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  • Hinxton Hall, Wellcome Trust Genome Campus, Cambridgeshire, UK

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Meeting of the ICTV Executive Committee and Study Group Chairs

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by admin on February 01, 2016
Brief notes of the meeting of the ICTV Executive Committee (EC) and Study Group (SG) chairs held on 1-2 February 2016 at Hinxton Hall, Wellcome Trust Genome Campus, Cambridgeshire, UK
Hinxton Hall, Wellcome Trust Genome Campus, Cambridgeshire, UK

This meeting was the first ever to bring together the EC and SG chairs to discuss current issues in virus taxonomy.

This meeting provided a very appropriate start to the year in which ICTV celebrates its 50th anniversary. The excellent conference facilities provided by the Wellcome Trust Genome Campus enhanced the success of the meeting.

As explained by Andrew Davison (ICTV President) and Peter Simmonds (meeting organiser), the meeting was funded as part of a 5-year Wellcome Trust grant that is helping to develop ICTV resources, in particular by initiating an open-access online version of the ICTV Report. The meeting provided the opportunity to explain and discuss how the working of ICTV can be improved and how the Report can be developed. Some sessions addressed various problems that virus classification is facing, and added interest came from plenary sessions from a range of external speakers.

Many of the Powerpoint presentations are available for downloading from the website.

 

Monday 1 February 

In the introductory plenary lecture, Paul Kellam from the Wellcome Trust Sanger Centre illustrated how next-generation sequencing is transforming viral epidemiology and clinical studies.

This was followed by a series of short presentations from EC members outlining the history of ICTV taxonomy, the current procedures for maintaining and updating ICTV taxonomy, and the ways in which this is made available to the scientific community.

George Garrity from Michigan State University then gave a plenary lecture on bacterial classification that provided insights into the management of nomenclature and taxonomy in a different biological arena.

A further series of short presentations from EC members then focused on plans for developing the ICTV Report into an online open-access resource, using an example chapter. Most chapters would correspond to a family, and it was planned to publish citeable 2-page summaries as open access articles in an appropriate journal as the online chapters become available. The summaries would provide authors with a publication indexed in PubMed. It is hoped to have 30 chapters prepared by the end of 2016.

After lunch, there was a wide-ranging open session in which SG chairs were invited to raise issues related to the ICTV. The key points noted for action from this session and other discussions during the meeting are listed at the end of these notes.

The formal business of the day ended with a plenary lecture from Chris Stringer of the London Natural History Museum on hominid evolution. This raised issues of classification in palaeontology and proved to be of great general interest.

 

Tuesday 2 February 

The day began with a plenary lecture in which Guy Cochrane of the European Nucleotide Archive explained the challenge posed by vast quantities of NGS data that need to be captured and made available in appropriate ways to the scientific community.

The next session concentrated on sequence-related issues, including bioinformatics tools for sequence analysis in taxonomy, and served as a preview for dedicated meeting(s) on these topics to be held in the future. It included presentations from two EC members and two researchers employed through the grant. Overviews of multiple sequence alignments and phylogenetic trees were presented. SG chairs were encouraged to co-operate in providing standard sequence alignments appropriate for use in classifying viruses in their remit and in publishing criteria used to discriminate between species (and other taxa). Bioinformatics tools to assist users in examining the taxonomic implications of virus sequence data were presented, including one which has been extensively validated and used for taxonomy development in two virus families. Where appropriate, SGs could make use of linked wikipages to provide related information that is not appropriate to the main Report chapters and may change more frequently. These could include, for example, genotype and strain classifications below the species level or lists of viruses or sequences not yet formally classified. 

Two sessions were devoted to selected issues raised in advance by SG chairs. Key points arising from these discussions are included in the list at the end of these notes.

The plenary lecture after lunch was given by Curtis Suttle from the University of British Columbia, who demonstrated the vast diversity of viruses in the ocean. As well as being a fascinating story, this helped to highlight the challenge that virus taxonomy faces from the discovery of so many potential new taxa.

