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

• Published in: Emerging infectious diseases Vol. 25; no. 3; pp. 465 - 472
• Main Authors: Karo-karo, Desniwaty, Bodewes, Rogier, Wibawa, Hendra, Artika, Made, Pribadi, Eko Sugeng, Diyantoro, D., Pratomo, Widya, Sugama, Agus, Hendrayani, Nani, Indasari, Iin, Wibowo, Michael Haryadi, Muljono, David Handojo, Stegeman, Jan Arend, Koch, Guus
• Format: Journal Article
• Language: English
• Published: United States U.S. National Center for Infectious Diseases 01.03.2019; Centers for Disease Control and Prevention
• Subjects: Amino Acid Sequence; Analysis; Animals; Avian influenza; Avian influenza viruses; CVI Virologie; CVI Virology; Disease Outbreaks; Genes; Genomes; Genomics; Genotype; Hemagglutinin Glycoproteins, Influenza Virus - genetics; HPAI; Humans; Indonesia - epidemiology; Influenza; Influenza A Virus, H5N1 Subtype - classification; Influenza A Virus, H5N1 Subtype - genetics; Influenza in Birds - epidemiology; Influenza in Birds - virology; Lectins; phylogenetic analysis; Phylogeny; Poultry; Poultry Diseases - epidemiology; Poultry Diseases - virology; Public Health Surveillance; Reassortant Viruses - classification; Reassortant Viruses - genetics; reassortment; Sequence Analysis, DNA; Virologie; Virology; viruses; West Java; Indonesia; Netherlands; influenza; HPAI; highly pathogenic avian influenza; reassortment; phylogenetic analysis; viruses; West Java; respiratory infections; Indonesia
• ISSN: 1080-6040; 1080-6059; 1080-6059
• DOI: 10.3201/eid2503.180167

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.