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. 2020 Apr;92(4):433-440.
doi: 10.1002/jmv.25682.

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

Wei Ji  1 , Wei Wang  2 , Xiaofang Zhao  3 , Junjie Zai  4 , Xingguang Li  5
Affiliations

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

Wei Ji et al. J Med Virol. 2020 Apr.

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.

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Conflict of interest statement

The authors declare that there are no conflict of interests.

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/)
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