Epidemiology of highly pathogenic avian influenza virus H5N1 in Indonesian poultry

Highly Pathogenic Avian Influenza (HPAIv) H5N1 virus of the A/Goose/Guandong/1/96 lineage was first reported in Asia in 1996 and has been circulating in Indonesia since 2003. Its spread caused a global impact on poultry health and severe losses to the poultry industry. Furthermore, 200 laboratory-confirmed human cases were reported alone in Indonesia with a case-fatality rate of 84%. Analysis of the contact structure facilitating the transmission of HPAIv(A)H5N1 between different types of poultry farms in West Java showed that visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits or contact during their visits in the farms. These results suggest that backyard chicken farms are most at risk for transmission of HPAIv compared to farms of the other poultry production types and also serve as a vector for transmitting HPAIv H5N1 to commercial poultry. Passive surveillance from outbreak farms in six regions of West Java from November 2015 to November 2016 showed the highest mortality in backyard chickens with dermal apoptosis and lesions and respiratory signs. Neurological signs were most frequently observed in ducks. The rate of visitor contacts onto a farm was positively associated with the odds of HPAI infection. Duck farms had higher odds of being infected than backyard farms. The larger farms had lower odds than small farms. Results indicate that better external biosecurity is needed to reduce transmission of HPAIvA(H5N1) in Indonesia. The phylogenetic analyses of the analysis of 39 full-genome HPAIv(A)H5N1 viruses with additional reference sequences revealed 2 genetic clusters in clade 2.3.2.1c based on the hemagglutinin gene as well as the neuraminidase, nucleoprotein, polymerase, and polymerase basic 1 gene. The polymerase basic 2 gene had a close relation with Eurasian low pathogenic avian influenza virus (LPAIv). Also, several matrix, nonstructural protein and polymerase basic 2 genes were detected in HPAIv with higher identity with clade 2.1.3 than with clade 2.3.2.1c. The phylogenetic analysis of the samples in 2015-2016 thus identified 13 types of reassortment in HPAIv in Indonesia, mostly in native chickens in Indramayu. The BEAST analysis of the Indonesian poultry HPAIvA(H5N1) sequences collected from 2003-2016 were performed with a set of represented global H5Nx that have identities greater than 98%. Temporal dynamic analysis revealed that most likely only two introductions of HPAIvA(H5N1) occurred in Indonesia. The common ancestor (TMRCA) of the first introduction to Indonesian poultry HPAIvA(H5N1) emerged about five to seven years after the global common ancestor of HPAIv A(H5Nx). The divergences and TMRCA of H5N1 clade 2.3.2.1c and clade 2.3.2.1b were identified. The TMRCA of clade 2.3.2.1c and clade 2.3.2.1 indicate that the second introduction of both HPAIvA(H5N1) into Indonesian poultry originated from viruses from the same clade as viruses. detected in China and other Asian countries. Results of studies presented the importance of continued and improved (genomic) surveillance in poultry, live bird markets and wild birds. Adequate control measures such poultry farm biosecurity and poultry reconstruction are required to prevent a new emerging pandemic threat