Abstract
BackgroundRodents represent the most diverse mammals on the planet and are important reservoirs of human pathogens. Coronaviruses infect various animals, but to date, relatively few coronaviruses have been identified in rodents worldwide. The evolution and ecology of coronaviruses in rodent have not been fully investigated.ResultsIn this study, we collected 177 intestinal samples from thress species of rodents in Jianchuan County, Yunnan Province, China. Alphacoronavirus and betacoronavirus were detected in 23 rodent samples from three species, namely Apodemus chevrieri (21/98), Eothenomys fidelis (1/62), and Apodemus ilex (1/17). We further characterized the full-length genome of an alphacoronavirus from the A. chevrieri rat and named it as AcCoV-JC34. The AcCoV-JC34 genome was 27,649 nucleotides long and showed a structure similar to the HKU2 bat coronavirus. Comparing the normal transcription regulatory sequence (TRS), 3 variant TRS sequences upstream the spike (S), ORF3, and ORF8 genes were found in the genome of AcCoV-JC34. In the conserved replicase domains, AcCoV-JC34 was most closely related to Rattus norvegicus coronavirus LNRV but diverged from other alphacoronaviruses, indicating that AcCoV-JC34 and LNRV may represent a novel alphacoronavirus species. However, the S and nucleocapsid proteins showed low similarity to those of LRNV, with 66.5 and 77.4% identities, respectively. Phylogenetic analysis revealed that the S genes of AcCoV-JC34, LRNV, and HKU2 formed a distinct lineage with all known coronaviruses.ConclusionsBoth alphacoronaviruses and betacoronaviruses were detected in Apodemus chevrieri in the Yunnan Province of China, indicating that Apodemus chevrieri is an important host for coronavirus. Several new features were identified in the genome of an Apodemus chevrieri coronavirus. The phylogenetic distance to other coronaviruses suggests a variable origin and evolutionary route of the S genes of AcCoV-JC34, LRNV, and HKU2. These results indicate that the diversity of rodent coronaviruses is much higher than previously expected. Further surveillance and functional studies of these coronaviruses will help to better understand the importance of rodent as host for coronaviruses.
Highlights
Rodents represent the most diverse mammals on the planet and are important reservoirs of human pathogens
By Reverse transcription PCR (RT-PCR), targeting a 440 base pairs partial RNA-dependent RNA polymerase gene (RdRp) gene sequence of CoVs, 23 rodents were identified as CoV positive, which included 21 of 98 (21.4%) A. chevrieri, 1 of 17 (5.9%) A. ilex, and 1 of 62 (1.6%) E. fidelis samples (Table 1)
Partial RdRp sequences were searched against the CoV database, and the results indicated that 21 out of 23 sequences were β-CoVs, whereas the remaining two were α-CoVs
Summary
Rodents represent the most diverse mammals on the planet and are important reservoirs of human pathogens. Coronaviruses infect various animals, but to date, relatively few coronaviruses have been identified in rodents worldwide. The evolution and ecology of coronaviruses in rodent have not been fully investigated. CoVs consist of 4 genera and have been identified in a wide range of animals and in humans. CoVs have been recognized in human and animals and cause upper respiratory diseases in most cases. 6 human CoVs were discovered: 4 of them (HCoV-229E, NL63, OC43, and HKU1) mainly cause mild respiratory diseases, and the other 2, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) cause severe respiratory diseases [5, 6].
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