Thottapalayam virus (TPMV), a member of the genus Hantavirus in the family Bunyaviridae, was isolated from an insectivore, Suncus murinus (musk shrew), captured in southern India in 1964. While the isolation of TPMV predates the discovery of the prototype Hantaan virus, little is known about its genetics and biology. To date, preliminary evidence suggests that TPMV differs significantly, both antigenically and genetically, from all known rodent-borne hantaviruses. However, since detailed epizootiological studies have not been conducted, it is unclear if TPMV is naturally harbored by an insectivore host or if TPMV represents a "spillover" from its natural rodent reservoir host. Moreover, to what extent TPMV causes infection and/or disease in humans is not known. To address these issues, we first studied the antigenic profile of TPMV using monoclonal antibodies against Hantaan and Seoul viruses and polyclonal immune sera against Puumala virus and TPMV. Armed with this newfound information, we developed an enzymelinked immunosorbent assay system for the diagnosis of TPMV infections in shrews and humans, using a recombinant TPMV N antigen manipulated to have an E5/G6 epitope to be captured by monoclonal antibody clone E5/G6. Using this assay, we found anti-TPMV antibodies in sera from a patient with high fever of unknown etiology in Thailand and from two shrews captured in Indonesia. Seropositivity was verified by the indirect immunofluorescence antibody test, Western blotting analysis, and focus reduction neutralization test. Collectively, our data indicate that TPMV is harbored by Suncus murinus as its host in nature and is capable of infecting humans.

During febrile surveillance in the western Java City of Bandung, Indonesia, a patient with clinical symptoms consistent with hantavirus infection was found to have elevated titers of hantavirus-specific immunoglobulin M (IgM) and IgG antibodies. A subsequent epizoological investigation demonstrated a higher prevalence of hantavirus IgG antibodies in rodents trapped in the vicinity of the patient's home compared with rodents from a control area (13.2% vs. 4.7%, p = 0.036). The Old World Seoul hantavirus was detected by reverse transcriptase-polymerase chain reaction in the organs of 71% of the seropositive rodents tested. This is the first report of a Seoul virus infection in Indonesia supported by clinical, serological, and epizoological evidences. These findings suggest that hantavirus infection should be on the clinical differential diagnosis when acutely ill febrile patients report for care in western Java.

We sought to elucidate the role of migratory birds in transmission of H5N1 in an enzoonotic area. Resident, captive, and migratory birds were sampled at five sites in Java, Indonesia. Mist nets were used to trap birds. Birds were identified to species. RNA was extracted from swabs and reverse transcriptase polymerase chain reaction (RT-PCR) conducted for the HA and M genes of H5N1. Antibodies were detected by enzyme-linked immunosorbent assay and hemagglutination inhibition test. Between October 2006 and September 2007, a total of 4,067 captive, resident, and migratory birds comprising 98 species in 23 genera were sampled. The most commonly collected birds were the common sandpiper (6% of total), striated heron (3%), and the domestic chicken (14%). The overall prevalence of H5N1 antibodies was 5.3%. A significantly higher percentage of captive birds (16.1%) showed antibody evidence of H5N1 exposure when compared to migratory or resident birds. The greatest number of seropositive birds in each category were Muschovy duck (captive), striated heron (resident), and the Pacific golden plover (migratory). Seven apparently well captive birds yielded molecular evidence of H5N1 infection. Following amplification, the HA, NA, and M genes were analyzed. Phylogenetic analysis of the HA gene showed that the isolates were 97% similar to EU124153.1 A/chicken/West Java/Garut May 2006, an isolate obtained in a similar region of West Java. While no known markers of neuraminidase inhibitor resistance were found within the NA gene, M segment analysis revealed the V27A mutation known to confer resistance to adamantanes. Our results demonstrate moderate serologic evidence of H5N1 infection in captive birds, sampled in five sites in Java, Indonesia, but only occasional infection in resident and migratory birds. These data imply that in an enzoonotic region of Indonesia the role of migratory birds in transmission of H5N1 is limited.

