Viral Metagenomic Analysis Of Bats In Yili Prefecture,Xinjiang

As important natural hosts of viruses,bats can carry and spread a variety of zoonotic viruses,such as SARS-like coronavirus,Marburg virus,Hendra virus,Nipah virus and so on.These viruses continue to pose a great threat to the health of humans and other animals.At present,the background of bat-borne viruses in southern China have been well investigated,which provides very important reference to the prevention of bat-borne zoonosis and rapid tracing of the source of new virus transmission in China.However,as to bats in Northeast of China,especially Xinjiang,we know very little about viruses harbored by these creatures.In this study,122 bats were collected from two sites in Yili Prefecture,Xinjiang.The diversity of viruses carried by these bats was preliminarily obtained using viral metagenomic combined with specific PCR detection,which provided basic data for understanding the pathogenic background of viruses carried by bats in Yili Prefecture,Xinjiang.In 2016,46 and 76 bats were collected from two abandoned residential houses in Xinyuan County and Qapqal County,Ili Prefecture,Xinjiang.After species identification,all bats are Pipistrellus pipistrellus.Through high-throughput sequencing,a total of 141,023 reads were classified as viruses of 18 families and some unclassified,such as Myoviridae,Podoviridae,Siphoviridae,Adenoviridae,Papillomaviridae,Polyomaviridae,Anelloviridae,Circoviridae,Parvoviridae,Coronaviridae,Astroviridae,Flaviviridae,Picornaviridae,Dicistroviridae,Iflaviridae,Bornaviridae,Paramyxoviridae and Rhabdoviridae.According to the results of viral metagenomic analysis,coronavirus,circovirus,astrovirus,parechovirus and adenovirus were selected to PCR screening.As a result,their positive rates ranged from 1.3% to 39.1%.Coronavirus here was identified as alphacoronavirus,and compared with other bat coronaviruses in China,these two viruses are more closely related to French bat virus,reflecting the different evolutionary history of bat coronavirus in Xinjiang Ili Prefecture and other parts of China;Circovirus formed an evolutionary branch with bat circoviruses from Guangdong,Ningxia,Jiangsu and Hubei,indicating that this group of bat circoviruses has a wide geographical distribution;The genetic relationship between adenovirus in Yili Prefecture and adenovirus in other parts of China is far,reflecting the different evolutionary history of bat adenovirus in Xinjiang Ili Prefecture and other parts of China.Astroviruses exhibited rich genetic diversity with some showing high identity with porcine astroviruses(suggesting possible cross-species transmission),whereas parechovirus was discovered for the first time in bats.For the first time,we found parechovirus in bats,which expanded the host range of parechovirus and increased our understanding of parechovirus.Belonging to the genus Parechovirus within the family Picornaviridae,Parechoviruses have been divided into 4 species,which mainly infects humans,rodents,birds and ferrets.In order to further analyze bat parechovirus,we selected one of the positive samples to amplify the whole genome of bat parechovirus.Its genome length is 7,174 nt,and it has a typical genome structure of parechovirus.Based on the homology analysis of polyproteins,the nucleotide and amino acid homology of bat parechovirus and Dutch ferret parechovirus were the highest.Phylogenetic analysis using the complete amino acid sequence of the polyprotein showed that the bat parechovirus clustered nearly together with ferret parechovirus within the clade of Parechovirus D.In this study,three strains of mammalian orthoreoviruses were obtained by virus isolation,which belong to the genus orthoreovirus within the family Reoviridae.The virions were observed by electron microscopy and their genomes were obtained by high-throughput sequencing.The genomes of three strains of mammalian orthoreoviruses were divided into 10 segments,and phylogenetic analysis using the complete nucleotide sequence of the S1 gene showed that the mammalian orthoreoviruses found in this study belong to serotypes 2.We profiled the viromic composition harbored by bats in Xinjiang,and it reveals that bats in this area carry a large number of viruses and show regional characteristics.Strikingly,we first identified bat parechovirus and obtained it's nearly whole genome.In addition,some new adenoviruses had been found.The study provides fundamental data for understanding of the diversity and background of the virus carried by bats in this region.Due to long border lines of Xinjiang with other Central Asian Countries and the ability to flying of bats,bats are very easy to migrate across borders,this research contributes to monitor the background of the viruses carried by bats in surrounding countries.