receptor-binding domain, the latter containing the key determinants to induce neutralizing antibodies (NAbs). It is therefore critical to assess if vaccine or infection-induced NAbs to SARS-CoV-2 protect against the highly mutated Omicron variant of concern (VOC).
Dec. 17, 2021By Vito Martella, DVM, Ph.D., professor of veterinary medicine, University Aldo Moro of Bari, Italy. Martella is a curator of the registry.
"Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer" by Kuchipudi, S., et al. published on bioRxiv on Nov. 6, 2021.
As soon as the COVID-19 pandemic started in early 2020, SARS-CoV-2 has been identified repeatedly in pets, in captive animals (i.e. large felids and nonhuman primates) and in mink farms, due to contact with and or exposure to infected persons. Also, experimental infections have identified several susceptible animal species. A major concern for researchers and health authorities, however, was also the possibility of transmission of SARS-CoV-2 to free-living animals, and eventual formation of a stable virus reservoir able to generate novel, non-predictable epidemiological pathways.
White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. By screening retropharyngeal lymph node samples collected from free-living and captive deer in Iowa from April 2020 through Dec. 2020, SARS-CoV-2 RNA was detected in 94 of the 283 deer (33.2%) samples. Whole genome sequencing identified 12 SARS-CoV-2 lineages, with B.1.2 and B.1.311 accounting for about 75% of the sequenced strains. These findings indicate that the massive viral pressure generated by replication of SARS-CoV-2 in human population has given rise in a short time span to multiple human-to-animal spillover events, eventually followed by deer-to-deer transmission. This is 1 of the worst-case scenarios and has surely important implications for the ecology of SARS-CoV-2, in terms of persistence in the ecosystem and potential for spillover to other animals and spillback into humans. These findings highlight the need for a proactive "One Health" approach in the study of SARS-CoV-2.
Dec. 3, 2021
By Frederick G. Hayden, M.D., Stuart S. Richardson professor emeritus of clinical virology and professor emeritus of medicine in the Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Va. Hayden is a curator of the registry.
"An oral SARS-CoV-2 Mpro inhibitor clinical candidate for the treatment of COVID-19" by Owen, D., et al. published in Science on Nov. 2, 2021.
The SARS-CoV-2 Mpro (or 3CLpro) is a cysteine protease responsible for 11 distinct polyprotein cleavage sites that release proteins including the polymerase subunits essential for viral replication. Mpro has a unique substrate preference, cleaving polypeptide sequences at 11 Gln P1 sites, that provides high selectivity of action. These features and conservation of the active enzyme site across coronaviruses makes the Mpro an excellent target for antivirals. The current paper details the synthesis strategy and pre-clinical characterization of a novel orally administered SARS-CoV-2 Mpro inhibitor designated PF-7321332. Its precursor molecule PF-0835231, initially developed as a SARS-CoV-1 inhibitor, potently inhibits the Mpro of multiple coronaviruses and is a sub-micromolar inhibitor of SARS-CoV-2 in cell cultures. PF-7304814, the intravenously administered phosphate prodrug of PF-0835231, entered clinical trials in hospitalized COVID-19 patients in Sept. 2020 (NCT04535167) and is part of the NIH-sponsored ACTIV3 adaptive platform trial (NCT04501978).
Launched in July 2021, the Pfizer Phase 2/3 EPIC-HR (Evaluation of Protease Inhibition for COVID-19 in High-Risk Patients) was a randomized, placebo-controlled, double-blind study of non-hospitalized adults with COVID-19 who had at least 1 risk factor for progression to severe illness (NCT04960202). Initiating treatment with PF-7321332/ritonavir (trade name Paxlovid™) within 3 days of symptom onset reduced the risk of COVID-19-related hospitalization or death from any cause (primary endpoint) by 89% (0.8% of 389 vs 7.0% of 385 placebo; p<0.0001). Starting treatment within 5 days of symptom onset showed similar reductions (1.0% of 607 vs 6.7% of 612 placebo; p<0.0001). No deaths occurred in the active group compared to 10 in the placebo group. Treatment-emergent adverse events, mostly mild, were comparable between the 2 groups, with fewer serious adverse events reported with PF-7321332/ritonavir (1.7%) than placebo (6.6%). The trial was stopped early because of clear evidence of efficacy, and Pfizer announced plans to submit the data to the U.S. FDA for Emergency Use Authorization (EUA) as soon as possible.
Trials testing the efficacy of oral PF-7321332/ritonavir for early treatment in low-risk COVID-19 outpatients (NCT05011513) and for post-exposure prophylaxis (NCT05047601) are ongoing. Of note, PF-0835231 showed some evidence of enhanced antiviral activity in vitro when combined with remdesivir, suggesting combinations of PF-7321332 with other inhibitors warrant study.
Disclosures: Hayden is a nonpaid consultant for Pfizer and multiple other companies involved in developing SARS-CoV-2 antivirals, therapeutics, or vaccines (Aphrodite/Daewoong, Appili, Arcturus, Atea, FujiFilm, Gilead, GSK, Janssen/JNJ, Merck, Pardes Bio, Primmune, Ridgeback, Roche, Shin Poong Pharm, Takeda, Vir). Shionogi has made charitable contributions for his consulting. The University of Virginia has received payments from CytoDyn for his work on a data safety and monitoring board.
Nov. 12, 2021
By Jonathan D. Dinman, Ph.D., Professor of Cell Biology and Molecular Genetics, University of Maryland, College Park, Md. Dinman is a curator of the registry.
"SARS-CoV-2 Nsp5 Demonstrates Two Distinct Mechanisms Targeting RIG-I and MAVS To Evade the Innate Immune Response" by Liu, Y., et al., published in mBio on Sept. 21, 2021.Double-stranded RNA (dsRNA) intermediates are produced during the replication phase of RNA viral developmental programs. This creates a problem for these viruses because dsRNA activates the innate immune response. To counter this, most RNA viruses have evolved strategies to inactivate the innate immune response prior to replicating their genomes. Elucidating the viral proteins so involved, their modes of action, and their cellular targets can create new opportunities for therapeutic intervention.
The report by Liu, Y., et al. begins with the observation that SARS-CoV-2 infection fails to induce a strong type I interferon response, the hallmark of innate immunity. A genetic screen identified the viral Nsp5 protease as a strong inhibitor IFN-β expression. Subsequent experiments revealed that Nsp5 had broad cytokine inhibitory activity, and that its primary cellular targets are RIG-I and MAVS. Proteloytic cleavage of RIG-I not only abrogated its activity, but that it also conferred a dominant negative phenotype, effectively shutting down this entire arm of the antiviral reaction. In parallel, Nsp5 was found to target MAVS for ubiquitination and subsequent degradation, thus shutting down a second immune response pathway. Given that Nsp5 is a cysteine protease, the authors leveraged vinyl sulfone "electrophilic warhead" chemistry, developing 2 small molecules that covalently target the catalytic residue of this class of proteases. Both molecules restored the innate immune response and inhibited SARS-CoV-2 replication in a dose-dependent manner. Importantly, the SARS-CoV-2 replication IC50s of these small-molecule Nsp5 inhibitors were ~200-fold greater than their CC50s, suggesting that that antiviral activity was not due to nonspecific cytotoxicity. These findings provide a proof of concept for targeting Nsp5 to treat COVID-19.
Oct. 29, 2021
By C. Brandon Ogbunu, Ph.D., Assistant Professor, Department of Ecology and Evolutionary Biology, Yale University. Ogbunu is a curator of the registry.
"The association of community mobility with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 330 local UK authorities" by Li, Y., et al., published in The Lancet Digital Health on Aug. 31, 2021.Since very early in the COVID-19 pandemic, the science of epidemiology has offered a detailed picture of the actors, forces and contexts that shape the dynamics of disease transmission. Much of this has been possible because of increasingly diverse sources of data, which have offered windows into the many ways that behavior and social networks play a role in outbreaks.
In their article, Li and colleagues produce a fine-grained picture of the COVID-19 epidemic in the U.K. using community mobility data from Google, in combination with estimations of the time-varying reproductive value (R), a proxy for the how rapidly infection spread in a given setting. Using multivariate log-linear regression, the authors calculated statistical relationships between visitation patterns to certain local authorities, and this R. The local authorities included retail and recreation spaces, grocery and pharmacy stores, transit stations, parks, workplaces and residential spaces. For each, the authors calculated the relationship between visitation patterns and changes in the time-varying R. They found that increased visits to retail and recreation spaces, and workplaces, were associated with the greatest increases in time-varying R. By contrast, increased visits to parks were associated with lower R, as were longer stays in residential areas.
The findings offer a window into disease dynamics that is intuitive. For example, the lower transmission rates associations occur when people visit outdoor settings (parks), and when people are inside homes (likely with few people) for longer periods of time. While visits to transit stations were not associated with increased R overall, they were associated with increased R in cities, where people use mass transit with greater frequency. The study provides a granular and actionable set of findings with regards to the types of settings that are associated with increased risk of transmission. Furthermore, the study supports previous findings about the importance of social distancing and other methods to prevent transmission, and fortifies the importance of new data sources and "digital epidemiology" towards improvements in public health practice.
Oct. 15, 2021
By Richard L. Hodinka, Ph.D., Professor Emeritus, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania. Hodinka is a curator of the registry.“Ultrarapid detection of SARS-CoV-2 RNA using a reverse transcription-free exponential amplification reaction, RTF-EXPAR” by Carter, J., et al., published in the Proceedings of the National Academy of Sciences on Aug. 16, 2021.
Fast and simple-to-use SARS-CoV-2 molecular diagnostic assays are being developed and implemented at an accelerated pace to meet the needs of the current pandemic.
