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

Published on 2024-02-23 00:00:00

Updated on 2024-04-10 00:00:00

Meeting dates: April 8-10, 2024 Registration  

Bacterial and Viral Bioinformatics Resource Center

Workshop is funded in part by National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. 75N93019C00076, in collaboration with the Centers for Disease Control and Prevention (CDC) and The National Center for Biotechnology Information, National Library of Medicine.

Community Forum for follow up discussions and feedback:

Please visit the following reddit thread for follow up discussions on viral sub-species classification and share your suggestions and/or feedback with the workshop committee.

• Introduction

• Workshop Logistics

• Registration

• Pathogens

• Workshop Speakers

• Workshop Agenda

Introduction

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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, are hosting 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 out breaks and potential pandemics. The valuable insights and best practices from this workshop will be widely disseminated.

Workshop Logistics

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Date & Time

• Apr 8, 2024 | 09:30 AM - 6:00 PM

• Apr 9, 2024 | 09:30 AM - 5:30 PM

• Apr 10, 2024 | 09:00 AM - 12:00 PM

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• Time shows in Eastern Time (US and Canada)

Registration

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Please register for virtual workshop participation here . The virtual workshop participants can actively participate by providing feedback and ask questions throughout the event.

Pathogens

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The focus of the workshop will be on viral pathogens. The viruses discussed will include those with established classification schemes as well as viruses defined by NIH/NIAID as prototype pathogens with pandemic potential (PMCID: PMC9384504).

Workshop Speakers

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Name	Affiliation
Anderson, Tavis	U.S. Department of Agriculture
Bahl, Justin	University of Georgia, U.S.
Beck, Andrew	U.S. Centers for Disease Control and Prevention (CDC)
Brown, Liliana	NIH/NIAID
Colquhoun, Rachel	University of Edinburgh, U.K.
Donato, Celeste	Murdoch Children’s Research Institute, Australia
Hatcher, Eneida	National Center for Biotechnology Information (NCBI), U.S.
Hinrichs, Angie	University of California Santa Cruz, U.S.
Korber, Bette	Los Alamos National Labs, U.S.
Kuhn, Jens H.	NIH/NIAID/DCR Integrated Research Facility at Fort Detrick, U.S.
Le Mercier, Philippe	Swiss-Prot group, Swiss Institute of Bioinformatics, Switzerland
Lefkowitz, Elliot	University of Alabama at Birmingham (UAB), U.S.
Lewis, Rosamund	World Health Organization
Neher, Richard	University of Basel, Switzerland
O’Toole, Áine	University of Edinburgh, U.K.
Queen, Krista	LSU Health Shreveport, U.S.
Roemer, Cornelius	University of Basel, Switzerland
Seto, Donald	George Mason University, U.S.
Simmonds, Peter	University of Oxford, U.K.
Smith, Derek J	University of Cambridge, U.K.
Wang, Sean	Minnesota Department of Health, U.S.
Warren, Andrew	University of Virginia, U.S.
Zmasek, Christian	J.Craig Venter Institute, U.S.

Workshop Agenda

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Agenda, Questions and Discussions at Reddit here

