First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

Abstract

The SARS-CoV-2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here we describe the first cases diagnosed with this variant in south-eastern France. We identified thirteen cases using variant-specific qPCR and next-generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travellers returning from Tanzania. Overall, viral genomes displayed a mean (+/-standard deviation) number of 65.9+/-2.5 (range, 61-69) nucleotide substitutions and 31.0+/-8.3 (27-50) nucleotide deletions, resulting in 49.6+/-2.2 (45-52) amino acid substitutions (including 28 in the spike protein) and 12.4+/-1.1 (12-15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions pointed out a significant enlargement and flattening of the 21L/BA.2 N-terminal domain surface compared with that of the 21K/BA.2 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.

Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France

“…qPCR assays that screen for SARS-CoV-2 variants were performed as recommended by French public health authorities (https://www.data.gouv.fr/fr/datasets/donnees-de-laboratoires-pour-le-depistage-indicateurs-sur-les-mutations/). In our center this included the detection of spike mutation among which K417N (Thermo Fisher Scientific, Waltham, USA), combined with testing with the TaqPath COVID-19 kit (Thermo Fisher Scientific) that target viral genes ORF1, N (nucleocapsid) and S (spike), as previously reported (Colson et al, 2022b; Colson et al, 2022a). The private medical laboratory used the ID SARS-CoV-2/VOC Revolution Pentaplex assay (ID Solutions, Grabels, France) that detects spike mutations K417N, L452R, and E484K (Pentaplex assay, ID Solution, France).…”

“…SARS-CoV-2 genomes were sequenced in the framework of genomic surveillance implemented since February 2020 (Colson et al, 2022b) in our institute and as recommended by French public health authorities since 2021 (https://www.santepubliquefrance.fr/dossiers/coronavirus-covid-19/consortium-emergen#block-356295). Next-generation sequencing was performed with the Illumina COVID-seq protocol on the NovaSeq 6000 instrument (Illumina Inc., San Diego, CA, USA) or with the Oxford Nanopore technology (ONT) on a GridION instrument (Oxford Nanopore Technologies Ltd., Oxford, UK) combined with prior multiplex PCR amplification according to the ARTIC procedure (https://artic.network/), as previously described (Colson et al, 2022b; Colson et al, 2022a), with the ARTIC nCoV-2019 Amplicon Panel v4.1 of primers (IDT, Coralville, IA, USA). Then, sequence read processing and genome analysis were performed as previously described (Colson et al, 2022b; Colson et al, 2022a).…”

“…Next-generation sequencing was performed with the Illumina COVID-seq protocol on the NovaSeq 6000 instrument (Illumina Inc., San Diego, CA, USA) or with the Oxford Nanopore technology (ONT) on a GridION instrument (Oxford Nanopore Technologies Ltd., Oxford, UK) combined with prior multiplex PCR amplification according to the ARTIC procedure (https://artic.network/), as previously described (Colson et al, 2022b; Colson et al, 2022a), with the ARTIC nCoV-2019 Amplicon Panel v4.1 of primers (IDT, Coralville, IA, USA). Then, sequence read processing and genome analysis were performed as previously described (Colson et al, 2022b; Colson et al, 2022a). Briefly, for Illumina NovaSeq reads, base calling was performed with the Dragen Bcl Convert pipeline [v3.9.3; https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html (Illumina Inc.)], mapping was performed with the bwa-mem2 tool (https://github.com/bwa-mem2/bwa-mem2) on the Wuhan-Hu-1 isolate genome (GenBank accession no.…”

“…This period spanned between December 27 th , 2021 and February 14 th , 2022 in our geographical area, as assessed by our SARS-CoV-2 genotypic surveillance based on variant-specific qPCR and next-generation genomic sequencing. 3,28,29 In January 2022, genomes harboring mutations from both Delta and Omicron 21K/BA.1 variants were reported in Cyprus but it was questioned whether sequences might have resulted from contamination. 23 Still, 15 genomes as of 27/02/2022 being hybrids of these two variants and highly similar between each other were reported since February 2022 (https://github.com/cov-lineages/pango-designation/issues/444).…”

“…Two pandemic variants, Delta and Omicron 21K [Nextclade classification (Aksamentov et al, 2021)]/BA.1 [Pangolin classification (Rambaut et al, 2020)], recently succeeded each other as the predominant viruses but co-circulated for a period of several weeks, creating conditions for co-infections and subsequently recombinations. This period spanned between December 27 th , 2021 and February 14 th , 2022 in our geographical area, as assessed by our SARS-CoV-2 genotypic surveillance based on variant-specific qPCR and next-generation genomic sequencing (Colson et al, 2022b;Colson et al, 2022a). In January 2022, genomes harboring mutations from both Delta and Omicron 21K/BA.1 variants were reported in Cyprus but it was questioned whether sequences might have resulted from contamination (Kreier, 2022).…”