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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...

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Autores principales: Colson, Philippe, Lavagna, Christian, Delerce, Jérémy, Groshenry, Guillaume, Yahi, Nouara, Fantini, Jacques, La Scola, Bernard, Althaus, Thomas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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.
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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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