CEIRS Short Nomenclature for Influenza Viruses Generated by Reverse Geneticsv1.00
CEIRS Short Nomenclaturefor Influenza Viruses Generated by Reverse Genetics
Final Document 10-31-2008 by the CEIRS IOWG Short Nomenclature Working Group*
A unique, consistent nomenclature for describing influenza viruses and submission to public data repositories has been discussed in CEIRS IOWG and is proposed here. Please consider:
I.New wild-type virus isolates should be named according to the WHO convention.
wild-type isolate: A/mallard/Vietnam/1203/2009(H5N1)
II.A virus generated by reverse genetics has a short unique name consistent with the WHO nomenclature standard but includes additional information in the isolate field.
reverse genetics: A/Vietnam/1203-CIP045_RG225/2004(H5N1)
The reverse genetics-generated virus isolate field contains the following additional information: after the parental virus isolate number (“1203”), there are a [-] separator, a unique institutional code (for example, "CIP045” for CRIP-Mt Sinai; please refer to BioHealthBase documentation for your institutional code), another separator [_], the letters "RG" for “reverse genetics”, and a clone number.
The virus A/Vietnam/1203-CIP045_RG225/2004(H5N1) is a reverse genetics-generated derivative of the parental virus A/Vietnam/1203/2004(H5N1). cDNA rescue plasmids encoding each of the gene segments exist. The format of the nomenclature is the same as the parental virus except for the isolate field, and in some cases, the subtype. The year is the same as the isolation year for the parental virus. The subtype should reflect the HA and NA segments present in the reverse genetics virus, which may have been altered by reassortment.
Use of CEIRS Short Nomenclature: Allreverse genetics-generated virus sequencessubmitted by CEIRS investigators to public databases must conform to this nomenclature.
Only RG-generated strains with a distinct biological phenotypeshould be named usingthis nomenclature and submitted to BioHealthBase, through the BioHealthBase submission portal. Determining what is considered a distinct biological phenotype is up to the scientific discretion of the investigator and NIAID.
The naming of reassortants within the CEIRS short nomenclature format is also up to the scientific discretion of the investigator. It is suggested that the virus contributing the HA gene (segment 4) be given priority as the parental name. Note that the subtype provided in the short nomenclature reflects the actual subtype of the reverse genetics virus.
A long genotypic nomenclature will exist in BioHealthBase, but at present it has not been finalized yet. The long genotypic name will describe the origin of each influenza gene segment exactly, with Accession numbers linking to sequence data. Adopting these nomenclature conventions will simplify and standardize hierarchal descriptions of reverse genetics-generated viruses and variants derived from them.
*Contributors to the CEIRS IOWG Short Nomenclature Working Group include Eric Bortz (1), Alex Roth (2),Randy Albrecht (1), Ron Fouchier (3), Scott Krauss (4),Gavin Smith (5), Vanessa Whitehurst (6), Dave Halverson (7), Falk Huettmann (8), Torsten Staab (2), Adolfo Garcia-Sastre (1), Ed Klem (9), Richard Scheuermann (9),Aihui Wang (10), Jonathan Dietrich (10), Valentina Di Francesco (11), and Yiming Bao (12).
1. Center for Research on Influenza Pathogenesis (CRIP), Mount Sinai School of Medicine, New York
2. Center for Rapid Influenza Surveillance and Research (CRISAR), University of California, Los Angeles
3. Center for Research on Influenza Pathogenesis (CRIP), ErasmusUniversity, Rotterdam, Netherlands
4. CEIRS St. Jude Children’s ResearchHospital, Memphis, Tennessee
5. CEIRS St. Jude, University of Hong Kong, Hong Kong, China
6. Influenza Pathogenesis and ImmunologyResearchCenter (IPIRC), EmoryUniversity, Atlanta
7. Center for Infectious Disease Research and Policy (CIDRAP), U. of Minnesota, Minneapolis
8. Center for Rapid Influenza Surveillance and Research (CRISAR), University of Alaska, Fairbanks
9. BioHealthBase, University of Texas-Southwestern, Dallas
10. Northrop Grumman Corporation, Maryland
11. National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health
12.NationalCenter for Biotechnology Information (NCBI), National Institutes of Health
We would also like to thank all CEIRS investigators as well as Tina Parker, Leyfou Dabo, and Diane Post at NIAID for their valuable comments.
Final10-31-2008Page 1 of 2