We 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.
Variants 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.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We analyzed 324,734 SARS-CoV-2 variant screening tests from France enriched with 16,973 whole-genome sequences sampled during September 1, 2021-February 28, 2022. Results showed the estimated growth ...advantage of the Omicron variant over the Delta variant to be 105% (95% CI 96%-114%) and that of the BA.2 lineage over the BA.1 lineage to be 49% (95% CI 44%-52%). Quantitative PCR cycle threshold values were consistent with an increased ability of Omicron to generate breakthrough infections. Epidemiologic modeling shows that, in spite of its decreased virulence, the Omicron variant can generate important critical COVID-19 activity in hospitals in France. The magnitude of the BA.2 wave in hospitals depends on the level of relaxing of control measures but remains lower than that of BA.1 in median scenarios.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Standardized, reproducible and validated Mucorales quantitative PCR (qPCR) assays are needed in the context of routine testing in diagnostic labs. We, therefore, compared the commercial MucorGenius® ...assay (PathoNostics, Maastricht) targeting five genera of Mucorales to our in-house qPCR targeting Rhizomucor spp., Lichtheimia spp. and Mucor/Rhizopus spp. To assess their analytical sensitivity, 25 frozen leftover serum specimens, which had already tested positive based on our in-house assay, were selected. These sera were from 15 patients with probable or proven mucormycosis. For analytical specificity, 0.5 pg from 15 purified fungal DNAs from nine different Mucorales genera were spiked into pooled qPCR-negative leftover serum specimens. All samples were tested in parallel with both assays and the quantitative cycles (Cq) were compared. A total of 13/25 (52%) serum samples were amplified by one of the two assays with only four of them detected with the MucorGenius® assay. In spiked specimens, all targeted strains were successfully amplified by our in-house qPCR. The MucorGenius® assay was not able to detect Lichtheimia corymbifera but successfully amplified all other species targeted by the kit and two additional non-targeted species (Syncephalastrum monosporum and Saksenaea vasiformis). The MucorGenius® assay showed lower analytical sensitivity compared to our in-house assay. Indeed, the MucorGenius® assay amplified more species, as expected, but showed a decreased detection of the frequent species Lichtheimia corymbifera.
•SARS-CoV-2 variants replaced the wild type in France between January and March 2021•The Alpha variant is associated with a 40% increase in transmission on average•The mean transmission advantage of ...the Beta/Gamma variants is estimated to 28%•Infections by SARS-CoV-2 Alpha, Beta and Gamma variants exhibit lower Ct values•These results suggest these variants have a double viral load compared to wild type
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 Alpha variant and that its transmission advantage over wild type strains was between 38 and 44%. We also find that tests positive for Alpha and Beta/Gamma variants exhibit significantly lower cycle threshold (Ct) values.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
From April 2023 to May 2024, an unusual epidemic of parvovirus B19 (B19V) infections occurred in France. The number of B19V IgM-positive serologies was four times higher than in the previous epidemic ...in 2019. Clinical data from emergency networks corroborated this observation. Morbidity and mortality consequences were observed in children through all data sources. In adults, the increase was only observed in laboratory-confirmed data. Physicians and decisionmakers should be informed in order to better prevent, diagnose and manage at-risk patients.
Phylodynamic 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.
In 2023, dengue virus serotype 2 (DENV2) affected most French overseas territories. In the French Caribbean Islands, viral circulation continues with > 30,000 suspected infections by March 2024. ...Genome sequence analysis reveals that the epidemic lineage in the French Caribbean islands has also become established in French Guiana but not Réunion. It has moreover seeded autochthonous circulation events in mainland France. To guide prevention of further inter-territorial spread and DENV introduction in non-endemic settings, continued molecular surveillance and mosquito control are essential.
BackgroundSuccessive epidemic waves of COVID-19 illustrated the potential of SARS-CoV-2 variants to reshape the pandemic. Detecting and characterising emerging variants is essential to evaluate their ...public health impact and guide implementation of adapted control measures.AimTo describe the detection of emerging variant, B.1.640, in France through genomic surveillance and present investigations performed to inform public health decisions.MethodsIdentification and monitoring of SARS-CoV-2 variant B.1.640 was achieved through the French genomic surveillance system, producing 1,009 sequences. Additional investigation of 272 B.1.640-infected cases was performed between October 2021 and January 2022 using a standardised questionnaire and comparing with Omicron variant-infected cases.ResultsB.1.640 was identified in early October 2021 in a school cluster in Bretagne, later spreading throughout France. B.1.640 was detected at low levels at the end of SARS-CoV-2 Delta variant's dominance and progressively disappeared after the emergence of the Omicron (BA.1) variant. A high proportion of investigated B.1.640 cases were children aged under 14 (14%) and people over 60 (27%) years, because of large clusters in these age groups. B.1.640 cases reported previous SARS-CoV-2 infection (4%), anosmia (32%) and ageusia (34%), consistent with data on pre-Omicron SARS-CoV-2 variants. Eight percent of investigated B.1.640 cases were hospitalised, with an overrepresentation of individuals aged over 60 years and with risk factors.ConclusionEven though B.1.640 did not outcompete the Delta variant, its importation and continuous low-level spread raised concerns regarding its public health impact. The investigations informed public health decisions during the time that B.1.640 was circulating.
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