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. 2017 Jul:507:1-10.
doi: 10.1016/j.virol.2017.03.019. Epub 2017 Apr 3.

Extensive diversity of coronaviruses in bats from China

Xian-Dan Lin  1 , Wen Wang  2 , Zong-Yu Hao  3 , Zhao-Xiao Wang  4 , Wen-Ping Guo  2 , Xiao-Qing Guan  2 , Miao-Ruo Wang  5 , Hong-Wei Wang  6 , Run-Hong Zhou  2 , Ming-Hui Li  2 , Guang-Peng Tang  4 , Jun Wu  7 , Edward C Holmes  8 , Yong-Zhen Zhang  9
Affiliations

Extensive diversity of coronaviruses in bats from China

Xian-Dan Lin et al. Virology. 2017 Jul.

Abstract

To help reveal the diversity and evolution of bat coronaviruses we collected 1067 bats from 21 species in China. A total of 73 coronaviruses (32 alphacoronaviruses and 41 betacoronaviruses) were identified in these bats, with an overall prevalence of 6.84%. All newly-identified betacoronaviruses were SARS-related Rhinolophus bat coronaviruses (SARSr-Rh-BatCoV). Importantly, with the exception of the S gene, the genome sequences of the SARSr-Rh-BatCoVs sampled in Guizhou province were closely related to SARS-related human coronavirus. Additionally, the newly-identified alphacoronaviruses exhibited high genetic diversity and some may represent novel species. Our phylogenetic analyses also provided insights into the transmission of these viruses among bat species, revealing a general clustering by geographic location rather than by bat species. Inter-species transmission among bats from the same genus was also commonplace in both the alphacoronaviruses and betacoronaviruses. Overall, these data suggest that high contact rates among specific bat species enable the acquisition and spread of coronaviruses.

Keywords: Bats; Coronavirus; Evolution; Phylogeny; SARS; Transmission.

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Figures

Fig. 1.
Fig. 1
A map of China illustrating the location of trap sites in which bats (red circles) were captured.
Fig. 2.
Fig. 2
Phylogenetic analysis of the nucleotide sequences of the RdRp and S genes including those CoVs obtained here. Bootstrap values (>70%) are shown at relevant nodes. The trees were mid-point rooted for clarity only. The scale bar depicts the number of nucleotide substitutions per site.
Fig. 3.
Fig. 3
Genome organization of coronaviruses. The four CoVs discovered in this study are shown in bold.
Fig. 4.
Fig. 4
Recombination within the genome of the Longquan-140 virus. A sequence similarity plot (A) reveals two recombination breakpoints shown by black arrows with their locations. The plot shows genome-scale similarity comparisons of the Longquan-140 (query) against HKU3 and other selected SARS-related CoVs. Phylogenies of regions A, B and C are shown below the similarity plot. Numbers (>70%) above or below branches indicate percentage bootstrap values.
Fig. 5.
Fig. 5
Phylogenetic analyses of the amino acid sequences of the RdRp including those CoVs obtained here. Numbers (>70%) above or below branches indicate percentage bootstrap values. The trees were mid-point rooted for clarity only. The scale bar represents the number of amino acid substitutions per site.
Fig. 6.
Fig. 6
Co-phylogenetic analyses of bats hosts and their associated coronaviruses. (A) SARS-related coronaviruses from bats, (B) alphacoronaviruses from bats. The coronavirus tree is shown in blue while the host phylogeny is shown in black. The host tree was based on mitochondrial cytochrome b gene sequences, and the coronavirus trees were based on the RdRp gene. Filled circles at the nodes indicate co-divergence events, empty circles indicate lineage duplication events, arrows indicate host-switching events, while dotted lines indicate loss events.
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