Abstract
Abstract Novel coronavirus (nCoV) namely “SARS-CoV-2” is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the “SARS-CoV-2” although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among “SARS-CoV-2” and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that “SARS-CoV-2” has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.
Highlights
World Health Organization (WHO) defines, continuous emergences of viral ailments possess a serious problem to the public health
During whole period which extends till today, an epidemic characterized by inexplicable low respiratory infections was identified in a largest cosmopolitan area in Wuhan (Hubei province), was first time reported on December 31, 2019, to the Country Office of WHO in China
Phylogenetic analysis exhibited that “SARS-CoV-2” belongs to genus “βCoV” and subgenus “sarbecovirus” along with other SARS and SARS-CoV viruses isolated from human, bat and other animals
Summary
World Health Organization (WHO) defines, continuous emergences of viral ailments possess a serious problem to the public health. Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was latest and firstly recognized in Saudi Arabia (2012). These epidemics like SARS-CoV triggered an epidemic in China affecting many other countries with about 8,000 cases MERS-CoV has about 2,500 cases while about 8,00 deaths in both (Cascella et al, 2020). The causative agent of the etiology of this infection is a “novel” virus member of coronavirus (CoV) family. It was called 2019-nCoV, latter on International Committee on Taxonomy of Viruses (ICTV) termed it as “SARS-CoV-2” virus due to its great similarity with that virus caused SARS outbreak (SARS-CoVs) (Gorbalenya et al, 2020)
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