Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022

Hiie Soeorg; Aare Abroi; Taavi Päll; Liidia Dotsenko; Erik Jaaniso; Katrin Kaarna; Andrio Lahesaare; Paul Naaber; Heiki Niglas; Ott Eric Oopkaup; Hedi Peterson; Tuuli Reisberg; Olga Sadikova; Steven Smit; Ulvi Gerst Talas; Radko Avi; Irja Lutsar; Kristi Huik

doi:10.1371/journal.pone.0316213

Dynamics of SARS-CoV-2 lineages in children and adults in 2021 and 2022

PLoS One. 2024 Dec 20;19(12):e0316213. doi: 10.1371/journal.pone.0316213. eCollection 2024.

Authors

Hiie Soeorg^{1

2}, Aare Abroi³, Taavi Päll¹, Liidia Dotsenko⁴, Erik Jaaniso⁵, Katrin Kaarna^{6

7}, Andrio Lahesaare⁸, Paul Naaber^{1

8}, Heiki Niglas⁴, Ott Eric Oopkaup⁹, Hedi Peterson⁵, Tuuli Reisberg¹⁰, Olga Sadikova⁴, Steven Smit¹⁰, Ulvi Gerst Talas⁹, Radko Avi¹, Irja Lutsar¹, Kristi Huik¹

Affiliations

¹ Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
² Infection, Immunity and Inflammation Research & Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.
³ Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia.
⁴ Department of Communicable Diseases, Health Board, Tallinn, Estonia.
⁵ Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia.
⁶ Clinical Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.
⁷ Tartu University Hospital, Tartu, Estonia.
⁸ SYNLAB Eesti OÜ, Tallinn, Estonia.
⁹ High Performance Computing Center, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia.
¹⁰ Faculty of Science and Technology, Institute of Genomics, University of Tartu, Tartu, Estonia.

Abstract

Purpose: We aimed to describe SARS-CoV-2 lineages and diversity in children and adults in Estonia and similarity to travel-related cases and neighbouring countries.

Methods: SARS-CoV-2 sequences in 2021-2022 from a nationwide study were included. The proportion of predominant lineages in Estonian regions and among travel-related cases was described by multinomial logistic regression. Simpson's indices of diversity were compared using linear regression. Dynamics of Bray-Curtis dissimilarity was described by applying fuzzy clustering to non-metrical dimensional scaling results.

Results: A total of 2,630 sequences from children (<15 years) and 23,031 from adults (≥15 years) were included. The increase in the proportion of Alpha/Delta/Omicron BA.1/BA.2 lineages was delayed in smaller regions (by 3.5-27.5 days). The proportion of Alpha/Delta/Omicron BA.1 increased earlier among travel-related (n = 4,654) than non-travel-related cases (10.5 days). Diversity was lower in non-travel-related than travel-related cases until Delta period by 0.066. Dynamics of lineages and diversity were similar in adults and children. Similarity of lineages was delayed compared to Finland during Alpha/Omicron BA.1/BA.2 periods and different from all neighbouring countries during Delta period.

Conclusion: SARS-CoV-2 lineages in children and adults were similar. Differences between regions and travel-related cases and varying similarity to neighbouring countries suggest the importance of mobility in the spread.

Copyright: © 2024 Soeorg et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

MeSH terms

Adolescent
Adult
COVID-19* / epidemiology
COVID-19* / virology
Child
Child, Preschool
Estonia / epidemiology
Female
Humans
Male
Middle Aged
Phylogeny
SARS-CoV-2* / genetics
SARS-CoV-2* / isolation & purification
Travel
Young Adult

Grants and funding

This work is part of the VERDI project (101045989), which is funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. The work described in this manuscript was co-financed through the DURABLE project. The DURABLE project has been co-funded by the European Union, under the EU4Health Programme (EU4H), Project no. 101102733. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or the European Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. The work described in this manuscript was co-financed by the European Union through HORIZON Coordination and Support Actions under grant agreement № 101079349 “Boosting the One Health Research Excellence and Management Capacity of the Estonian University of Life Sciences. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. https://european-union.europa.eu/index_en The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.