Foot and mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed animals which has been well documented as one of the major animal diseases that causing serious economic loss of livestock sectors. The disease is endemic in many countries, particularly in Asia and Africa. Indonesia has declared disease-free country since 1986 and the World Organization of Animal Health (WOAH/OIE) has recognised Indonesia as FMD-free country without vaccination in 1990. However, FMD virus was detected from a number of disease outbreaks in cattle and goat in Indonesia in May 2022. This study report for the first time the detection and identification of serotype O/ME-SA/Ind-2001 lineage in Indonesia. Although the Indonesian serotype O/ME-SA/Ind-2001 viruses appeared belonging to the Ind-2001e sublineage, they formed a unique cluster with 95.3% average nucleotide sequence similarity to Ind-2001e viruses from other Asia countries. The source of virus incursion into Indonesia is still unresolved; however, illegal trade of live animals from endemic areas in Southeast Asia is the suspected route which should be further investigated.
HPAI is endemic across parts of Indonesia, but the mechanisms of viral persistence in the poultry production system have not been well investigated. This mixed methods research conducted in Purbalingga District, Java characterised poultry populations and trade and contact networks and performed risk-based sampling for the active detection of HPAI virus in live bird markets, collector yards, backyard poultry, nomadic ducks and commercial farms. Approximately 60% of households kept birds, about half of which contributed towards household income. Traders tended to use multiple collector yards and live bird markets, and poultry might be presented at multiple markets before sale. Only the commercial farm sector implemented biosecurity practices and vaccination. Samples were screened for avian influenza virus (AIV) and positive samples were tested for the H5 and H9 sub-types. H5 virus was detected in all enterprise types, although there were few positive results in commercial farms, the backyard sector and nomadic duck flocks. The highest numbers of AIV, H5 and H9 viruses were found in the live bird markets and collector yards. The odds of detection of H5 in live bird markets and collector yards were similar; however, these were 3½ to 4 times higher than in backyard birds and nomadic ducks and 25 to 30 times higher than in commercial poultry. This suggests that transmission of infection in backyard poultry and duck production was likely to be driven more strongly by the value chain than by direct or indirect contacts at source. We could not determine whether the value chain concentrates or amplifies virus along its length, or whether AIV persists and actively circulates in live bird markets and collector yards. H5 and H9 viruses were detected year-round and were co-circulating in the different enterprise types, although no inference can be drawn regarding interactions between these HPAI and LPAI viruses.