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

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.

Figure 1

Locations of sampling areas and of different hemagglutinin (HA) clades in study of avian influenza A(H5N1) viruses circulating in Indonesia, 2015–2016. A) West Java Province; B) location of province in Indonesia (box). Data were compiled from this study and additional sequence data of Directorate General for Livestock Services, the Indonesian Ministry of Agriculture, and submitted to GenBank (accession nos. EPI1009273–463).

Figure 2

Number of samples in study of avian influenza A(H5N1) viruses circulating in Indonesia, 2015–2016, by district (A), time (B), poultry type (C), poultry sector (D), and farm size (E) from which the complete HPAIV H5N1 genome could be obtained.

Figure 3

Reassortment events of avian influenza A(H5N1) viruses in samples from Indonesia, 2015–2016, some of which were confirmed using maximum-likelihood analysis with parent strains clade 2.3.2.1c, 2005-11 (clade 2.1.3.2a), and Asia low pathogenicity avian influenza virus. Parent strains appear above the dotted line and 13 detected reassortment types below the dotted line. HA, hemagglutinin; LPAI, low pathogenicity avian influenza virus; MP, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, nonstructural protein; PA, polymerase; PB1, polymerase basic 1; PB2; polymerase basic 2. Green bars indicate clade 2.1.3.1a; blue, clade 2.1.3.2c subgroup A; red, clade 2.1.3.2c subgroup B; violet, Asia LPAI.