The circulating H5N1 Highly Pathogenic Avian Influenza in chicken has created devastating problems in Indonesia since 2003. Although human cases of Avian Influenza could be exceptionally reduced, however, it remains unsettled in poultry. Phylogenetic analysis of H5N1 virus (2003–2011) revealed the introduction of a single ancestral of 2.1 HA clade before 2003. The enzootic clade subsequently evolved into fourth order with predominantly 18.104.22.168. Pathological lesions showed cyanotic wattle, torticollis and haemorrhage in chicken feet and multi-internal organs. However, the introduction of vaccination and stringent biosecurity resulted in milder manifestations compared to classical lesions. In 2012, unusual high mortality in duck farms revealed the introduction of exotic clade 22.214.171.124. Despite the inefficient transmission of avian virus to humans and experimental receptor binding of 126.96.36.199 virus that showed avian preference, substitution of N158D and E190D in HA gene indicates possible threat to humans. In the same year, the Government of Indonesia announced the introduction of H9N2. Furthermore, a recent publication (2018) has reported new reassortant between HPAIV H5N1 and LPAIV H3N8 with resulting virulence attenuation in chicken.
Part of the book: Viruses and Viral Infections in Developing Countries