---
title: "Detection of Zoonotic Pteropine orthoreovirus in Rousettus amplexicaudatus Bats in Indonesia"
id: "cdc-emerging-infectious-diseases-journal-0-identification-of-zoonotic-pteropine-orthoreovirus-in-rousettus-amplexicaudatus"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-0-identification-of-zoonotic-pteropine-orthoreovirus-in-rousettus-amplexicaudatus"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article"
published_at: "2026-10-23T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Detection of Zoonotic Pteropine orthoreovirus in Rousettus amplexicaudatus Bats in Indonesia
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-0-identification-of-zoonotic-pteropine-orthoreovirus-in-rousettus-amplexicaudatus
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article)
- **Published At:** 2026-10-23T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- Investigators sampled 182 fruit bats from animal markets and suppliers across Java, Indonesia, during 2020–2021; species were identified by morphological criteria. - Rectal swabs were cultured on Vero cells; two isolates produced cytopathic effects and were selected for whole-genome sequencing. - Next-generation sequencing recovered nine of ten genomic segments for both isolates; 9 segments were >99%–100% identical between isolates, while the S2 segment showed 88.9% identity. - Phylogenetic analyses placed the isolates in close association with known bat-associated PRVs, including Nelson Bay, Melaka, Kampar, Pulau, and Garut-69 strains. - The two virus isolations originated from Rousettus amplexicaudatus bats sold for human consumption in Cianjur, West Java—highlighting wildlife trade at the human–bat interface. - Laboratory workflow: nonlethal rectal swab and serum collection, RNA extraction with QIAamp kit, RT-PCR screening for influenza and coronaviruses, blinded Vero cell culture isolation, Illumina NextSeq 550 paired-end sequencing, and EsViritu bioinformatics for detection and genome assembly. - The study team observed that PRVs are circulating in Indonesian fruit bats and recommended continued surveillance at the human–bat interface to monitor for emergence of novel viruses and to mitigate zoonotic risk. - The source did not report specific patient infections, disease incidence among humans, or detailed infection experiments; clinical pathogenicity in humans was not assessed in this study.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1348) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F12%2F25-1991_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F12%2F25-1991_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F12%2F25-1991_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/12/25-1991_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 12—December 2026 ##### _Research_ ### Identification of Zoonotic _Pteropine orthoreovirus_ in _Rousettus amplexicaudatus_ Fruit Bats, Indonesia On This Page [Materials and Methods](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) * * * [Results](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) * * * [Discussion](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f2) * * * [Figure 3](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f3) * * * [Figure 4](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f4) * * * [Figure 5](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f5) * * * [Figure 6](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f6) * * * [Figure 7](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f7) * * * [Figure 8](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f8) * * * [Figure 9](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f9) * * * [Figure 10](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f10) * * * [Figure 11](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f11) * * * [Figure 12](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-f12) Tables [Table 1](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-t1) * * * [Table 2](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-t2) Downloads [Appendix ](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-app1.pdf) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/12/25-1991.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article) Ni Luh Putu Indi Dharmayanti[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#comment) , Diana Nurjanah, and Yustinus Maladan Author affiliation: National Research and Innovation Agency, Cibinong, Indonesia [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#suggestedcitation) ### Abstract _Pteropine orthoreovirus_ (PRV) is an emerging batborne virus with zoonotic potential increasingly linked to human respiratory illness. During 2020–2021, we sampled 182 fruit bats from animal markets and suppliers across Java, Indonesia, and identified species morphologically. We cultured rectal swab samples on Vero cells and sequenced samples showing cytopathic effects by using next-generation technology. We recovered 2 isolates from _Rousettus amplexicaudatus_ bats sold for human consumption in Cianjur, West Java. Comparative analysis of 9 of 10 genomic segments showed the isolates were nearly identical (>99%–100%), except for the S2 segment (88.9%). Phylogenetic analysis indicated close clustering with Nelson Bay, Melaka, Kampar, Pulau, and Garut-69 bat-associated PRVs. We found PRV in _R. amplexicaudatus_ bats in Indonesia, which highlights the zoonotic risk of wildlife trade. Continued surveillance of PRVs at the human–bat interface will be needed to assess the emergence of novel viruses and mitigate potential zoonotic threats. Fruit bats, particularly large flying foxes (_Pteropus vampyrus_), are well documented as natural reservoirs of a wide range of viruses that have zoonotic potential, including herpesviruses, parvoviruses, polyomaviruses, paramyxoviruses, coronaviruses, and orthoreoviruses ([_1_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r1 "1"),[_2_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r2 "2")). Orthoreoviruses, specifically those classified as _Pteropine orthoreovirus_ (PRV), have increasingly been associated with respiratory diseases in humans ([_3_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r3 "3")–[ _5_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r5 "5")). The zoonotic potential of batborne orthoreoviruses was first recognized in 2006, when a febrile illness along with respiratory symptoms were reported in a patient who had known exposure to a flying fox. The causative agent, later named Melaka virus, marked the first identification of a PRV responsible for human respiratory disease ([_6_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r6 "6")). After 2006, several genetically and antigenically related virus strains, such as Kampar, Sikamat, HK23629/07, and