Project description: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.
Project description:We compared vaccine effectiveness against severe COVID-19 between December 2021 and March 2022 when Omicron BA.1 and BA.2 were the dominating SARS-CoV-2 variants in Scania county, Sweden. Effectiveness remained above 80% after the transition from BA.1 to BA.2 among people with at least three vaccine doses but the point estimate decreased markedly to 54% among those with only two doses. Protection from prior infection was also lower after the transition to BA.2. Booster vaccination seems necessary to maintain sufficient protection.
Project description:Our analysis of data collected from multiple epidemics in Hong Kong indicated a shorter serial interval and generation time of infections with the SARS-CoV-2 Omicron variant. The age-specific case-fatality risk for Omicron BA.2.2 case-patients without complete primary vaccination was comparable to that of persons infected with ancestral strains in earlier waves.
Project description:The largest wave of infection with SARS-CoV-2 virus in Ecuador was observed in mid-December 2021 and early January 2022, driven by B.1.1.529/BA (Omicron) variant. During the second half of March, an increase in the number of daily cases was observed and coincided with the emergence of the BA.2 variant, which we describe in the present study. The first sequenced five cases of SARS-CoV-2 21L/BA.2 in Ecuador were identified using variant specific genotyping by qPCR and confirmed by whole genome sequencing (WGS). The first sequenced Ecuadorian BA.2 isolate was obtained from a person with international travel history who became symptomatic 3 days after travelling, whereas in the other cases no travel history was recorded.
Project description:Between 9 December 2021 and 15 March 2022, 2,653 highly pathogenic avian influenza (HPAI) virus detections were reported in 33 EU/EEA countries and the UK in poultry (1,030), in wild (1,489) and in captive birds (133). The outbreaks in poultry were mainly reported by France (609), where two spatiotemporal clusters have been identified since October 2021, followed by Italy (131), Hungary (73) and Poland (53); those reporting countries accounted together for 12.8 of the 17.5 million birds that were culled in the HPAI affected poultry establishments in this reporting period. The majority of the detections in wild birds were reported by Germany (767), the Netherlands (293), the UK (118) and Denmark (74). HPAI A(H5) was detected in a wide range of host species in wild birds, indicating an increasing and changing risk for virus incursion into poultry farms. The observed persistence and continuous circulation of HPAI viruses in migratory and resident wild birds will continue to pose a risk for the poultry industry in Europe for the coming months. This requires the definition and the rapid implementation of suitable and sustainable HPAI mitigation strategies such as appropriate biosecurity measures, surveillance plans and early detection measures in the different poultry production systems. The results of the genetic analysis indicate that the viruses currently circulating in Europe belong to clade 2.3.4.4b. Some of these viruses were also detected in wild mammal species in the Netherlands, Slovenia, Finland and Ireland showing genetic markers of adaptation to replication in mammals. Since the last report, the UK reported one human infection with A(H5N1), China 17 human infections with A(H5N6), and China and Cambodia 15 infections with A(H9N2) virus. The risk of infection for the general population in the EU/EEA is assessed as low, and for occupationally exposed people, low to medium.
Project description:Since the first reports in summer 2020, SARS-CoV-2 reinfections have raised concerns about the immunogenicity of the virus, which will affect SARS-CoV-2 epidemiology and possibly the burden of COVID-19 on our societies in the future. This study provides data on the frequency and characteristics of possible reinfections, using the French national COVID-19 testing database. The Omicron variant had a large impact on the frequency of possible reinfections in France, which represented 3.8% of all confirmed COVID-19 cases since December 2021.