The article by Carter and colleagues describes the development and evaluation of a rapid single temperature (isothermal) method for the amplification of SARS-CoV-2 RNA that uniquely bypasses the reverse-transcription step used in RT-PCR to convert viral RNA into DNA. In the process, an RNA/DNA heteroduplex is formed and selectively cleaved by the restriction enzyme BstNI to generate a short DNA trigger strand containing a sequence complementary to the conserved Orf1ab gene in the SARS-CoV-2 genome. The trigger strand binds to a DNA template and large quantities of short double-stranded DNA sequences are then cyclically amplified using an exponential amplification reaction (EXPAR) that involves a DNA polymerase to extend the sequence and a DNA nicking endonuclease to cut it, leaving an intact template. This reverse-transcription-free (RTF) alternative isothermal approach involves a single step, and the authors report that RTF-EXPAR can accurately detect 7.25 SARS-CoV-2 RNA copies/µl in less than 10 minutes using a SYBR Green fluorescence read out.
Direct comparison of the RTF-EXPAR test with existing RT-PCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays demonstrated a high amplification efficiency, producing up to 108 strands of DNA in minutes, with comparable specificity and sensitivity. The assay is much simpler and faster than RT-PCR and has a shorter test time than RT-LAMP, which is considered to be one of the fastest methods currently in use (e.g., RTF-EXPAR, 8.8 min < RT-LAMP, 13.8 min < RT-PCR, 42.7 min to detect 7.25 SARS-CoV-2 RNA copies/µl when tested in target dilution studies).
Overall, the described assay may be of high value and appears to be especially suited for applications where rapid turnaround and decentralized testing are most desirable. Similar to other rapid molecular assays, the test is performed on unprocessed samples with no sophisticated instruments or operations and results are available in real time. The assay also has the potential to be widely applicable to the detection of many other pathogens. However, larger comparison studies will be needed to appreciate fully the diagnostic accuracy of this method and whether use of a SYBR Green intercalating dye for signal detection will be adequately specific.
Sept. 24, 2021
By Catherine J. Pachuk, Ph.D., Chief Science Officer, Marizyme, Inc., Jupiter, Fla. Pachuk is one of the curators of the Registry.
"Durability of antibody responses elicited by a single dose of Ad26.COV2.S and substantial increase following late boosting" by Sadoff, J., et al., published on medRxiv on Aug. 26, 2021.SARS-CoV-2 vaccines have been shown to be safe and to confer high protective efficacy against severe COVID-19 disease, hospitalization and death; however, concerns of waning immunity following vaccination and potentially less protection against emerging variants of concern (VoCs) have prompted significant debate regarding the need for booster immunizations.
Sadoff, J., et al. recently reported findings on both the durability of vaccine-induced SARS-CoV-2-specific antibody (Ab) responses and the impact of booster immunization on these responses in Phase 1/2a and Phase 2 Janssen vaccine trial participants. SARS-CoV-2-specific Ab responses were found to be mostly stable for at least 8-9 months post-vaccination and comparable to day 29 post-immunization titers. A 2.3-fold reduction in GMT for neutralizing Ab was however observed by 9 months in > 65-year-old participants and the percentage of those in this age group with detectable neutralizing Ab at 9 months was lower compared to those in the 18–55-year-old age group; 68% versus 95%.
Booster immunization at 6 months post-vaccination elicited rapid and strong increases in spike-specific binding Ab levels in all study participants. Up to 9-fold higher Ab levels were generated compared to levels induced by primary vaccination and may be important in conferring additional protection against emerging VoCs more resistant to neutralization by vaccine-induced Abs. The rapid anamnestic response to boost, observed even in individuals with undetectable Abs at time of boost, indicates that robust immune memory was established following primary vaccination. Such anamnestic responses would likely also occur in response to infection and vaccinated individuals with substantially diminished Ab titers who experience breakthrough infection may still be protected from severe disease.
While boost-induced neutralizing Ab data were not yet available at the time of this report, past analyses demonstrated a strong correlation between spike-specific binding Ab and neutralizing Ab levels following primary vaccination and it is predicted that neutralizing Ab titers will also be substantially increased following booster immunization. Lastly, the study addresses questions regarding the feasibility of using the Janssen vaccine for both primary and booster vaccination given the potential for booster-vaccine inactivation due to adenovector-specific immune responses. The data clearly support the use of the vaccine as a booster when administered approximately 6months after primary vaccination. Feasibility of other boosting schedules would need to be further evaluated.
The long-lived humoral response and the establishment of robust immune memory following primary vaccination give confidence that protection against severe disease will also be long-lived. However, boosting offers the significant advantage of substantially increasing Ab levels over those achieved by primary vaccination alone. Higher Ab titers may be beneficial for certain populations and may ultimately be important in affording more protection against emerging variants, both in terms of protection from disease and perhaps in curbing viral transmission by reducing viral load in those with breakthrough infections.
Sept. 3, 2021
By Tom Gallagher, Ph.D., Professor of Microbiology and Immunology, Loyola University Chicago, Maywood, Il. Gallagher is one of the curators of the registry.
"SARS-CoV-2 variant B.1.617 is resistant to bamlanivimab and evades antibodies induced by infection and vaccination" by Hoffmann, M., et al., published in Cell Reports on July 20, 2021.SARS-CoV-2 variants of concern (VOCs) emerge continuously. Those with increased fitness expand with remarkable speed to establish worldwide dominance, replacing the previously prevailing version. Currently there is no evidence for the ascendance of a durable and temperate form of SARS-CoV-2 to replace the alarming VOCs. Therefore, at present we are faced with highly dynamic virus variation, which clearly complicates COVID19 control programs. Tremendous research efforts are rising to these challenges, with aims to reveal mechanisms of fitness advantage and establish antiviral approaches that disable current and future VOCs.
Amongst the research enterprises are those of Hoffmann et al., who focused on SARS-CoV-2 variant B.1.617, a member of the currently widespread "delta" cluster. As with previous VOCs, the B.1.617 viruses are set apart by several changes in their spike proteins. Investigators compared B.1.617 spikes with those of previously extant VOCs using established pseudovirus transduction assays and found that B.1.617 spikes supported increased virus entry into cell types that may reflect those targeted during natural infections. Importantly, they recognized enhanced entry by B.1.617 spikes only when ACE2 receptor levels were low–arguing for receptor limitations as selective forces driving spike VOC adaptations. The investigators also discovered that the B.1.617 spike-directed transductions were modestly less sensitive to neutralization by antibodies from vaccinees and from those who have recovered from COVID19. Consistent with antibody escape, the B.1.617 spikes fully supported virus entry in the presence of bamlanivimab (LY-CoV555), a monoclonal antibody with emergency use authorization for COVID-19 therapy.
With several outstanding research groups advancing on similar fronts, there will soon be ever greater clarity on VOC spikes in relation to viral fitness and antibody evasion. Hypervariable spike domains will be further recognized relative to virus transmission and initial infection events and to the process of antibody-driven antigenic drift. These discoveries will be needed to distinguish the extensive antigenic drifts that may give rise to breakthrough infections. Amongst the VOC combat strategies will be novel vaccines eliciting neutralizing antibodies that target invariant, possibly "universal" SARS-CoV-2 epitopes.
Aug. 20, 2021
By Zhengli Shi, Ph.D., Senior Scientist, Wuhan Institute of Virology, Chinese Academy of Sciences. Shi is one of the curators of the registry.
"ACE2 binding is an ancestral and evolvable trait of sarbecoviruses" by Starr, T., et al., published on bioRxiv on July 19, 2021.
SARS-CoV and SARS-CoV-2, both belonging to sarbecovirues, utilize human ACE2 as their receptor. It is suggested that horseshoe bats are natural reservoirs of SARS-CoV-1, and probably SARS-CoV-2. Previous studies have demonstrated that bat SARS-related CoV (SARSr-CoV) clade 1, not clade 2, utilize ACE2 orthologs for cell entry. It is unclear how did some groups of virus acquire or lose the ACE2 binding.
July 30, 2021
By Sonia Navas-Martin, Ph.D., Professor of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pa. Navas-Martin is one of the curators of the Registry."SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans" by Turner, J., et al., published in Nature on May 24, 2021.
It is well established that protective immunity against seasonal coronaviruses is short-lived. Since the SARS-CoV-2 pandemic began, researchers around the world investigated the intriguing plethora of host responses to this novel coronavirus. Although impressive progress has been made during the past 18 months, defining whether SARS-CoV-2 infection induces short- or long-lived humoral immune memory is paramount to develop protective vaccines and eradicate the COVID-19 pandemic.
Turner et al., investigated if individuals who had recovered from mild COVID-19 develop long-lived protective immunity. To address this question, they analyzed blood and bone marrow aspirates from individuals convalescing from mild COVID-19 and healthy volunteers. Long-lived bone marrow plasma cells (BMPCs) are non-replicating, antigen-specific plasma cells that maintain serum antibody titers and are detected in the bone marrow long after the clearance of an antigen. Importantly, SARS-CoV-2 S-specific BMPCs were detected in bone marrow aspirates from 15 out of 19 convalescent individuals approximately 7 and 11 months after infection for anti-SARS-CoV-2 S-specific BMPCs. Overall, their results suggest that early transient burst of extrafollicular plasmablasts generates a first wave of serum antibodies that decline quickly, followed by stably maintained levels of serum antibodies that are supported by long-lived BMPCs.
The study by Turner et al., provides the first direct evidence for the induction of antigen-specific BMPCs after a viral infection in humans. Because SARS-CoV-2 S protein is the main target of neutralizing antibodies, a key question that remains to be determined is the fraction of the S-binding BMPCs that encodes neutralizing antibodies. Moreover, do severe SARS-CoV-2 infection or vaccination induce a long-lived BMPC response?
July 16, 2021By Frederick G. Hayden, M.D., Stuart S Richardson Professor Emeritus of Clinical Virology and Professor Emeritus of Medicine in the Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Va. Hayden is one of the curators of the registry.
"Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial" by the RECOVERY Collaborative Group, published on medRxiv on June 16, 2021.
Investigators for RECOVERY, the UK-wide, open-label adaptive platform trial for hospitalized COVID-19 patients, have recently posted their findings in patients randomized to standard of care (SOC) or to SOC plus a single intravenous infusion of the anti-Spike receptor binding domain monoclonal antibodies casirivimab 4,000 mg and imdevimab 4,000 mg (aka REGN-COV2 or REGEN-COVTM). The arms enrolled 9,785 patients, 61% of whom required supplemental oxygen and 32% higher levels of respiratory support at entry. SOC included low-dose dexamethasone in 94%; remdesivir was used in 24%. In the pre-specified analysis of 3,153 (32%) SARS-CoV-2 seronegative patients (based on validated ELISA), mortality was reduced (24% vs 30%; rate ratio 0.80; 95% CI 0.70-0·91; p=0·0010) and the secondary outcome of hospital discharge by day 28 increased (64% vs 58%). In contrast, no reduction in 28-day mortality was found in seropositives or in the whole cohort (20% vs 21%) No data on SARS-CoV-2 variant-specific clinical responses were given but are of obvious interest.
Several randomized controlled trials (RCTs) by the ACTIV-3 investigators that found no mortality reduction or clinical benefits with other anti-S monoclonal products in hospitalized COVID-19 patients. A key difference is that these studies were smaller and neither reported outcomes nor were powered to examine the subset of seronegative patients. An ongoing company-sponsored RCT in seronegative hospitalized patients has reported preliminary findings of a lower risk of death or receiving mechanical ventilation (HR: 0.78; 80% CI: 0.51-1.2). Time to initiating treatment and antibody quantity and potency, as demonstrated in both seronegative outpatients and inpatients with the casirivimab and imdevimab cocktail, are also important variables. For example, RECOVERY’s study of higher titer convalescent plasma did not find reduced mortality overall or in seronegative patients. In outpatient placebo-controlled RCTs, REGEN-COV 1,200 mg shortened the time to symptom resolution, and reduced COVID-19-related hospitalization or all-cause mortality by approximately 70%. No important safety signals have been identified to date, and REGEN-CoV is authorized for clinical use by both the FDA and the European Medicines Agency.
Declaration of interest: Previously Hayden was a nonpaid consultant for Regeneron on their influenza and MERS antibody programs but not for SARS-CoV-2. During the pandemic, he served as nonpaid advisor to multiple groups regarding potential therapeutics including NIH's ACTIV 2 and 3 subpanels, UK CTAP (recommendations for RECOVERY, AGILE, and other UK platforms), CETF, WHO, several academic groups, and multiple companies (including Aphrodite, Arcturus, Cidara, Fujifilm, Gilead, GSK, Janssen/JNJ, Merck, Pfizer, Pardes Bio, Primmune, resTORbio, Ridgeback, Shionogi, Takeda, Vir). He served on DSMB for phase 3 clinical trial of immunomodulator in severe COVID-19 by Cytodyn (fees to UVA) and is currently serving on two DSMBs (Imperial College, U Oxford) involved with human challenge studies with SARS-CoV-2 (no compensation). Hayden has received personal honoraria for serving as a member of the SAB for the NIH-sponsored Antiviral Drug Discovery and Development Consortium, University of Alabama.
July 2, 2021By Yi-Wei Tang, M.D., Ph.D., F(AAM), FIDSA, Chief Medical Officer, Danaher Diagnostic Platform and Cepheid (China), Shanghai. Tang is one of the curators of the registry.
"A Generic, Scalable, and Rapid Time-Resolved Förster Resonance Energy Transfer-Based Assay for Antigen Detection—SARS-CoV-2 as a Proof of Concept" by Rusanen, J., et al., published in mBio on May 18, 2021.
Although nucleic acid-based molecular assays have been considered gold standards for laboratory diagnosis of COVID-19, it is generally accepted that antigen-based assays remained useful and supplemental in the diagnosis procedure. Current antigen testing is relatively rapid and can usually be completed with turnaround times of 30 minutes or less. In addition, clinical relevance of an antigen test result can be fundamentally different from nucleic acid detection. However, antigen-based testing has suffered from relatively poor sensitivity and, on some platforms, low specificity, which is usually the major bottleneck for disease surveillance in which higher sensitivity is desirable.
In this study, Rusanen et al. from the University of Helsinki described a generic, scalable, and rapid time-resolved Förster resonance energy transfer (TR-FRET)-based assay for SARS-CoV-2 antigen detection. The energy transfer method has been widely used for real-time nucleic acid amplification product detection and identification. The authors adapted the energy transfer method to detect directly antigens of the infectious agent in as short as 10 minutes. The method is based on the detection of SARS-CoV-2 nucleoprotein (NP) and S protein (SP) via TR-FRET with donor- and acceptor-labeled polyclonal anti-NP and -SP antibodies. Using recombinant proteins and cell culture-grown SARS-CoV-2, the limits of detection were established as 25 pg of NP or 20 infectious units (IU) and 875 pg of SP or 625 IU. Testing of RT-PCR-positive (n = 48, with cycle threshold [CT] values from 11 to 30) or -negative (n = 96) nasopharyngeal swabs (NPS), demonstrated that the assay yielded positive results for all samples with CT values of 25 and for a single RT-PCR-negative sample. In a pilot study, the NP-based assay showed 97.4% sensitivity and 100% speciﬁcity in comparison with virus isolation and 77.1% sensitivity and 99.0% speciﬁcity in comparison with SARS-CoV-2 RT-PCR.
While the results are encouraging from this proof-of-concept study, two concerns must be addressed before the assay can be successfully applied to diagnosis of COVID-19. First, current data suggests that the sensitivity of the antigen assay remains lower than that of RT-PCR. Additional optimization is needed to further enhance the test sensitivity. Second, there is no data on whether the antigens from variants can be correctly identified by the monoclonal antibodies used in the study. Larger studies including different and representative SARS-CoV-2 variants are needed.
June 18, 2021
By Vito Martella, DVM, Ph.D., Professor of Veterinary Medicine, Universita degli studi di Bari Aldo Moro, Bari, Italy. Martella is one of the curators of the registry.
"Infection, recovery and re-infection of farmed mink with SARS-CoV-2" by Rasmussen, T., et al., published on bioRxiv on May 7, 2021.
Farmed minks (Neovison vison) are highly susceptible to infection by SARS-CoV-2. The clinical course of infection in minks ranges from inapparent forms to respiratory distress and, in some cases, increased mortality. SARS-CoV-2 infection in farmed minks was initially observed in the Netherlands in April 2020, in Denmark in June 2020 and subsequently it has been reported in several countries globally. Data on the patterns of SARS-CoV-2 infection in the farms have been mostly collected from observational studies in the initial outbreaks, suggesting that SARS-CoV-2 may quickly spread in minks of an infected farm and that, when most animals seroconvert, virus circulation comes to an end.
However, thus far long-term observational data in infected mink farms are not available. Ramussen et al. report follow up data on a Danish mink farm with about 15,000 animals where in August 2020 an outbreak of SARS-CoV-2 had occurred. The infected minks recovered and remained seropositive. The minks from the farm were not culled and during follow-up studies, after a virus-free period of more than 2 months, over 75% of tested animals scored positive again for SARS-CoV-2 RNA. Whole genome sequencing showed that the SARS-CoV-2 viruses circulating in the 2 phases in the farm were closely related to each other. These findings may be compared with cases of apparent re-infections reported anecdotally in COVID-19 patients and are relevant for control measures and strategies in mink farms.
June 4, 2021By Jonathan D. Dinman, Ph.D., Professor of Cell Biology and Molecular Genetics, University of Maryland, College Park, Md, USA. Dinman is one of the curators of the registry.
“SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis” by Finkel, Y., et al., published in Nature on May 12, 2021.
Shortly after a virus like SARS-CoV-2 infects a cell, its (+) stranded RNA genome is released into the cytoplasm. Because the genomes of these viruses also function as mRNAs, the first and critical battle is for control of the translational apparatus: whoever owns the ribosomes wins.
This study leveraged the power of RNA sequencing, ribosome profiling and RNA metabolic labeling to examine comprehensively how SARS-CoV-2 outfoxes the cell to win this war. Global translation was significantly reduced due to the activity of the viral NSP1 protein. This is known to block translation through its interaction with the mRNA entry channel of the ribosome, triggering endonucleolytic cleavage and mRNA degradation. Intriguingly, viral mRNAs, which contain a common 5’ leader that is added during (-) strand synthesis, were found to dominate the translationally active pool. A clever genetic experiment using GFP reporters revealed that those containing the leader were refractory to ectopic NSP1 expression, thus demonstrating that the addition of this sequence helps the virus to dominate the translational apparatus. Additionally, cellular fractionation studies revealed an increase in unprocessed pre-mRNAs in the nucleus, indicating that SARS-CoV-2 infection disrupts their export to the cytoplasm. This is critical because the highly structured viral RNAs are recognized by TLR3 and TLR10 as pathogen-associated molecular patterns (PAMPS), activating the immune response through transcription of cytokines and interferon induced genes. Thus, in addition to selectively degrading cellular mRNAs in the cytoplasm, by blocking their export from the nucleus the virus appears to have evolved a second front in the war over the ribosomes.
May 21, 2021
By Paul G. Thomas, PhD., Department of Immunology Member, St. Jude Children's Research Hospital, Memphis, Tenn. Thomas is one of the curators of the Registry.
“Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant” by Graham, C., et al., published in Immunity on April 1, 2021.
The emergence of SARS-CoV-2 variants has created concern about the possibility of immune escape based on prior infection- or vaccine-induced memory. The B.1.1.7 variant, sometimes referred to as the "UK variant," has quickly spread and become the primary strain in many areas of the world, with demonstrated increase transmissibility and some conflicting evidence of increased pathogenicity. Given the current prevalence of this strain, it is important to identifying its antigenicity relative to the original "wild-type" strains from the early stages of the pandemic that were the basis for vaccine design.