The final session attempted to look forward. Andrew Davison (President) summarised the current position of the ICTV about classifying viruses based on sequence data alone. This continues to be one of the major issues faced and will be the subject of a specialist meeting of invited experts and EC members in June 2016 in Boston. It is hoped that this meeting will result in a publication and recommendations to inform future ICTV policy. Andrew King (Proposals Secretary) recognised the importance of simplifying and accelerating the proposal process, especially for new species in well-established genera. Mike Adams (Business Secretary) discussed some of the advantages and disadvantages of adopting a latinized binomial nomenclature as used in other branches of biology and envisaged by the founders of ICTV 50 years ago. Elliot Lefkowitz (Data Secretary) outlined the provision of high quality taxonomic information and associated tools that the new online Report will be able to provide, together with links to other biological and sequence databases.

Key issues noted

  • Diversity within the ranks of the ICTV: SG chairs are overwhelmingly white males. Chairs are encouraged to ensure that membership of SGs reflects the current activity in virus discovery and classification (e.g. from Asia).
  • National Representatives: these have often had a purely symbolic role and the EC will discuss ways to involve them more actively.
  • Educating the scientific community: journal editors and others need to be made more aware of the importance of taxonomy and the role of the ICTV.
  • Taxonomic delay: ICTV will always be behind the curve, as sequences have to be deposited and given a provisional classification before a taxonomic decision can be made. Co-ordination between databases and direct contact between SG chairs and NCBI can improve the situation.
  • SGs have the option of using linked wikipages in the new online Report at least to provide listings (and perhaps other data) on nascent information.
  • Proposing new species needs to be made easier. The EC will be discussing this.
  • A 50th anniversary publication should be prepared incorporating information from the present meeting.
  • The EC should note the need for new SG chairs to be mentored (usually the responsibility of the SC chair and the outgoing SG chair).
  • Classifying viruses from metagenomic data is a major issue.
  • Demarcation of higher ranks in taxonomy remains extremely challenging and may generate contrasting opinions.
  • Incorporation of virus and virus-related host elements, e.g. EVEs, in a single classification scheme within virus taxonomy requires further discussion.
  • The provision of multiple sequence alignments (curated and kept up-to-date by SGs) and bioinformatics tools for taxonomy will be important and valuable features of the new online Report. In addition to clarifying the criteria used by SGs for taxonomic assignments, these will facilitate the analysis of new sequence data and the creation of proposals.

 

Immediate action

  • Further opinions about ICTV developments are always welcome!
  • Work is in progress to finalise the publication strategies for the Report chapter summaries.
  • The management committee will co-ordinate the writing and production of chapters for the online Report but will welcome volunteers! A template will be provided for the summaries.
  • Wikipages can already be provided for SGs and can be linked to the online Report as this facility develops.
  • A procedure will be developed and circulated to help SGs provide their sequence alignments in a suitable standard format.  
     

 

Invite-1

Invite-2

Agenda 1

Agenda 2

Presentations

  • Executive Committee Presentations
  • Paul Kellam: The transformation of viral epidemiology and clinical studies by next-generation sequencing
  • George Garrity: Bacterial taxonomy: Current developments
  • Guy Cochrane: The challenge of NGS data
  • Sead Sabanadzovic: ICTV Proposal Submission
  • Yves Bigot and Bas Dutilh: Evolutionary relationships between virus families - core genes and methods for homology detection
  • Jean-Michel Claverie: Challenges in classifying newly discovered viruses
  • Welkin Johnson and Pierre-Yves Teycheney: Classification of endogenous viral elements

Download the presentations

Group Picture

Group Picture Outline

 

