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Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan

Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable...

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Autores principales: Tamim, Sana, Trovao, Nidia S., Thielen, Peter, Mehoke, Tom, Merritt, Brian, Ikram, Aamer, Salman, Muhammad, Alam, Muhammad Masroor, Umair, Massab, Badar, Nazish, Khurshid, Adnan, Mehmood, Nayab
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier B.V. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8277555/
https://www.ncbi.nlm.nih.gov/pubmed/34271187
http://dx.doi.org/10.1016/j.meegid.2021.105003
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author Tamim, Sana
Trovao, Nidia S.
Thielen, Peter
Mehoke, Tom
Merritt, Brian
Ikram, Aamer
Salman, Muhammad
Alam, Muhammad Masroor
Umair, Massab
Badar, Nazish
Khurshid, Adnan
Mehmood, Nayab
author_facet Tamim, Sana
Trovao, Nidia S.
Thielen, Peter
Mehoke, Tom
Merritt, Brian
Ikram, Aamer
Salman, Muhammad
Alam, Muhammad Masroor
Umair, Massab
Badar, Nazish
Khurshid, Adnan
Mehmood, Nayab
author_sort Tamim, Sana
collection PubMed
description Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable in-depth global phylogenetic analysis. To contribute to these efforts, we established an Oxford Nanopore Technologies (ONT) sequencing capability at the National Institutes of Health (NIH), Pakistan. This study highlights multiple SARS-CoV-2 lineages co-circulating during the peak of a second COVID-19 wave in Pakistan (Nov 2020-Feb 2021), with virus origins traced to the United States of America and Saudi Arabia. Ten SARS-CoV-2 positive samples were used for ONT library preparation. Sequence and phylogenetic analysis determined that the patients were infected with lineage B.1.1.250, originally identified in the United Kingdom and Bangladesh during March and April of 2020, and in circulation until the time of this study in Europe, USA and Australia. Lineage B.1.261 was originally identified in Saudi Arabia with widespread local dissemination in Pakistan. One sample clustered with the parental B.1 lineage and the other with lineage B.6 originally from Singapore. In the future, monitoring the evolutionary dynamics of circulating lineages in Pakistan will enable improved tracing of the viral spread, changing trends of their expansion trajectories, persistence, changes in their demographic dynamics, and provide guidance for better implementation of control measures.
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spelling pubmed-82775552021-07-14 Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan Tamim, Sana Trovao, Nidia S. Thielen, Peter Mehoke, Tom Merritt, Brian Ikram, Aamer Salman, Muhammad Alam, Muhammad Masroor Umair, Massab Badar, Nazish Khurshid, Adnan Mehmood, Nayab Infect Genet Evol Article Genomic epidemiology of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has provided global epidemiological insight into the COVID-19 pandemic since it began. Sequencing of the virus has been performed at scale, with many countries depositing data into open access repositories to enable in-depth global phylogenetic analysis. To contribute to these efforts, we established an Oxford Nanopore Technologies (ONT) sequencing capability at the National Institutes of Health (NIH), Pakistan. This study highlights multiple SARS-CoV-2 lineages co-circulating during the peak of a second COVID-19 wave in Pakistan (Nov 2020-Feb 2021), with virus origins traced to the United States of America and Saudi Arabia. Ten SARS-CoV-2 positive samples were used for ONT library preparation. Sequence and phylogenetic analysis determined that the patients were infected with lineage B.1.1.250, originally identified in the United Kingdom and Bangladesh during March and April of 2020, and in circulation until the time of this study in Europe, USA and Australia. Lineage B.1.261 was originally identified in Saudi Arabia with widespread local dissemination in Pakistan. One sample clustered with the parental B.1 lineage and the other with lineage B.6 originally from Singapore. In the future, monitoring the evolutionary dynamics of circulating lineages in Pakistan will enable improved tracing of the viral spread, changing trends of their expansion trajectories, persistence, changes in their demographic dynamics, and provide guidance for better implementation of control measures. Published by Elsevier B.V. 2021-10 2021-07-14 /pmc/articles/PMC8277555/ /pubmed/34271187 http://dx.doi.org/10.1016/j.meegid.2021.105003 Text en © 2021 Published by Elsevier B.V. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Tamim, Sana
Trovao, Nidia S.
Thielen, Peter
Mehoke, Tom
Merritt, Brian
Ikram, Aamer
Salman, Muhammad
Alam, Muhammad Masroor
Umair, Massab
Badar, Nazish
Khurshid, Adnan
Mehmood, Nayab
Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title_full Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title_fullStr Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title_full_unstemmed Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title_short Genetic and evolutionary analysis of SARS-CoV-2 circulating in the region surrounding Islamabad, Pakistan
title_sort genetic and evolutionary analysis of sars-cov-2 circulating in the region surrounding islamabad, pakistan
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8277555/
https://www.ncbi.nlm.nih.gov/pubmed/34271187
http://dx.doi.org/10.1016/j.meegid.2021.105003
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