Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Roquebert B

PROVIDER: S-EPMC8484004 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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

Roquebert Benedicte B Haim-Boukobza Stéphanie S Trombert-Paolantoni Sabine S Lecorche Emmanuel E Verdurme Laura L Foulongne Vincent V Burrel Sonia S Alizon Samuel S Sofonea Mircea T MT

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 20211001

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 th ...[more]

PMID: 34601145

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Project description:IntroductionThe emergence of novel SARS-CoV-2 has caused a pandemic of Coronavirus Disease 19 (COVID-19) which has spread exponentially worldwide. A robust surveillance system is essential for correct estimation of the disease burden and containment of the pandemic. We evaluated the performance of COVID-19 case-based surveillance system in FCT, Nigeria and assessed its key attributes.MethodsWe used a cross-sectional study design, comprising a survey, key informant interview, record review and secondary data analysis. A self-administered, semi-structured questionnaire was administered to key stakeholders to assess the attributes and process of operation of the surveillance system using CDC's Updated Guidelines for Evaluation of Public Health Surveillance System 2001. Data collected alongside surveillance data from March 2020 to January 2021 were analyzed and summarized using descriptive statistics.ResultsOut of 69,338 suspected cases, 12,595 tested positive with RT-PCR with a positive predictive value (PPV) of 18%. Healthcare workers were identified as high-risk group with a prevalence of 23.5%. About 82% respondents perceived the system to be simple, 85.5% posited that the system was flexible and easily accommodates changes, 71.4% reported that the system was acceptable and expressed willingness to continue participation. Representativeness of the system was 93%, stability 40%, data quality 56.2% and timeliness 45.5%, estimated result turnaround time (TAT) was suboptimal.ConclusionThe system was found to be useful, simple, flexible, sensitive, acceptable, with good representativeness but the stability, data quality and timeliness was poor. The system meets initial surveillance objectives but rapid expansion of sample collection and testing sites, improvement of TAT, sustainable funding, improvement of electronic database, continuous provision of logistics, supplies and additional trainings are needed to address identified weaknesses, optimize the system performance and meet increasing need of case detection in the wake of rapidly spreading pandemic. More risk-group persons should be tested to improve surveillance effectiveness.

Dataset Information

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

Publications

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

Similar Datasets

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