Extensive genetic diversity and host range of rodent-borne coronaviruses
#MMPMID33318860
Wang W
; Lin XD
; Zhang HL
; Wang MR
; Guan XQ
; Holmes EC
; Zhang YZ
Virus Evol
2020[Jul]; 6
(2
): veaa078
PMID33318860
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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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