Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins

Lam, Tommy Tsan-Yuk; Jia, Na; Zhang, Yawei; Shum, Marcus Ho-Hin; Jiang, Jia-Fu; Zhu, Hua; Tong, Yigang; Shi, Yongxia; Ni, Xue-Bing; Liao, Yunshi; Li, Wenjuan; Jiang, Bao-Gui; Wei, Wei; Yuan, Tingting; Zheng, Kui; Cui, Xiaoming; Li, Jie; Pei, Guangqian; Xin, Qiang; Cheung, Y. M.; Li, Lian-Feng; Sun, Fangfang; Qin, Si; Huang, Jicheng; Leung, Gabriel M.; Holmes, Edward C.; Hu, Yanling; Guan, Yi; Cao, Wu‐Chun

doi:10.1038/s41586-020-2169-0

Cited by 1,681 publications

(1,783 citation statements)

References 38 publications

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“…Notably, while the NTD domain of both GX and GD pangolin sequences fell to 88% and 67% identity, respectively, the RBD domain of the GD domain was confirmed to be remarkably well conserved compared to SARS-CoV-2 (97% identity compared to 87% identity for GX pangolin and 89% for BatCoV-RaTG13). These observations are in line with previously reported putative recombination events occurring between pangolin, bat, and human betacoronavirus sequences [22]. Phylogenetically, pangolin spike sequences from 2017 (GX) form a subclade that groups with RaTG13 (Figure 2(b)).…”

Section: Phylogenetic Analysis Of Sars-cov-2 S With Other Betacoronavsupporting

confidence: 90%

“…While bat coronaviruses are the established reservoir for SARS-CoV-2, the presumed intermediate host remains to be determined. Based on the high degree of sequence identity in the RBD of sequences found in Malayan pangolins (M. javanica), it was proposed that these mammals could be intermediate hosts [20][21][22]. Subsequent wholegenome analysis revealed 85.5%-92.% identity to SARS-CoV-2, which is less than what is observed for Bat-SL-RaTG13 (96.3%) [34].…”

Section: Phylogenetic Analysis Of Sars-cov-2 S With Other Betacoronavmentioning

confidence: 93%

“…Origination of SARS-CoV-2 from bats has been strongly supported, but the presumed intermediate host remains to be identified. Recent reports have suggested the Malayan pangolins (Manis javanica) as a possible intermediate host for SARS-CoV-2, with putative recombination signals found between pangolin, bat, and human coronavirus sequences [7,9,[20][21][22]. However, the direct precursor sequence to the currently circulating human SARS-CoV-2 and putative intermediate host remain to be identified.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

Jaimes

André

Chappie

et al. 2020

Journal of Molecular Biology

453

499

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The 2019 novel coronavirus (2019-nCoV/SARS-CoV-2) originally arose as part of a major outbreak of respiratory disease centered on Hubei province, China. It is now a global pandemic and is a major public health concern. Taxonomically, SARS-CoV-2 was shown to be a Betacoronavirus (lineage B) closely related to SARS-CoV and SARS-related bat coronaviruses, and it has been reported to share a common receptor with SARS-CoV (ACE-2). Subsequently, betacoronaviruses from pangolins were identified as close relatives to SARS-CoV-2. Here, we perform structural modeling of the SARS-CoV-2 spike glycoprotein. Our data provide support for the similar receptor utilization between SARS-CoV-2 and SARS-CoV, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV and all other coronaviruses in Betacoronavirus lineage B, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains. We suggest this loop confers fusion activation and entry properties more in line with betacoronaviruses in lineages A and C, and be a key component in the evolution of SARS-CoV-2 with this structural loop affecting virus stability and transmission.

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Section: Phylogenetic Analysis Of Sars-cov-2 S With Other Betacoronavsupporting

confidence: 90%

Section: Phylogenetic Analysis Of Sars-cov-2 S With Other Betacoronavmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop

Jaimes

André

Chappie

et al. 2020

Journal of Molecular Biology

453

499

View full text Add to dashboard Cite

show abstract

“…The whole genome-wide nucleotide sequence of SARS-CoV-2 is 96% identical to a bat CoV [26] . Importantly, SARS-CoV-2 has been isolated from pangolins and it was found that the isolated pangolin CoV genomes have ~85.5-92.4% similarity to SARS-CoV-2 [36] , suggesting that pangolin may be a potential intermediate host for SARS-CoV-2. However, whether SARS-CoV-2 is transmitted directly from bats or by an intermediate host requires further confirmation.…”

Section: Origin Of Sars-cov-2mentioning

confidence: 99%

Coronavirus disease 2019 (COVID-19): current status and future perspectives

Liu

et al. 2020

International Journal of Antimicrobial Agents

1,001

893

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“…The results illustrated that bat and mink might be two candidate reservoirs of SARS-CoV-2. Lam et al identified pangolinassociated coronaviruses belonging to two sublineages of SARS-CoV-2-related coronaviruses, including one very closely related to SARS-CoV-2 in the RBD by metagenomic sequencing [15] . Hence, pangolins should be considered as possible intermediate hosts and should be removed from markets to prevent such zoonotic transmission.…”

Section: Potential Hostsmentioning

confidence: 99%