From the Curator-in-Chief's Desk

April 14, 2020


Dear Colleagues,

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 to 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.

Sincerely,

Lynn Enquist, Ph.D., 
Curator-in-Chief
Lynn Enquist, Ph.D., Curator-in-Chief
 
Harold Varmus, M.D., 
Chief Consultant
Harold Varmus, M.D., Chief Consultant

 


​Biweekly Commentary Letters

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.



Aug. 14, 2020

By Tom Gallagher, Ph.D., Professor, Loyola University Chicago
 
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, 2020

By 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, 2020

By 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, 2020

By 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, 2020

By 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, 2020

By 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:

  1. Combined synergistic therapies are needed to inhibit both virus infection and regulate the dysfunctional immune responses.
  2. 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.
  3. 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:

  1. SARS-CoV-2 test performance is already troubled by false negative results, so greater reliability is clearly indicated.
  2. Nasopharyngeal swabs, considered the gold standard of COVID-19 testing, have been in short supply. Dispensing with swabs will streamline test logistics.
  3. 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.