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

Abstract

The H1 subtype of influenza A viruses (IAVs) has been circulating in swine since the 1918 human influenza pandemic. Over time, and aided by further introductions from nonswine hosts, swine H1 viruses have diversified into three genetic lineages. Due to limited global data, these H1 lineages were named based on colloquial context, leading to a proliferation of inconsistent regional naming conventions. In this study, we propose rigorous phylogenetic criteria to establish a globally consistent nomenclature of swine H1 virus hemagglutinin (HA) evolution. These criteria applied to a data set of 7,070 H1 HA sequences led to 28 distinct clades as the basis for the nomenclature. We developed and implemented a web-accessible annotation tool that can assign these biologically informative categories to new sequence data. The annotation tool assigned the combined data set of 7,070 H1 sequences to the correct clade more than 99% of the time. Our analyses indicated that 87% of the swine H1 viruses from 2010 to the present had HAs that belonged to 7 contemporary cocirculating clades. Our nomenclature and web-accessible classification tool provide an accurate method for researchers, diagnosticians, and health officials to assign clade designations to HA sequences. The tool can be updated readily tomore » track evolving nomenclature as new clades emerge, ensuring continued relevance. A common global nomenclature facilitates comparisons of IAVs infecting humans and pigs, within and between regions, and can provide insight into the diversity of swine H1 influenza virus and its impact on vaccine strain selection, diagnostic reagents, and test performance, thereby simplifying communication of such data.« less

Authors:

Anderson, Tavis K.  ^[1];

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• Search DOE PAGES for ORCID "0000-0002-3138-5535"

Macken, Catherine A. ^[2]; Lewis, Nicola S. ^[3]; Scheuermann, Richard H.  ^[4];

• Search DOE PAGES for author "Scheuermann, Richard H."
• Search DOE PAGES for ORCID "0000-0003-1355-892X"

Van Reeth, Kristien ^[5]; Brown, Ian H. ^[6]; Swenson, Sabrina L. ^[7]; Simon, Gaëlle ^[8]; Saito, Takehiko ^[9]; Berhane, Yohannes ^[10]; Ciacci-Zanella, Janice ^[11]; Pereda, Ariel ^[12]; Davis, C. Todd ^[13]; Donis, Ruben O. ^[13]; Webby, Richard J. ^[14]; Vincent, Amy L. ^[1]; Lowen, ed., Anice C.

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+ Show Author Affiliations

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, Department of Pathology, University of California, San Diego, California, USA
5. Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
6. Animal and Plant Health Agency, Weybridge, United Kingdom
7. National Veterinary Services Laboratories, USDA-APHIS, Ames, Iowa, USA
8. ANSES, Ploufragan-Plouzané Laboratory, Swine Virology Immunology Unit, Ploufragan, France
9. Division of Transboundary Animal Disease, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
10. Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada
11. Embrapa Swine and Poultry, Animal Health and Genetic Laboratory, Concórdia, SC, Brazil
12. Instituto de Patobiología, CICVyA INTA, Hurlingham, Buenos Aires, Argentina
13. Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
14. Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA

Publication Date:

Wed Dec 28 00:00:00 EST 2016

Research Org.:

Oak Ridge Associated Univ., Oak Ridge, TN (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1618366

Alternate Identifier(s):

OSTI ID: 1626157

Grant/Contract Number:  

AC05-06OR23100

Resource Type:

Published Article

Journal Name:

mSphere

Additional Journal Information:

Journal Name: mSphere Journal Volume: 1 Journal Issue: 6; Journal ID: ISSN 2379-5042

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

Microbiology; H1N1; H1N2; influenza A virus; molecular epidemiology; nomenclature; swine; virus evolution