Detection and molecular identification of blood parasites in rodents captured from urban areas of southern Sarawak, Malaysian Borneo.

BACKGROUND: Rodent species are well known for their potential as hosts and reservoirs for various zoonotic diseases. Studies on blood parasite infection in small mammals focused on urban cities in Peninsular Malaysia and have been conducted over the years. In contrast, there are information gaps related to molecular detection of blood parasites in urban areas of Sarawak that are associated with veterinary importance and zoonotic spillover potential. Increasing prevalence and transmission of blood parasite diseases is the most crucial public health issue, particularly in developing urban areas of Sarawak. Therefore, molecular identification studies were performed to determine and identify the blood parasites infecting rodents. METHODS: A total of 40 rodent blood samples were analysed for blood parasite infection and a combined approach using polymerase chain reaction-based technique, and traditional microscopic examination (blood smear test) was conducted. 18s rRNA (Plasmodium spp.) and cytochrome b (Hepatocystis spp.) gene marker were used to identify the blood parasites. RESULTS: Note that 67.5% (n = 27) blood samples were tested negative for blood parasites, while 32.5% (n = 13) blood samples collected were infected with at least one protozoan parasite. Out of 13 samples, 69.2% (n = 9) were detected with Hepatocystis sp., while 15.4% (n = 2) were positive with Hepatozoon ophisauri. Two individuals had multiple infections from both species. No Plasmodium spp. have been detected throughout this study using universal primer (targeted Plasmodium spp.); however, different parasite species which were H. ophisauri were detected. CONCLUSION: Although there is no evidence of human infection from H. ophisauri and Hepatocystis sp. detected from the study, the data show the host species are heavily infected, and the information is essential for future prevention of zoonotic outbreaks and surveillance programmes. Therefore, it is suggested that the surveillance programmes should be incorporated in targeted areas with a high risk of disease emergence.

Ecological surveillance of bat coronaviruses in Sarawak, Malaysian Borneo.

OBJECTIVE: Coronaviruses (CoVs) are natural commensals of bats. Two subgenera, namely Sarbecoviruses and Merbecoviruses have a high zoonotic potential and have been associated with three separate spillover events in the past 2 decades, making surveillance of bat-CoVs crucial for the prevention of the next epidemic. The study was aimed to elucidate the presence of coronavirus in fresh bat guano sampled from Wind Cave Nature Reserve (WCNR) in Sarawak, Malaysian Borneo. Samples collected were placed into viral transport medium, transported on ice within the collection day, and preserved at - 80 °C. Nucleic acid was extracted using the column method and screened using consensus PCR primers targeting the RNA-dependent RNA polymerase (RdRp) gene. Amplicons were sequenced bidirectionally using the Sanger method. Phylogenetic tree with maximum-likelihood bootstrap and Bayesian posterior probability were constructed. RESULTS: CoV-RNA was detected in ten specimens (47.6%, n = 21). Six alphacoronavirus and four betacoronaviruses were identified. The bat-CoVs can be phylogenetically grouped into four novel clades which are closely related to Decacovirus-1 and Decacovirus-2, Sarbecovirus, and an unclassified CoV. CoVs lineages unique to the Island of Borneo were discovered in Sarawak, Malaysia, with one of them closely related to Sarbecovirus. All of them are distant from currently known human coronaviruses.

Bedbugs Evolved before Their Bat Hosts and Did Not Co-speciate with Ancient Humans.

All 100+ bedbug species (Cimicidae) are obligate blood-sucking parasites [1, 2]. In general, blood sucking (hematophagy) is thought to have evolved in generalist feeders adventitiously taking blood meals [3, 4], but those cimicid taxa currently considered ancestral are putative host specialists [1, 5]. Bats are believed to be the ancestral hosts of cimicids [1], but a cimicid fossil [6] predates the oldest known bat fossil [7] by >30 million years (Ma). The bedbugs that parasitize humans [1, 8] are host generalists, so their evolution from specialist ancestors is incompatible with the "resource efficiency" hypothesis and only partially consistent with the "oscillation" hypothesis [9-16]. Because quantifying host shift frequencies of hematophagous specialists and generalists may help to predict host associations when vertebrate ranges expand by climate change [17], livestock, and pet trade in general and because of the previously proposed role of human pre-history in parasite speciation [18-20], we constructed a fossil-dated, molecular phylogeny of the Cimicidae. This phylogeny places ancestral Cimicidae to 115 mya as hematophagous specialists with lineages that later frequently populated bat and bird lineages. We also found that the clades, including the two major current urban pests, Cimex lectularius and C. hemipterus, separated 47 mya, rejecting the notion that the evolutionary trajectories of Homo caused their divergence [18-21]. VIDEO ABSTRACT.

