Current understanding of an emerging coronavirus using in silico approach: Severe acute respiratory syndrome-coronavirus-2 (sars-cov-2)

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dc.contributor.authorKhalid, S.
dc.contributor.authorSiddique, R.
dc.contributor.authorShaheen, S.
dc.contributor.authorShahid, M.N.
dc.contributor.authorShamim, Z.
dc.contributor.authorKhan, M.K.A.
dc.contributor.authorSerçe, Ç. Ulubaş
dc.date.accessioned2024-11-07T10:40:01Z
dc.date.available2024-11-07T10:40:01Z
dc.date.issued2023
dc.departmentNiğde Ömer Halisdemir Üniversitesi
dc.description.abstractNovel 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. © 2023, Instituto Internacional de Ecologia. All rights reserved.
dc.identifier.doi10.1590/1519-6984.247237
dc.identifier.issn1519-6984
dc.identifier.pmid34495154
dc.identifier.scopus2-s2.0-85115614374
dc.identifier.scopusqualityQ2
dc.identifier.urihttps://doi.org/10.1590/1519-6984.247237
dc.identifier.urihttps://hdl.handle.net/11480/11351
dc.identifier.volume83
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.language.isoen
dc.publisherInstituto Internacional de Ecologia
dc.relation.ispartofBrazilian Journal of Biology
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.snmzKA_20241106
dc.subjectBat-SARS-CoVs
dc.subjectCOVID-19
dc.subjectNovel coronavirus (nCoV)
dc.subjectPhylogenetic relationship
dc.subjectRecombination detection program-4
dc.titleCurrent understanding of an emerging coronavirus using in silico approach: Severe acute respiratory syndrome-coronavirus-2 (sars-cov-2)
dc.title.alternativeCompreensão atual de um coronavírus emergente usando abordagem in silico: Síndrome respiratória aguda grave-coronavírus-2 (sars-cov-2)
dc.typeArticle

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