Genomic Epidemiology of SARS-CoV-2 in Ukraine from May 2022 to March 2024 Reveals Omicron Variant Dynamics

Abstract

In Ukraine, SARS-CoV-2 detection and national genomic surveillance have been complicated by full-scale war, limited resources, and varying levels of public health infrastructure impacted across the country. Following the Spring of 2022, only a paucity of data have been reported describing the prevalence and variant dynamics of SARS-CoV-2 in the country. Comparative whole genome analysis has overtaken diagnostics as the new gold standard for detecting and tracing emerging variants while showing utility to rapidly inform diagnostics, vaccine strategies, and health policy. Herein, we provide an updated report characterizing the dynamics and prevalence of SARS-CoV-2 in Ukraine from 1 May 2022 to 31 March 2024. The present study extends previous reports for disease incidence Waves 1-4 in Ukraine with the addition herein of Waves 5, 6, and 7, occurring from August to November 2022 (Wave 5), February to May 2023 (Wave 6), and October 2023 to January 2024 (Wave 7). During the study period, the national Case Fatality Rate (CFR) fluctuated between 0.46% and 1.74%, indicating a consistent yet modest rate when compared to the global average. The epidemiological dynamics of Variants of Concern (VOCs) in Ukraine reflected global patterns over this period, punctuated by the rise of the BA.5 lineage and its subsequent replacement by the Omicron subvariants XBB and JN.1. Our analysis of variant dispersal patterns revealed multiple potential spatiotemporal introductions into Ukraine from Europe, Asia, and North America. Our results highlight the importance of ongoing genomic surveillance to monitor variant dynamics and support global efforts to control and mitigate COVID-19 disease risks as new variants arise.

Keywords: COVID-19 surveillance; Omicron; SARS-CoV-2; SARS-CoV-2 introductions; genomic epidemiology; genomic surveillance; pandemic; public health; variant dynamics; whole genome sequencing.

Figure 1

Epidemic curve of confirmed COVID-19 cases registered in Ukraine from May 2022 to March 2024. Waves 5–7 are highlighted by colors. Arrows show the first detected cases of the indicated VOC/VOI. The data gap is elaborated in the discussion section. The number of cases is plotted along the y-axis.

Figure 2

Variant frequencies of SARS-CoV-2 samples collected in Ukraine in May 2022–March 2024. The graph shows the monthly variant frequencies as a percentage relative to the total number of sequenced samples per month. Variants per PANGO nomenclature are represented by distinct colors, as indicated in the legend. Sample collection dates are plotted along the x-axis. The percentage of variant frequency relative to the total number of samples per month is plotted along the y-axis. The total number of sequenced samples for each month is shown above the bars (“Month total”).

Figure 3

Phylogenetic relationships among Omicron SARS-CoV-2 genomes included in this study. Phylogenetic reconstructions and clade assignment were performed using the Nextclade web server v3.1.0 under default settings.

Figure 4

Proportions of inferred SARS-CoV-2 introductions into Ukraine by continent of origin, stratified by major clade (BA.5, XBB, JN). The percentage of introductions from different continents relative to the total number of introductions within each clade is plotted along the y-axis.

Figure 5

(A) Number of confirmed cases of COVID-19 by oblasts of Ukraine, May 2022–March 2024. (B) Number of hospitalizations due to COVID-19 by oblasts of Ukraine, May 2022–March 2024. (C) Case Fatality Rate (CFR) for COVID-19 in Ukraine from May 2022 to March 2024, calculated using a 5-week moving average for cases and deaths, with an applied 2-week lag between case and death registration. (D) Scaled number of death cases per week, plotted against the number of confirmed cases per week (left axis for confirmed cases, right axis for death cases). The graph for death cases was magnified using a different scale to make the variability visible.

Figure 6

Correlation between variants and normalized severity metrics. This heatmap illustrates the correlation between SARS-CoV-2 variants and two normalized severity metrics: hospitalization rate (HR) and Case Fatality Rate (CFR) per 100 cases. SARS-CoV-2 variants are displayed chronologically. Correlation coefficients are represented along the x-axis, with red indicating positive correlations (stronger associations with increased severity) and blue showing negative correlations (weaker associations or reduced severity).