COVID-19 Research Registry

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Lynn Enquist, Ph.D.
Curator-in-Chief

Keeping up with the most recent research publications is challenging for any investigator, but when hundreds of publications and preprints are appearing every week on SARS-CoV-2, the task can be overwhelming. The launch of the ASM COVID-19 Research Registry (Registry) was a milestone for ASM in response to the needs of the scientific community.

The goal of the Registry is not to be a simple collection of publications. We seek to provide a "one-stop shop" of authoritative information of fundamental research on SARS-CoV-2. We want the Registry to bring together traditional and non-traditional microbiology researchers and experts and provide them with reliable and up-to-date scientific information about SARS-CoV-2 studies. Moreover, the Registry aims to be the go-to source for educators and students who want to find solid materials for teaching and learning about SARS-CoV-2 and COVID-19.

In a short time, we have established the Registry site and system that provides aggregated access to vetted fundamental research on SARS-CoV-2, and other selected viruses. Every week, the ASM Registry staff funnel research articles to our expert curators who chose the best preprints and publications. These items are added continuously to the site. Our curators continue to recommend previously published and impactful papers. Collectively, you can find over 120 high quality papers on the Registry today.

We hope new connections and new ideas will develop. A new feature, Research Resources, was added to the Registry. There, we will include research tools and information for the research community.  For example, for those who want to see a more encyclopedic account of what is being reported about COVID-19, the NIH Office of Portfolio Analysis has a good dashboard to follow the numbers of publications and preprints.

Sincerely,

Lynn Enquist, Ph.D.
Curator-in-Chief

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Bi-weekly Commentary

Published on June 26th, 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.

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Video & other curricular resources for COVID-19

• Antimicrobial Agents and Chemotherapy (AAC) Podcast: Therapeutic approaches for COVID-19: Myths and Facts.
• Science Forum: SARS-CoV-2 (COVID-19) by the numbers.
• Vaughn Cooper: “The ongoing evolution of SARS-CoV-2” April 1, 2020 (YouTube11:21).
• Dr. Pamela Bjorkman: Intro to Viruses, Antivirals, and Vaccines April 10, 2020 (YouTube 52:57).
• Scott Page: Understanding Fatality Rate Models  April 3, 2020 (YouTube 10:12).
• Minute Physics: "How to tell if we’re beating Covid-19"  March 27, 2020 (YouTube 7:15).
• 3 Blue 1 Brown "Simulating an Epidemic"  March 27, 2020 (YouTube 2:07).
• Britt Glaunsinger: "Coronaviruses 101, Focus on Molecular Virology"  March 25, 2020 (YouTube 1:02:18).
• Vaughn Cooper: "Evolutionary Biology of Novel Coronavirus SARS-CoV-2"  March 24, 2020 (YouTube 11:48).
• Pennings and colleagues: "How does SARS-CoV-2 spread?"  March 24, 2020 (Vimeo 8:25).
• Nick Jewell "The Exponential Power of Now"  March 19, 2020 (YouTube 1:06:00).
• Online Marty: "Disease Spread Simulation"  March 18, 2020 (YouTube 2:52).
• Pennings and colleagues: "Coronavirus in numbers"  March 11, 2020 (Vimeo 10:18).
• Pennings: "SARS-CoV-2 and phylogenetic trees"  March 2, 2020 (Vimeo 14:15).
• University of Pennsylvania: "Coronavirus Outbreak Symposium"  April 3, 2020 (YouTube).
• Coursera: Fighting COVID-19 with Epidemiology: A Johns Hopkins Teach-Out  (Free Course).

Blogs, Articles, and Opinions

• Atul Gawande: Amid the Coronavirus Crisis, a Regimen for Re-entry.
• Dougan and Holt: “How to make a new COVID-19 vaccine starting from scratch” April 9, 2020.