Published March 26, 2020 | Version v1
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Identifying SARS-CoV-2related coronaviruses in Malayan pangolins

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Lam, Tommy Tsan-Yuk, Shum, Marcus Ho-Hin, Zhu, Hua-Chen, Tong, Yi-Gang, Ni, Xue-Bing, Liao, Yun-Shi, Wei, Wei, Cheung, William Yiu-Man, Li, Wen-Juan, Li, Lian-Feng, Leung, Gabriel M., Holmes, Edward C., Guan, Yi (2020): Identifying SARS-CoV-2related coronaviruses in Malayan pangolins. Nature 2020: 1-15, DOI: 10.1038/s41586-020-2169-0

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References

  • 1. Wu,F.et al. A new coronavirus associated with human respiratory disease in China. Nature (2020). https://doi.org/10.1038/s41586-020-2008-3.
  • 2. Lu,R.et al. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.Lancet, (2020).https://doi. org/10.1016/S0140-6736(20)30251-8.
  • 3. World Health Organization. WHO Novel Coronavirus (2019-nCoV) situation reports. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/
  • 4. Cohen,J. Mining coronavirus genomes for clues to the outbreak's origins.Science, (2020) https://www.sciencemag.org/news/2020/01/mining-coronavirus-genomes-clues-outbreak-s-origins.
  • 5. Wang,M. et al. SARS-CoV infection in a restaurant from palm civet. Emerg Infect Dis 11:1860-5,(2005).
  • 6. Zhou,P.et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature (2020).https://doi.org/10.1038/s41586-020-2012-7.
  • 7. Liu,P.et al. Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica). Viruses 11, (2019).
  • 8. Hon,C.C. et al. Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.J Virol 82, 1819-1826,(2008).
  • 9. Wan, Y.et al. Receptor recognition by novel coronavirus from Wuhan: An analysis based on decade-long structural studies of SARS.J Virol, (2020).
  • 10. Coutard,B.et al. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade.Antiviral Res, 104742,https://doi. org/10.1016/j.antiviral.2020.104742 (2020).
  • 11. Heinrich,S.et al. The global trafficking of pangolins:A comprehensive summary of seizures and trafficking routes from 2010-2015.Trafficking, (2017).
  • 12. Wang,W.et al. 2017.Discovery of a highly divergent coronavirus in the Asian house shrew from China illuminates the origin of the alphacoronaviruses.J Virol 91, (2017).
  • 13. Li,D. et al. MEGAHIT:an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.Bioinformatics 31, 1674-1676, (2015).
  • 14. Li,H.and Durbin,R.Fast and accurate long-read alignment with Burrows-Wheeler transform.Bioinformatics 26, 589-595, (2010).
  • 15. Rozewicki,J. et al. MAFFT-DASH:integrated protein sequence and structural alignment. Nucleic Acids Res 47, W5-W10,(2019).
  • 16. Stamatakis,A.RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.Bioinformatics 30, 1312-1313,(2014).
  • 17. Lole,KS.et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India,with evidence of intersubtype recombination.J Virol 73(1):152-60, (1999).
  • 18. He,R. et al. Analysis of multimerization of the SARS coronavirus nucleocapsid protein. Biochem Biophys Res Commun 316, 476-483,(2004).
  • 19. Snijder,E.J. et al. Unique and conserved features of genome and proteome of SARScoronavirus, an early split-off from the coronavirus group 2 lineage.J Mol Biol 331, 991-1004,(2003).
  • 20. Marra,M. A.et al. The Genome sequence of the SARS-associated coronavirus.Science 300, 1399-1404,(2003).
  • 21. Song, H. D.et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human.Proc Natl Acad Sci U S A 102, 2430-2435,(2005).
  • 22. Han,Y.et al. Identification of Diverse Bat Alphacoronaviruses and Betacoronaviruses in China Provides New Insights Into the Evolution and Origin of Coronavirus-Related Diseases. Front Microbiol 10, 1900, (2019).
  • 23. Tao,Y.& Tong,S.Complete Genome Sequence of a Severe Acute Respiratory Syndrome- Related Coronavirus from Kenyan Bats.Microbiol Resour Announc 8, (2019).
  • 24. Hu, D.et al. Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats. Emerg Microbes Infect 7, 154,(2018).
  • 25. Hu, B.et al.Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus.PLoS Pathog 13, e1006698,(2017).
  • 26. Wu,Z.et al. ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus.J Infect Dis 213, 579-583, (2016).
  • 27. Wu, Z. et al. Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases.ISME J 10, 609-620,(2016).
  • 28. Yang,L. et al. Novel SARS-like betacoronaviruses in bats, China,2011. Emerg Infect Dis 19, 989-991, (2013).
  • 29. Xu,L. et al. Detection and characterization of diverse alpha- and betacoronaviruses from bats in China. Virol Sin 31, 69-77,(2016).
  • 30. He,B. et al. Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China.J Virol 88, 7070-7082,(2014).
  • 31. Ge,X. Y.et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor.Nature 503, 535-538,(2013).
  • 32. Li,W.et al. Bats are natural reservoirs of SARS-like coronaviruses.Science 310, 676-679, (2005).
  • 33. Drexler,J. F.et al. Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences.J Virol 84, 11336-11349, (2010).
  • 34. Lau, S. K. et al. Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute,self-limiting infection that allows recombination events. J Virol 84, 2808-2819,(2010).
  • 35. Yuan,J.et al. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans.J Gen Virol 91, 1058-1062, (2010).
  • 36. Guan, Y.et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China.Science 302, 276-278,(2003).
  • 37. Tang,X. C.et al. Prevalence and genetic diversity of coronaviruses in bats from China. J Virol 80, 7481-7490,(2006).
  • 38. Yeh,S.H. et al. Characterization of severe acute respiratory syndrome coronavirus genomes in Taiwan:molecular epidemiology and genome evolution.Proc Natl Acad Sci U S A 101, 2542-2547,(2004).
  • 39. Vega,V.B.et al. Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003.BMC Infect Dis 4, 32,(2004).