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.
References
Jan 29, 2002·Archives of Virology·E HoffmannD R Perez
Jul 16, 2004·Journal of Virology·Chang-Won LeeDavid L Suarez
May 9, 2008·PLoS Pathogens·Martha I NelsonEdward C Holmes
May 26, 2009·Virology·Ryo TakanoYoshihiro Kawaoka
Jun 12, 2010·Transboundary and Emerging Diseases·E BasunoN Ilham
Feb 5, 2011·Vaccine·F RauwT van den Berg
Jul 8, 2011·Journal of Virology·Giovanni CattoliIlaria Capua
Aug 5, 2011·Preventive Veterinary Medicine·Leo LothXiangming Xiao
Jan 21, 2012·Influenza and Other Respiratory Viruses·R Burke SquiresRichard H Scheuermann
Jun 13, 2012·Epidemiology and Infection·J HenningJ Meers
Nov 6, 2012·Virology·Maria Serena BeatoIlaria Capua
Dec 6, 2012·Biology Open·U Chandimal de SilvaTeruo Yasunaga
Feb 5, 2013·Veterinary Microbiology·Kunkun ZhaoXiufan Liu
May 1, 2013·Emerging Infectious Diseases·Trevon L FullerThomas B Smith
Jun 4, 2013·Virology·Michelle WilleJonas Waldenström
Oct 18, 2013·Molecular Biology and Evolution·Koichiro TamuraSudhir Kumar
Oct 29, 2013·Biochimica Et Biophysica Acta·Caroline M MairChristian Sieben
Nov 5, 2013·Lancet·Hongjie YuGabriel M Leung
May 13, 2015·Influenza and Other Respiratory Viruses·Gavin J D SmithUNKNOWN World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5 Evolution
Jul 8, 2015·The Journal of Infection·Xiaoyan ZhouRicardo J Soares Magalhaes
May 14, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Chakradhar ToshDiwakar D Kulkarni
May 24, 2016·One Health·Vittoria OffedduJ S Malik Peiris
Dec 6, 2016·Cell Host & Microbe·Yuhai BiGeorge Fu Gao
Jan 31, 2017·Virology·Ben PeetersCornelis A M de Haan
Aug 7, 2017·Vaccine·Juan P Villanueva-CabezasJodie McVernon
Nov 8, 2017·PLoS Pathogens·Mara Villa, Michael Lässig
Jan 11, 2018·PloS One·Simson TariganJagoda Ignjatovic
Jun 13, 2018·Preventive Veterinary Medicine·Hendra WibawaArjan Stegeman
Aug 23, 2018·Emerging Microbes & Infections·Ni Luh Putu Indi DharmayantiC Todd Davis
Citations
Sep 11, 2019·Microorganisms·Desniwaty Karo-KaroJan Arend Stegeman
Nov 27, 2019·Transboundary and Emerging Diseases· LestariAlongkorn Amonsin
Aug 18, 2020·Veterinary World·Imas YuyunWidagdo Sri Nugroho
Jun 4, 2020·Viruses·Yunyueng Jang, Sang Heui Seo
Aug 25, 2020·Heliyon·I Made ArtikaAgeng Wiyatno
Feb 2, 2020·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·I Made ArtikaChairin Nisa Ma'roef
Feb 28, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Xiao LiWeixin Jia
Aug 10, 2021·Frontiers in Public Health·Beatriz Delgado-HernándezPastor Alfonso