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JVI Accepted Manuscript
Posted Online 25 August 2021
Xin Li, Liang Wang, Peipei Liu, Hongying Li, Shuting Huo, Kexin Zong, Shiyan Zhu, , Yuanyuan Guo, Libiao Zhang, Ben Hu, Yu Lan, Aleksei Chmura https://orcid.org/0000-0001-5544-0431, GuizhenWu, Peter Daszak, William J. Liu https://orcid.org/0000-0003-3605-4070, and George F. Gao
https://doi.org/10.1128/JVI.01173-21
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. We sampled 297 rodents and shrews representing eight species in three municipalities of southern China. We report coronavirus prevalence of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalence than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus RCoV-GCCDC3, an Alphacoronavirus RCoV-GCCDC5 and a novel Betacoronavirus RCoV-GCCDC4. Recombination analysis suggests that there was a potential recombinant event involving RCoV-GCCDC4, Murine hepatitis virus and Longquan Rl rat coronavirus. Furthermore, we uncovered a polybasic cleavage site RARR in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for inter-species transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery.
Importance
Surveillance of viruses among rodents within rural and urban areas of South China identified three rodent coronaviruses RCoV-GCCDC3, 4 and 5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription PCR screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for inter-species transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
Posted Online 25 August 2021
Xin Li, Liang Wang, Peipei Liu, Hongying Li, Shuting Huo, Kexin Zong, Shiyan Zhu, , Yuanyuan Guo, Libiao Zhang, Ben Hu, Yu Lan, Aleksei Chmura https://orcid.org/0000-0001-5544-0431, GuizhenWu, Peter Daszak, William J. Liu https://orcid.org/0000-0003-3605-4070, and George F. Gao
https://doi.org/10.1128/JVI.01173-21
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. We sampled 297 rodents and shrews representing eight species in three municipalities of southern China. We report coronavirus prevalence of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalence than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus RCoV-GCCDC3, an Alphacoronavirus RCoV-GCCDC5 and a novel Betacoronavirus RCoV-GCCDC4. Recombination analysis suggests that there was a potential recombinant event involving RCoV-GCCDC4, Murine hepatitis virus and Longquan Rl rat coronavirus. Furthermore, we uncovered a polybasic cleavage site RARR in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for inter-species transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery.
Importance
Surveillance of viruses among rodents within rural and urban areas of South China identified three rodent coronaviruses RCoV-GCCDC3, 4 and 5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription PCR screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for inter-species transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
