Extensive Genetic Diversity and Host Range of Rodent-borne Coronaviruses

To better understand the genetic diversity, host association and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on the reverse transcriptase PCR-based CoV screening CoVs of fecal samples and subsequent sequence analysis of the RdRp gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus latronum, Bandicota indica, Eothenomys miletus, E. eleusis, Rattus andamanesis, Rattus norvegicus, and R. tanezumi. Apodemus chevrieri was a particularly rich host, harboring 25 rodent CoVs. Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat coronavirus (LRNV), China Rattus coronavirus HKU24 (ChRCoV_HKU24) and Longquan Rl rat coronavirus (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative nonstructural NS2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the ORF1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and greatly extend our knowledge of these major wildlife virus reservoirs.

Extensive genetic diversity and host range of rodent-borne coronaviruses

To better understand the genetic diversity, host associations and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on reverse transcriptase PCR-based CoV screening of fecal samples and subsequent sequence analysis of the RNA-dependent RNA polymerase gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus chevrieri, Apodemus latronum, Bandicota indica, Eothenomys cachinus, Eothenomys miletus, Rattus andamanensis, Rattus norvegicus, and Rattus tanezumi. CoVs were particularly commonplace in A. chevrieri, with a detection rate of 12.44 per cent (24/193). Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat CoV (LRNV), China Rattus CoV HKU24 (ChRCoV_HKU24), and Longquan Rl rat CoV (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative non-structural (NS)2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the open reading frame (ORF) 1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and extend our knowledge of these major wildlife virus reservoirs.

Comparative Study on Phenotypic Differences in Eothenomys Miletus Under Food Restriction and Refeeding Between Xianggelila and Jianchuan from Hengduan Mountain Regions

Body mass regulation may be appeared regional differences, in order to investigate the physiological and behavioral changes in Eothenomys miletus from Shanggelila (XGLL) and Jianchuan (JC) under food restriction (FR) and refeeding (Re), body mass, food intake, resting metabolic rate (RMR), serum leptin levels, hypothalamic neuropeptides expression and activity behavior were measured. The results showed that areas and FR had significant effects on body mass, food intake, RMR, activity behavior, serum leptin levels, hypothalamic neuropeptides expression, masses of liver and small intestine in E. miletus. Body mass and serum leptin levels in XGLL were lower than that of JC, food intake, activity behavior, liver mass and RMR in XGLL were higher relative to in JC. All the indexes of the two areas of E. miletus can be restored to control levels after refeeding, showing phenotypic plasticity. In conclusion, physiological and behavioral characteristics illustrated that the influences of food and different regions on phenotypic plasticity, which had important significance for in-depth understanding of the survival and adaptation strategies of E. miletus in Hengduan mountain regions.

Metabolomics of Eothenomys miletus from five Hengduan Mountains locations in summer

Climatic characteristics of Hengduan Mountains region were diverse, and Eothenomys miletus was a native species throughout this region. To investigate adaptive strategies of E. miletus to environmental factors in different locations in this region, five locations were selected, including Deqin (DQ), Xianggelila (XGLL), Lijiang (LJ), Jianchuan (JC) and Ailaoshan (ALS). Then, body mass, visceral organ masses, and serum and liver metabolomes of E. miletus from each location were examined. The results showed that body mass was significantly different among these five sites. Liver mass was lower in ALS than in other locations. PLS-DA analysis, metabolite tree maps and heat maps of serum and liver metabolites showed that samples from DQ and XGLL clustered together, as did the samples from LJ, JC and ALS. Serum concentrations of lipid and amino acid metabolites, concentrations of TCA cycle intermediates, lipid metabolites and amino acid metabolites in livers from DQ and XGLL were higher than those from other three regions. However, the concentrations of glycolytic metabolites were lower in DQ and XGLL. All these results indicated that E. miletus adapts to changes in environmental temperature and altitude of this region by adjusting body mass and serum and liver metabolite concentrations.