BV-BRC Viral Sub-species Classification Workshop at NIAID Rockville, MD, April 8-10, 2024


A critical aspect of the response to the COVID-19 pandemic was to trace, classify, and understand the evolving virus lineages, their phenotypic differences, and their impact on diagnostics, vaccines, and therapeutics. Classification and tracing of sub-species level variation has also been similarly important in outbreaks of viruses such as influenza, HIV, and monkeypox, and has informed public health risk assessment and communication strategies. To prepare for the next inevitable outbreak of virus disease, the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), along with the CDC, NCBI, and NIAID, HOSTED a hybrid workshop on viral sub-species classification. Workshop objectives include the review of various classification schemes developed for SARS-CoV-2 and other viruses, examination of the methods and tools developed for classification, discussion of the utility and impact of classification schemes on the public health response, and review of lessons learned from past and current outbreaks. The outcome of the workshop will be to define best practices for establishing sub-species classification systems for these and other viruses that will be important in controlling future outbreaks and potential pandemics. The valuable insights and best practices from this workshop will be widely disseminated.

All video recordings of the workshop can be found here, in the YouTube Playlist BV-BRC Viral Sub-species Classification Workshop at NIAID Rockville, MD, April 8-10, 2024.

Workshop Highlights

Session One, led by Elliot Lefkowitz, tracked virus evolution and its impact on sub-species. Dr. Richard Neher discussed RNA virus spread, followed by Dr. Bette Korber’s insights on SARS-CoV-2 and HIV variants.

Session Two, moderated by Dr. Rodney Brister, explored RNA and DNA virus complexity. Dr. Justin Bahl discussed RNA virus evolution, Dr. Tavis Anderson spoke on influenza A virus, and Dr. Jens Kuhn covered Filovirus nomenclature.

Session Three, moderated by Dr. Conrad Schoch, explored diverse perspectives on virus classification, featuring discussions on Influenza, SARS-CoV-2, and virus classification from Dr. Derek Smith and Dr. Peter Simmonds, respectively.

Session Four, moderated by Dr. Richard Scheuermann, delved into classification schemes, featuring discussions from Dr. Jens H. Kuhn on ICTV taxonomy, Dr. Krista Queen about GISAID classification, Dr. Áine O’Toole, on the Pango system development, and its future beyond the SARS-CoV-2 pandemic from Dr. Rachel Colquhoun.

Session Five, moderated by Dr. Eneida Hatcher, focused on tools for viral evolution classification. Dr. Cornelius Roemer discussed Clade and lineage assignment, Dr. Angie Hinrichs presented UShER and autolin, and Dr. Christian Zmasek discussed BV-BRC sub-species classification tools.

Session Six, moderated by Indresh Singh, explored analytical and visualization tools for studying virus evolution during outbreaks. Dr. Eneida Hatcher discussed NCBI Virus and Taxonomy, Dr. Philippe Le Mercier presented Virus sub-species in ViralZone and UniProtKB, and Dr. Andrew Warren discussed virus mutational spectra visualization.

Session Seven, led by Dr. Paul Eder, addressed public health responses. Dr. Brown discussed NIAID’s disease prevention efforts, Dr. Beck shared CDC’s perspective, Dr. Rosamund Lewis explored viral evolution’s impact on pox outbreaks, and Dr. Xiong (Sean) Wang provided insights from the Minnesota Department of Health on virus surveillance.

Workshop Speakers amd Reading List





Bioinformatics Bottleneck

PMID: 33649511

Anderson, Tavis

U.S. Department of Agriculture

PMID: 37208300

Bahl, Justin

University of Georgia, U.S.

Beck, Andrew

U.S. Centers for Disease Control and Prevention (CDC)

PMID: 37516478

Brown, Liliana


Colquhoun, Rachel

University of Edinburgh, U.K.

PMID: 32669681

Donato, Celeste

Murdoch Children’s Research Institute, Australia

PMID: 37323680

Hatcher, Eneida

National Center for Biotechnology Information (NCBI), U.S.

Hinrichs, Angie

University of California Santa Cruz, U.S.

PMID: 38316930, PMID: 38155331

Korber, Bette

Los Alamos National Labs, U.S.

Kuhn, Jens H.

NIH/NIAID/DCR Integrated Research Facility at Fort Detrick, U.S.

PMID: 23001720, PMID: 37141106

Le Mercier, Philippe

Swiss-Prot group, Swiss Institute of Bioinformatics, Switzerland

PMID: 37897348

Lefkowitz, Elliot

University of Alabama at Birmingham (UAB), U.S.

PMID: 37710003

Lewis, Rosamund

World Health Organization

PMID: 37710003

Neher, Richard

University of Basel, Switzerland

O’Toole, Áine

University of Edinburgh, U.K.

PMID: 35998195

Queen, Krista

LSU Health Shreveport, U.S.

Roemer, Cornelius

University of Basel, Switzerland

JOSS 03773

Seto, Donald

George Mason University, U.S.

PMID: 38275969, PMID: 34618969

Simmonds, Peter

University of Oxford, U.K.

PMID: 36780432

Smith, Derek J

University of Cambridge, U.K.

PMID: 36780432

Wang, Sean

Minnesota Department of Health, U.S.

Warren, Andrew

University of Virginia, U.S.

PMID: 34520557, PMID: 38361813

Zmasek, Christian

J.Craig Venter Institute, U.S.

PMID: 27981236, PMID: 21034504, PMID: 33972780

Full details of publications from pre-reading list can be found here.