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Feb 21, 12h ago
Edward C. Holmes1, Kristian G. Andersen2,3, Andrew Rambaut4 and Robert F. Garry5,6,*...
Introduction
SARS-CoV and SARS-CoV-2 are members of the Sarbecovirus subgenus of betacoronaviruses (family Coronaviridae). Two sarbecoviruses lineages, GX (Guangxi) and GD (Guangdong), have been identified in Malayan pangolins, Manis javanica, illegally imported into China (Liu, Chen and Chen, 2019; Lam et al., 2020). A variety of sarbecoviruses have also been described in bats of the genus Rhinolophus, although it is evident that the diversity of this subgenus in wildlife species has been greatly under-sampled (Boni et al., 2020). While close relatives of SARS-CoV have been identified in bats, civets and other animals (Li, 2008), the immediate progenitor of SARS-CoV-2 is unknown (Andersen et al., 2020). The bat coronavirus RaTG13 genome was sequenced from a sample from a Rhinolophus affinis captured at Mojiang cave in Yunnan province, China in 2013 (Ge et al., 2016; Zhou P et al., 2020a,b). RaTG13 remains the virus with the highest overall sequence similarity to SARS-CoV-2, although because of frequent recombination patterns of sequence similarity vary across the genome. Recently, new sarbecoviruses have been sequenced from bats sampled in Cambodia, Thailand and Japan (Hul et al., 2021, Wacharapluesadee et al., 2021; Murakami et al., 2020). Here, we reveal more of the natural evolution of sarbecoviruses by analyzing the spike protein sequences of these viruses. We also discuss some implications of these new sequences for understanding the proximal origin of SARS-CoV-2.
Methods
Spike protein sequences from a variety of sarbecoviruses were selected for comparative analysis as described in Table 1.
...
Edward C. Holmes1, Kristian G. Andersen2,3, Andrew Rambaut4 and Robert F. Garry5,6,*...
Introduction
SARS-CoV and SARS-CoV-2 are members of the Sarbecovirus subgenus of betacoronaviruses (family Coronaviridae). Two sarbecoviruses lineages, GX (Guangxi) and GD (Guangdong), have been identified in Malayan pangolins, Manis javanica, illegally imported into China (Liu, Chen and Chen, 2019; Lam et al., 2020). A variety of sarbecoviruses have also been described in bats of the genus Rhinolophus, although it is evident that the diversity of this subgenus in wildlife species has been greatly under-sampled (Boni et al., 2020). While close relatives of SARS-CoV have been identified in bats, civets and other animals (Li, 2008), the immediate progenitor of SARS-CoV-2 is unknown (Andersen et al., 2020). The bat coronavirus RaTG13 genome was sequenced from a sample from a Rhinolophus affinis captured at Mojiang cave in Yunnan province, China in 2013 (Ge et al., 2016; Zhou P et al., 2020a,b). RaTG13 remains the virus with the highest overall sequence similarity to SARS-CoV-2, although because of frequent recombination patterns of sequence similarity vary across the genome. Recently, new sarbecoviruses have been sequenced from bats sampled in Cambodia, Thailand and Japan (Hul et al., 2021, Wacharapluesadee et al., 2021; Murakami et al., 2020). Here, we reveal more of the natural evolution of sarbecoviruses by analyzing the spike protein sequences of these viruses. We also discuss some implications of these new sequences for understanding the proximal origin of SARS-CoV-2.
Methods
Spike protein sequences from a variety of sarbecoviruses were selected for comparative analysis as described in Table 1.
...