Graham, C., et al. characterized over 100 monoclonal antibodies isolated from three individuals who had infection with SARS-CoV-2, and divided them into those targeting epitopes in the N-terminal domain (NTD), Receptor Binding Domain (RBD), and Spike 2 region (S2). Prior work from others confirmed here show that anti-S2 antibodies are not neutralizing. Approximately 20% of the antibodies that were neutralizing in this study targeted the NTD, which could be further divided into two groups, one that was strongly neutralizing and the other that was less potent and glycan-dependent. The authors then introduced mutations associated with the B.1.1.7 lineage and found that NTD-mutations caused a significant reduction in neutralization activity against the NTD-targeting antibodies. In contrast, the RBD-mutations associated with the B.1.1.7 lineage did not cause immune escape from antibodies elicited by infection with "earlier" era strains.
These data indicate that the B.1.1.7 variant has escaped important neutralizing responses targeting the NTD, but is still susceptible to the immunodominant RBD specificities. As new variants emerge, careful consideration of the accumulation of mutations across the full length of the Spike protein, particularly the NTD and RBD, is necessary to assess the potential risk of immune escape.
May 7, 2021
By Catherine J. Pachuk, Ph.D., Chief Science Officer, Marizyme, Inc., Jupiter, Fla. Pachuk is one of the curators of the Registry.
“Neutralizing Response against Variants after SARS-CoV-2 Infection and One Dose of BNT162b2” by Lustig, Y., et al., published in The New England Journal of Medicine on April 7, 2021.
Several vaccines have been authorized in the U.S. and elsewhere for prevention of COVID-19 disease; however, concerns exist regarding the potential for emerging viral variants to escape vaccine protection. The concerns are largely driven by reductions in variant-specific neutralizing antibody (Ab) titers in vaccinated and convalescent individuals compared to responses directed against the original lineage virus. Relative reductions in neutralizing Ab titers vary depending upon the variant, ranging from only modest reductions observed for B.1.1.7 to more significant reductions observed for B.1.351.
Recently, Lustig et al. reported substantial increases in neutralizing responses to original and variant viruses in previously infected individuals following administration of a single dose of the Pfizer BNT162b2 vaccine. Neutralizing Ab titers were measured in serum samples obtained from subjects 1-12 weeks following natural infection, immediately prior to vaccination and 1-2 weeks after single dose vaccine administration, in microneutralization assays using isolates of the original virus or variants. Geometric mean titers for neutralizing activity in serum samples collected post-natural infection were 456, 256, 71 and 8 respectively for the original B1 lineage virus, B.1.1.7, P1 and B.1.351. Prior to vaccination, titers dropped to 81, 40, 36 and 7, but following vaccination substantially increased to 9195, 8192, 2896 and 1625 respectively for B.1, B.1.1.7, P1 and B.1.351. These data demonstrate the potential of the current vaccine, when administered to those with prior infection, to drive high neutralizing Ab titers against current variants of concern, including B.1.351 for which there was low to undetectable neutralization activity prior to vaccination.
Likewise, a previously published study documented significant increases in anti-spike Abs following a single dose of the Pfizer vaccine in individuals with prior infection. It is not known if prior infection is required to achieve these increased responses post-vaccination or whether a series of vaccine boosters can achieve similar results. The study, although limited by small sample size, minimally underscores the importance of vaccinating previously infected individuals.
April 23, 2021
By Benjamin Neuman, Ph.D., Professor of Biology and GHRC Chief Virologist, Texas A&M University, College Station, Texas. Neuman is one of the curators of the registry.
“In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs” by Sun, L., et al., published in Cell on April 1, 2021.
When heading into an unfamiliar place, it helps to have a map. The study by Sun and coworkers provides exactly that—a map of RNA secondary structure in the SARS-CoV-2 genome that shows the ways that the long-strand viral RNA twists and folds. This study brings some new and impressive technology to bear on the question of viral RNA structure, and the decision of the authors to go the extra step and characterize RNA folding both in solution and inside an infected cell is an important step in SARS-CoV-2 RNA cartography.
The reason why this could be important is that we knew from previous work that coronavirus genomes contain multiple layers of encoded information. In addition to genes that can be expressed, sometimes from within other genes, there are also signals that help the viral replicase recognize and copy its own genome and shorter mRNAs, and help those genomes to be selectively packaged into new virions. Some RNA secondary structure elements serve as anchor points for binding of viral or possibly host proteins that functionalize and protect the viral genome. Notably, part of the 3’-untranslated region of betacoronaviruses is hypothesized to switch between 2 different conformations, which seem to be both an anchor point for the conserved nonstructural protein 9 and an essential feature for successful viral RNA replication. In other RNA viruses, like poliovirus, RNA structures serve as a base and template on which the primers for viral RNA synthesis are built. A recent study from Slanina, H., et al. brings new evidence that coronavirus replication may begin through a similar protein-primed RNA synthesis mechanism—if that turns out to be the case, then having an accurate map of RNA secondary structure could turn out to be even more valuable than anticipated.
Another idea that coronavirus researchers may be able to take from picornavirus research is that modified or isolated versions of key RNA secondary structure elements can be expressed in cells as powerful dominant negative inhibitors of virus growth. Next steps are likely to include a combination of reverse genetics analysis to better understand the implication of each conserved RNA structure element, aided by bioinformatics to highlight conserved structures and populate this map with important features. Development of RNA structure-based inhibitors, and further experiments to map which of the many folds in the SARS-CoV-2 genome are important for virus growth, could be a long journey. But at least now, for this journey, we have a map.
April 9, 2021
By Seema S. Lakdawala, Ph.D., Assistant Professor of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pa.
“Increased transmission of SARS-CoV-2 lineage B.1.1.7 (VOC 2020212/01) is not accounted for by a replicative advantage in primary airway cells or antibody escape” by Brown, J., et al., published on bioRxiv on March 1, 2021.
The rapid rise of the SARS-CoV-2 B.1.1.7 variant world-wide clearly demonstrates the increased fitness for community spread. Many characteristics explaining this increased transmissibility have been proposed. In particular, an increase in ACE2 receptor affinity has been proposed to account for this increased transmissibility.
In the manuscript by Brown et al, the authors address a variety of potential reasons for the increased transmission fitness for the B.1.1.7 variant. In a series of elegant studies, the authors test a wide range of SARS-CoV-2 virus strains for replication capacity in human airway epithelial cells at an air-liquid-interface. The authors demonstrate that viral growth is equivalent between the B.1.1.7 variant and other contemporaneous strains in human airway epithelial cultures. The authors further explore the efficiency of protease cleavage and demonstrate the substitutions in the SARS-CoV-2 spike do not drastically impact the efficiency of spike cleavage in the context of a full virus. In contrast, use of pseudotype viruses expressing single or combined spike mutants presented a stronger phenotype, solidifying the need to study important aspects of SARS-CoV-2 biology in the full viral context. Finally, in concert with other recent publications, the group demonstrates that convalescent sera from vaccinated and infected individuals was capable of neutralizing current B.1.1.7 isolates.
Taken together, this manuscripts dispels important notions about the emergence and success of B.1.1.7 variant and strengthens the argument that vaccination will also function to limit the spread of this virus.
March 26, 2021By Richard L. Hodinka, Ph.D., Professor, University of South Carolina School of Medicine Greenville, S.C.; Emeritus Professor, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pa. Hodinka is one of the curators of the Registry.
“Quantifying Absolute Neutralization Titers against SARS-CoV-2 by a Standardized Virus Neutralization Assay Allows for Cross-Cohort Comparisons of COVID-19 Sera” by Oguntuyo, K.Y., et al., published in mBio on Feb. 16, 2021.
Infection with SARS-CoV-2 elicits an immune response in the host that includes the production of neutralizing antibodies to the spike glycoprotein on the surface of the virus. Neutralizing antibodies represent a correlate of protection since they can block attachment of the virus to the ACE2 cellular receptor and prevent viral entry into the cell.
The article by Oguntuyo and colleagues describes the development and evaluation of a standardized assay to accurately quantify absolute neutralizing antibody titers against SARS-CoV-2. The assay is of high value and should provide meaningful comparative information for monitoring neutralizing antibody responses of acutely infected patients, screening convalescent-phase plasma from patients recovered from COVID-19, determining the efficacies of various vaccines and therapeutic entry inhibitors and studying naturally occuring spike mutants.
Pseudotyped viral particles bearing the SARS-CoV-2 spike glycoprotein (CoV2pp) were generated using vesicular stomatitis virus as a surrogate virus core bearing the Renilla luciferase reporter gene in place of its G glycoprotein to generate a measurable luminescent signal. A CoV2pp-based virus neutralization assay (VNA) was then developed and parameters impacting the performance of the assay were examined and standardized. The standardized VNA was evaluated by 4 independent groups using serum samples from geographically distinct and ethnically diverse COVID-19 patient cohorts. Quantitative measures of absolute 50% inhibitory concentration (absIC50), absIC80 and absIC90 were compared between laboratories. Two ultrapermissive 293T cell clones were also identified, allowing for ~150,000 infections per week in a 96-well format that can generate full neutralization curves for ~4,600 to ~6,200 samples.
Overall, this article will be invaluable to those interested in pseudotype virus production for SARS-CoV-2 and its use to quantify neutralizing antibody responses and study virus entry into host cells. Detailed and optimized protocols for producing the CoV2pp were provided. The produced CoV2pp circumvents the need for restrictive, expensive and limited biosafety level 3 (BSL 3) facilities, and the CoV2pp-based VNA represents a highly standardized, safe, reasonably simple, scalable and high-throughput system with robust metrics.
