Epidemiology and genetic characteristics of murine kobuvirus from faecal samples of Rattus losea, Rattus tanezumi and Rattus norvegicus in southern China

Recently, murine kobuvirus (MuKV), a novel member of the family Picornaviridae, was identified in faecal samples of Rattus norvegicus in China. The limited information on the circulation of MuKV in other murine rodent species prompted us to investigate its prevalence and conduct a genetic characterization of MuKV in Rattus losea, Rattus tanezumi and Rattus norvegicus in China. Between 2015 and 2017, 243 faecal samples of these three murine rodent species from three regions in southern China were screened for the presence of MuKV. The overall prevalence was 23.0% (56/243). Three complete MuKV polyprotein sequences were acquired, and the genome organization was determined. Phylogenetic analyses suggested that our sequences were closely related to Chinese strains and belong to the species Aichivirus A in the genus Kobuvirus. Additional studies are required to understand the true prevalence of MuKV in murine rodent populations in China.

Infestation and Related Ecology of Chigger Mites on the Asian House Rat (Rattus tanezumi) in Yunnan Province, Southwest China

This paper is to illustrate the infestation and related ecological characteristics of chigger mites on the Asian house rat (Rattus tanezumi). A total of 17,221 chigger mites were collected from 2,761 R. tanezumi rats, and then identified as 131 species and 19 genera in 2 families. Leptotrombidium deliense, the most powerful vector of scrub typhus in China, was the first major dominant species on R. tanezumi. All the dominant mite species were of an aggregated distribution among different individuals of R. tanezumi. The species composition and infestations of chiggers on R. tanezumi varied along different geographical regions, habitats and altitudes. The species-abundance distribution of the chigger mite community was successfully fitted and the theoretical curve equation was. Ŝ (R)=37e–(0.28R)2 The total chigger species on R. tanezumi were estimated to be 199 species or 234 species, and this further suggested that R. tanezumi has a great potential to harbor abundant species of chigger mites. The results of the species-plot relationship indicated that the chigger mite community on R. tanezumi in Yunnan was an uneven community with very high heterogeneity. Wide geographical regions with large host samples are recommended in the investigations of chigger mites.

Epidemiology, Genetic Characterization, and Evolution of Hunnivirus Carried by Rattus norvegicus and Rattus tanezumi: The First Epidemiological Evidence from Southern China

Hunnivirus is a novel member of the family Picornaviridae. A single species, Hunnivirus A, is currently described. However, there is limited information on the identification of Hunnivirus to date, and thereby the circulation of Hunnivirus is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of Hunnivirus from urban rats (Rattus norvegicus and Rattus tanezumi) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in Rattus norvegicus and 15.6% in Rattus tanezumi. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of Hunnivirus A4. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.

Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene

Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’s D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.

Diversity of Rodent Species and Its Potency as the Vector for Transmitting Rodent Borne Parasitic Disease in Households

Rodent species have been known as the major pest in the agricultural sector leading to economic losses. They are also identified as the vector for several rodent -borne zoonotic diseases. However, a specific study on observing their diversity in households closed to lowland irrigated agroecosystems that correspond to disease distribution’s role is limited. To address this issue, a field study was performed during the 2019 -2020 cropping season in two sites (Yogyakarta and West Java) which were categorized as the rice production centers. Trapping was conducted consecutively for 13-30 days using 65-75 snap traps. Roasted coconut and salty fish were used to attract rodents. In West Java, 3 rodent species ( Rattus argentiventer, Rattus tanezumi, Bandicota indica) and insectivore small mammal (Suncus murinus) were discovered from 1,950 trap nights. Meanwhile, the setting of 900 trap nights in Yogyakarta indicated less diverse rodents with only one species (Rattus tanezumi) and the same insectivore discovered. All captured animals were dissected and observed for the endoparasites. We obtained two potent species of parasites ( Taenia taeniaeformis and Capillaria hepatica), which can be transmitted by rodents to the local people if they do not apply a proper health practice.