Number in PictureNameStudy Group
1Rosemary DorringtonChair - Tetraviridae Study Group
2Matthias G. FischerChair - Mimiviridae Study Group
3Robert D. BurkChair - Papillomaviridae Study Group
4Jens KuhnElected member
5Eeva VainioChair - Partitiviridae Study Group
6Petar KnezevicChair - Inoviridae Study Group
7Annika GillisChair - Tectiviridae Study Group
8Jeremy ThompsonChair - Secoviridae Study Group
9Michael A. PurdyChair - Hepeviridae Study Group
10Richard KormelinkChair - Tospoviridae Study Group
11Michael StrandChair - Polydnaviridae Study Group
12Thomas BrieseChair - Bunyaviridae Study Group
13Finn K. VogensenChair - Lactic Acid Bacteria (LAB) Bacteriophage Study Group
14F. Murilo ZebriniElected Member
15Yves BigotMember - Ascoviridae Study Group
16David PrangishviliChair - Archaeal viruses Study Group
17Francesco Di SerioChair - Viroids Study Group
18Balázs HarrachChair - Animal DNA Viruses and Retroviruses Subcommittee
19Bas DutilhChair - Metagenomics Study Group
20John ThomasChair - Nanoviridae Study Group
21Rodrigo ValverdeChair - Endornaviridae Study Group
22Andrew KropinskyElected Member
23Arcady MushegianElected member
24Stuart SiddellChair - Animal dsRNA and ssRNA- Viruses Subcommittee
25Lars MagniusChair - Hepadnaviridae & Hepatitis delta virus Study Group
26George GarrityKeynote speaker
27Covadonga AlonsoChair - Asfarviridae Study Group
28Donald SmithEdinburgh bioinformatics
29Mike AdamsBusiness Secretary
30Elliot LefkowitzData Secretary
31Jean-Michel ClaverieChair – “Pandoraviridae” Study Group
32Han-Ching WangChair - Nimaviridae Study Group
33Andrew DavisonICTV President
34Nick KnowlesChair - Animal ssRNA+ Viruses Subcommittee
35Stacey Shultz-CherryChair - Astroviridae Study Group
36Jelle MatthijnssensChair - Reoviridae Study Group
37Toufic ElbeainoChair - Emaravirus Study Group
38Roland ZellChair - Picornaviridae Study Group
39Dennis RubbenstrothChair - Bornaviridae Study Group
40Sead SabanadzovicElected member
41Robert HarrisonElected member
42James StewartChair - Herpesvirales Study Group
43Sasha GorbalenyaVice-President
44Mart KrupovicElected member
45Mária BenköChair - Adenoviridae Study Group
46Hélène SanfaçonChair - Plant Viruses Subcommittee
47Stephen WylieChair - Potyviridae Study Group
48Max NibertChair - Fungal and Protist Viruses Subcommittee
49Massimo TurinaChair - Ourmiavirus Study Group
50Jan KreuzeChair - Alpha-, Beta-, Gammaflexiviridae Study Group
51Andrew LangChair - Marnaviridae Study Group
52W. Allen MillerChair - Luteoviridae Study Group
53Welkin JohnsonChair - Retroviridae Study Group
54Arvind VarsaniElected member
55Bradley HillmanChair - Narnaviridae Study Group
56John ZiebuhrChair - Coronaviridae
57V. Gregory CincharChair - Iridoviridae Study Group
58Jan VinjéChair - Caliciviridae Study Group
59Richard OrtonGlasgow bioinformatics
60Pierre-Yves TeycheneyChair - Caulimoviridae Study Group
61Bert RimaChair – Paramyxoviridae Study Group
62Philippe ColsonChair - Marseilleviridae Study Group
63Bernhard EhlersChair - Polyomaviridae Study Group
64Nobuhiro SuzukiChair - Partitiviridae Study Group
65Peter SimmondsElected member
66Micheal MelzerChair - Cilevirus Study Group

 

NameStudy Group
Meeting attendees not in photo
Margo A. BrintonChair – Arteriviridae Study Group
Bernard DelmasChair – Birnaviridae & Picobirnaviridae Study Groups
Andrew KingProposals Secretary
Juan Carlos de la TorreChair – Arenaviridae Study Group
Peter WalkerChair – Rhabdoviridae Study Group
Johannes WittmannChair – N4-like phages Study Group
  
Invited speakers not in photo
Paul KellamKeynote speaker
Chris StringerKeynote speaker
Guy CochraneKeynote speaker
Curtis SuttleKeynote speaker

 

International Committee on Taxonomy of Viruses

 

Unless otherwise noted, this work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License

Support is provided by the National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health, Award U24AI162625

 

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