March 12, 2021
By Tom Gallagher, Ph.D., Professor of Microbiology and Immunology, Loyola University Chicago, Maywood, Ill. Gallagher is one of the curators of the registry.
“Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics” by Pillon, M., et al., published in Nature Communications on Jan. 27, 2021.
Several coronavirus (CoV)-encoded accessory and “non-structural” proteins (nsps) operate to conceal infections from host-encoded antiviral factors and sensors that activate immune systems. CoV nsp15 is amongst these proteins facilitating virus proliferation within immunocompetent hosts. Nsp15 is an endo-uridine (endoU) specific ribonuclease that degrades polyuridine tracts from the 5’ ends of minus-strand viral RNAs, thereby quickly eliminating an RNA activator of innate immunity. Without endoU activity, CoV infections induce powerful host interferon responses, which limits their amplification in vivo. Tipping the balance towards host advantage has clinical implications. For example, live-attenuated CoV vaccines may be engineered by disabling endoU activity. Similarly, endoU-inhibiting drugs may induce interferons that quickly extinguish CoV spread and pathogenicity.
The findings reported in Pillon, M., et al. will promote nsp15-targeted antiviral drug discovery. The manuscript provides cryo-EM structures of SARS-CoV-2 nsp15 hexamers, with and without bound uridine triphosphate (UTP), in ways that further define endoU active sites and uridine substrate discrimination. The works also delineate a catalytic mechanism for endonucleolytic cleavage that brings out parallels with other endonucleases, including well-described RNase A. Importantly, the study also reveals a conformational flexibility in the hexamers that may be essential for capturing RNA substrates and mediating subsequent endonucleolytic cleavage. The findings provide frameworks for developing enzyme active-site inhibitors; i.e., uridine derivatives, as well as allosteric inhibitors that restrict the flexible “wobbling” of hexameric subunits. Finally, this study nicely illustrates how x-ray crystallography and cryo-EM techniques can be combined to reveal the conformational landscapes of complex protein machinery.
Feb. 26, 2021
By C.A.M. (Xander) de Haan, Ph.D., Associate Professor in virus-host interactions at the Faculty of Veterinary Medicine, Utrecht University, the Netherlands. de Haan is one of the curators of the registry.
“Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces shedding of SARS-CoV-2 D614G in rhesus macaques” by van Doremalen, N., et al., published on bioRxiv on Jan. 11, 2021.
Ideally, SARS-CoV-2 vaccines provide sterilizing immunity, meaning that they not only protect against disease, but also prevent replication in the upper respiratory tract and onward transmission. Within 1 year after the emergence of SARS-CoV-2, many vaccines targeting this virus are in clinical trials and several have already been approved. These vaccines protect against disease with different efficacies, but not necessarily prevent shedding of virus, as least as determined in non-human primates. This is probably associated with the intramuscular (IM) administration of these vaccines, which results in the induction of systemic IgG antibodies that protect the lungs, but not of mucosal IgA antibodies needed to inhibit replication in the nasal epithelium.
In a study by Neeltje van Doremalen and coworkers, intranasal (IN) and IM administration of the ChAdOx1 nCoV-19 vaccine was compared in a hamster challenge model. Both administration routes protected hamsters against disease, while IN vaccination resulted in significantly less virus shedding compared to IM vaccination. IN vaccination of rhesus macaques also protected against disease and resulted in systemic immunity comparable to that of IM-vaccinated animals. In addition, IN vaccination elicited SARS-CoV-2-specific mucosal immunity and reduced virus shedding.
Reducing virus replication and interrupting the chain of transmission is important to limit the emergence of variants, against which the currently approved vaccines may be less effective. Emergence of antigenic drift variants may even be accelerated by imperfect vaccines. Currently approved vaccines should therefore be analyzed for their ability to prevent onward transmission, and vaccines that do so should be further developed. In this respect, it is worthwhile to further investigate IN administration of adenovirus-vectored vaccines in a clinical setting.
Feb. 12, 2021
By Leo Poon, Professor, School of Public Health, The University of Hong Kong. Poon is one of the curators of the registry.
“Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice” by Cohen, A., et al., published in Science on Jan. 12, 2021.
The recent emergence of SARS-CoV-2 antigenic variants pose some serious concerns about the protective effect of COVID-19 vaccines recently rolled out in different countries. Data from preliminary studies suggest that some of these variants may partially escape neutralization by antibodies from recovered COVID-19 patients. Besides, several SARS-like betacoronaviruses (sarbecoviruses) are still circulating in animals and they continue to pose zoonotic threats to humans. Thus, there is a need to develop new strategies to control this group of pathogens.
Cohen and colleagues recently reported the use of multivalent nanoparticles containing the receptor binding domains (RBDs) of SARS-CoV-2 and other sarbecoviruses for immunization. Although the RBD of SARS-CoV-2 is a well-known neutralization target, its soluble form is not highly immunogenic. The authors found that SARS-CoV-2 RBD-specific antibody responses can be enhanced by conjugating the RBD of SARS-CoV-2 to nanoparticles. Mice treated with this nanoparticle vaccine have more robust neutralizing antibody titers than those vaccinated with the soluble form of SARS-CoV-2 RBD. In addition, serum samples from mice vaccinated with this homotypic nanoparticle vaccine can neutralize pseudoviruses of other sarbecoviruses and a boosting vaccination can further enhance such effects. Most interestingly, the authors found that mosaic nanoparticles decorated with different RBDs of sarbecoviruses (N=4/8) have even more pronounced effects in eliciting these cross-reactive responses. By contrast, convalescent plasma samples from COVD-19 patients do not have such activities.
This study from Cohen and colleagues provides a promising direction in developing pan-sarbecovirus vaccine. Further work using live virus in virus neutralization or animal studies will help to assess the potential use of this interesting approach. In particular, there is a high priority of using SARS-CoV-2 Variants of Concern (e.g. 501Y.V2 variant) for such investigations.
Jan. 22, 2021
By Jonathan D. Dinman, Ph.D., Professor of Cell Biology and Molecular Genetics, University of Maryland, College Park, Md., U.S. Dinman is one of the curators of the registry.
“SARS-CoV-2 protein ORF3a is pathogenic in Drosophila and causes phenotypes associated with COVID-19 post-viral syndrome” by Yang, S., et al., published in bioRxiv on Dec. 20, 2020.
A majority of COVID-19 patients suffer from post-recovery neurological complications including extreme fatigue and neuropsychiatric symptoms. Although a growing number of animal models, including non-human primates and hACE2 transgenic mice, have been developed to elucidate molecular mechanisms underlying the acute disease, the relatively long generation times of these mammalian systems render dissection of the bases for the long-term sequelae impractical, especially in light of the urgency attending the growing number of potential patients.
This study leveraged the power of Drosophila molecular genetics and developmental biology to address this pressing issue. Additionally, the rapid lifecycle of this model organism enables the types of longitudinal studies that would take months if not years in humans and non-human primate models. In this proof of principle work, Drosophila strains were constructed expressing the SARS-CoV-2 ORF3a protein in tissue specific manner. The authors found significant phenotypes only in flies’ expression of ORF3a in the nervous system. These included reduced lifespan, impaired motor function, abdominal swelling and partial larval lethality. Follow-up studies revealed that ORF3a expression induced apoptosis, neuroinflammation and neurotropism though immunoinflammatory pathways. The ability of ORF3a to cause lysosome deacidification suggested that this may be a source of toxic stress in neural cells. As proof of principle, transgenic flies treated with chloroquine phosphate, which blocks lysosome deacidification, increased ORF3a expressing fly lifespan, improved motor function and larval survival suggesting that chloroquine treatment may ameliorate symptoms associated with SARS-CoV-2 associated post-viral syndrome in humans. This study also validates the fly system as a platform for targeting specific proteins and pathways for drug screening.
Dec. 18, 2020
By Zhengli Shi, Ph.D., Senior Scientist, Wuhan Institute of Virology, Chinese Academy of Sciences. Dr. Shi is one of the curators of the Registry.
“Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan” by Murakami, S., et al., published in Emerging Infectious Diseases in Dec. 2020.
Coronaviruses phylogenetically related to SARS-CoV-2 were reported from 2 rhinolophus bat species in China, as well as pangolins smuggled to China from South Asian countries. This suggests that the progenitors of SARS-CoV-2 may exist in bats and other animals outside of China.
The article by Murakami, S., et. al., reported the discovery of a novel sarbecovirus (Rc-o319) in Rhinolophus cornututs, Japan, in 2 out of 4 samples collected in 2013. Rc-o319 shares 81.47% genome sequence identity with human SARS-CoV-2 and is positioned within a specific clade that includes SARS-CoV-2 and related coronaviruses from bats and pangolins. Interestingly, the Rc-o319 spike protein possesses a unique sequence variation from the known sarbecoviruses in the region corresponding to SARS-CoV and SARS-CoV-2 receptor binding domains. The authors also performed an analysis of receptor usage of this virus by using the vesicular stomatitis virus (VSV)-pseudovirus and demonstrated that Rc-o319 spike can use ACE2 of R. cornututs, but not that from human and other rhinolophus bat species. This is the first full-length genome sequence of bat sarbecovirus reported in an Asian country other than China, and highlights the necessity of much wider geographical investigations on sarbecoviruses in wildlife to find out the origins of SARS-CoV-2.
Dec. 4, 2020
By Vito Martella, Ph.D., Professor of Veterinary Medicine, Universita degli studi di Bari Aldo Moro, Bari, Italy. Dr. Martella is one of the curators of the registry.
Comparison of SARS-CoV-2 infection in two non-human primate species: rhesus and cynomolgus macaques by Böszörményi K., et al. published on bioRxiv on Nov. 5, 2020.
