Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event
By D. Paraskevis, E. Kostaki, Gkikas Magiorkinis, G. Panayiotakopoulos, G. Sourvinos, Sotirios Tsiodras. bioRxiv, 2020
697 citations recorded by the source corpus.
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.
Subfields: Animal Science and Zoology, Infectious Diseases
View Paper: https://www.semanticscholar.org/paper/d6620e2e6054877fb520e9dca908877a56fc4f2c
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In Infectious Diseases
Citations in the corpus
- The deadly coronaviruses: The 2003 SARS pandemic and the 2020 novel coronavirus epidemic in China (2020, positive): “This rejects the hypothesis of emergence as a result of a recombination event [94, 96] .”
- Coronavirus disease 2019 (COVID-19): A literature review (2020, neutral): “some studies linked the virus to bat [72, 73] while others associated the virus with snake [74]), contacts with these animal fluids or tissues or consumption of wild caught animal meet should be avoided.”
- A Review of SARS-CoV-2 and the Ongoing Clinical Trials (2020, background): “By contrast, both ground-glass opacification and consolidation were present relatively early in SARS [6].”
- COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives (2020, positive): “These viruses exhibit rich genetic diversity and frequent recombination events, which may increase the potential for cross-species transmission [7, 42, [51] [52] [53] [54] [55] .”
- The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control (2020, background): “This agrees with previous conclusions regarding the evolutionary analysis of SARS-CoV-2 [11,44].”
- Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study (2020, background): “Within the RdRp region, it was found that another bat coronavirus, RaTG13, was the closest relative to COVID-19 and formed a distinct lineage from other bat SARS-like coronaviruses [39,41].”
- On the origin and continuing evolution of SARS-CoV-2 (2020, neutral): “PublishedbyOxfordUniversityPressonbehalfofChinaSciencePublishing&MediaLtd.”