Investigating the first stage of the COVID-19 pandemic in Ukraine using epidemiological and genomic data

Abstract

The novel coronavirus SARS-CoV-2 emerged in China in December 2019 and has rapidly spread around the globe. The World Health Organization declared COVID-19 a pandemic in March 2020 just three months after the introduction of the virus. Individual nations have implemented and enforced with varying degrees of success a variety of social distancing interventions to slow the virus spread. Investigating the role of non-pharmaceutical interventions on COVID-19 transmission in different settings is an important research. While most transmission modeling studies have focused on the dynamics in China, neighboring Asian counties, Western Europe, and North America, there is a scarcity of studies for Eastern Europe. This study starts to fill this gap by analyzing the characteristics of the first epidemic wave in Ukraine using mathematical and statistical models together with epidemiological and genomic sequencing data. Using an agent-based model, the trajectory of the first wave in terms of cases and deaths and explore the impact of quarantine strategies via simulation studies have been characterized. The implemented stochastic model for epidemic counts suggests, that even a small delay of weeks could have increased the number of cases by up to 50\%, with the potential to overwhelm hospital systems. The genomic data analysis suggests that there have been multiple introductions of SARS-CoV-2 into Ukraine during the early stages of the epidemic with eight distinct transmission clusters identified. The basic reproduction number for the epidemic has been estimated independently both from case counts data and from genomic data. The findings support the hypothesis that, the public health measures did not have a decreasing effect on the existing viral population number at the time of implementation, since strains were detected after the quarantine date. However, the public health measures did help to prevent the appearance of new (and potentially more virulent) SARS-CoV-2 variants in Ukraine.

SARS-CoV-2 transmission dynamics in Belarus in 2020 revealed by genomic and incidence data analysis

“…The median UkrainianR e over the same time period was estimated to beR e ¼ 1:64 (95% HPD interval: (1.49; 1.81)). This assessment agrees with the previous estimation based on the Exponential Coalescent model 46 and appeared to be comparable tô R e estimates for Belarus. Numbers of sequences (Y-axis) in 11 genomic lineages present in Belarus (X-axis).…”

“…The same Birth-Death Skyline Serial model was applied to two best-sampled Ukrainian clusters with a total of 28 sequences defined as in ref. 46 (Table S3). The median UkrainianR e over the same time period was estimated to beR e ¼ 1:64 (95% HPD interval: (1.49; 1.81)).…”

Tracking SARS-COV-2 Variants Using Nanopore Sequencing in Ukraine in Summer 2021

“…Currently, only one study on the phylodynamic analysis of the SARS-CoV-2 sequences obtained from Ukrainian patients has been reported, describing the rst four months of the pandemic. It showed that the initial rise in the number of COVID-19 cases was likely led by multiple independent introductions of the virus into Ukraine prior to border closures [27], similar to the ndings of the importation and circulation of SARS-CoV-2 lineages in the UK [7]. For the rst time, our study aimed to build local and sustainable SARS-COV-2 sequencing capacity and genomic epidemiology expertise in Kyiv, Ukraine using the Nanopore MinION sequencing platform.…”

“…Ukraine has experienced three COVID-19 epidemic waves between the identi cation of the rst case on March 3rd 2020 and at the time of writing. Compared to other European countries, the epidemic waves in Ukraine were lagging behind by several months as Ukraine did not experience many cases in spring 2020, likely due to a combination of a timely lockdown and a restriction of movement policy [27,28]. The border closure was applied to both foreign citizens and Ukrainian nationals in March 2020, three weeks after the rst case was diagnosed in the country.…”

SARS-CoV-2 transmission dynamics in Belarus revealed by genomic and incidence data analysis

“…The obtained HPD intervals, however, are rather wide due to the relatively small genome sample size. Thus, we also to two best-sampled Ukrainian clusters with the total of 28 sequences defined as in [25] 202 (Supplemental Table S3). The median UkrainianR e over the same tine period was es- The results of the complementary analysis based on the number of officially reported cases D(t) and conducted tests T (t) over time are presented in Fig.…”