Genetic characteristics of avian influenza viruses isolated from ducks in Java Island, Indonesia year 2015-2017

Abstract

Avian influenza becomes public health concern over years due to the serious impacts in both animal and human health. This study aimed to identify and characterize avian influenza viruses isolated from ducks in Java Indonesia during 2015-2017. Total 50 samples of previously identified as avian influenza viruses were acquired from the virus/culture collections of Disease Investigation Center (DIC) Wates Yogyakarta, Indonesia. The samples were recovered from either the avian influenza surveillance or avian influenza outbreaks in ducks in 3 provinces, East Java (n=26), Central Java (n=16), and Yogyakarta (n=8). Then the samples were processed for influenza A virus screening by realtime RT-PCR using M gene specific primers. The results showed that 46 out of 50 samples (92%) were positive for influenza A virus screening. The positive samples were then subjected for influenza A virus isolation. Seven out of 46 samples were positive for influenza A virus confirmation by using multi-segment reverse transcription PCR (M-RTPCR). All 7 avian influenza viruses were subjected to whole genome sequencing by next generation sequencing. The viruses were then identified as avian influenza subtype H5N1 (n=6) and H9N2 (n=1). Phylogenetic analysis showed that the avian influenza viruses were clustered into H5N1 virus of clade 2.3.2.1c (n=6) and H9N2 viruses of Y280-like group (n=1). Phylogenetic analysis of internal genes indicated that among the H5N1 of clade 2.3.2.1c (n=1), the evidence of inter-lineage reassortment by acquiring the M gene from H5N1 of clade 2.1.3.2 could be observed. On the other hand, phylogenetic analysis of H9N2 showed that all internal genes of H9N2 were closely related to the human H7N9 virus isolated from China. Genetic analysis showed that the H5N1 and H9N2 viruses were categorized as HPAI and LPAI, respectively. In conclusion, our results suggested that both HPAI-H5N1 and LPAI-H9N2 were circulated in ducks in Java, Indonesia. Routine surveillance and genetic characterization are important to monitor the dynamic and genetic diversity of avian influenza viruses and possibility of novel reassortment strains.