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1.
PLoS One ; 19(5): e0303176, 2024.
Article in English | MEDLINE | ID: mdl-38728305

ABSTRACT

BACKGROUND: The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. METHODS: We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. RESULTS: We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. CONCLUSIONS: COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.


Subject(s)
COVID-19 , Hospitalization , SARS-CoV-2 , Humans , COVID-19/epidemiology , COVID-19/virology , Hospitalization/statistics & numerical data , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , SARS-CoV-2/classification , Male , Female , Middle Aged , Adult , Aged , Estonia/epidemiology , Genome, Viral , Young Adult , Phylogeny , Pandemics , Adolescent , Child , Infant , Child, Preschool , Aged, 80 and over
2.
Euro Surveill ; 27(7)2022 02.
Article in English | MEDLINE | ID: mdl-35177166

ABSTRACT

Despite high COVID-19 vaccine coverage in the EU/EEA, there are increasing reports of SARS-CoV-2 infections and hospitalisations in vaccinated individuals. Using surveillance data from Estonia, Ireland, Luxembourg and Slovakia (January-November 2021), we estimated risk reduction of severe outcomes in vaccinated cases. Increasing age remains the most important driver of severity, and vaccination significantly reduces risk in all ages for hospitalisation (adjusted relative risk (aRR): 0.32; 95% confidence interval (CI): 0.26-0.39) and death (aRR: 0.20; 95% CI: 0.13-0.29).


Subject(s)
COVID-19 , COVID-19 Vaccines , Estonia/epidemiology , Hospitalization , Humans , Ireland/epidemiology , Luxembourg , Risk Reduction Behavior , SARS-CoV-2 , Slovakia/epidemiology
3.
Euro Surveill ; 26(48)2021 12.
Article in English | MEDLINE | ID: mdl-34857068

ABSTRACT

Prioritisation of elderly people in COVID-19 vaccination campaigns aimed at reducing severe outcomes in this group. Using EU/EEA surveillance and vaccination uptake, we estimated the risk ratio of case, hospitalisation and death notifications in people 80 years and older compared with 25-59-year-olds. Highest impact was observed for full vaccination uptake 80% or higher with reductions in notification rates of cases up to 65% (IRR: 0.35; 95% CI: 0.13-0.99), hospitalisations up to 78% (IRR: 0.22; 95% CI: 0.13-0.37) and deaths up to 84% (IRR: 0.16; 95% CI: 0.13-0.20).


Subject(s)
COVID-19 Vaccines , COVID-19 , Aged , Hospitalization , Humans , SARS-CoV-2 , Vaccination
4.
Euro Surveill ; 26(16)2021 04.
Article in English | MEDLINE | ID: mdl-33890566

ABSTRACT

We compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).


Subject(s)
COVID-19 , SARS-CoV-2 , Critical Care , Europe/epidemiology , Humans
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