Miyazaki-Bali/2007, were isolated from patients who had similar respiratory tract infections ([_7_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r7 "7")–[ _9_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r9 "9")). Those findings strongly support a role for PRVs as emerging zoonotic pathogens that have a capacity for interspecies transmission. In 2010, a novel PRV strain, designated as Indonesia/2010, was isolated from a _P. vampyrus_ bat imported from Indonesia to Italy ([_10_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r10 "10")). Whole-genome sequencing (WGS) revealed close genetic similarity to Melaka virus, reinforcing the hypothesis that Southeast Asia, particularly Indonesia, serves as a major ecologic reservoir for orthoreoviruses that have zoonotic potential. That discovery was followed by the identification of additional strains from Indonesia, such as Garut-69 ([_11_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r11 "11")), further highlighting the genetic diversity and ongoing circulation of PRVs in fruit bat populations. A study in 2022 reported the isolation and characterization of a novel PRV strain from fruit bats in the Paguyaman region of Sulawesi, Indonesia; that strain was designated as _Paguyaman orthoreovirus_ ([_12_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r12 "12")). In vitro and in vivo characterization of that virus revealed evidence of potential reassortment events with previously described Nelson Bay virus–related strains ([_8_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r8 "8")). Intranasal inoculation of laboratory mice with _Paguyaman orthoreovirus_ resulted in severe pneumonia, underscoring its pathogenic potential in mammal hosts ([_12_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r12 "12")). Mammal orthoreoviruses were first detected in Southeast Asia within fecal samples from _P. vampyrus_ bats in Central Java Province, Indonesia ([_13_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r13 "13")). We report the detection of 2 PRV isolates in _Rousettus amplexicaudatus_ bats collected in West Java, Indonesia. _R. amplexicaudatus_ is a medium-sized fruit bat distributed throughout Indonesia. We conducted next-generation sequencing and phylogenetic analysis to determine associations between the 2 isolates and other orthoreoviruses. ### Materials and Methods ##### Sample Collection The Institutional Animal Care and Use Committee of the Indonesian Agency for Agricultural Research and Development approved all animal handling procedures (protocol nos. Balitbangtan/BB Litvet/M/01/2020 and Balitbangtan/BB Litvet/M/01/2021). We performed sampling nonlethally and obtained both rectal swab and blood serum samples from 182 bats. We placed rectal swab samples in virus transport medium consisting of Dulbecco’s modified Eagle medium (Thermo Fisher Scientific, [External Link](https://www.thermofisher.com)) supplemented with 10,000 U/mL penicillin/streptomycin, 250 μg/mL amphotericin B, and 10 mg/mL gentamycin (Thermo Fisher Scientific). We stored all samples at −20°C in a portable freezer and transported them to the Indonesia Research Center for Veterinary Science laboratory in Bogor, Indonesia. ##### Bat Species Identification We identified bat species by using photographic records combined with established external morphologic assessments ([_14_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r14 "14")). Key morphometric parameters included forearm, tibia, hind limb, and ear lengths; overall body size and coloration; presence of a claw on the second wing digit; tail length; body mass; and distinctive features of the muzzle, tongue, and ear margins. We used those parameters to distinguish between bat species. ##### Virus Isolation, RNA Extraction, and WGS We extracted virus RNA by using the QIAamp Viral RNA Mini Kit (QIAGEN, [External Link](https://www.qiagen.com)), according to the manufacturer’s protocol. We preserved the RNA extracts at −20°C for reverse transcription PCR (RT-PCR). We screened total RNA extracts from collected samples for influenza A virus ([_15_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r15 "15")) and for RNA-dependent RNA polymerase (RdRp) and spike genes of bat coronaviruses by RT-PCR ([_16_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r16 "16")). In addition, we screened for SARS-CoV-2 by using the SensiFAST Probe No-ROX One-Step Real-Time PCR Kit (Bioline, [External Link](https://www.bioline.com)) on an Applied Biosystems 7300 Real-Time PCR System (Thermo Fisher Scientific). The SARS-CoV-2 assay targeted the nucleocapsid (N) 1 and N2 gene regions, and we used the human RNase P gene as an internal control, according to the manufacturer’s protocol. We used the SARS-CoV-2 assay for qualitative real-time RT-PCR to detect the presence of the virus; the assay was not intended for virus load quantification. After screening, we selected a subset of samples that tested positive for a virus and performed virus isolation through a blinded cell culture procedure. We inoculated Vero cell monolayers with each sample separately and incubated the cells at 37°C in a humidified 5% CO2 atmosphere under standard cell culture conditions. We monitored cultures daily for the appearance of cytopathic effects (CPEs). Among the cultured samples, we selected 2 isolates exhibiting prominent CPEs for further genomic analysis. We reextracted virus RNA directly from clarified culture supernatants and performed WGS using next-generation sequencing technology. A commercial sequencing service provider performed the library preparation and sequencing by using the Illumina NextSeq 550 platform with paired-end 150-bp reads. We used the resulting sequencing data for virus genome assembly and downstream molecular characterization. In addition, we also performed RT-PCR targeting the small (S) 1 and S2 genome segments as previously described ([_11_](https://wwwnc.cdc.gov/eid/article/32/12/25-1991_article#r11 "11")) to confirm the presence of those segments in the isolates ([Appendix](https://wwwnc.cdc.gov/eid/article/32/12/25-1991-app1.pdf) Figure 1). ##### Bioinformatics Analysis We detected and quantified animal virus pathogens from short-read sequencing data by using EsViritu version 3.1.0 ( [External Link](https://github.com/cmmr/EsViritu)). EsViritu is a sensitive and specific bioinformatics pipeline designed to explore the presence, absence, and diversity of viruses within and between metagenomic or clinical samples. The database used by EsViritu includes all human and animal viruses available in GenBank. The output of the pipeline consists of consensus genomes or segments of detected viruses along with an interactive table that includes vi
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