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

Abstract

A B S T R A C TBackground: 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.

Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species

“…Furthermore, the amino acid homologies of ORF1ab, N, S proteins of the two viruses are 98.55, 99.05 and 97.41% respectively. These results suggest the two viruses have a high genetic relationship, which is consistent with the results reported previously Li et al, 2020;Paraskevis et al, 2020;Zhou et al, 2020). Moreover, the N protein of SARS-CoV-2 and bat coronavirus RaTG13 had 4 different amino acids, which were 37S/P, 215G/S, 243G/S, and 267A/Q, respectively.…”

“…Notably, although the whole genome sequence of SARS-CoV-2 is almost identical, with a similarity rate of 99.9% (Ceraolo and Giorgi, 2020;Li et al, 2020;Lu et al, 2020;Paraskevis et al, 2020), the virus begins to mutate in patients . Mutations of different SARS-CoV-2 isolates mainly occurs in five genes, including S, N, ORF8, ORF3a, and ORF1ab, with about 42% of the variations are non-synonymous mutation ).…”

Investigation into SARS-CoV-2 Resistance of Compounds in Garlic Essential Oil

“…9,10 The ACE2 protein is the same functional host-cell receptor shared by SARS-CoV-2 and SARS. 8,11,12 The structural database of ACE2 can be referenced from UniProtKB. 13 Therefore, besides inhibiting SARS-CoV-2, the inhibition of the ACE2 protein is absolutely necessary to reduce the operability of the host receptor of SARS-CoV-2.…”

<p>Epidemiologic and Clinical Characteristics of 26 Cases of COVID-19 Arising from Patient-to-Patient Transmission in Liaocheng, China</p>

“…4 Human-to-human transmission has accounted for most of the infections outside Wuhan. 5 Most studies to date on COVID-19 have focused on disease etiology and the genomics of 2019-nCoV, [6][7][8] with few reports on the epidemiologic and clinical characteristics of infected patients. 5,9 Here we report early clinical features of 25 patients with confirmed COVID-19 who were admitted to Liaocheng Infectious Disease Hospital in Shandong Province.…”