|Title||Reassortments among avian influenza A(H5N1) viruses circulating in Indonesia, 2015-2016|
|Author(s)||Karo-Karo, Desniwaty; Bodewes, Rogier; Wibawa, Hendra; Artika, I.M.; Pribadi, Eko Sugeng; Diyantoro, D.; Pratomo, Widya; Sugama, Agus; Hendrayani, Nani; Indasari, Iin; Wibowo, Michael Haryadi; Muljono, David Handojo; Stegeman, Jan Arend; Koch, Guus|
|Source||Emerging Infectious Diseases 25 (2019)3. - ISSN 1080-6040 - p. 465 - 472.|
|Publication type||Refereed Article in a scientific journal|
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 184.108.40.206c. 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 220.127.116.11c, 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.