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Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) / Compreensão atual de um coronavírus emergente usando abordagem in silico: síndrome respiratória aguda grave - coronavírus-2 (SARS-CoV-2)
Khalid, S; Siddique, R; Shaheen, S; Shahid, M N; Shamim, Z; Khan, M K A; Serçe, Ç. Ulubas.
Affiliation
  • Khalid, S; Lahore College for Women University. Department of Botany. Jail Road. PK
  • Siddique, R; Lahore College for Women University. Department of Botany. Jail Road. PK
  • Shaheen, S; Lahore College for Women University. Department of Botany. Jail Road. PK
  • Shahid, M N; University of Education. Department of Botany. Division of Science and Technology. Lahore. PK
  • Shamim, Z; Mirpur University of Science and Technology. Department of Biotechnology. Mirpur. PK
  • Khan, M K A; University of Okara. Department of Zoology. Okara. PK
  • Serçe, Ç. Ulubas; Niğde Ömer Halisdemir Üniversitesi. Tarım Bilimleri ve Teknolojileri Fakültesi. Bitkisel Üretim ve Teknolojileri Bölümü. Niğde. TR
Braz. j. biol ; 83: e247237, 2023. tab, graf
Article in English | MEDLINE, LILACS, VETINDEX | ID: biblio-1339386
Responsible library: BR1.1
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.
RESUMO
Resumo O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.
Subject(s)


Full text: Available Collection: Tematic databases Database: LILACS / MEDLINE / VETINDEX Main subject: Chiroptera / COVID-19 Language: English Journal: Braz. j. biol Year: 2023 Document type: Article Institution/Affiliation country: Lahore College for Women University/PK / Mirpur University of Science and Technology/PK / Niğde Ömer Halisdemir Üniversitesi/TR / University of Education/PK / University of Okara/PK

Full text: Available Collection: Tematic databases Database: LILACS / MEDLINE / VETINDEX Main subject: Chiroptera / COVID-19 Language: English Journal: Braz. j. biol Year: 2023 Document type: Article Institution/Affiliation country: Lahore College for Women University/PK / Mirpur University of Science and Technology/PK / Niğde Ömer Halisdemir Üniversitesi/TR / University of Education/PK / University of Okara/PK
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