Basic Research
Genomic characteristics and phylogenetic analysis of a novel rat astrovirus strain
Li Lili, Xu Yalong, Liu Mengmeng, Duan Zhaojun
Published 2020-06-25
Cite as Int J Virol, 2020, 27(3): 205-209. DOI: 10.3760/cma.j.issn.1673-4092.2020.03.007
Abstract
ObjectiveTo inverstigate the genome characteristics of a novel astrovirus strain and to analyze its phylogenetic relationship with known virus.
MethodsA total of 221 rat intestinal content samples were collected in Shandong province. High throughput sequencing method was used to study the viral genomes.
ResultsA novel astrovirus strain was discovered and a nearly complete genome was obtained. The strain was named as RoAstV/CHN/S3. RoAstV/CHN/S3 showed typical genomic structure of astrovirus. The similarity analysis showed that RoAstV/CHN/S3 was the most closely related to rodent astrovirus and porcine astrovirus 4. The results of genetic distance by amino acids in ORF2 showed that the genetic distances of RoAstV/CHN/S3 to rodent astrovirus and porcine astrovirus 4 were 0.557-0.655. Since the genetic distances of species in mammalian astrovirus was 0.338-0.783, RoAstV/CHN/S3 should be classified as novel species. The result of phylogenetic tree for ORF1a, ORF1b and ORF2 showed that RoAstV/CHN/S3 was clustered with rodent astroviruses and porcine astrovirus 4, suggesting these viruses shared potential common ancestor and potential cross-species transmission. The screen results to 221 intestinal content samples showed that 4 samples were positive and the positive rate was 1.8%. Three of the 4 rats were sewer rat while the rest one was striped field mouse. All these samples were from the Jining city of Shandong province.
ConclusionsThe discovery of RoAstV/CHN/S3 has expand the diversity of astroviruses and provided the important information to control and prevent emerging infectious disease in the future.
Key words:
Rat; Astrovirus; Genome characteristics; Evolution
Contributor Information
Li Lili
NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
Xu Yalong
School of Public Health, Shaanxi University of Chinese Medicine, Xi'an 712046, China
Liu Mengmeng
Department of Medical Microbiology, Medical College of Qingdao University, Qingdao 266021, China
Duan Zhaojun
NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