Animal models are essential for progress in SARS-CoV-2 research. Non-human primates (NHPs) have been employed for preclinical evaluation of vaccines and antiviral or immunomodulatory compounds to combat SARS-CoV-2. Thus far, 5 species of NHPs have been used in SARS-CoV-2 studies, including rhesus and cynomolgus macaques. Both macaque species are the 2 most widely-used NHP species in biomedical research and have been successfully used in studies of other human hypervirulent coronaviruses.
The use of different NHP species may generate variability and hamper a precise comparison of data in the study of SARS-CoV-2 infection, influencing the disease outcome considerably, as observed in other disease NHP models. In this study, the researchers made a comparative experimental infection in standardized conditions to assess which macaque species is best suited to investigate specific aspects of SARS-CoV-2 research. Rhesus and cynomolgus macaques were infected in parallel with the same virus stock, received completely identical treatment and the course of infection was followed using the same analyses and instruments. Both species showed moderate disease symptoms. Cynomolgus macaques showed elevated body temperature in the first 8 to 10 days following infection. A decrease in physical activity was only observed in the rhesus macaque. Pulmonary lesions were observed in most animals, as evidenced by computer tomography imaging. Shedding of infectious virus from the respiratory system was also documented. Immunoglobulins were detected in all animals by day 10 post-infection and the cytokine responses were highly comparable between species.
The authors conclude that both rhesus and cynomolgus macaques represent valid models for evaluation of COVID-19 vaccine and antiviral candidates in a preclinical setting.
Nov. 19, 2020
By Aaron G. Schmidt, Ph.D., Assistant Professor of Microbiology, Harvard Medical School and Ragon Institute of MGH, MIT and Harvard. Dr. Schmidt is one of the curators of the Registry.
Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants by Weisblum, Y., et al., published in eLife on Oct. 28, 2020.
In response to natural infection or vaccination, the human immune system often mounts a protective humoral response that helps prevent future infections. Viruses, however, can vary the antigenicity of their surface-exposed proteins. This serves as an effective evasion strategy to avoid host immune surveillance. Understanding how viruses might escape the mounted immune response is essential as it can directly influence the selection of antibody therapeutics as well as vaccine development.
Hatziioannou, Bieniasz and colleagues in their recent paper identify variants of the SARS-CoV-2 Spike protein that can escape neutralization by human monoclonal antibodies as well as convalescent sera. Using a chimeric vesicular stomatitis virus (VSV)/SARS-CoV-2 replication competent reporter virus, they obtained a “library” of Spike variants due to the lack of proof-reading activity of the VSV polymerase. They used this library to identify mutations that conferred resistance to three different monoclonal antibodies and convalescent sera from which the monoclonals were obtained. Key findings of their study include the observation that resistance populations were readily selected and clustered around the receptor binding domain. These mutations, however, did not impact interactions with its receptor, ACE-2. Mutations conferring escape from monoclonal antibodies remained sensitive to neutralization by the sera. Importantly, they found that cocktails of monoclonals could suppress viral escape. Lastly, through analysis of SARS-CoV-2 sequences, they also identified naturally occurring variants that are resistant to the monoclonals. Collectively, these data help further our understanding of the potential escape pathways of SARS-CoV-2 and have implications for developing therapies and vaccines.
Nov. 6, 2020
By Linda J. Saif, Distinguished University Professor, The Ohio State University, Wooster.
The effect of influenza vaccination on trained immunity: impact on COVID-19 by P. A. Debisarun, et al. medRxiv 2020.
Trained immunity is the concept that innate immune cells are trained via epigenetic and metabolic reprogramming during primary exposure to a vaccine or infection to produce enhanced secondary responses to an unrelated infection. This confers non-specific innate immune memory. Certain live vaccines, such as Bacille Calmette-Guérin (BCG), measles and oral polio, are reported to induce innate memory and cross-protection against unrelated viral infections. Currently, clinical trials are ongoing to assess if BCG vaccination may protect against COVID-19, since previous studies indicate that it can protect against certain viral respiratory tract infections in children; likewise for influenza vaccines and COVID-19.
The authors investigated the effects of an inactivated influenza vaccine ± BCG on trained immunity in vitro using peripheral blood mononuclear cells (PBMCs) from healthy volunteers. Variable and vaccine dose-related cytokine responses were observed when the primed, but not the unprimed, PBMCs were stimulated with SARS-CoV-2, suggesting varying patterns and levels of trained immunity. However, the in vitro data were limited to a few cytokines and did not include interferon responses (except Interferon (IFN)-gamma) that play key roles in innate immunity; nor were the contributing PBMC myeloid innate cell types defined. In an in vivo study, based on observation data with potential confounders, a significantly lower incidence of SARS-CoV-2 infection was reported among relatively young Dutch hospital employees (mean of 39-44 years) who received the inactivated influenza vaccine vs non-vaccines. However, there is other contradictory information on the impact of influenza vaccines on COVID-19 cases (De Wals and Divangahi, medRxiv 2020). The type of influenza vaccine (live vs. inactivated), the heterologous respiratory infection and its timing relative to vaccination, and most critically the influenza vaccinated age group and vaccine efficacy, may all influence both trained immunity and the impact of influenza vaccines.
More detailed in vitro and in vivo studies are warranted to define the impact of influenza vaccines on both trained immunity and SARS-CoV-2 infection. Relevant in vivo studies include investigations using animal models, such as ferrets susceptible to influenza and SARS-CoV-2 infections, in addition to well-designed epidemiologic studies in humans receiving influenza vaccines and exposed to SARS-CoV-2. Furthermore, as emphasized by the World Health Organization (WHO), because both positive and negative “off-target” effects of vaccines are evident (especially in children), it is critical to investigate the nonspecific effects of vaccines and trained innate immunity on subsequent infections.
Oct. 23, 2020
By Yi-Wei Tang, M.D., Ph.D., F(AAM), FIDSA, Chief Medical Officer, Danaher Diagnostic Platform and Cepheid (China), Shanghai. Dr. Tang is one of the curators of the Registry.
Saliva as a Candidate for COVID-19 Diagnostic Testing: A Meta-Analysis by Czumbel, L. M. et al. from Frontiers in Medicine.
Although the use of nasopharyngeal swab (NPS) specimens remains the “gold standard” for upper respiratory system sampling, the use of alternative specimens has been widely explored to overcome the supply shortages and to avoid clinician exposure. Saliva, which can be tracked back to 2003 in Hong Kong, when the SARS outbreak occurred, has been proposed as a promising alternative that could simplify and accelerate COVID-19 diagnosis.
The article by Czumbel and colleagues conducted a meta-analysis on the reliability and consistency of SARS-CoV-2 viral RNA detection in saliva specimens. The systematic search revealed 96 records after removal of duplicates. Twenty-six records were eventually included for analysis. Overall the sensitivity was 91% (CI 80–99%) for saliva tests and 98% (CI 89–100%) for NPS tests in previously conﬁrmed COVID-19 patients, with moderate heterogeneity among the studies. Additionally, 18 registered, ongoing clinical trials of saliva-based tests were also identified for detection of the SARS-CoV-2 virus. The authors concluded that saliva tests offer a promising alternative to NPS for COVID-19 diagnosis; however, further diagnostic accuracy studies are needed to improve their speciﬁcity and sensitivity.
Due to the nature of the metanalysis, the authors were not able to address the definition and quality control of the saliva. Instead of a simple spit, the ideal “saliva” specimen covering upper respiratory tract for SARS-CoV-2 testing should be a “hock a loggie” specimen, i.e., to cough up and spit out phlegm or saliva. To set up a standard of procedure for collecting the ideal saliva is difficult, especially for patient self collection (accessed Oct. 7, 2020). In addition, determination and standardization of saliva quality remains an unmet issue in quality assurance and quality control. Regulatory bodies need to catch up to address this deficiency. Until April 2020, the U.S. Food and Drug Administration (FDA) granted emergency use authorization (EUA) to 2 devices for use of saliva specimens for COVID-19 infection. Saliva testing on other EUA SARS-CoV-2 devices has been reported and we are looking forward to more independent, scientiﬁc analyses to establish their eﬀectiveness.
The authors acknowledged a limitation of their paper is the relatively small number of studies and small sample sizes available regarding this topic. Several relevant studies have been published after April 25, 2020 and we are looking forward to next version of metanalysis and literature review covering larger study numbers and sample sizes.
Oct. 9, 2020
By Sonia Navas-Martin, Ph.D., Associate Professor, Drexel University College of Medicine, Philadelphia. Dr. Navas-Martin is one of the curators of the Registry.
Loss of Bcl-6-Expressing T Follicular Helper Cells and Germinal Centers in COVID-19 by Kaneko, N. et al. Published in Cell on Oct. 1, 2020.
The immune response to coronaviruses remains poorly understood. Endemic human coronaviruses associated with the common cold are known to induce non-durable humoral immune responses. Similarly, there is rapid decay of anti–SARS-CoV-2 IgG in early infection in patients with mild COVID-19. Previous studies in COVID-19 autopsies have identified splenic white pulp atrophy and lymphocyte depletion in spleen and lymph nodes. Pillai, Pradera, and colleagues provide novel mechanistic insights into a paramount, unresolved question: Why humoral immunity to human coronaviruses’ infection is short lived?
