Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq

Detalhes bibliográficos
Autor(a) principal: Ahmed,Jivan Qasim
Data de Publicação: 2022
Outros Autores: Maulud,Sazan Qader, Al-Qadi,Rawand, Mohamed,Teroj Abdulrahman, Tayib,Gahin Abdulraheem, Hassan,Akheenk Mustafa, Taha,Luqman Saleh, Qasim,Khairi Mohammed, Tawfeeq,Mohammed Abid
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Brazilian Journal of Infectious Diseases
Texto Completo: http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702022000500200
Resumo: Abstract Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.
id BSID-1_9f1434fddb5fd258d0ac7e77193ab274
oai_identifier_str oai:scielo:S1413-86702022000500200
network_acronym_str BSID-1
network_name_str Brazilian Journal of Infectious Diseases
repository_id_str
spelling Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in IraqCOVID-19SARS-CoV-2Variant of concernOmicron variantAbstract Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.Brazilian Society of Infectious Diseases2022-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702022000500200Brazilian Journal of Infectious Diseases v.26 n.5 2022reponame:Brazilian Journal of Infectious Diseasesinstname:Brazilian Society of Infectious Diseases (BSID)instacron:BSID10.1016/j.bjid.2022.102677info:eu-repo/semantics/openAccessAhmed,Jivan QasimMaulud,Sazan QaderAl-Qadi,RawandMohamed,Teroj AbdulrahmanTayib,Gahin AbdulraheemHassan,Akheenk MustafaTaha,Luqman SalehQasim,Khairi MohammedTawfeeq,Mohammed Abideng2022-11-08T00:00:00Zoai:scielo:S1413-86702022000500200Revistahttps://www.bjid.org.br/https://old.scielo.br/oai/scielo-oai.phpbjid@bjid.org.br||lgoldani@ufrgs.br1678-43911413-8670opendoar:2022-11-08T00:00Brazilian Journal of Infectious Diseases - Brazilian Society of Infectious Diseases (BSID)false
dc.title.none.fl_str_mv Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
title Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
spellingShingle Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
Ahmed,Jivan Qasim
COVID-19
SARS-CoV-2
Variant of concern
Omicron variant
title_short Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
title_full Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
title_fullStr Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
title_full_unstemmed Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
title_sort Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq
author Ahmed,Jivan Qasim
author_facet Ahmed,Jivan Qasim
Maulud,Sazan Qader
Al-Qadi,Rawand
Mohamed,Teroj Abdulrahman
Tayib,Gahin Abdulraheem
Hassan,Akheenk Mustafa
Taha,Luqman Saleh
Qasim,Khairi Mohammed
Tawfeeq,Mohammed Abid
author_role author
author2 Maulud,Sazan Qader
Al-Qadi,Rawand
Mohamed,Teroj Abdulrahman
Tayib,Gahin Abdulraheem
Hassan,Akheenk Mustafa
Taha,Luqman Saleh
Qasim,Khairi Mohammed
Tawfeeq,Mohammed Abid
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Ahmed,Jivan Qasim
Maulud,Sazan Qader
Al-Qadi,Rawand
Mohamed,Teroj Abdulrahman
Tayib,Gahin Abdulraheem
Hassan,Akheenk Mustafa
Taha,Luqman Saleh
Qasim,Khairi Mohammed
Tawfeeq,Mohammed Abid
dc.subject.por.fl_str_mv COVID-19
SARS-CoV-2
Variant of concern
Omicron variant
topic COVID-19
SARS-CoV-2
Variant of concern
Omicron variant
description Abstract Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.
publishDate 2022
dc.date.none.fl_str_mv 2022-01-01
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702022000500200
url http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702022000500200
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 10.1016/j.bjid.2022.102677
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv text/html
dc.publisher.none.fl_str_mv Brazilian Society of Infectious Diseases
publisher.none.fl_str_mv Brazilian Society of Infectious Diseases
dc.source.none.fl_str_mv Brazilian Journal of Infectious Diseases v.26 n.5 2022
reponame:Brazilian Journal of Infectious Diseases
instname:Brazilian Society of Infectious Diseases (BSID)
instacron:BSID
instname_str Brazilian Society of Infectious Diseases (BSID)
instacron_str BSID
institution BSID
reponame_str Brazilian Journal of Infectious Diseases
collection Brazilian Journal of Infectious Diseases
repository.name.fl_str_mv Brazilian Journal of Infectious Diseases - Brazilian Society of Infectious Diseases (BSID)
repository.mail.fl_str_mv bjid@bjid.org.br||lgoldani@ufrgs.br
_version_ 1754209245465673728