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Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK

Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations th...

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Autores principales: Pacchiarini, Nicole, Cronin, Michelle, Sawyer, Clare, Williams, Catie, Beazer, Andrew, Cottrell, Simon, Morgan, Mari, Saunders, Vince, Moore, Catherine, Connor, Thomas R., Williams, Christopher
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Microbiology Society 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210960/
https://www.ncbi.nlm.nih.gov/pubmed/37052600
http://dx.doi.org/10.1099/mgen.0.000984
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author Pacchiarini, Nicole
Cronin, Michelle
Sawyer, Clare
Williams, Catie
Beazer, Andrew
Cottrell, Simon
Morgan, Mari
Saunders, Vince
Moore, Catherine
Connor, Thomas R.
Williams, Christopher
author_facet Pacchiarini, Nicole
Cronin, Michelle
Sawyer, Clare
Williams, Catie
Beazer, Andrew
Cottrell, Simon
Morgan, Mari
Saunders, Vince
Moore, Catherine
Connor, Thomas R.
Williams, Christopher
author_sort Pacchiarini, Nicole
collection PubMed
description Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations that may increase transmissibility, severity or vaccine escape. We present a genomic and epidemiological description of a new recombinant lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), XR, first identified in Wales. The Pathogen Genomics Unit (Public Health Wales, UK) sequences positive SARS-CoV-2 PCR tests using the ARTIC SARS-CoV-2 sequencing protocol. Recombinants were detected using an in-house pipeline and the epidemiological data analysed in R. Nosocomial cases were defined as those with samples taken after >7 days in hospital. Between February and March 2022, we identified 78 samples with highly similar genomes, comprising a BA.1-like 5' end, a BA.2-like 3' end and a BA.2-like spike protein. This signature is consistent with recombination and was defined as XR by Pangolin (PANGO v1.8). A total of 50 % of cases had a sample collected whilst in hospital and the first three cases were immunocompromised patients. The patient median age was 58 years (range: 4–95 years) and most of the patients were fully vaccinated against SARS-CoV-2 (74 % third dose/booster). Three patients died within 28 days of their sample collection date, one of whom had COVID-19 listed amongst ICD10 (International Classification of Diseases 10) coded causes of death. Our integrated system enabled real-time monitoring of recombinant SARS-CoV-2 for early detection, in order to rapidly risk assess and respond. This work highlights the importance of setting-based surveillance of recombinant SARS-CoV-2, as well as the need to monitor immunocompromised populations through repeat testing and sequencing.
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spelling pubmed-102109602023-05-26 Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK Pacchiarini, Nicole Cronin, Michelle Sawyer, Clare Williams, Catie Beazer, Andrew Cottrell, Simon Morgan, Mari Saunders, Vince Moore, Catherine Connor, Thomas R. Williams, Christopher Microb Genom Short Communications Recombination, the process whereby a segment of genetic material from one genome is inserted into another, producing a new chimeric genome, is an important evolutionary mechanism frequently observed in coronaviruses. The risks posed by recombination include the shuffling of advantageous mutations that may increase transmissibility, severity or vaccine escape. We present a genomic and epidemiological description of a new recombinant lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), XR, first identified in Wales. The Pathogen Genomics Unit (Public Health Wales, UK) sequences positive SARS-CoV-2 PCR tests using the ARTIC SARS-CoV-2 sequencing protocol. Recombinants were detected using an in-house pipeline and the epidemiological data analysed in R. Nosocomial cases were defined as those with samples taken after >7 days in hospital. Between February and March 2022, we identified 78 samples with highly similar genomes, comprising a BA.1-like 5' end, a BA.2-like 3' end and a BA.2-like spike protein. This signature is consistent with recombination and was defined as XR by Pangolin (PANGO v1.8). A total of 50 % of cases had a sample collected whilst in hospital and the first three cases were immunocompromised patients. The patient median age was 58 years (range: 4–95 years) and most of the patients were fully vaccinated against SARS-CoV-2 (74 % third dose/booster). Three patients died within 28 days of their sample collection date, one of whom had COVID-19 listed amongst ICD10 (International Classification of Diseases 10) coded causes of death. Our integrated system enabled real-time monitoring of recombinant SARS-CoV-2 for early detection, in order to rapidly risk assess and respond. This work highlights the importance of setting-based surveillance of recombinant SARS-CoV-2, as well as the need to monitor immunocompromised populations through repeat testing and sequencing. Microbiology Society 2023-04-13 /pmc/articles/PMC10210960/ /pubmed/37052600 http://dx.doi.org/10.1099/mgen.0.000984 Text en © 2023 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.
spellingShingle Short Communications
Pacchiarini, Nicole
Cronin, Michelle
Sawyer, Clare
Williams, Catie
Beazer, Andrew
Cottrell, Simon
Morgan, Mari
Saunders, Vince
Moore, Catherine
Connor, Thomas R.
Williams, Christopher
Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title_full Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title_fullStr Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title_full_unstemmed Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title_short Novel recombinant SARS-CoV-2 lineage detected through genomic surveillance in Wales, UK
title_sort novel recombinant sars-cov-2 lineage detected through genomic surveillance in wales, uk
topic Short Communications
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210960/
https://www.ncbi.nlm.nih.gov/pubmed/37052600
http://dx.doi.org/10.1099/mgen.0.000984
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