Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak

Overview

Journal Curr Biol

Publisher Cell Press

Specialty Biology

Date 2020 Mar 21

PMID 32197085

Citations 555

Authors

Tao Zhang

Qunfu Wu

Zhigang Zhang

Affiliations

Soon will be listed here.

Abstract

An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) began in the city of Wuhan in China and has widely spread worldwide. Currently, it is vital to explore potential intermediate hosts of SARS-CoV-2 to control COVID-19 spread. Therefore, we reinvestigated published data from pangolin lung samples from which SARS-CoV-like CoVs were detected by Liu et al. [1]. We found genomic and evolutionary evidence of the occurrence of a SARS-CoV-2-like CoV (named Pangolin-CoV) in dead Malayan pangolins. Pangolin-CoV is 91.02% and 90.55% identical to SARS-CoV-2 and BatCoV RaTG13, respectively, at the whole-genome level. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site that can be observed in the SARS-CoV-2. Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs.

Citing Articles

Effect of Exportin 1/XPO1 Nuclear Export Pathway Inhibition on Coronavirus Replication.

Rahman M, Estifanos B, Glenn H, Gutierrez-Jensen A, Kibler K, Li Y Viruses. 2025; 17(2).

PMID: 40007039 PMC: 11860411. DOI: 10.3390/v17020284.

Coronavirus nucleocapsid protein enhances the binding of p-PKCα to RACK1: Implications for inhibition of nucleocytoplasmic trafficking and suppression of the innate immune response.

Xue W, Chu H, Wang J, Sun Y, Qiu X, Song C PLoS Pathog. 2024; 20(11):e1012097.

PMID: 39602452 PMC: 11633972. DOI: 10.1371/journal.ppat.1012097.

Veterinary medicine under COVID-19: a mixed-methods analysis of student and practitioner experiences in Austria.

Humer E, Winter S, Probst T, Pieh C, Dale R, Bruhl D Front Vet Sci. 2024; 11:1460269.

PMID: 39568480 PMC: 11576337. DOI: 10.3389/fvets.2024.1460269.

SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.

Eldin P, David A, Hirtz C, Battini J, Briant L Int J Mol Sci. 2024; 25(21).

PMID: 39519170 PMC: 11546939. DOI: 10.3390/ijms252111614.

Detection of Mycotoxin Contamination in Foods Using Artificial Intelligence: A Review.

Aggarwal A, Mishra A, Tabassum N, Kim Y, Khan F Foods. 2024; 13(20).

PMID: 39456400 PMC: 11507438. DOI: 10.3390/foods13203339.

References

Abecasis G, Altshuler D, Auton A, Brooks L, Durbin R, Gibbs R . A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061-73. PMC: 3042601. DOI: 10.1038/nature09534. View

Li D, Liu C, Luo R, Sadakane K, Lam T . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10):1674-6. DOI: 10.1093/bioinformatics/btv033. View

Ge X, Li J, Yang X, Chmura A, Zhu G, Epstein J . Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013; 503(7477):535-8. PMC: 5389864. DOI: 10.1038/nature12711. View

Millet J, Whittaker G . Host cell proteases: Critical determinants of coronavirus tropism and pathogenesis. Virus Res. 2014; 202:120-34. PMC: 4465284. DOI: 10.1016/j.virusres.2014.11.021. View

Liu P, Chen W, Chen J . Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (). Viruses. 2019; 11(11). PMC: 6893680. DOI: 10.3390/v11110979. View

Lole K, Bollinger R, Paranjape R, Gadkari D, Kulkarni S, Novak N . Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1998; 73(1):152-60. PMC: 103818. DOI: 10.1128/JVI.73.1.152-160.1999. View

Tortorici M, Veesler D . Structural insights into coronavirus entry. Adv Virus Res. 2019; 105:93-116. PMC: 7112261. DOI: 10.1016/bs.aivir.2019.08.002. View

Langmead B, Salzberg S . Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9. PMC: 3322381. DOI: 10.1038/nmeth.1923. View

Coutard B, Valle C, de Lamballerie X, Canard B, Seidah N, Decroly E . The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade. Antiviral Res. 2020; 176:104742. PMC: 7114094. DOI: 10.1016/j.antiviral.2020.104742. View

10.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

11.

Albertsen M, Hugenholtz P, Skarshewski A, Nielsen K, Tyson G, Nielsen P . Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013; 31(6):533-8. DOI: 10.1038/nbt.2579. View

12.

Wu F, Zhao S, Yu B, Chen Y, Wang W, Song Z . A new coronavirus associated with human respiratory disease in China. Nature. 2020; 579(7798):265-269. PMC: 7094943. DOI: 10.1038/s41586-020-2008-3. View

13.

Zhou P, Yang X, Wang X, Hu B, Zhang L, Zhang W . A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-273. PMC: 7095418. DOI: 10.1038/s41586-020-2012-7. View

14.

Kumar S, Stecher G, Li M, Knyaz C, Tamura K . MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Mol Biol Evol. 2018; 35(6):1547-1549. PMC: 5967553. DOI: 10.1093/molbev/msy096. View

15.

Talavera G, Castresana J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56(4):564-77. DOI: 10.1080/10635150701472164. View

16.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

17.

Wong S, Li W, Moore M, Choe H, Farzan M . A 193-amino acid fragment of the SARS coronavirus S protein efficiently binds angiotensin-converting enzyme 2. J Biol Chem. 2003; 279(5):3197-201. PMC: 7982343. DOI: 10.1074/jbc.C300520200. View

18.

Cui J, Li F, Shi Z . Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 2018; 17(3):181-192. PMC: 7097006. DOI: 10.1038/s41579-018-0118-9. View

19.

Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y . Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020; 395(10223):497-506. PMC: 7159299. DOI: 10.1016/S0140-6736(20)30183-5. View

20.

Yan R, Zhang Y, Li Y, Xia L, Guo Y, Zhou Q . Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science. 2020; 367(6485):1444-1448. PMC: 7164635. DOI: 10.1126/science.abb2762. View