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

by 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

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.

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.

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.

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.