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USDA-commons-2023-01-03.fasta (15.71 kB)

Data from: Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential

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posted on 2023-12-18, 20:08 authored by Alexey Markin, Giovana Ciacci Zanella, Zebulun W. Arendsee, Jianqiang Zhang, Karen M. Krueger, Phillip C. Gauger, Amy L. Vincent Baker, Tavis K. Anderson

Influenza A virus in swine hemagglutinin (HA) gene sequence data for 9 virus strains.

Resources in this dataset:

  • Resource Title: H1N1pdm09 HA gene sequences.

    File Name: USDA-commons-2023-01-03.fasta

    Resource Description: 9 hemagglutinin (HA) gene sequences of influenza A virus collected from swine.


USDA-ARS: 5030-32000-231-000D

USDA-APHIS: 5030-32000-231-080-I

National Institute of Allergy and Infectious Diseases: 75N93021C00015

Defense Advanced Research Projects Agency: HR00112020034

Oak Ridge Institute for Science and Education: DE-AC05-06OR23100

Centers for Disease Control and Prevention: 21FED2100395IPD

USDA-ARS: 0500-00093-001-00-D


Data contact name

Anderson, Tavis

Data contact email


Ag Data Commons

Intended use

These data include hemagglutinin (HA) gene sequence data for nine influenza A virus strains collected from United States pigs. Following incorporation into a larger gene sequence dataset they may be used to study the evolutionary history of H1 subtype influenza A viruses in swine.

Use limitations

The 9 hemagglutinin genes are sourced from clinically sick pigs, were not isolated, and archival samples are not available. The sequence quality is not adequate to submit these strains to NCBI Genbank as sequence errors have introduced frameshifts and premature stop codons. They should not be used as representative of H1 influenza A virus in swine data. However, when studied in the context of other swine H1 subtype HA genes, the data may be aligned, and phylogenetic methods may be applied to make appropriate evolutionary inference.

Temporal Extent Start Date


Temporal Extent End Date



  • notPlanned


  • Not specified

Geographic Coverage


Geographic location - description


ISO Topic Category

  • biota
  • farming
  • health

National Agricultural Library Thesaurus terms

pandemic; Influenza A virus; swine; viruses; zoonoses; hemagglutinins; nucleotide sequences; phylogeny; swine influenza; United States; virulent strains

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 103

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Markin, Alexey; Ciacci Zanella, Giovana; Arendsee, Zebulun W.; Zhang, Jianqiang; Krueger, Karen M.; Gauger, Phillip C.; Vincent Baker, Amy L.; Anderson, Tavis K. (2023). Data from: Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential. Ag Data Commons.

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