Détail du document
Identifiant

oai:HAL:hal-03959816v1

Sujet
influenza A/H3N2 virus qPCR diagnosis matrix gene M1 gene genetic diversity [SDV]Life Sciences [q-bio]
Auteur
Le Targa, Lorlane Hikmat, Houmadi Boschi, Céline La Scola, Bernard Colson, Philippe
Langue
en
Editeur

HAL CCSD;MDPI

Catégorie

CNRS - Centre national de la recherche scientifique

Année

2022

Date de référencement

29/09/2023

Mots clés
2a 93 commercialized influenza genomes clade qpcr 2a1b 3c virus assays
Métrique

Résumé

As for the case of SARS-CoV-2, genome sequencing of influenza viruses is of potential interest to raise and address virological issues.

Recently, false-negativity of real-time reverse transcription-PCR (qPCR) assays that detect influenza A/H3N2 virus RNA were reported and associated with two mutations (A37T and C161T) in the Matrix-encoding (M1) gene located on viral segment 7.

This triggered a national alert in France.

The present study sought to assess the association between the presence of these mutations and potential false negative results of influenza A/H3N2 virus RNA detection by commercialized qPCR assays at the clinical virology laboratory of our university hospitals in southern France.

This study focused on the genetic diversity in the M1 gene and segment 7 of 624 influenza A/H3N2 virus genomes obtained from respiratory samples having tested qPCR-positive with M1 gene-targeting assays in our clinical virology laboratory.

A total of 585 among the 624 influenza A/H3N2 virus genomes (93.7%) were of clade 3C.2a1b.2a.2, and 39 (6.3%) were of clade 3C.2a1b.1a. M1 gene substitutions A37T and C161T were both present in 582 (93.3%) genomes, only of clade 3C.2a1b.2a.2.

Substitution A37T was present in 621 (99.5%) genomes.

Substitution C161T was present in 585 genomes (93.8%), all of clade 3C.2a1b.2a.2.

Moreover, 21 other nucleotide positions were mutated in ≥90% of the genomes.

The present study shows that A37T/C and C161T mutations, and other mutations in the M1 gene and segment 7, were widely present in influenza A/H3N2 virus genomes recovered from respiratory samples diagnosed qPCR-positive with commercialized assays.

Le Targa, Lorlane,Hikmat, Houmadi,Boschi, Céline,La Scola, Bernard,Colson, Philippe, 2022, Matrix-Encoding Gene Diversity of 624 Influenza A/H3N2 Genomes Does Not Show Association with Impaired Viral Detection by Commercialized qPCR Assays, HAL CCSD;MDPI

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