A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses

Author:

Anderson Tavis K.1ORCID,Macken Catherine A.2,Lewis Nicola S.3,Scheuermann Richard H.45ORCID,Van Reeth Kristien6,Brown Ian H.7,Swenson Sabrina L.8,Simon Gaëlle9,Saito Takehiko10,Berhane Yohannes11,Ciacci-Zanella Janice12,Pereda Ariel13,Davis C. Todd14,Donis Ruben O.14,Webby Richard J.15,Vincent Amy L.1

Affiliation:

1. Virus and Prion Research Unit, National Animal Disease Center, USDA-ARS, Ames, Iowa, USA

2. Bioinformatics Institute, University of Auckland, Auckland, New Zealand

3. Department of Zoology, University of Cambridge, Cambridge, United Kingdom

4. J. Craig Venter Institute, La Jolla, California, USA

5. Department of Pathology, University of California, San Diego, California, USA

6. Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium

7. Animal and Plant Health Agency, Weybridge, United Kingdom

8. National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA

9. ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France

10. Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan

11. Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada

12. Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil

13. Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina

14. Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

15. Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA

Abstract

A fundamental goal in the biological sciences is the definition of groups of organisms based on evolutionary history and the naming of those groups. For influenza A viruses (IAVs) in swine, understanding the hemagglutinin (HA) genetic lineage of a circulating strain aids in vaccine antigen selection and allows for inferences about vaccine efficacy. Previous reporting of H1 virus HA in swine relied on colloquial names, frequently with incriminating and stigmatizing geographic toponyms, making comparisons between studies challenging. To overcome this, we developed an adaptable nomenclature using measurable criteria for historical and contemporary evolutionary patterns of H1 global swine IAVs. We also developed a web-accessible tool that classifies viruses according to this nomenclature. This classification system will aid agricultural production and pandemic preparedness through the identification of important changes in swine IAVs and provides terminology enabling discussion of swine IAVs in a common context among animal and human health initiatives.

Funder

HHS | NIH | National Institute of Allergy and Infectious Diseases

European Commission

USDA | Agricultural Research Service

DOE | LDRD | Oak Ridge Institute for Science and Education

USDA | Animal and Plant Health Inspection Service

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

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