key: cord-0712717-bavbzplh authors: Houhamdi, Linda; Gautret, Philippe; Hoang, Van Thuan; Fournier, Pierre‐Edouard; Colson, Philippe; Raoult, Didier title: Characteristics of the first 1119 SARS‐CoV‐2 Omicron variant cases, in Marseille, France, November−December 2021 date: 2022-02-03 journal: J Med Virol DOI: 10.1002/jmv.27613 sha: 7883065913fea9c6efa21401e14899776877dac3 doc_id: 712717 cord_uid: bavbzplh One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) Omicron variant cases have been diagnosed at the Institut Hospitalo‐Universitaire Méditerranée Infection, Marseille, France, between November 28, 2021, and December 31, 2021. Among the 825 patients with known vaccination status, 383 (46.4%) were vaccinated, of whom 91.9% had received at least two doses of the vaccine. Interestingly, 26.3% of cases developed SARS‐CoV‐2 infection within 21 days following the last dose of vaccine suggesting possible early production of anti‐SARS‐CoV‐2 facilitating antibodies. Twenty‐one patients have been hospitalized, one patient required intensive care, and another patient who received a vaccine booster dose died. were fully vaccinated and experienced clinically-mild infections. 2, 3 The objective of this study was to describe the first 1119 Omicron cases diagnosed at the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection located in Marseille, France that manages the vast majority of patients in the area and to provide preliminary information on its severity. We conducted a single-center retrospective cohort study at IHU Méditerranée Infection, which is part of the network of public hospitals in Marseille (AP-HM). All available SARS-CoV-2 positive results obtained by our laboratory between November 28, 2021 (the date of the first identification of the Omicron variant) and SARS-CoV-2 genotyping was performed from nasopharyngeal samples as previously described. 4 The Omicron variant was identified first by the absence of detection of amino acid substitutions L452R and P681R with TaqMan SARS-CoV-2 mutation assays (Thermo Fisher Scientific) and by positivity of ORF1 and N genes but negativity of the S gene with the TaqPath COVID-19 kit (Thermo Fisher Scientific). 4, 5 Then, SARS-CoV-2 genomes were obtained and analyzed as previously described. 4 Briefly, next-generation sequencing was performed using either the Illumina COVID-seq protocol and the NovaSeq. 6000 instrument (Illumina Inc.) or the Oxford Nanopore Technology (ONT) and the GridION instrument (Oxford Nanopore Technologies Ltd.). Genome sequences were assembled by mapping on the SARS-CoV-2 genome GenBank accession no. NC_045512.2 (Wuhan-Hu-1 isolate) using Minimap2 (https://github.com/lh3/ minimap2). 6 Samtools (https://www.htslib.org/) were used to soft clip primers (https://artic.network/) and remove sequence duplicates. 7 Consensus genomes were generated using Sam2consensus (https://github.com/vbsreenu/Sam2Consensus) through a first inhouse script written in Python language (https://www.python.org/). Mutation detection was performed with Nextclade web application (https://clades.nextstrain.org/) 8 and freebayes (https://github.com/ freebayes/freebayes). 9 SARS-CoV-2 genotype was determined with a second in-house Python script. Nextstrain clades and Pangolin lineages were determined using Nextclade and Pangolin web application (https://cov-lineages.org/pangolin.html), 10 respectively. Genome sequences were deposited in the GISAID sequence database (https://www.gisaid.org/). 11 Demographics and clinical data retrospectively obtained from electronic medical files were anonymized before analysis ( We observed a rapid increase in the proportion of the SARS-CoV-2 Omicron variant among SARS-CoV-2-infected patients during December 2021, exceeding the Delta variant at the end of 2021 and supporting its higher transmissibility. 3 Unfortunately, we are unable to calculate the transmission dynamics due to the lack of necessary epidemiological data. It has been hypothesized that superspreading events may account for the increased transmissibility of the Omicron variant. 2 High-Technologies Corporation, Tokyo, Japan from 2018 to 2020. The remaining authors declare that there are no conflict of interests. Didier Raoult designed the study. Linda Houhamdi, Philippe Gautret, Philippe Colson, and Didier Raoult wrote the paper. All authors contributed to materials/analysis, reviewed, and approved the manuscript. The authors confirm that the data supporting the findings of this study are available within the article. COVID-19: point épidémiologique du 30 décembre 2021 Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark Outbreak caused by the SARS-CoV-2 Omicron variant in Norway Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics. 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Antibody-dependent enhancement and SARS-CoV-2 vaccines and therapies The puzzling mutational landscape of the SARS-2-variant Omicron Characteristics of the first 1119 SARS-CoV-2 Omicron variant cases