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Ticks are one of the arthropods that play an important role in the transmission of numerous pathogens to livestock and humans. We investigated the presence of tick‐borne bacteria in 23 Amblyomma varanense that fed on a water monitor (Varanus salvator) in Indonesia. Anaplasmataceae and borreliae were detected by PCR in 17.4% and 95.7% of ticks, respectively. "Candidatus Rickettsia sepangensis", spotted fever group of Rickettsia, was detected in 21.7% of ticks. The water monitor is a common reptile that is widely encountered in city areas in Asian countries. Our results suggested that Am. varanense on water monitor in Indonesia harbored several kinds of bacteria. [ABSTRACT FROM AUTHOR]

Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.

Post-import from the Republic of Indonesia to Japan in 2017, two juvenile, captive bred Asian small-clawed otters (Aonyx cinereus) exhibited gastrointestinal symptoms, including vomiting, diarrhea, and hematemesis, and died. One of them was examined postmortem. Microscopically, the small intestinal mucosa was necrotic with crypts lined by regenerating large epithelial cells. A gastric cardiac mucosal ulcerative lesion containing fungal yeasts and pseudohyphae morphologically indicated Candida spp. The lymph nodes exhibited marked lymphoid depletion. Canine parvovirus 2 (CPV-2) was isolated from an oral swab, and virus protein 2 (VP2) gene sequencing revealed new CPV-2a. To our knowledge, this is the first new CPV-2a infection report in Asian small-clawed otters. This infection should be considered in gastrointestinal symptom-related cases in this species.

Mosquitoes transmit many kinds of arboviruses (arthropod-borne viruses), and numerous arboviral diseases have become serious problems in Indonesia. In this study, we conducted surveillance of mosquito-borne viruses at several sites in Indonesia during 2016-2018 for risk assessment of arbovirus infection and analysis of virus biodiversity in mosquito populations. We collected 10,015 mosquitoes comprising at least 11 species from 4 genera. Major collected mosquito species were Culex quinquefasciatus, Aedes albopictus, Culex tritaeniorhynchus, Aedes aegypti, and Armigeres subalbatus. The collected mosquitoes were divided into 285 pools and used for virus isolation using two mammalian cell lines, Vero and BHK-21, and one mosquito cell line, C6/36. Seventy-two pools showed clear cytopathic effects only in C6/36 cells. Using RT-PCR and next-generation sequencing approaches, these isolates were identified as insect flaviviruses (family Flaviviridae, genus Flavivirus), Banna virus (family Reoviridae, genus Seadornavirus), new permutotetravirus (designed as Bogor virus) (family Permutotetraviridae, genus Alphapermutotetravirus), and alphamesoniviruses 2 and 3 (family Mesoniviridae, genus Alphamesonivirus). We believed that this large surveillance of mosquitoes and mosquito-borne viruses provides basic information for the prevention and control of emerging and re-emerging arboviral diseases.

During 2016-2018, we conducted surveillance for Japanese encephalitis virus (JEV) in mosquitoes and pigs in Japan, Thailand, the Philippines, and Indonesia. Phylogenetic analyses demonstrated that our isolates (genotypes Ia, Ib, III, IV) were related to JEV isolates obtained from the same regions many years ago. Indigenous JEV strains persist in Asia.

Flying foxes belonging to the genus Pteropus are known to be reservoirs of zoonotic viruses. In this study, we describe the isolation of Pteropine orthoreovirus (PRV) from rectal swab samples of Pteropus vampyrus in Indonesia. PRV is an emerging zoonotic respiratory virus that can be transmitted from bats to humans. Rectal swabs (n = 91) were screened by PCR for PRV and 10 (11%) were positive. Phylogenetic analysis based on nucleotide sequences indicated that the S2, S3, S4, M3, L2, and L3 segments of one isolate (Garut-69) were closely related to previously isolated strains in Indonesia. The remaining gene segments showed both similarity and genetic divergence with other PRV strains, suggesting that re-assortment events had occurred. This is the first report of PRV infection to P. vampyrus in West Java, Indonesia.