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First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco
The Omicron BA.5/22B variant has been designated as a “variant of concern” by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination of non-BA.5/22B...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9607325/ https://www.ncbi.nlm.nih.gov/pubmed/36296228 http://dx.doi.org/10.3390/microorganisms10101952 |
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author | Colson, Philippe Lavagna, Christian Delerce, Jérémy Groshenry, Guillaume Yahi, Nouara Fantini, Jacques La Scola, Bernard Althaus, Thomas |
author_facet | Colson, Philippe Lavagna, Christian Delerce, Jérémy Groshenry, Guillaume Yahi, Nouara Fantini, Jacques La Scola, Bernard Althaus, Thomas |
author_sort | Colson, Philippe |
collection | PubMed |
description | The Omicron BA.5/22B variant has been designated as a “variant of concern” by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination of non-BA.5/22B signature amino acid changes. SARS-CoV-2 neutralizing antibodies were measured with a surrogate virus neutralization test. SARS-CoV-2 genotype screening was performed on nasopharyngeal samples with a multiplex qPCR assay. The SARS-CoV-2 genome was obtained by next-generation sequencing with the Illumina COVID-seq protocol, then assembly using bioinformatics pipelines and software was performed. The BA.5/22B spike protein structure was obtained by molecular modeling. Two spouses were SARS-CoV-2-diagnosed the day they returned from a one-week trip in the Republic of Seychelles. SARS-CoV-2 qPCR screening for variant-specific mutations identified an Omicron variant BA.1/21K, BA.4/22A, or BA.5/22B. A SARS-Co-2 BA.5/22B variant genome was recovered from one of the spouses. Aside from BA.5/22B-defining amino acid substitutions, four other amino acid changes were encoded including Q556K in ORF1a, K2557R in ORF1b, and A67V and A829T in spike; only 13 genomes in sequence databases harbored these four mutations concurrently. Structural analysis of this BA.5/22B variant predicted that A829T in spike may result in a compaction that may affect conformational plasticity. Overall, our findings warrant performing genome-based genotypic surveillance to survey accurately the emergence and circulation of SARS-CoV-2 variants worldwide and point out that their first occurrence in a country is often through international travel despite implemented countermeasures. |
format | Online Article Text |
id | pubmed-9607325 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96073252022-10-28 First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco Colson, Philippe Lavagna, Christian Delerce, Jérémy Groshenry, Guillaume Yahi, Nouara Fantini, Jacques La Scola, Bernard Althaus, Thomas Microorganisms Case Report The Omicron BA.5/22B variant has been designated as a “variant of concern” by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination of non-BA.5/22B signature amino acid changes. SARS-CoV-2 neutralizing antibodies were measured with a surrogate virus neutralization test. SARS-CoV-2 genotype screening was performed on nasopharyngeal samples with a multiplex qPCR assay. The SARS-CoV-2 genome was obtained by next-generation sequencing with the Illumina COVID-seq protocol, then assembly using bioinformatics pipelines and software was performed. The BA.5/22B spike protein structure was obtained by molecular modeling. Two spouses were SARS-CoV-2-diagnosed the day they returned from a one-week trip in the Republic of Seychelles. SARS-CoV-2 qPCR screening for variant-specific mutations identified an Omicron variant BA.1/21K, BA.4/22A, or BA.5/22B. A SARS-Co-2 BA.5/22B variant genome was recovered from one of the spouses. Aside from BA.5/22B-defining amino acid substitutions, four other amino acid changes were encoded including Q556K in ORF1a, K2557R in ORF1b, and A67V and A829T in spike; only 13 genomes in sequence databases harbored these four mutations concurrently. Structural analysis of this BA.5/22B variant predicted that A829T in spike may result in a compaction that may affect conformational plasticity. Overall, our findings warrant performing genome-based genotypic surveillance to survey accurately the emergence and circulation of SARS-CoV-2 variants worldwide and point out that their first occurrence in a country is often through international travel despite implemented countermeasures. MDPI 2022-09-30 /pmc/articles/PMC9607325/ /pubmed/36296228 http://dx.doi.org/10.3390/microorganisms10101952 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Case Report Colson, Philippe Lavagna, Christian Delerce, Jérémy Groshenry, Guillaume Yahi, Nouara Fantini, Jacques La Scola, Bernard Althaus, Thomas First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title_full | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title_fullStr | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title_full_unstemmed | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title_short | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco |
title_sort | first detection of the sars-cov-2 omicron ba.5/22b in monaco |
topic | Case Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9607325/ https://www.ncbi.nlm.nih.gov/pubmed/36296228 http://dx.doi.org/10.3390/microorganisms10101952 |
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