April 8, Day 1: Virus Sub-species Classification: What and Why

Time	Topic	Title	Presenter
9:30 AM - 10:00 AM	Welcome and Introduction	Goals, Expectations, and Logistics	Elliot Lefkowitz (UAB) Wiriya Rutvisuttinunt (NIAID) on behalf of the Organizing Committee
10:00 AM - 12:00 PM	Session I: Tracking virus evolution through sub-species classification The evolution of viruses during disease outbreaks and the impact this process has on sub-species classification, especially considering rapid rates of virus evolution. Moderator Elliot Lefkowitz, PhD, University of Alabama at Birmingham Panel and Session Topics [30-minute talks] Tracking and predicting the spread and evolution of RNA viruses Richard Neher, PhD, University of Basel, Switzerland   SARS-CoV-2 and HIV variant evolution Bette Korber, PhD, Los Alamos National Labs, U.S. Break [15 minutes] Q&A Panel Discussions [45 Minutes] How are viruses classified below the level of species? How does virus evolution impact outbreak response? How have past outbreaks challenged traditional/current virus classification? What are the implications of these findings for future outbreak preparedness and response? Use Reddit for questions and discussions here.
12:00 PM - 1:00 PM	Lunch
1:00 PM - 3:05 PM	Session II: Unraveling the complexities of RNA and DNA viruses Examples of the evolution of virus disease, the impact of lineage evolution on pathogenicity, and the consequences for classifying and responding to particular virus threats. Moderator James Rodney Brister, PhD, NCBI Panel and Session Topics [15-minute talks] Evolution, epidemiology, and RNA virus disease Justin Bahl, PhD, University of Georgia   The evolution of influenza A virus at the human-animal interface Tavis Anderson, PhD, U.S. Department of Agriculture   Filovirus sub-species nomenclature Jens H. Kuhn, PhD, NIH/NIAID/DCR Integrated Research Facility at Fort Detrick   Rotavirus diversity, evolution, and lineage classification Celeste Donato, PhD, Murdoch Children's Research Institute Break Update on Human Adenoviruses Donald Seto, PhD, George Mason University   Monkeypox virus sub-species evolution Elliot Lefkowitz, PhD, University of Alabama at Birmingham Q&A Panel Discussions [20 Minutes] How are viruses classified? What biological and genetic features are used to support classification? Are complete genomic sequences required to support classification or are specific subgenomic regions sufficient? Are there common characteristics that can be used to classify all viruses or do distinguishing characteristics require multiple classification schemes? Is the current sub-species classification system for each virus sufficient to capture the relevant genetic diversity now and in the future? During disease outbreaks, are there specific mutations or common patterns of genetic variation observed in RNA or DNA viruses that impact pathogenesis? Use Reddit for questions and discussions here.
3:05 PM - 3:45 PM	Break Darkness descends on us all; big and small. Alive? Not necessarily all.
3:45 PM - 5:00 PM	White Board Brainstorming Session Moderators: Elodie Ghedin, PhD, NIAID Session Moderators Questions: To what extent can we leverage our understanding of virus evolution to improve classification, predict novel, impactful strains, develop more effective diagnostics and vaccines, and ultimately inform control and response strategies?

