Enzootic frog pathogen Batrachochytrium dendrobatidis in Asian tropics reveals high ITS haplotype diversity and low prevalence

Emerging Infectious Diseases (EIDs) are a major threat to wildlife and a key player in the declining amphibian populations worldwide. One such EID is chytridiomycosis caused by Batrachochytrium dendrobatidis (Bd), a fungal pathogen. Aetiology of Bd infection is poorly known from tropical frogs in Asian biodiversity hotspots. Surveys were carried out in four biodiversity hotspots to ascertain the status of Bd fungus. We collected a total of 1870 swab samples from frogs representing 32 genera and 111 species. Nested PCRs revealed low prevalence (8.4%) and high Bd haplotype richness was revealed after sequencing. We document 57 Bd Internal Transcribed Spacer region (ITS) haplotypes, of which 46 were unique to the global database. Bd ITS region showed indels at the Taqman binding site and qPCR reverse primer binding site, suggesting qPCR is unsuitable for diagnosis in Asian Bd coldspots. Our median-joining network and Bayesian tree analyses reveal that the Asian haplotypes, with the exception of Korea, formed a separate clade along with pandemic BdGPL (Bd Global Panzootic Lineage) haplotype. We hypothesise that the frog populations in Asian tropics might harbour several endemic strains of Bd, and the high levels of diversity and uniqueness of Bd haplotypes in the region, probably resulted from historical host-pathogen co-evolution.