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Päll T, Abroi A, Avi R, Niglas H, Shablinskaja A, Pauskar M, Jõgeda EL, Soeorg H, Kallas E, Lahesaare A, Truusalu K, Hoidmets D, Sadikova O, Ratnik K, Sepp H, Dotsenko L, Epštein J, Suija H, Kaarna K, Smit S, Milani L, Metspalu M, Oopkaup OE, Koppel I, Jaaniso E, Kuzmin I, Inno H, Raudvere U, Härma MA, Naaber P, Reisberg T, Peterson H, Talas UG, Lutsar I, Huik K. SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic. PLoS One 2024; 19:e0303176. [PMID: 38728305 PMCID: PMC11086870 DOI: 10.1371/journal.pone.0303176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 04/20/2024] [Indexed: 05/12/2024] Open
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.
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Affiliation(s)
- Taavi Päll
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Aare Abroi
- Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Radko Avi
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Heiki Niglas
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Arina Shablinskaja
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Merit Pauskar
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ene-Ly Jõgeda
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hiie Soeorg
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eveli Kallas
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | | | - Kai Truusalu
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Dagmar Hoidmets
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Olga Sadikova
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | | | - Hanna Sepp
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Liidia Dotsenko
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Jevgenia Epštein
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Heleene Suija
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Katrin Kaarna
- Clinical Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Tartu University Hospital, Tartu, Estonia
| | - Steven Smit
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Mait Metspalu
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ott Eric Oopkaup
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivar Koppel
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Erik Jaaniso
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Heleri Inno
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mari-Anne Härma
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Paul Naaber
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- SYNLAB Eesti OÜ, Tallinn, Estonia
| | - Tuuli Reisberg
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ulvi Gerst Talas
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Irja Lutsar
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristi Huik
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Funk T, Pharris A, Spiteri G, Bundle N, Melidou A, Carr M, Gonzalez G, Garcia-Leon A, Crispie F, O'Connor L, Murphy N, Mossong J, Vergison A, Wienecke-Baldacchino AK, Abdelrahman T, Riccardo F, Stefanelli P, Di Martino A, Bella A, Lo Presti A, Casaca P, Moreno J, Borges V, Isidro J, Ferreira R, Gomes JP, Dotsenko L, Suija H, Epstein J, Sadikova O, Sepp H, Ikonen N, Savolainen-Kopra C, Blomqvist S, Möttönen T, Helve O, Gomes-Dias J, Adlhoch C. Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021. Euro Surveill 2021; 26:2100348. [PMID: 33890566 PMCID: PMC8063589 DOI: 10.2807/1560-7917.es.2021.26.16.2100348] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
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).
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Affiliation(s)
- Tjede Funk
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anastasia Pharris
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Gianfranco Spiteri
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Nick Bundle
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Angeliki Melidou
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Michael Carr
- National Virus Reference Laboratory (NVRL), University College Dublin, Dublin, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Gabriel Gonzalez
- National Virus Reference Laboratory (NVRL), University College Dublin, Dublin, Ireland
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Alejandro Garcia-Leon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland on behalf of the All Ireland Infectious Diseases (AIID) Cohort
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland on behalf of the Irish Coronavirus Sequencing Consortium (ICSC)
| | - Lois O'Connor
- Health Service Executive - Health Protection Surveillance Centre (HPSC), Dublin, Ireland
| | - Niamh Murphy
- Health Service Executive - Health Protection Surveillance Centre (HPSC), Dublin, Ireland
| | | | | | | | | | | | | | | | | | | | - Pedro Casaca
- Directorate of Analysis and Information, Directorate-General of Health, Lisbon, Portugal
| | - Joana Moreno
- Directorate of Analysis and Information, Directorate-General of Health, Lisbon, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Rita Ferreira
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | | | | | | | | | | | - Niina Ikonen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Carita Savolainen-Kopra
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Soile Blomqvist
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Teemu Möttönen
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Otto Helve
- Finnish Institute for Health and Welfare (THL), Department of Health Security, Helsinki, Finland
| | - Joana Gomes-Dias
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Cornelia Adlhoch
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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