BV-BRC Viral Sub-species Classification Workshop at NIAID Rockville, MD, April 8-10, 2024 ========================================================================================= .. raw:: html - `Introduction <#introduction-section>`_ - `Workshop Highlights <#highlights-section>`_ - `Workshop Agenda and Presentations <#agenda-section>`_ - `Workshop Speakers and Reading List <#speakers-section>`_ .. _introduction-section: ------------------ Introduction ------------------ --------------------- 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. .. _highlights-section: ------------------ 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. .. _agenda-section: --------------- Workshop Agenda with Links to Recordings and Presentations --------------- --------------------- .. raw:: html

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

Time Topic Title Presenter
9:30 AM - 10:00 AM Welcome and Introduction

Watch Recording Here 		Goals, Expectations, and Logistics Download Presentation Here
  • 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.

Watch Recording Here


Moderator

  • Elliot Lefkowitz, PhD, University of Alabama at Birmingham

Panel and Session Topics

  • Tracking and predicting the spread and evolution of RNA viruses
  • Richard Neher, PhD, University of Basel, Switzerland
  • Download Presentation Here
  •  
  • SARS-CoV-2 and HIV variant evolution
  • Bette Korber, PhD, Los Alamos National Labs, U.S.
  • Download Presentation Here

Break


Q&A Panel Discussions

  • 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.

Watch Recording Here

Moderator

  • James Rodney Brister, PhD, NCBI

Panel and Session Topics

  • Evolution, epidemiology, and RNA virus disease
  • Justin Bahl, PhD, University of Georgia
  • Download Presentation Here
  •  
  • The evolution of influenza A virus at the human-animal interface
  • Tavis Anderson, PhD, U.S. Department of Agriculture
  • Download Presentation Here
  •  
  • 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
  • Download Presentation Here

Break



Q&A Panel Discussions

  • 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

Watch Recording Here

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.

Watch Recording Here

Moderator

  • Conrad Schoch, PhD, NCBI

Panel and Session Topics

  • Influenza and SARS-CoV-2: Evolution, Immunity, and Surveillance
  • Derek Smith, PhD, University of Cambridge
  • Download Presentation Here
  •  
  • Virus classification and support for different stakeholders
  • Peter Simmonds, PhD, University of Oxford
  • Download Presentation Here

Q&A Panel Discussions

  • 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.

Watch Recording Here

Moderator

  • Richard Scheuermann, PhD, National Library of Medicine (NLM)

Panel and Session Topics

  • 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)
  • Download Presentation Here
  •  
  • Perspectives on the development of the Pango system and software
  • Áine O'Toole, PhD, The University of Edinburgh
  • Download Presentation Here
  •  

  • Pango beyond the SARS-CoV-2 pandemic
  • Rachel Colquhoun, PhD, The University of Edinburgh
  • Download Presentation Here

Q&A Panel Discussion

  • 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.

Watch Recording Here

Moderator

  • Eneida Hatcher, PhD, NCBI

Panel and Session Topics


Q&A Panel Discussion

  • 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.

Watch Recording Here

Moderator

  • Indresh Singh, J. Craig Venter Institute, BV-BRC

Panel and Session Topics


Q&A Panel Discussion

  • 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

Watch Recording Here
  • 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.

Watch Recording Here

Moderator

  • Paul Eder, PhD, NIAID

Panel and Session Topics

  • 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
  • Download Presentation Here
  •  
  • WHO Global Program (remote)
  • Rosamund Lewis, PhD, WHO
  • Download Presentation Here
  •  
  • Boots on the ground: State public health laboratory’s perspective on virus pathogen surveillance
  • Sean Wang, Minnesota Department of Public Health
  • Download Presentation Here

Q&A Panel Discussions

  • 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

Watch Recording Here
  • 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
Agenda, Questions and Discussions at Reddit https://www.reddit.com/r/BRC_users/ .. _speakers-section: ------------------ Workshop Speakers amd Reading List ------------------ --------------------- .. list-table:: :widths: 25 60 15 :header-rows: 1 * - Name - Affiliation - Papers * - **General** - 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** - NIH/NIAID - * - **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 `_.