This study examined post mortem thoracic lymph nodes and spleens in acute severe SARS-CoV-2 infection. Germinal centers in secondary lymphoid organs are responsible for the induction of high-affinity pathogen-specific antibodies and long-lasting B cell memory. Using quantitative multi-color immunofluorescence combined with multispectral imaging and cell-cell interaction analyses of autopsy specimens as well as analyses of peripheral blood samples in parallel cohorts with acute, severe SARS-CoV-2 infection, this study demonstrates dysregulated humoral immune induction early in COVID-19, including absence of germinal centers in the earliest stages of infection, defective Bcl6+ T follicular helper (TFH) cell generation, and aberrant lymphoid TNF (Tumor Necrosis Factor)-alpha production. Interestingly, although there is a marked reduction of germinal center B cells, activation-induced cytidine deaminase (AID)-expressing B cells are preserved, indicating that activated helper T cells are still likely to be in contact with antigen-specific B cells. Therefore, although there is robust T-cell-mediated activation of B cells, germinal centers do not form. Thus, robust activation of non-germinal center type B cell responses does not give rise to long-lived memory or high-affinity B cells. The study suggest a link between changes in the extra-follicular cytokine milieu driven by TH1 cells and the aberrant local production of TNF-a in lymphoid organs and the failure of differentiation of Bcl-6+ TFH cells. A potential hypothesis is that circulating factors in severely ill COVID-19 patients may impair GCTFH cell differentiation and thus abrogate the generation of germinal centers. Overall, these findings have implications for heard immunity and the development of efficient SARS-CoV-2 vaccines. It will be important to continue these studies in suitable SARS-CoV-2 animal models.
Sept. 17, 2020
By Dr. Catherine J. Pachuk, Chief Scientific Officer at Somahlution, Inc.
COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing by To, K. et al. published on the Clinical Infectious Diseases on August 25, 2020.
Accounts of reinfection have been reported in individuals following apparent recovery from initial infection with SARS-CoV-2. In the absence of sufficient supporting data, it is not clear whether these reports documented reinfection or have instead described cases of prolonged viral shedding.
To et al. present the first well-documented case of SARS-CoV-2 reinfection in a patient who first tested positive in mid-March, became ill, was hospitalized and later released following two serial negative nasopharyngeal swabs. Approximately 4.5 months later, upon border screening in Hong Kong, he tested positive again, but remained asymptomatic. Whole genome sequencing on samples collected during both episodes demonstrated that the two viral genomes were phylogenetically distinct, mapping to two different GISAID clades indicating the patient was re-infected opposed to shedding virus over an extended time.
It is not known if reinfection is associated with differences in viral load compared to initial infection, however, the case for active infection during the second episode was supported by elevated CRP values and relatively high viral RNA load with gradual decline; the patient was therefore presumably still infectious. Asymptomatic reinfection or reinfection associated with milder disease is consistent with the presence of pre-existing adaptive immune responses induced following first exposure and is consistent with studies in which vaccination of Rhesus macaques conferred protection against disease but not viral infection.
The results demonstrate that reinfection is possible (at least with viruses having sufficient sequence differences) and may be associated with asymptomatic or milder disease, although the generalizability of this is not known. The results suggest that immune responses elicited by natural infection (and perhaps vaccination) may not confer “sterilizing immunity” against future infections and individuals may still become infected and transmit virus after vaccination and/or resolution of initial infection.
Sept. 4, 2020
By Dr. Ben Neuman, Professor of Biology & Chair of Biological Sciences, Texas A&M University — Texarkana
Camostat mesylate inhibits SARS-CoV-2 activation by TMPRSS2-related proteases and its metabolite GBPA exerts antiviral activity by Hoffmann, M. et al., posted on BioRxiv on August 5, 2020.
Most kitchens have an “everything drawer” – a wonderful place where you can find batteries, binder clips or spare keys. The search for SARS-CoV-2 antivirals has led many groups to search the everything drawer of experimental medicine - screening libraries of approved compounds for serendipitous antiviral effects.
Among the first potential antivirals to come out of the drawer are the serine protease inhibitors nafamostat and camostat, originally developed to inhibit coagulation and treat pancreatitis. In a series of papers (Zhou Y. et al., Hoffmann M. et al., Hoffmann M. et al., culminating with the recent preprint by Hoffmann M. et al.), Stefan Pöhlmann’s lab has identified nafamostat mesylate and camostat mesylate as potent inhibitors of SARS-CoV-2 entry in cell culture. Both nafamostat and camostat prevent host transmembrane serine proteases (TMPRSS) including TMPRSS2 from cleaving the viral spike protein to free the viral fusion peptide and initiate the post-attachment steps of viral entry.
This study is the most careful and mechanistic to date on the effects of camostat. Four additional TMPRSS isoforms are identified as facilitators of SARS-CoV-2 entry. This study even tracks the conversion and potency of camostat metabolites 4-(4-guanidinobenzoyloxy)phenylacetic acid (GBPA) and guanidino-benzoate (GBA).
Perhaps the greatest value in a study like this is to work out a clear mechanism of action. While we wait for the results of clinical trials to find out if camostat is effective in COVID-19 patients, there is some comfort in its relative mechanistic simplicity. Even though we cannot be sure camostat will work in people, if it does, at least we will have a good idea why.
By Tom Gallagher, Ph.D., Professor, Loyola University Chicago
Aug. 14, 2020
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin by Krafcikova, P. et al. and Structural basis of RNA cap modification by SARS-CoV-2 by Viswanathan, T., et al., both published July 24, 2020 in Nature Communications.
Combination therapies simultaneously targeting several SARS-CoV-2 infection events can provide synergistic antiviral efficacy. Hence there are incentives for drugs disabling virus entry, polyprotein proteolysis and ribonucleic acid (RNA) replication. Additional drugs may effectively compromise the viral RNA modifications taking place as 5’ RNA caps are constructed. Coronavirus nonstructural protein 14 (nsp14) and nonstructural protein 16 (nsp16) enzymes methylate viral RNA caps, which increases RNA translation and decreases RNA recognition by the innate immune system. Therapeutics inhibiting these viral methyltransferases are promising antivirals.
Structural resolution of antiviral targets advances COVID19 therapeutic development. The articles by Krafcikova et al. and Viswanathan et al. are 2 of several recent reports on the structure of the SARS-CoV-2 nsp16. The 2 reports provide several insights. Krafcikova et al. show how nsp16 interfaces with a nonstructural protein 10 (nsp10) cofactor, revealing the challenges and the possibilities for drugs preventing nsp10-mediated methyltransferase activation. They also provide the position of a pan-methyltransferase inhibitor (sinefungin) within nsp16, along with modeled RNA substrate in a positively charged groove. This sets the stage for developing virus-specific active site inhibitors. Viswanathan et al. report RNA cap and methyl donor (SAM) locations within nsp16, and they reveal an induced fit model of RNA substrate binding. They also document a distal ligand binding site on nsp16, suggesting drug targets beyond the location of methyltransferase action. The reports provide frameworks for drug discovery, and with medicinal chemistry and clinical studies, there will be ever greater potential to bring methyltransferase inhibitors into the arsenal of therapeutics suppressing SARS-CoV-2 and related coronavirus infections.
July 31, 2020By Leo Poon, Professor, School of Public Health, The University of Hong Kong
Comprehensive mapping of immune perturbations associated with severe COVID-19 by Kuri-Cervantes, L. et al, Science Immunology 2020.
Most COVID-19 patients develop mild (40%) or moderate (40%) symptoms, whereas some can have severe (15%) or critical clinical outcomes. Such heterogeneity of disease spectrum is very different from the one of SARS. The underlying reasons accounting for this are not clear.
In order to determine immune parameters that might associate with the disease severity of COVID-19, a team from Philadelphia have conducted a comprehensive immune profiling analysis in 42 COVID-19 patients (7 mild, 28 severe and 7 recovered cases). Similar to others’ findings, several immune parameters (e.g., neutrophil-to-lymphocyte ratio and neutrophil:T cell ratio) correlate with disease severity. They also report severe COVID-19 cases tend to have reduced expression of CD16 on some innate immune cells (e.g., neutrophil, NK cells and monocytes). In addition, they report severe COVID-19 patients have increased activation of T cells and pronounced oligoclonal expansion of plasmablasts with long and divergent complementarity determining regions (CDR3) sequences. These results indicate that the immune responses of severe COVID-19 cases are different from those of mild ones. Some of these new parameters might be used as immune correlates for disease severity. Nonetheless, further systematic investigations on these immune subsets are needed to explain the pathogenesis of severe COVID-19 infection.
Several studies have demonstrated that severe COVID-19 patients have robust Immunoglobulin G (IgG) and Immunoglobulin M (IgM) responses. With the findings on B cells from the above study, it is of great interest to know the quality of antibodies produced by severe COVID-19 patients. In particular, long CDR3 sequences may relate to non-specific cross reactivity and/or immunopathology. Such analysis might provide useful information to advice clinical treatment, prognosis and vaccine development.
July 17, 2020By Michael Loeffelholz, Ph.D., D(ABMM), Senior Director, Medical Affairs, Cepheid and Adjunct Professor, Department of Pathology, University of Texas Medical Branch. Dr. Loeffelholz is one of the curators of the Registry.
“Diagnostic technology for COVID-19: comparative evaluation of antigen and serology-based SARS-CoV-2 immunoassays, and contact tracing solutions for potential use as at-home products” by Jorfi, M. et al. from medRxiv preprint server.
Testing and contact tracing are essential components of the approach to control the COVID-19 pandemic. Access to testing is crucial. At-home testing is a potential means to increase access. Manual contact tracing is labor intensive and requires a considerable amount of human resources. Personal electronic device-based contact tracing employing smartphones and wearable sensors is another potential approach. The preprint by Jorfi and colleagues describes their horizon scan, a systematic process to identify new technology with the potential for future impact, for antigen and serology diagnostics with the potential for use as at-home testing. The authors also assessed personal electronic technologies for contact tracing.
A systematic review of diagnostic tests, including literature and internet review, interviews of subject matter experts, and application of diagnostic test specification criteria such as performance characteristics, specimen types, and scalability identified over 300 candidates, including 138 serology and 44 antigen tests. The horizon scan, consisting of an algorithm to score tests identified in the systematic review, identified 24 antibody tests potentially suitable for at-home use, for further laboratory evaluation. Additionally, personal device-based electronic platforms were evaluated for potential contact tracing and the authors identified 26 potential smartphone solutions.
