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. 2020 Apr:79:104212.
doi: 10.1016/j.meegid.2020.104212. Epub 2020 Jan 29.

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

D Paraskevis  1 , E G Kostaki  2 , G Magiorkinis  2 , G Panayiotakopoulos  3 , G Sourvinos  4 , S Tsiodras  5
Affiliations

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

D Paraskevis et al. Infect Genet Evol. 2020 Apr.

Abstract

Background: A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus.

Methods: Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods.

Results: Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5'-part spanning the first 11,498 nucleotides and the last 3'-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3'-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch.

Conclusions: The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.

Keywords: Genomic sequence analysis; Molecular epidemiology; Novel coronavirus; Origin; Phylogenetic analysis; Recombination.

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Conflict of interest statement

Declaration of Competing Interest All authors report no conflict of interest related to the submitted work.

Figures

Fig. 1
Fig. 1
A. Genomic organization of the novel coronavirus (2019-nCoV) according to the positions in the edited alignment. B. Simplot of 2019-nCoV (NC_045512_Wuhan_Hu-1) against sequences within the subgenus sarbecovirus. Different colours correspond to the nucleotide similarity between the 2019-nCoV and different groups. The regions with discordant phylogenetic clustering of the 2019-nCoV with Bats_SARS-like sequences are shown in different colours. C. Maximum likelihood (ML) phylogenetic trees inferred in different genomic regions as indicated by the Simplot analysis. The genomic regions are shown in numbers at the top or at the left of the trees. The 2019-nCoV sequence is shown in red and stars indicate important nodes received 100% bootstrap and 1 posterior probability support. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
Fig. 2
Fig. 2
Neighbor joining distance tree of the BLAST search results of the 2019-nCoV (NC_0455_Wuhan_Hu_1) sequence in the genomic region 10,901–22,830 of the alignment.
See this image and copyright information in PMC

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