April 9, Day 2: Virus Sub-species Classification: How

9:30 AM - 9:35 AM	Welcome back and Recap of Day 1
9:35 AM - 10:45 AM	Session III: Diverse Viewpoints: Exploring Classification from Different Perspectives Exploring and understanding different virus classification systems and how they impact our responses to disease outbreaks. Moderator Conrad Schoch, PhD, NCBI Panel and Session Topics [20-minute talks] Influenza and SARS-CoV-2: Evolution, Immunity, and Surveillance Derek Smith, PhD, University of Cambridge   Virus classification and support for different stakeholders Peter Simmonds, PhD, University of Oxford Q&A Panel Discussions [30 Minutes] Can virus classification systems be designed to be both clear and adaptable, allowing for consistent communication while effectively tracking virus evolution? Can these sometimes conflicting goals be effectively addressed, especially during a disease outbreak? How does rapid virus evolution during outbreaks hinder current sub-species classification methods? Are there alternative approaches better suited for tracking these dynamic changes? Use Reddit for questions and discussions here.
10:45 AM - 11:00 AM	Break
11:00 AM - 12:15 PM	Session IV: Virus classification schemes Species and sub-species: Different approaches and schemes for the classification of viruses. Moderator Richard Scheuermann, PhD, National Library of Medicine (NLM) Panel and Session Topics [15-minute talks] The ICTV taxonomy: Classification and nomenclature Jens H. Kuhn, PhD, NIH/NIAID/DCR Integrated Research Facility at Fort Detrick   GISAID classification Krista Queen, PhD, LSU Health Shreveport (remote)   Perspectives on the development of the Pango system and software Áine O'Toole, PhD, The University of Edinburgh   Pango beyond the SARS-CoV-2 pandemic Rachel Colquhoun, PhD, The University of Edinburgh Q&A Panel Discussion [15 Minutes] How do the existing classification schemes impact our ability to track and respond to virus outbreaks? In what ways do these classification schemes influence public health interventions and vaccine development? Use Reddit for questions and discussions here.
12:15 PM - 1:15 PM	Lunch
1:15 PM - 2:30 PM	Session V: Virus classification tools Tools to explore virus evolution and their classification. Moderator Eneida Hatcher, PhD, NCBI Panel and Session Topics [20-minute talks] Clade and lineage assignment with Nextclade Cornelius Roemer, University of Basel, Switzerland   UShER and autolin: Identifying virus lineages Angie Hinrichs, University of California Santa Cruz   BV-BRC sub-species classification tools Christian Zmasek, J. Craig Venter Institute, BV-BRC Q&A Panel Discussion [15 Minutes] How do different classification systems impact our understanding of virus evolution and disease emergence? Do current classification systems capture sufficient genetic variation and associated phenotypic impact to support prediction of future disease outcomes? Are there emerging classification approaches that hold promise for improved prediction, control and response to virus disease? Use Reddit for questions and discussions here.
2:30 PM - 2:45 PM	Break
2:45 PM - 4:00 PM	Session VI: Analytical and visualization tools User tools and platforms available to study virus evolution during an outbreak. Moderator Indresh Singh, J. Craig Venter Institute, BV-BRC Panel and Session Topics [20-minute talks] NCBI Virus / Taxonomy Eneida Hatcher, PhD, NCBI   Virus sub-species in ViralZone and UniProtKB Philippe Le Mercier, PhD, Swiss-Prot group, Swiss Institute of Bioinformatics, Switzerland   Thinking about virus mutational spectra through visualization Andrew Warren, PhD, University of Virginia, BV-BRC Q&A Panel Discussion [15 Minutes] What role do data repository and analytical platforms provide to support basic research and outbreak response? Are there research and response needs not supported by these platforms? How can these platforms be extended to provide a more complete spectrum of biomedical data and analytical tools? Use Reddit for questions and discussions here.
4:00 PM - 4:15 PM	Break
4:15 PM - 5:15 PM	White Board Brainstorming Session [60 minutes] Moderators: Wiriya Rutvisuttinunt, PhD, NIAID Session Moderators Questions: What are the limitations of current classification systems? Are they able to track rapidly evolving viruses? Are they able to track associated phenotypic changes? Can they be used to effectively model future genotypic and phenotypic changes are their impact on disease? Can we use an existing classification approach for all viruses? If not, how many unique approaches need to be provided/supported? What new tools need to be developed to support classification of all human disease-causing viruses? To what extent can classification be automated and support large volumes of data? Do we need a standardized nomenclature for evolving lineages? How do we implement a standardized scheme? In what ways do these classification schemes influence the public health response?

April 10, Day 3: Responding to Public Health Needs

9:00 AM - 9:05 AM	Welcome back and Recap of Day 1 & 2
9:05 AM - 10:40 AM	Session VII: The Public Health Impact, Challenges and the Path Forward The role of virus classification to support the public health response to disease and how that classifications helps us identify new threats, track outbreaks, and develop targeted interventions. Moderator Paul Eder, PhD, NIAID Panel and Session Topics [20-minute talks] NIAID: To better understand, treat, and ultimately prevent infectious diseases Liliana Brown, Ph.D. NIAID   CDC: Public Health Perspective: Federal Level Andrew Beck, PhD, U.S. Centers for Disease Control and Prevention   WHO Global Program (remote) Rosamund Lewis, PhD, WHO   Boots on the ground: State public health laboratory’s perspective on virus pathogen surveillance Sean Wang, Minnesota Department of Public Health Q&A Panel Discussions [15 Minutes] How does an understanding of virus evolution during outbreaks improve and/or complicate outbreak preparedness and response? How can we improve our understanding of virus evolution to inform the development of more effective vaccines and treatments? Are there any ethical considerations related to the classification and naming of evolving virus lineages with respect to the public health response and the development of interventions? Use Reddit for questions and discussions here.
10:40 AM - 10:55 AM	Break
10:55 AM - 12:00 PM	White Board Brainstorming Session [65 minutes] Moderator: Alison St John, PhD, CDC Panel discussion What are the needs of the Public Health community? How do we best meet those needs Who should develop, implement, and maintain the classification system(s)? Will one approach/system suffice, or do multiple systems need to be developed and supported? What other responsibilities need to be supported (e.g., making the tools available along with outreach efforts to publicize the system and train people in their use.)? Preparing for the next pandemic How do we bring all of this together in a timely manner? How do we test the proposed response? How will this effort be supported? Meeting outcomes and next steps Conclusion