Multilocus analyses indicate a mosaic distribution of hybrid populations in ground squirrels (genus Ictidomys).

DNA sequence data from mitochondrial cytochrome-b (Cytb) and Y-linked structural maintenance of chromosomes (SmcY) genes were combined with 478 nuclear loci obtained from amplified fragment length polymorphisms (AFLP) to assess the extent of hybridization and genetic spatial structure of populations in two hybridizing species of ground squirrel (Ictidomys parvidens and Ictidomys tridecemlineatus). Based on AFLP analyses of 134 individuals from 28 populations, 10 populations were identified that possessed hybrid individuals. Overall estimates of F ST values revealed strong support for population structure in the Cytb data set; however, analyses of the SmcY gene and the AFLP data indicated ongoing gene flow between species. Pairwise F ST comparisons of populations were not significant for the SmcY gene; although they were significant for the Cytb gene, indicating that these populations were structured and that gene flow was minimal. Therefore, gene flow between I. parvidens and I. tridecemlineatus appeared to be restricted to populations that exhibited hybridization. In addition, the fragmented nature of the geographic landscape suggested limited gene flow between populations. As a result, the distributional pattern of interspersed parental and hybrid populations were compatible with a mosaic hybrid zone model. Because ground squirrels display female philopatry and male-biased dispersal, the ecology of these species is compatible with this hypothesis.

Single-locus species delimitation: a test of the mixed Yule-coalescent model, with an empirical application to Philippine round-leaf bats.

Prospects for a comprehensive inventory of global biodiversity would be greatly improved by automating methods of species delimitation. The general mixed Yule-coalescent (GMYC) was recently proposed as a potential means of increasing the rate of biodiversity exploration. We tested this method with simulated data and applied it to a group of poorly known bats (Hipposideros) from the Philippines. We then used echolocation call characteristics to evaluate the plausibility of species boundaries suggested by GMYC. In our simulations, GMYC performed relatively well (errors in estimated species diversity less than 25%) when the product of the haploid effective population size (N(e)) and speciation rate (SR; per lineage per million years) was less than or equal to 10(5), while interspecific variation in N(e) was twofold or less. However, at higher but also biologically relevant values of N(e) × SR and when N(e) varied tenfold among species, performance was very poor. GMYC analyses of mitochondrial DNA sequences from Philippine Hipposideros suggest actual diversity may be approximately twice the current estimate, and available echolocation call data are mostly consistent with GMYC delimitations. In conclusion, we consider the GMYC model useful under some conditions, but additional information on N(e), SR and/or corroboration from independent character data are needed to allow meaningful interpretation of results.

Do time, heterochromatin, NORs, or chromosomal rearrangements correlate with distribution of interstitial telomeric repeats in Sigmodon (cotton rats)?

We studied the chromosomal distribution of telomere repeats (TTAGGG)(n) in 8 species of Sigmodon (cotton rats) using chromosome paints fluorescent in situ hybridization (FISH) from Sigmodon hispidus. In 2 species with the proposed primitive karyotype for the genus, telomere repeats were restricted to telomeric sites. But in the other 6 species that include 3 with proposed primitive karyotypes and 3 with highly rearranged karyotypes, telomere repeats were found on both telomeric sites and within interstitial telomeric sites (ITSs). To explain the distribution of ITS in Sigmodon, we gather data from C-bands, silver nitrate staining, G-bands, and chromosomal paint data from previous published studies. We did find some correlation with ITS and heterochromatin, euchromatic chromosomal rearrangements, and nucleolar organizing regions. No one type of chromosomal structure explains all ITS in Sigmodon. Multiple explanations and mechanisms for movement of intragenomic sequences are required to explain ITS in this genus. We rejected the hypothesis that age of a lineage correlates with the presence of ITS using divergence time estimate analyses. This multigene phylogeny places species with ITS (S. arizonae, S. fulviventer, S. hispidus, S. mascotensis, S. ochrognathus, and S. toltecus) in the clade with a species without ITS (S. hirsutus). Lineages with ITS (S. arizonae and S. mascotensis) arose independently from a lineage absent of ITS (S. hirsutus) around 0.67 to 0.83 Ma. The rearranged karyotypes of S. mascotensis and S. arizonae appear to be an independently derived autapomorphic characters, supporting a fast rate of chromosomal changes that vary among species.