Nipah virus causes periodic livestock and human disease with high case fatality rate, and consequent major economic, social and psychological impacts. Fruit bats of the genus Pteropus are the natural reservoir. In this study, we used real time PCR to screen the saliva and urine of P. vampyrus from North Sumatera for Nipah virus genome. A conventional reverse transcriptase (RT-PCR) assay was used on provisionally positive samples to corroborate findings. This is the first report of Nipah virus detection in P. vampyrus in Sumatera, Indonesia.

Compared to other viruses, research on Nipah virus has been limited in Indonesia because attributable disease outbreaks have not been reported. However, Nipah virus is a zoonotic Biosafety Level 4 (BSL4) agent, so strategic monitoring is prudent. Farmer interviews and a serologic survey of 610 pig sera and 99 bat sera from West Kalimantan province were conducted. Farmers reported no recent or historic encephalitic or respiratory disease in themselves, their families, workers or pigs. The survey found no evidence of exposure to Nipah virus in pigs. In contrast, 19% of the 84 Pteropus vampyrus bat sera reacted in the ELISA, but none of 15 Cynopterus brachyotis bats reacted.

African swine fever (ASF) is a highly lethal and contagious viral haemorrhagic disease of domestic and wild pigs, caused by the ASF virus (ASFV). After entering China in 2018, the disease has continued to spread through Asia. In September 2019, a team from the Indonesian Research Center for Veterinary Science, Bogor, investigated outbreaks in backyard pigs in the Dairi and Humbang Hasundutan districts of North Sumatra province. In January 2020, three pigs purchased from a pig seller in Bogor District, West Java province were also tested. Real‐time PCR results confirmed ASFV DNA in sixteen out of twenty‐nine samples, with nine positive samples from North Sumatra and seven from West Java. Four partial or full‐length genes (i.e. p72, p54, pB602L and CD2v) and a 356‐bp fragment between the I73R and I329L genes were sequenced from representative samples. Phylogenetic analysis established that the ASFV in the samples from both North Sumatra and West Java were identical, indicating a common source of infection, and that they belonged to the p72 genotype II and serogroup 8. The sequences from the Indonesian ASFVs were also identical to other genotype II ASFV from domestic pigs in Vietnam, China and Russia.

The highly pathogenic avian influenza (HPAI) A(H5N1) virus is endemic in Indonesian poultry and has caused sporadic human infection in Indonesia since 2005. Surveillance of H5N1 viruses in live bird markets (LBMs) during 2012 and 2013 was carried out to provide epidemiologic and virologic information regarding viral circulation and the risk of human exposure. Real-time RT-PCR of avian cloacal swabs and environmental samples revealed influenza A-positive specimens, which were then subjected to virus isolation and genomic sequencing. Genetic analysis of specimens collected at multiple LBMs in Indonesia identified both low pathogenicity avian influenza (LPAI) A(H3N8) and HPAI A(H5N1) viruses belonging to clade 2.1.3.2a. Comparison of internal gene segments among the LPAI and HPAI viruses revealed that the latter had acquired the PB2, PB1, and NS genes from LPAI progenitors and other viruses containing a wild type (wt) genomic constellation. Comparison of murine infectivity of the LPAI A(H3N8), wt HPAI A(H5N1) and reassortant HPAI A(H5N1) viruses showed that the acquisition of LPAI internal genes attenuated the reassortant HPAI virus, producing a mouse infectivity/virulence phenotype comparable to that of the LPAI virus. Comparison of molecular markers in each viral gene segment suggested that mutations in PB2 and NS1 may facilitate attenuation. The discovery of an attenuated HPAI A(H5N1) virus in mice that resulted from reassortment may have implications for the capability of these viruses to transmit and cause disease. In addition, surveillance suggests that LBMs in Indonesia may play a role in the generation of reassortant A(H5) viruses and should be monitored.

Background: The live bird market (LBM) plays an important role in the dynamic evolution of the avian influenza H5N1 virus. Objectives: The main objective of this study was to monitor the genetic diversity of the H5N1 viruses in LBMs in Indonesia. Methods: Therefore, the disease surveillance was conducted in the area of Banten, West Java, Central Java, East Java, and Jakarta Province, Indonesia from 2014 to 2019. Subsequently, the genetic characterization of the H5N1 viruses was performed by sequencing all 8 segments of the viral genome. Results: As a result, the H5N1 viruses were detected in most of LBMs in both bird' cloacal and environmental samples, in which about 35% of all samples were positive for influenza A and, subsequently, about 52% of these samples were positive for H5 subtyping. Based on the genetic analyses of 14 viruses isolated from LBMs, genetic diversities of the H5N1 viruses were identified including clades 2.1.3 and 2.3.2 as typical predominant groups as well as reassortant viruses between these 2 clades. Conclusions: As a consequence, zoonotic transmission to humans in the market could be occurred from the exposure of infected birds and/or contaminated environments. Moreover, new virus variants could emerge from the LBM environment. Therefore, improving pandemic preparedness raised great concerns related to the zoonotic aspect of new influenza variants because of its high adaptivity and efficiency for human infection.