Cargando…

Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021

The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-...

Descripción completa

Detalles Bibliográficos
Autores principales: Merhi, Georgi, Trotter, Alexander J., de Oliveira Martins, Leonardo, Koweyes, Jad, Le-Viet, Thanh, Abou Naja, Hala, Al Buaini, Mona, Prosolek, Sophie J., Alikhan, Nabil-Fareed, Lott, Martin, Tohmeh, Tatiana, Badran, Bassam, Jupp, Orla J., Gardner, Sarah, Felgate, Matthew W., Makin, Kate A., Wilkinson, Janine M., Stanley, Rachael, Sesay, Abdul K., Webber, Mark A., Davidson, Rose K., Ghosn, Nada, Pallen, Mark, Hasan, Hamad, Page, Andrew J., Tokajian, Sima
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455693/
https://www.ncbi.nlm.nih.gov/pubmed/35876490
http://dx.doi.org/10.1099/mgen.0.000838
_version_ 1784785634184921088
author Merhi, Georgi
Trotter, Alexander J.
de Oliveira Martins, Leonardo
Koweyes, Jad
Le-Viet, Thanh
Abou Naja, Hala
Al Buaini, Mona
Prosolek, Sophie J.
Alikhan, Nabil-Fareed
Lott, Martin
Tohmeh, Tatiana
Badran, Bassam
Jupp, Orla J.
Gardner, Sarah
Felgate, Matthew W.
Makin, Kate A.
Wilkinson, Janine M.
Stanley, Rachael
Sesay, Abdul K.
Webber, Mark A.
Davidson, Rose K.
Ghosn, Nada
Pallen, Mark
Hasan, Hamad
Page, Andrew J.
Tokajian, Sima
author_facet Merhi, Georgi
Trotter, Alexander J.
de Oliveira Martins, Leonardo
Koweyes, Jad
Le-Viet, Thanh
Abou Naja, Hala
Al Buaini, Mona
Prosolek, Sophie J.
Alikhan, Nabil-Fareed
Lott, Martin
Tohmeh, Tatiana
Badran, Bassam
Jupp, Orla J.
Gardner, Sarah
Felgate, Matthew W.
Makin, Kate A.
Wilkinson, Janine M.
Stanley, Rachael
Sesay, Abdul K.
Webber, Mark A.
Davidson, Rose K.
Ghosn, Nada
Pallen, Mark
Hasan, Hamad
Page, Andrew J.
Tokajian, Sima
author_sort Merhi, Georgi
collection PubMed
description The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks.
format Online
Article
Text
id pubmed-9455693
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Microbiology Society
record_format MEDLINE/PubMed
spelling pubmed-94556932022-09-09 Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021 Merhi, Georgi Trotter, Alexander J. de Oliveira Martins, Leonardo Koweyes, Jad Le-Viet, Thanh Abou Naja, Hala Al Buaini, Mona Prosolek, Sophie J. Alikhan, Nabil-Fareed Lott, Martin Tohmeh, Tatiana Badran, Bassam Jupp, Orla J. Gardner, Sarah Felgate, Matthew W. Makin, Kate A. Wilkinson, Janine M. Stanley, Rachael Sesay, Abdul K. Webber, Mark A. Davidson, Rose K. Ghosn, Nada Pallen, Mark Hasan, Hamad Page, Andrew J. Tokajian, Sima Microb Genom Research Articles The COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just 26 SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation. In total, 905 SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, sex, nationality and age. Although 16 PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97 % of samples. In the following 2 months, all samples contained the Alpha variant. However, this had changed dramatically by June and July 2021, when all samples belonged to the Delta variant. This study documents a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the country's largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under 6 weeks. Microbiology Society 2022-07-25 /pmc/articles/PMC9455693/ /pubmed/35876490 http://dx.doi.org/10.1099/mgen.0.000838 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
spellingShingle Research Articles
Merhi, Georgi
Trotter, Alexander J.
de Oliveira Martins, Leonardo
Koweyes, Jad
Le-Viet, Thanh
Abou Naja, Hala
Al Buaini, Mona
Prosolek, Sophie J.
Alikhan, Nabil-Fareed
Lott, Martin
Tohmeh, Tatiana
Badran, Bassam
Jupp, Orla J.
Gardner, Sarah
Felgate, Matthew W.
Makin, Kate A.
Wilkinson, Janine M.
Stanley, Rachael
Sesay, Abdul K.
Webber, Mark A.
Davidson, Rose K.
Ghosn, Nada
Pallen, Mark
Hasan, Hamad
Page, Andrew J.
Tokajian, Sima
Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title_full Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title_fullStr Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title_full_unstemmed Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title_short Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
title_sort replacement of the alpha variant of sars-cov-2 by the delta variant in lebanon between april and june 2021
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9455693/
https://www.ncbi.nlm.nih.gov/pubmed/35876490
http://dx.doi.org/10.1099/mgen.0.000838
work_keys_str_mv AT merhigeorgi replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT trotteralexanderj replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT deoliveiramartinsleonardo replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT koweyesjad replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT levietthanh replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT abounajahala replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT albuainimona replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT prosoleksophiej replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT alikhannabilfareed replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT lottmartin replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT tohmehtatiana replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT badranbassam replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT jupporlaj replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT gardnersarah replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT felgatemattheww replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT makinkatea replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT wilkinsonjaninem replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT stanleyrachael replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT sesayabdulk replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT webbermarka replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT davidsonrosek replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT ghosnnada replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT pallenmark replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT hasanhamad replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT pageandrewj replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021
AT tokajiansima replacementofthealphavariantofsarscov2bythedeltavariantinlebanonbetweenaprilandjune2021