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Extensive genetic diversity and host range of rodent-borne coronaviruses.
Wang, Wen; Lin, Xian-Dan; Zhang, Hai-Lin; Wang, Miao-Ruo; Guan, Xiao-Qing; Holmes, Edward C; Zhang, Yong-Zhen.
  • Wang W; Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.
  • Lin XD; Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang 325001, China.
  • Zhang HL; Yunnan Institute of Endemic Diseases Control and Prevention, Dali 671000, China.
  • Wang MR; Longquan Center for Disease Control and Prevention, Zhejiang Province, Longquan 323799, China.
  • Guan XQ; Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, China.
  • Holmes EC; Shanghai Public Health Clinical Center & School of Life Science, Fudan University, Shanghai 201052, China.
  • Zhang YZ; Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Virus Evol ; 6(2): veaa078, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-1383237
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ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Experimental Studies / Randomized controlled trials Topics: Variants Language: English Journal: Virus Evol Year: 2020 Document Type: Article Affiliation country: VE

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Experimental Studies / Randomized controlled trials Topics: Variants Language: English Journal: Virus Evol Year: 2020 Document Type: Article Affiliation country: VE