Cross-species transmission of the newly identified coronavirus 2019-nCoV

Wei Ji, Wei Wang, Xiaofang Zhao, Junjie Zai, Xingguang Li, Wei Ji, Wei Wang, Xiaofang Zhao, Junjie Zai, Xingguang Li

Abstract

The current outbreak of viral pneumonia in the city of Wuhan, China, was caused by a novel coronavirus designated 2019-nCoV by the World Health Organization, as determined by sequencing the viral RNA genome. Many initial patients were exposed to wildlife animals at the Huanan seafood wholesale market, where poultry, snake, bats, and other farm animals were also sold. To investigate possible virus reservoir, we have carried out comprehensive sequence analysis and comparison in conjunction with relative synonymous codon usage (RSCU) bias among different animal species based on the 2019-nCoV sequence. Results obtained from our analyses suggest that the 2019-nCoV may appear to be a recombinant virus between the bat coronavirus and an origin-unknown coronavirus. The recombination may occurred within the viral spike glycoprotein, which recognizes a cell surface receptor. Additionally, our findings suggest that 2019-nCoV has most similar genetic information with bat coronovirus and most similar codon usage bias with snake. Taken together, our results suggest that homologous recombination may occur and contribute to the 2019-nCoV cross-species transmission.

Keywords: 2019-nCoV; codon usage bias; cross-species transmission; phylogenetic analysis; recombination.

Conflict of interest statement

The authors declare that there are no conflict of interests.

© 2020 Wiley Periodicals, Inc.

Figures

Figure 1
Figure 1
Maximum likelihood phylogenetic tree of the 2019‐nCoV. Phylogenetic tree inferred from 272 near‐complete genome sequences of coronavirus was midpoint rooted and grouped into 4 clades (2019‐nCoV, Clades A, B, and C). Coronaviruses originating from different countries/regions are highlighted in colors
Figure 2
Figure 2
Sequence comparison among different coronaviruses. Similarity plot analysis was performed among coronaviruses in Clades A, B, and C. Recombination analysis was conducted with a sliding window of 500 bp and a step size of 30 bp. Recombination sites were located within the viral spike glycoprotein genes, as indicated by an orange box on the top
Figure 3
Figure 3
Comparison of relative synonymous codon usage (RSCU) between 2019‐nCoV and its putative wildlife animal reservoir(s). A, Heat map resulting from cluster analysis of the RSCU among the 2019‐nCoV, bat‐SL‐CoVZC45, Bungarus multicinctus, Naja atra, Rhinolophus sinicus, Gallus gallus, Marmota, Homo sapiens, Manis javanica, and Erinaceus europaeus. B, Comparison of squared euclidean distance between 2019‐nCoV and different animal species. Squared Euclidean distance was calculated based on the RSCU
Figure 4
Figure 4
Geographic distribution of Bungarus multicinctus and Naja atra in China. The geographic distribution of Bungarus multicinctus and Naja atra are highlighted in colors. Yellow color represents the common geographic distribution of Bungarus multicinctus and Naja atra. Green color represents additional geographic distribution of Bungarus multicinctus. The location of Wuhan city where the 2019‐nCoV outbreak occurs is indicated in red. Maps were obtained from Craft MAP website (http://www.craftmap.box-i.net/)

References

    1. Chan PK. Outbreak of avian influenza A (H5N1) virus infection in Hong Kong in 1997. Clin Infect Dis. 2002;34:S58‐S64.
    1. Guan Y. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302:276‐278.
    1. Yu XJ, Liang MF, Zhang SY, et al. Fever with thrombocytopenia associated with a novel bunyavirus in China. N Engl J Med. 2011;364:1523‐1532. 10.1056/NEJMoa1010095
    1. Lu H, Stratton CW, Tang YW. Outbreak of pneumonia of unknown etiology in Wuhan China: the mystery and the miracle. J Med Virol. 2020. 10.1002/jmv.25678
    1. World Health Organization . Coronavirus. 2019.
    1. Zhang N, Wang L, Deng X, et al. Recent advances in the detection of respiratory virus infection in humans. J Med Virol. 2020. 10.1002/jmv.25674
    1. MacLachlan NJ, Dubovi EJ. In: MacLachlan NJ, Dubovi EJ, eds. Fenner's Veterinary Virology. 5th ed. Cambridge, MA: Academic Press; 2017:393‐413.
    1. Howley DMKP. Fields Virology. 1 Lippincott Williams & Wilkins; 2013:830P.
    1. World Health Organization . Consensus Document on the Epidemiology of Severe Acute Respiratory Syndrome (SARS). Geneva: World Health Organization; 2003.
    1. Wang H, Liu S, Zhang B, Wei W. Analysis of synonymous codon usage bias of Zika virus and its adaption to the hosts. PLoS One. 2016;11:e0166260.
    1. Bahir I, Fromer M, Prat Y, Linial M. Viral adaptation to host: a proteome‐based analysis of codon usage and amino acid preferences. Mol Syst Biol. 2009;5:311.
    1. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772‐780. 10.1093/molbev/mst010
    1. Hall TA. BioEdit: a user‐friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95‐98.
    1. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post‐analysis of large phylogenies. Bioinformatics. 2014;30:1312‐1313. 10.1093/bioinformatics/btu033
    1. Lole KS, Bollinger RC, Paranjape RS, et al. Full‐length human immunodeficiency virus type 1 genomes from subtype C‐infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999;73:152‐160.
    1. Liu X, Zhang Y, Fang Y, Wang Y. Patterns and influencing factor of synonymous codon usage in porcine circovirus. Virol J. 2012;9:1‐9.
    1. Wright F. The ‘effective number of codons’ used in a gene. Gene. 1990;87:23‐29.
    1. Ji W, Niu D‐D, Si H‐L, Ding N‐Z, He C‐Q. Vaccination influences the evolution of classical swine fever virus. Infect Genet Evol. 2014;25:69‐77.
    1. Howe H, Holton K, Nair S, Schlauch D, Sinha R, Quackenbush J. In: Ochs MF, Casagrande JT, Davuluri RV, eds. Biomedical Informatics for Cancer Research. Boston, MA: Springer; 2019:267‐277.
    1. Tolou HJ, Couissinier‐Paris P, Durand JP, et al. Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences. J Gen Virol. 2001;82:1283‐1290.
    1. Clavel F, Hoggan MD, Willey RL, Strebel K, Martin MA, Repaske R. Genetic recombination of human immunodeficiency virus. J Virol. 1989;63:1455‐1459.
    1. Bollyky PL, Rambaut A, Harvey PH, Holmes EC. Recombination between sequences of hepatitis B virus from different genotypes. J Mol Evol. 1996;42:97‐102.
    1. Colina R, Casane D, Vasquez S, et al. Evidence of intratypic recombination in natural populations of hepatitis C virus. J Gen Virol. 2004;85:31‐37.
    1. Wikipedia . Many‐banded krait. 2020. .
    1. Wikipedia . Chinese cobra. 2020. .
    1. Smith RD. Responding to global infectious disease outbreaks: lessons from SARS on the role of risk perception, communication and management. Soc Sci Med. 2006;63:3113‐3123.
    1. Graham RL, Baric RS. Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross‐species transmission. J Virol. 2010;84:3134‐3146.
    1. Cunha CB, Opal SM. Middle East respiratory syndrome (MERS) A new zoonotic viral pneumonia. Virulence. 2014;5:650‐654.

Source: PubMed

Sponsors and Collaborators

Medical Conditions

Drug Interventions

3
Subscribe