With increasing need for more and faster SARS-CoV-2 testing, we must consider the possibility of future at-home products. The work described in this preprint provides a framework for the identification and assessment of current diagnostic and electronic contact tracing products for their potential suitability for at-home use.
June 26, 2020By Richard L. Hodinka, Ph.D., Professor, University of South Carolina School of Medicine Greenville; Emeritus Professor, Perelman School of Medicine at the University of Pennsylvania. Dr. Hodinka is one of the curators of the Registry.
Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit by Nalla, A.K. et al. published in the Journal of Clinical Microbiology on May 26, 2020.
Various primer-probe sets have been developed and are being used for molecular detection of SARS-CoV-2 RNA in clinical specimens. Validation of the performance characteristics of assays using these primers and probes is needed.
The article by Nalla and colleagues is of high value and provides useful information on the comparative performance of seven different primer-probe sets and one commercial reagent kit for the detection of SARS-CoV-2 RNA when used in laboratory-designed molecular assays. Laboratories pursuing their own development, validation and implementation of in-house molecular-based assays will find this information to be helpful and it may save them much needed time and resources as they work to rapidly optimize assay performance and increase their testing capacity to meet demands.
Panels of respiratory specimens positive and negative for SARS-CoV-2 and those positive for influenza A and B, respiratory syncytial virus, parainfluenza virus, adenovirus, metapneumovirus, rhinovirus, bocavirus, and coronaviruses other that SARS-CoV-2 were examined. Nucleic acid extraction was performed on Roche MagNA Pure LC 2.0 and MagNA Pure 96 systems. Primer/probe sets against the RdRp, E, N1, N2, and N3 genes were used for SARS-CoV-2 RNA detection. RT-PCR was performed using Life Technologies AgPath-ID One Step master mix and an Applied Biosystems ABI 7500 real-time PCR system. A complete detection kit from BGI targeting the ORF1ab gene was also examined.
Overall, the authors observed variability in the sensitivities of the testing when using the different primer-probe sets and commercial reagent kit. Assays using the E-gene primer-probe set described by Corman et al. (https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045) and the N2 set developed by the Division of Viral Diseases, Centers for Disease Control and Prevention (https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-primer-probes.pdf) were found to be the most sensitive. All assays tested were highly specific for SARS-CoV-2, showing no cross-reactivity with other commonly encountered respiratory viruses.
June 12, 2020By Dr. Frederick G. Hayden, Professor Emeritus, Medicine: Infectious Diseases and International Health at the University of Virginia. Dr. Hayden is one of the curators of the Registry.
Mechanism of baricitinib supports artificial intelligence-predicted testing in COVID-19 patients by Stebbing, J., et. al. published in EMBO Molecular Medicine on May 30, 2020.
The article by Stebbing and colleagues provides important new data on baricitinib, an immunomodulatory therapeutic of particular interest for COVID-19 treatment because of its documented anti-inflammatory properties and potential inhibition of coronavirus replication. The antiviral effect is postulated to be mediated by its affinity for AP2-associated protein AAK1 leading to reduced SARS-CoV-2 endocytosis. Baricitinib (trade name Olumiant, Eli Lilly and Company) is an oral inhibitor of Janus kinase (JAK)1 and JAK2 that is approved for the treatment of moderately to severely active rheumatoid arthritis in adults. Stebbing et al. show that baricitinib also inhibits numb-associated kinase (NAK) family members that includes AAK1 and that baricitinib exerts some antiviral effects against SARS-CoV-2 in in liver organoids, although at relatively high concentrations. The article also presents observational data from four baricitinib-treated COVID-19 patients.
Type I interferons trigger the Janus kinase/signal transducer and activator of transcription (Jak-Stat) signaling pathway that activates many antiviral genes, so that an inhibitor like baricitinib could facilitate virus replication. Baricitinib treatment causes dose-related decreases in interferon biomarkers in patients with interferonopathy-related auto-inflammatory disorders (Kim, 2018), and chronic therapy for rheumatoid arthritis has been associated with reactivation of latent herpes and polyomavirus infections and other serious infections (Favalli, 2020). Whether enhanced SARS-CoV-2 regulation might occur in an acute infection like COVID-19 remains to be determined.
A small, open-label observational trial of baricitinib added to lopinavir-ritonavir in hospitalized patients with moderate COVID-19 pneumonia reported that illness measures, respiratory function, and CRP elevations significantly improved both at week 1 and week 2 compared to baseline and to a historical control-group receiving lopinavir-ritonavir plus hydroxychloroquine (Cantini, 2020). A number of other clinical trials with baricitinib are in progress, including a large NIAID-sponsored randomized, placebo-controlled clinical trial (NCT04401579 ) is evaluating the safety and efficacy of a combination treatment regimen of remdesivir plus baricitinib compared to remdesivir for hospitalized COVID-19 patients.
May 29, 2020By Dr. C.A.M. de (Xander) Haan, Associate Professor, Utrecht University.
BCG-induced trained immunity: can it offer protection against COVID-19? by O’Neill, L.A. and Netea, M.G., Nature Review Immunology.
Bridging the SARS-CoV-2 vaccine gap by Bacille Calmette-Guérin (BCG) vaccination?
Development of a SARS-CoV-2 vaccine is expected to take at least 12-18 months. The authors of this comment propose that the BCG live attenuated vaccine, which was developed against tuberculosis a century ago, may be used to bridge this gap. Although currently there is no evidence that BCG protects against SARS-CoV-2 infection or disease, previous studies indicate that BCG can protect against viral respiratory tract infections in children.
This non-specific protective effect is proposed to be mediated by epigenetic changes that lead to long-term transcriptional programming of immune cells, resulting de facto in the induction of innate immune memory, termed trained immunity. Upon challenge with another pathogen, the trained immune cells then show an enhanced response, thereby promoting host defense.
Randomized controlled clinical trials are needed to provide evidence for the hypothesis that BCG vaccination may protect against COVID-19. Currently, such clinical trials are ongoing or being planned in different countries. Care should be taken that BCG vaccination to protect against COVID-19 will not cause, however, an increase of disease and deaths from tuberculosis resulting from vaccine shortages.
May 15, 2020
By Linda J Saif, Distinguished University Professor, The Ohio State University, Wooster, Ohio.
Trinity of COVID-19: Immunity, inflammation and intervention by Tay, M.Z., et al, Nat Rev Immunol 2020.
To date many approaches to therapeutic interventions for COVID-19 are empirical or based on only limited knowledge of SARS-CoV-2 infections. Based on increasing numbers of global reports, a clearer understanding of SARS-CoV-2 pathogenesis and pathophysiology is emerging to guide the rational design of targeted interventions. This is the topic of the selected review.
This review of the pathophysiology of SARS-CoV-2 infections is comprehensive and timely. The authors highlight the temporal sequence of coronavirus replication in respiratory tract cells and induction of healthy immune responses. They then characterize the chronology and potential contribution of dysfunctional immune responses to disease progression, focusing on the observed uncontrolled inflammation and cytokine storm leading to acute respiratory distress syndrome. Important and pertinent aspects of SARS and MERS coronavirus pathogenesis are compared to illuminate related data on SARS-CoV-2 infections. A table of relevant interventional clinical trials (March 2020) is included, but more updated versions are available on the WHO web site.
Significant conclusions include:
- Combined synergistic therapies are needed to inhibit both virus infection and regulate the dysfunctional immune responses.
- Studies of healthy versus dysfunctional outcomes and their chronology are critical to elucidate biomarkers of disease severity that will aid in the rational design of targeted interventions and a timeline for their application.
- Identification of biomarkers for immune correlates of protection and those related to disease severity are important for the design of safe and efficacious vaccines to circumvent immunopathology and to induce protection, respectively.
Unknowns that require additional research are how age, sex, genetics, co-morbidities, hypoxia, co-infections, immune landscape, microbiota, drug treatments, etc contribute to SARS-CoV-2 susceptibility, dysfunctional immune responses and disease severity. More information on innate immune responses is needed. A comprehensive, One Health, multi-disciplinary approach is highly relevant to answer these questions. Examples include: How do the coronavirus ancestor host species (bats) cope with SARS-like coronavirus infections to render them innocuous? How do the incidental hosts (cats, felids, ferrets, mink, non-human primates, etc) respond to SARS-CoV as a largely asymptomatic or mild infection? How do the above parameters influence the pathophysiology and severity of the disease and immune responses in humans compared with the animal disease models? Continued studies of the full spectrum of coronavirus disease (enteric, respiratory, systemic, and nervous systems) in naïve and partially immune natural host species are also warranted to delineate the impact of coronavirus infections on multiple organ systems and immune responses and to test potential targeted interventions, including vaccines.
May 1, 2020
By John J. Dennehy, Ph.D., Professor at Queens College and The Graduate Center of CUNY.
As the world struggles to overcome the COVID-19 pandemic, one fact is clear: testing and contact tracing will be a part of the solution. However, difficulties scaling up test capacity remain an issue. Test conductors are beset by logistical problems with every aspect of the workflow, from supply chains to operational coordination.
A preprint from a Yale University team suggests a way to alleviate some of these issues, while also increasing test reliability. Wyllie et al. report that tests of saliva for SARS-CoV-2 returned greater detection sensitivity and consistency throughout the course of infection than did patient-matched samples acquired from nasopharyngeal swabs. It is likely that larger sample volumes provided by saliva sampling reduce inconsistencies in sampler technique.
The results are significant for 3 reasons:
- SARS-CoV-2 test performance is already troubled by false negative results, so greater reliability is clearly indicated.
- Nasopharyngeal swabs, considered the gold standard of COVID-19 testing, have been in short supply. Dispensing with swabs will streamline test logistics.
- Nasopharyngeal swabbing is usually performed by trained medical personnel. Saliva sampling can be performed at home and submitted by post, alleviating demands on both patients and health care workers.
Further research of both COVID-19 positive and negative participants will reveal if saliva testing is ready for wider application.