Detection and Complete Genome Analysis of Circoviruses and Cycloviruses in the Small Indian Mongoose (Urva auropunctata): Identification of Novel Species

Fecal samples from 76 of 83 apparently healthy small Indian mongooses (Urva auropunctata) were PCR positive with circovirus/cyclovirus pan-rep (replicase gene) primers. In this case, 30 samples yielded high quality partial rep sequences (~400 bp), of which 26 sequences shared maximum homology with cycloviruses from an arthropod, bats, humans or a sheep. Three sequences exhibited maximum identities with a bat circovirus, whilst a single sequence could not be assigned to either genus. Using inverse nested PCRs, the complete genomes of mongoose associated circoviruses (Mon-1, -29 and -66) and cycloviruses (Mon-20, -24, -32, -58, -60 and -62) were determined. Mon-1, -20, -24, -29, -32 and -66 shared <80% maximum genome-wide pairwise nucleotide sequence identities with circoviruses/cycloviruses from other animals/sources, and were assigned to novel circovirus, or cyclovirus species. Mon-58, -60 and -62 shared maximum pairwise identities of 79.90–80.20% with human and bat cycloviruses, which were borderline to the cut-off identity value for assigning novel cycloviral species. Despite high genetic diversity, the mongoose associated circoviruses/cycloviruses retained the various features that are conserved among members of the family Circoviridae, such as presence of the putative origin of replication (ori) in the 5′-intergenic region, conserved motifs in the putative replication-associated protein and an arginine rich region in the amino terminus of the putative capsid protein. Since only fecal samples were tested, and mongooses are polyphagous predators, we could not determine whether the mongoose associated circoviruses/cycloviruses were of dietary origin, or actually infected the host. To our knowledge, this is the first report on detection and complete genome analysis of circoviruses/cycloviruses in the small Indian mongoose, warranting further studies in other species of mongooses.

Development and Characterization of Microsatellite Markers in The Small Indian Mongoose (Urva Auropunctata)

The small Indian mongoose (Urva auropunctata) is listed among 100 of the World’s Worst Invasive Alien Species and eradication programs are ongoing worldwide. The development of individual and sex identification markers will improve their management. Therefore, we searched for novel mongoose short simple repeat (SSR) markers using genome-wide screening and identified 115,265 tetra-nucleotide repeat loci. Of 96 loci tested, 17 were genotyped in 28 mongooses from the Okinawa population. The genetic diversity analysis showed that the average expected and observed heterozygosity and number of alleles were 0.55, 0.56, and 2.94, respectively. Of 17 loci, one deviated from Hardy–Weinberg equilibrium and six loci pairs were likely linked to each other. However, we succeed in identifying all individuals using all of the SSR loci. The novel sex identification markers worked successfully in a test using six known sex samples. These novel SSR and sex identification markers should be useful in studies of individual identification and population genetics of the mongoose.

First Report on Detection and Genetic Diversity of Picobirnaviruses in the Small Indian Mongoose (Herpestes auropunctatus)

Picobirnaviruses (PBVs), family Picobirnaviridae, are bi-segmented, double-stranded RNA viruses. PBVs are considered opportunistic enteric pathogens. Gene segment-1 of PBV encodes the capsid protein, whilst gene segment-2 codes for RNA-dependent RNA polymerase (RdRp). Based on differences in gene segment-2, PBVs are classified into genogroup-I (GI) and GII. Although PBVs have been detected in a wide variety of host species, there are no reports on PBVs from mongoose so far. We report here high rates of detection (35.36%, 29/82) of GI PBVs in fecal samples from the small Indian mongoose (Herpestes auropunctatus) on the Caribbean island of St. Kitts. Applying a combination of a non-specific primer-based amplification method and conventional RT-PCR using a newly designed primer targeting the 3′-untranslated region (UTR), we could amplify and sequence the complete/nearly complete gene segment-2 of eight mongoose PBV strains. Except for a single strain, the gene segment-2 of the remaining mongoose PBV strains contained the putative open reading frame encoding the RdRp. The gene segment-2/putative RdRps of the mongoose PBV strains retained various features that are conserved in other PBVs (5′- and 3′-terminal nucleotide sequences, bacterial ribosomal binding site sequence in 5′-UTR, and the three domains in putative RdRps). On the other hand, phylogenetic analysis and sequence identities of the putative RdRps revealed high genetic diversity among the mongoose PBV strains and with those of PBVs from other host species. To our knowledge, this is the first report on detection and genetic diversity of PBVs from the mongoose, expanding the host range of PBVs and providing vital insights into the various features and evolution of putative RdRps of PBVs in a new host species.

Temporal overlap of carnivorous mammal community and their prey in Khao Ang Rue Nai Wildlife Sanctuary, Chachoengsao Province, Thailand

Sukmasuang R, Charaspet K, Reontik J, Pla-ard M. 2020. Temporal overlap of carnivorous mammal community and their prey in Khao Ang Rue Nai Wildlife sanctuary, Chachoengsao Province, Thailand. Biodiversitas 21: 922-932. This study on the temporal overlap of the carnivorous community and their prey in Khao Ang Rue Nai Wildlife Sanctuary was conducted from March 2017 to February 2018. Camera traps were deployed systematically with a total of 4,463 trap nights. Fourteen carnivorous mammals were recorded, which were mainly present at night, with the exception of the dhole, small Indian mongoose, crab-eating mongoose, and yellow-throated marten. The clouded leopard's presence overlapped between day and night. Using the average coefficient overlap(Δ) between a carnivore, and the other carnivorous species, the leopard cat was found to have the highest Δ value, followed by the hog badger, Asiatic jackal, small Indian civet, Asian palm civet, large Indian civet, large spotted civet, Asiatic black bear, dhole, Malayan sun bear, yellow-throated marten, small Indian mongoose, crab-eating mongoose, and clouded leopard. The potential prey species that had the highest Δwith the carnivorous species, was the Siamese hare. This study shows the importance of preserving the carnivorous community within the area. An important threat is a likelihood that carnivorous species in the area may be exposed to external diseases from infected domestic animals when coming out to hunt in the communities surrounding the protected area.