Spot Survei Reservoir Leptospira di Daerah Dataran Rendah dan Dataran Tinggi

ENGLISHThe presence of rats and direct contact with rat is a risk factor of Leptospirosis. Rats play an important role in the transmission of Leptospira to humans. Rats are able to adapt in all habitats from the coast to the highlands. The purpose of this paper is to describe rats as Leptospira reservoirs in the lowlands and highlands as a picture of rats confirmed by the source of Leptospira transmission for animals, humans and their environment and serovar circulating in the lowlands and highlands. This research uses deskriptif approach with a cross-sectional design, carried out around the latest leptospirosis cases in Mojolawaran Village, Gabus District and Tajungsari Village, Tlogowungu District, Pati Regency. Data collection was carried out in April-May 2011. The Results of the research showed that the number of rats caught is higher in the lowlands with almost the same number of species between the lowlands and highlands with trap success 15,33%. Rats infected with Leptospira in the lowlands are Rattus tanezumi while in the highlands are Rattus tanezumi and Suncus murinus so that R. tanezumi and S. murinus act as reservoirs of Leptospira and sources of transmission at the survey sites with serovars infected are Hardjo, Autumnalis and Sejroe. INDONESIAKeberadaan tikus dan kontak dengan tikus merupakan salah satu faktor risiko terjadinya leptospirosis. Tikus berperan penting dalam menularkan Leptospira kepada manusia serta mampu beradaptasi di segala habitat dari daerah pantai hingga dataran tinggi. Tujuan penelitian ini untuk mendeskripsikan tikus sebagai reservoir Leptospira di dataran rendah dan dataran tinggi sebagai gambaran jenis tikus yang terkonfirmasi sumber penularan Leptospira bagi hewan, manusia, dan lingkungannya serta serovar yang bersirkulasi di dataran rendah dan dataran tinggi. Penelitian ini menggunakan pendekatan deskriptif dengan rancangan potong lintang. Penelitian dilakukan di sekitar kasus leptospirosis terbaru di Desa Mojolawaran Kecamatan Gabus dan Desa Tajungsari Kecamatan Tlogowungu Kabupaten Pati. Pengumpulan data dilakukan pada April-Mei 2011. Hasil penelitian menunjukkan jumlah tikus tertangkap lebih banyak di dataran rendah dengan jumlah spesies yang hampir sama antara dataran rendah dan tinggi dengan keberhasilan penangkapan 15,33%. Spesies tikus yang terinfeksi Leptospira di dataran rendah adalah Rattus tanezumi, sedangkan di dataran tinggi adalah Rattus tanezumi dan Suncus murinus. R. tanezumi dan S. murinus berperan sebagai reservoir Leptospira dan sumber penularan di lokasi survei dengan serovar yang menginfeksi adalah Hardjo, Autumnalis dan Sejroe.

Molecular detection and identification of “Candidatus Ehrlichia hainanensis”, a novel Ehrlichia species in rodents from Hainan province, China

Background: Ehrlichia is a genus of Rickettsiales bacteria closely related to human/animal disease and it plays an important role in public health. Naturally they are hosted by mammals such as canines, bovines, wild rodents and vectored by ticks. Results: In this study, we collected 121 rodent samples including 67 Niviventer fulvescens, 27 Rattus tanezumi, 24 Chiromyscus sp., 2 Rattus nitidus and 1 Leopoldamys edwardsi from Hainan province, which consists of the second largest island in China. The presence and genetic diversity of Ehrlichia was evaluated and characterized by amplifying and sequencing the 16S rRNA, groEL and gltA genes. An Ehrlichia species was detected in 5 of the 67 Niviventer fulvescens samples (7.46%). The 16S rRNA, groEL and gltA genes show highest 99.20%, 89.87% and 83.86% identity to known Ehrlichia sequences. In the phylogenetic trees they form a distinct cluster from any other species. Conclusions: We propose that this species present a putative novel Ehrlichia species nominated as ‘Candidatus Ehrlichia hainanensis’. Its pathogenicity to human is still to be further researched and molecular surveillance in local populations is needed.

Angiostrongylus cantonensis infection of non-native rats in Mount Makiling Forest Reserve, the Philippines

A number of studies had been conducted on rat species diversity in the Philippines, however, there is a dearth of information on the extent of Angiostrongylus spp. infection in various ecological niches. Collection of non-native rat samples occurred in various sampling sites categorized as residential, agricultural and agro-forest in Philippine Mount Makiling Forest Reserve (MMFR) and its adjacent areas . Three species of non-native rats were captured including Rattus tanezumi, Rattus norvegicus and Rattus exulans. Of the total 90 non-native rats collected, 24.4% were found infected with Angiostrongylus cantonensis. Statistical analysis showed significant difference among rat species with highest prevalence observed in R. exulans (42.9%) followed by R. tanezumi (29.8%) and R. norvegicus (7.7%) (P = 0.047). Angiostrongylus cantonensis infection was significantly higher in adults (29.4%) than in juvenile rats (9.1%) (P = 0.050). However, results showed no significant difference in A. cantonensis infection between male (43.3%) and female (18.3%) rats and between wet (31.6%) and dry seasons (19.2%) (P > 0.05). Moreover, this study also revealed that rats from agricultural and agro-forest areas showed significantly higher prevalence than residential areas. With urbanization and the everchanging landscape of MMFR watersheds and buffer zones, zoonotic transmission can pose health threats to the local people.