Phylodynamics of Highly Pathogenic Avian Influenza A(H5N1) Virus Circulating in Indonesian Poultry

Abstract

After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis sampling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the divergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and diverged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.

Keywords: Bayesian evolutionary analysis; H5N1; HPAI; Indonesia; phylodynamic.

Figure A1

Time-measured phylogeny of HA genes of Indonesian poultry HPAIv A(H5N1) 2003–2016. The estimated root of HA clade 2.3.2.1c was highlighted by asterisk symbol, the tMRCA of HA clade 2.3.2.1c is pointed out by the red arrow, and the tMRCA between HA clade 2.1.1 and 2.3.2.1c is pointed out by the green arrow. The HPAIv A(H5N1) clade 2.3.2.1c diverged into subgroups (A and B). The node labels display the posterior value. The two gray lines between the clades 2.1.1 and 2.3.2.1c represent the presence of multiple viruses between these two clades as presented in Figure 1. The original sequences (GISAID ID) of HA genes of Indonesian poultry HPAIv A(H5N1) 2003–2016 phylogeny is displayed in Supplementary Table S1.

Figure A2

Time-scale phylogeny of Indonesian HA of H5N1v of HA genes of Indonesian poultry HPAIv A(H5N1) clade 2.3.2.1c. The clade 2.3.2.1c subgroup A is highlighted in red and clade 2.3.2.1c subgroup B is highlighted in blue. Another clade, 2.3.2.1c, is highlighted in pink. The node labels display the posterior value.

Figure 1

Time-scale phylogeny of selected worldwide HA of H5N1v. The estimated origin of the divergence of the HA 2.3.2.1c clade is highlighted in the asterisk symbol. The tMRCA of HA clades 2.3.2.1b and 2.2.3.1a are pointed out by the arrow. The blue colour highlights the HA of H5N1v from Indonesia. The node labels display the posterior value. The original sequences (GISAID ID) for worldwide HA of H5N1v phylogeny are displayed in Supplementary Table S1.

Figure 2

The distribution of HA of HPAIv A(H5N1) was detected in poultry based on different clades and different provinces of Indonesia. The number of taxa per province and per years are displayed in Supplementary Tables S2 and S3.