Malik Yashpal Singh, Ansari Mohd Ikram, Karikalan Mathesh, Sircar Shubhankar, Selvaraj Ilayaraja, Ghosh Souvik, Singh Kalpana
ICAR-Indian Veterinary Research Institute, Bareilly 243122, India.
College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India.
Pathogens. 2023 Jul 13;12(7):934. doi: 10.3390/pathogens12070934.
The present study reports the detection and molecular characterisation of rotavirus C (RVC) in sloth bears (Melursus ursinus) rescued from urban areas in India. Based on an RVC VP6 gene-targeted diagnostic RT-PCR assay, 48.3% (42/87) of sloth bears tested positive for RVC infection. The VP6, VP7, and NSP4 genes of three sloth bear RVC isolates (UP-SB19, 21, and 37) were further analysed. The VP6 genes of RVC UP-SB21 and 37 isolates were only 37% identical. The sequence identity, TM-score from structure alignment, and selection pressure (dN/dS) of VP6 UP-SB37 with pig and human RVCs isolates were (99.67%, 0.97, and 1.718) and (99.01%, 0.93, and 0.0340), respectively. However, VP6 UP-SB21 has an identity, TM-score, and dN/dS of (84.38%, 1.0, and 0.0648) and (99.63%, 1.0, and 3.7696) with human and pig RVC isolates, respectively. The VP7 genes from UP-SB19 and 37 RVC isolates were 79.98% identical and shared identity, TM-score, and dN/dS of 88.4%, 0.76, and 5.3210, along with 77.98%, 0.77, and 4.7483 with pig and human RVC isolates, respectively. The NSP4 gene of UP-SB37 RVC isolates has an identity, TM-score, and dN/dS of 98.95%, 0.76, and 0.2907, along with 83.12%, 0.34, and 0.2133 with pig and human RVC isolates, respectively. Phylogenetic analysis of the nucleotide sequences of the sloth bear RVC isolates assigned the isolate UP-SB37 to genotype G12, I2 for RVC structural genes VP7 and VP6, and E1 for NSP4 genes, respectively, while isolates UP-SB19 and UP-SB21 were classified as genotype G13 and GI7 based on the structural gene VP7, respectively. The study suggests that the RVCs circulating in the Indian sloth bear population are highly divergent and might have originated from pigs or humans, and further investigation focusing on the whole genome sequencing of the sloth bear RVC isolate may shed light on the virus origin and evolution.
本研究报告了从印度城市地区救出的懒熊（马来熊）中轮状病毒C（RVC）的检测及分子特征。基于针对RVC VP6基因的诊断性逆转录聚合酶链反应（RT-PCR）检测，48.3%（42/87）的懒熊RVC感染检测呈阳性。对三只懒熊RVC分离株（UP-SB19、21和37）的VP6、VP7和NSP4基因进行了进一步分析。RVC UP-SB21和37分离株的VP6基因仅有37%的同源性。RVC UP-SB37与猪和人RVC分离株的VP6序列同源性、结构比对的TM分数及选择压力（dN/dS）分别为（99.67%、0.97和1.718）以及（99.01%、0.93和0.0340）。然而，VP6 UP-SB21与人和猪RVC分离株的同源性、TM分数及dN/dS分别为（84.38%、1.0和0.0648）以及（99.63%、1.0和3.7696）。UP-SB19和37 RVC分离株的VP7基因同源性为79.98%，与猪和人RVC分离株的同源性、TM分数及dN/dS分别为88.4%、0.76和5.3210以及77.98%、0.77和4.7483。UP-SB37 RVC分离株的NSP4基因与猪和人RVC分离株的同源性、TM分数及dN/dS分别为98.95%、0.76和0.2907以及83.12%、0.34和0.2133。对懒熊RVC分离株核苷酸序列的系统发育分析将分离株UP-SB37分别归为RVC结构基因VP7和VP6的G12基因型、I2基因型以及NSP4基因的E1基因型，而分离株UP-SB19和UP-SB21基于结构基因VP7分别被归类为G13基因型和GI7基因型。该研究表明，在印度懒熊种群中传播的RVC具有高度的差异性，可能起源于猪或人，对懒熊RVC分离株进行全基因组测序的进一步研究可能有助于揭示病毒的起源和进化。