Ectoparasites were sampled from small mammals collected in West Java, West Sumatra, North Sulawesi, and East Kalimantan, Indonesia, in 2007-2008 and were screened for evidence of infection from bacteria in the Rickettsaceae family. During eight trap nights at eight sites, 208 fleas were collected from 96 of 507 small mammals trapped from four orders (379 Rodentia; 123 Soricomorpha; two Carnivora; three Scandentia). Two species of fleas were collected: Xenopsylla cheopis (n = 204) and Nosopsyllus spp. (n = 4). Among the 208 fleas collected, 171 X. cheopis were removed from rats (Rattus spp.) and 33 X. cheopis from shrews (Suncus murinus). X. cheopis were pooled and tested for DNA from rickettsial agents Rickettsia typhi, Rickettsia felis, and spotted fever group rickettsiae. R. typhi, the agent of murine typhus, was detected in X. cheopis collected from small mammals in West Java and East Kalimantan. R. felis was detected in X. cheopis collected from small mammals in Manado, North Sulawesi. R. felis and spotted fever group rickettsiae were detected in a pool of X. cheopis collected from an animal in East Kalimantan. Sixteen percent of the X. cheopis pools were found positive for Rickettsia spp.; four (10.8%) R. typhi, one (2.7%) R. felis, and one (2.7%) codetection of R. felis and a spotted fever group rickettsia. These data suggest that rickettsial infections remain a threat to human health across Indonesia.

Dengue and other common tropical infectious diseases of similar clinical presentation are endemic in Indonesia, which may lead to an underestimation of the prevalence of hantavirus (HTV) infection in the country. To better understand the current burden of HTV infection, this study aimed to both identify acute HTV infection among hospitalized patients with fever and to determine the overall seroprevalence of HTV. These results were further considered within the context of previously reported HTV infection in humans and animals in Indonesia by conducting a review of published literature. As part of an observational cohort study of acute febrile illness, this sub-study retrospectively analyzed blood specimens obtained during admission, during the 2–4-week convalescent period, and three months after admission. Convalescent specimens from patients with clinical signs and symptoms of HTV infection were first screened for HTV IgG. When positive, convalescent specimens and paired acute specimens were screened for HTV IgM, and paired acute specimens were tested for HTV by Reverse Transcription Polymerase Chain Reaction (RT-PCR). A literature review of HTV in Indonesia was conducted on manuscripts manually reviewed for relevance after identification from a search using the terms “hantavirus/Seoul virus” and “Indonesia”. From patients at eight hospitals in seven provincial capitals, HTV IgG seroprevalence was 11.6% (38/327), with the highest being in Denpasar (16.3%, 7/43) and the lowest being in Yogyakarta (3.4%, 1/31). Anti-HTV IgG was most prevalent in adults (13.5%, 33/244) and males (15.6%, 29/186). Acute HTV infections were identified in two subjects, both of whom had Seoul virus. In Indonesia, HTVs have been studied in humans and animals since 1984. Over the past 35 years, the reported seroprevalences in rodents ranged from 0% to 34%, and in humans from 0% to 13%. Fourteen acute infections have been reported, including one in a tourist returning to Germany, but only two have been confirmed by RT-PCR. Almost all rodent and human surveillance results demonstrated serological and molecular evidence of Seoul virus infection. However, in Semarang, anti-Puumala virus IgM has been detected in humans and Puumala RNA in one rodent. In Serang, a new virus named Serang virus was identified due to its differences from Seoul virus. In Maumere, HTV and Leptospira spp. were identified simultaneously in rodents. The burden of HTV infection in Indonesia is underestimated, and additional studies are needed to understand the true prevalence. Seroprevalence data reported here, previous observations of HTV co-infections in rodents, and the prevalence of rodent-borne bacterial infections in Indonesia suggest that the population may be routinely encountering HTVs. While Seoul virus appears to be the most prevalent HTV in the country, further studies are needed to understand which HTVs are circulating.

The prevalence of antibodies against spotted fever group rickettsia (SFGR), murine typhus and Q fever were investigated in wild rats captured in Indonesia. Sera of 327 rats were collected from Jakarta and Boyolali on Java Island. The prevalences of antibodies against SFGR and murine typhus were 128 (39.1%) and 48 (14.7%), respectively. Antibodies against Q fever were not detected in these serum samples. Antibodies against SFGR were found in all species of rats (20.8-51.9%). The antibody positive rate against murine typhus in Rattus norvegicus (38.0%) was significantly higher than that in other rat species (0-4.8%, p<0.01). The antibody positive rates against SFGR and murine typhus in rats captured in Jakarta were significantly higher than those in rats captured in Boyolali (p<0.01). In this survey, all species of rats had antibodies against SFGR, indicating that the 4 species of tested rats (R. norvegicus, R. rattus, R. exulans, R. tiomanicus) were infected with SFGR and that SFGR may infest the whole of Java Island. Most of the rats that were antibody-positive against murine typhus were captured in Jakarta. Therefore, R. norvegicus and R. rattus are likely to be important hosts of murine typhus in Jakarta. The antibody-positive rates against SFGR and murine typhus in rats captured in the dry season were significantly higher than those in rats captured in the rainy season. This may coincide with the active periods of ticks and fleas in Indonesia.