RESUMEN
Phylodynamic analyses 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.
RESUMEN
We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmission advantage of the Omicron variant over the Delta variant is +105% (95% confidence interval: 96-114%). Based on these data, we use mechanistic mathematical modelling to explore scenarios for early 2022.
RESUMEN
Analysing 9,030 variant-specific tests performed on SARS-CoV-2 positive samples collected in France between 31 May and 21 June 2021 reveals a rapid growth of the {delta} variant in 3 French regions. The next weeks will prove decisive but the magnitude of the estimated transmission advantages could represent a major challenge for public health authorities.
RESUMEN
SARS-CoV-2 variants threaten our ability to control COVID-19 epidemics. We analyzed 36,590 variant-specific RT-PCR tests performed on samples collected between April 12 and May 7, 2021 in France to compare variant spread. Contrarily to January to March 2021, we found that the V2 variant had a significant transmission advantage over V1 in some regions (15.1 to 16.1% in Ile-de-France and 16.1 to 18.8% in Hauts-de-France). This shift in transmission advantage is consistent with the immune evasion abilities of V2 and the high levels of immunization in these regions.
RESUMEN
SARS-CoV-2 variants raise concern regarding the mortality caused by COVID-19 epidemics. We analyse 88,375 cycle amplification (Ct) values from variant-specific 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 V1 variant and that its transmission advantage over wild type strains was between 38 and 44%. We also find that tests positive for V1 and V2/V3 variants exhibit significantly lower cycle threshold (Ct) values.
RESUMEN
SARS-CoV-2 variants raise major concerns regarding the control of COVID-19 epidemics. We analyse 40,000 specific RT-PCR tests performed on SARS-CoV-2-positive samples collected between Jan 26 and Feb 16, 2021. We find a high transmission advantage of variants and show that their spread in the country is more advanced than anticipated.