Letter: liver transplantation for acute HEV infection in cirrhotic patients in France

International audienceno abstrac

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

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

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

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

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

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) β (B.1.351 lineage) and/or γ (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 β’s immune evasion abilities and high proportions of prior-SARS-CoV-2-infected persons in these regions

Cinétique intra-hôte des variants du SARS-CoV2

International audienceSince early 2021, SARS-CoV-2 variants of concern (VOCs) have been causing epidemic rebounds in many countries. Their properties are well characterised at the epidemiological level but the potential underlying within-host determinants remain poorly understood. We analyse a longitudinal cohort of 6,944 individuals with 14,304 cycle threshold (Ct) values of RT-qPCR VOC screening tests performed in the general population and hospitals in France between February 6 and August 21, 2021. To convert Ct values into numbers of virus copies, we performed an additional analysis using droplet digital PCR (ddPCR). We find that the number of viral genome copies reaches a higher peak value and has a slower decay rate in infections caused by Alpha variant compared to that caused by historical lineages. Following the evidence that viral genome copies in upper respiratory tract swabs are informative on contagiousness, we show that the kinetics of the Alpha variant translate into significantly higher transmission potentials, especially in older populations. Finally, comparing infections caused by the Alpha and Delta variants, we find no significant difference in the peak viral copy number. These results highlight that some of the differences between variants may be detected in virus load variations.Depuis le début de l'année 2021, les variants préoccupants du SRAS-CoV-2 (VOC) provoquent des rebonds épidémiques dans de nombreux pays. Leurs propriétés sont bien caractérisées au niveau épidémiologique, mais les déterminants potentiels au niveau intra-hôte restent mal compris. Nous analysons une cohorte longitudinale de 6 944 individus avec 14 304 valeurs de cycle threshold (Ct) de tests de dépistage des COV par RT-qPCR réalisés dans la population générale et les hôpitaux en France entre le 6 février et le 21 août 2021. Pour convertir les valeurs Ct en nombre de copies virales, nous avons effectué une analyse supplémentaire en utilisant la PCR digitale. Nous constatons que le nombre de copies du génome viral atteint un pic plus élevé et présente un taux de décroissance plus lent dans les infections causées par le variant Alpha par rapport à celles causées par les lignées historiques. En se basant sur certaines observations montrant que le nombre copies virales dans les écouvillons des voies respiratoires supérieures sont informatives sur la contagiosité, nous montrons que la cinétique du variant Alpha se traduit par des potentiels de transmission significativement plus élevés, en particulier dans les populations plus âgées. Enfin, en comparant les infections causées par les variants Alpha et Delta, nous ne trouvons pas de différence significative dans le nombre maximal de copies virales. Ces résultats soulignent que certaines des différences entre les variants peuvent être détectées dans les variations de la charge virale