Extensive Genetic Diversity and Host Range of Rodent-borne Coronaviruses
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Abstract
To better understand the genetic diversity, host association 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 the reverse transcriptase PCR-based CoV screening CoVs of fecal samples and subsequent sequence analysis of the RdRp gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus latronum, Bandicota indica, Eothenomys miletus, E. eleusis, Rattus andamanesis, Rattus norvegicus , and R. tanezumi. Apodemus chevrieri was a particularly rich host, harboring 25 rodent CoVs. 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 coronavirus (LRNV), China Rattus coronavirus HKU24 (ChRCoV_HKU24) and Longquan Rl rat coronavirus (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 nonstructural NS2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the ORF1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and greatly extend our knowledge of these major wildlife virus reservoirs.
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SciScore for 10.1101/2020.08.11.245415: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: 2.1 Sample collection: This study was reviewed and approved by the ethics committee of the National Institute for Communicable Disease Control and Prevention of the Chinese CDC.
IACUC: All animals were kept alive after capture and treated in strictly according to the guidelines for the Laboratory Animal Use and Care from the Chinese CDC and the Rules for the Implementation of Laboratory Animal Medicine (1998) from the Ministry of Health, China, under the protocols approved by the National Institute for Communicable Disease Control and Prevention.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. SciScore for 10.1101/2020.08.11.245415: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: 2.1 Sample collection: This study was reviewed and approved by the ethics committee of the National Institute for Communicable Disease Control and Prevention of the Chinese CDC.
IACUC: All animals were kept alive after capture and treated in strictly according to the guidelines for the Laboratory Animal Use and Care from the Chinese CDC and the Rules for the Implementation of Laboratory Animal Medicine (1998) from the Ministry of Health, China, under the protocols approved by the National Institute for Communicable Disease Control and Prevention.Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Nucleotide (nt) sequence similarities and deduced amino acid (aa) similarities to GenBank database sequences were determined using BLASTn and BLASTp. 2.4 Phylogenetic analysis: CoV reference sequences sets representing the RdRp, S and N genes were downloaded from GenBank. BLASTnsuggested: (BLASTN, RRID:SCR_001598)BLASTpsuggested: (BLASTP, RRID:SCR_001010)All viral sequences were aligned using the MAFFT algorithm (Katoh and Standley 2013). MAFFTsuggested: (MAFFT, RRID:SCR_011811)The best-fit model of nucleotide substitution was determined using jModelTest version 0.1 (Posada 2008). jModelTestsuggested: (jModelTest, RRID:SCR_015244)Phylogenetic trees were generated using the maximum likelihood (ML) method implemented in PhyML v3.0 (Guindon et al. 2010). PhyMLsuggested: (PhyML, RRID:SCR_014629)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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