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. 2022 Jun 28;13(3):e0046322.
doi: 10.1128/mbio.00463-22. Epub 2022 Apr 25.

Epidemiology and Genomic Characterization of Two Novel SARS-Related Coronaviruses in Horseshoe Bats from Guangdong, China

Affiliations

Epidemiology and Genomic Characterization of Two Novel SARS-Related Coronaviruses in Horseshoe Bats from Guangdong, China

Linmiao Li et al. mBio. .

Abstract

Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2, the causative agents of SARS, which broke out in 2003, and coronavirus disease 2019 (COVID-2019), which broke out in 2019, probably originated in Rhinolophus sinicus and R. affinis, respectively. Rhinolophus bats are important hosts for coronaviruses. Many SARS-related coronaviruses (SARSr-CoVs) have been detected in bats from different areas of China; however, the diversity of bat SARSr-CoVs is increasing, and their transmission mechanisms have attracted much attention. Here, we report the findings of SARSr-CoVs in R. sinicus and R. affinis from South China from 2008 to 2021. The full-length genome sequences of the two novel SARSr-CoVs obtained from Guangdong shared 83 to 88% and 71 to 72% nucleotide identities with human SARS-CoV and SARS-CoV-2, respectively, while sharing high similarity with human SARS-CoV in hypervariable open reading frame 8 (ORF8). Significant recombination occurred between the two novel SARSr-CoVs. Phylogenetic analysis showed that the two novel bat SARSr-CoVs from Guangdong were more distant than the bat SARSr-CoVs from Yunnan to human SARS-CoV. We found that transmission in bats contributes more to virus diversity than time. Although our results of the sequence analysis of the receptor-binding motif (RBM) and the expression pattern of angiotensin-converting enzyme 2 (ACE2) inferred that these viruses could not directly infect humans, risks still exist after some unpredictable mutations. Thus, this study increased our understanding of the genetic diversity and transmission of SARSr-CoVs carried by bats in the field. IMPORTANCE Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 probably originated from the SARS-related coronaviruses (SARSr-CoVs) carried by Rhinolophus bats from Yunnan, China. Systematic investigations of the reservoir hosts carrying SARSr-CoVs in Guangdong and the reservoir distribution and transmission are urgently needed to prevent future outbreaks. Here, we detected SARSr-CoV in Rhinolophus bat samples from Guangdong in 2009 and 2021 and found that the transmission of SARSr-CoV from different host populations contributes more to increased virus diversity than time. Bat SARSr-CoVs in Guangdong had genetic diversity, and Guangdong was also the hot spot for SARSr-CoVs. We once again prove that R. sinicus plays an important role in the maintenance of the SARS-CoVs. Besides, the SARSr-CoVs are mainly transmitted through the intestines in bats, and these SARSr-CoVs found in Guangdong could not use human ACE2 (hACE2), but whether they can pass through intermediate hosts or directly infect humans requires further research. Our findings demonstrate the ability of SARSr-CoVs to spread across species.

Keywords: SARS-related coronavirus; epidemiology; genetic diversity; horseshoe bats.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

FIG 1
FIG 1
Gene map of the two novel SARSr-CoVs and similarity plot based on the full-length genome sequence of SARS-CoV-SZ3. Full-length genome sequences of Bat-SARSr-CoV-RaCH025, Bat-SARSr-CoV-Rs56, Bat-SARSr-CoV-HKU3-7/HKU3-8, and Bat-SARSr-CoV-GD2016B/2017F/2017G/2017H/2017I/2017J/2017L/2017M/2017N/2017O/2017P/2017Q/2017W/2019A/2019B/2019D were used as reference sequences. The analysis was performed with the Kimura model, with a window size of 1,500 bp and a step size of 150 bp.
FIG 2
FIG 2
Detection of potential recombination events by similarity plot and bootscan analyses. (A) The full-length genome sequence of SARSr-CoV-Rs56 was used as the query sequence, and the sequences of GX2013, HKU3-1, and RaCH025 were used as the reference sequences. (B) The full-length genome sequence of HKU3-1 was used as the query sequence, and SARSr-CoVs HuB2013, Rs56, and RaCH025 were used as the reference sequences. All analyses were performed with a Kimura model, with a window size of 1,500 bp and a step size of 150 bp.
FIG 3
FIG 3
Phylogenetic trees based on nucleotide sequences of the whole genome (A) and the S gene (B). The trees were constructed by the maximum likelihood method using the MrBayes approach employing the GTR+I+G nucleotide substitution model. The red letters represent the SARSr-CoV strains isolated from Guangdong in this study. GD, Guangdong; FJ, Fujian; JX, Jiangxi; HK, Hongkong; HB, Hubei; YN, Yunnan; GX, Guangxi; GZ, Guizhou; LN, Liaoning; HN, Hunan; ZJ, Zhejiang.
FIG 4
FIG 4
Sequence alignment of the receptor-binding motif (RBM) region. The red font represents the sequences obtained in this study. Yellow highlighting represents the 5 key sites where SARS-CoV binds to angiotensin-converting enzyme 2 (ACE2). Green shading represents amino acid (aa) deletions. The red words represent the sequences obtained in this study.
FIG 5
FIG 5
mRNA expression of ACE2 in different organs of Rhinolophus sinicus and R. affinis.

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