9 research outputs found

    Rapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021

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    International audienceWe analysed 9,030 variant-specific RT-PCR tests performed on SARS-CoV-2-positive samples collected in France between 31 May and 21 June 2021. This analysis revealed rapid growth of the Delta variant in three of the 13 metropolitan French regions and estimated a +79% (95% confidence interval: 52–110%) transmission advantage compared with the Alpha variant. The next weeks will prove decisive and the magnitude of the estimated transmission advantages of the Delta variant could represent a major challenge for public health authorities

    The SARS-CoV-2 B.1.351 lineage (VOC ÎČ) is outgrowing the B.1.1.7 lineage (VOC α) in some French regions in April 2021

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    International audienceTo assess SARS-CoV-2 variants spread, we analysed 36,590 variant-specific reverse-transcription-PCR tests performed on samples from 12 April–7 May 2021 in France. In this period, contrarily to January–March 2021, variants of concern (VOC) ÎČ (B.1.351 lineage) and/or Îł (P.1 lineage) had a significant transmission advantage over VOC α (B.1.1.7 lineage) in Île-de-France (15.8%; 95% confidence interval (CI): 15.5–16.2) and Hauts-de-France (17.3%; 95% CI: 15.9–18.7) regions. This is consistent with VOC ÎČ’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions

    COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences

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    International audiencePhylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest

    Detecting Rapid Spread of SARS-CoV-2 Variants, France, January 26–February 16, 2021

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    International audienceVariants of severe acute respiratory syndrome coronavirus 2 raise concerns regarding the control of coronavirus disease epidemics. We analyzed 40,000 specific reverse transcription PCR tests performed on positive samples during January 26–February 16, 2021, in France. We found high transmission advantage of variants and more advanced spread than anticipated

    SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

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    International audienceSARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplication (Ct) values from variant-specic RT-PCR tests performed between January 26 and March 13, 2021. We estimate that on March 12, nearly 85% of the infections were caused by the Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also nd that tests positive for Alpha and Beta/Gamma variants exhibit signicantly lower cycle threshold (Ct) values

    Epidemiological and clinical study of microsporidiosis in French kidney transplant recipients from 2005 to 2019: TRANS‐SPORE registry

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    International audienceMicrosporidiosis is an emerging opportunistic infection in renal transplantation (RT) recipients. We aimed to describe its clinical presentation and treatment
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