Reassortments among Avian Influenza A(H5N1) Viruses Circulating in Indonesia, 2015-2016

Emerg Infect Dis. 2019 Mar;25(3):465-472. doi: 10.3201/eid2503.180167.

Abstract

Highly pathogenic avian influenza (HPAI) A(H5N1) viruses have been circulating since 2003 in Indonesia, with major impacts on poultry health, severe economic losses, and 168 fatal laboratory-confirmed human cases. We performed phylogenetic analysis on 39 full-genome H5N1 virus samples collected during outbreaks among poultry in 2015-2016 in West Java and compared them with recently published sequences from Indonesia. Phylogenetic analysis revealed that the hemagglutinin gene of all samples belonged to 2 genetic groups in clade 2.3.2.1c. We also observed these groups for the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 genes. Matrix, nonstructural protein, and polymerase basic 2 genes of some HPAI were most closely related to clade 2.1.3 instead of clade 2.3.2.1c, and a polymerase basic 2 gene was most closely related to Eurasian low pathogenicity avian influenza. Our results detected a total of 13 reassortment types among HPAI in Indonesia, mostly in backyard chickens in Indramayu.

Keywords: HPAI; Indonesia; West Java; highly pathogenic avian influenza; influenza; phylogenetic analysis; reassortment; respiratory infections; viruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Disease Outbreaks
  • Genotype
  • Hemagglutinin Glycoproteins, Influenza Virus / genetics
  • Humans
  • Indonesia / epidemiology
  • Influenza A Virus, H5N1 Subtype / classification
  • Influenza A Virus, H5N1 Subtype / genetics*
  • Influenza in Birds / epidemiology*
  • Influenza in Birds / virology*
  • Phylogeny
  • Poultry
  • Poultry Diseases / epidemiology*
  • Poultry Diseases / virology*
  • Public Health Surveillance
  • Reassortant Viruses / classification
  • Reassortant Viruses / genetics*
  • Sequence Analysis, DNA

Substances

  • Hemagglutinin Glycoproteins, Influenza Virus