Uninvited Guest: Arrival and Dissemination of Omicron Lineage SARS-CoV-2 in St. Petersburg, Russia

Abstract

Following its emergence at the end of 2021, the Omicron SARS-CoV-2 variant rapidly spread around the world and became a dominant variant of concern (VOC). The appearance of the new strain provoked a new pandemic wave with record incidence rates. Here, we analyze the dissemination dynamics of Omicron strains in Saint Petersburg, Russia's second largest city. The first case of Omicron lineage BA.1 was registered in St. Petersburg on 10 December 2021. Rapid expansion of the variant and increased incidence followed. The peak incidence was reached in February 2022, followed by an observed decline coinciding with the beginning of spread of the BA.2 variant. SARS-CoV-2 lineage change dynamics were shown in three categories: airport arrivals; clinical outpatients; and clinical inpatients. It is shown that the distribution of lineage BA.1 occurred as a result of multiple imports. Variability within the BA.1 and BA.2 lineages in St. Petersburg was also revealed. On the basis of phylogenetic analysis, an attempt was made to trace the origin of the first imported strain, and an assessment was made of the quarantine measures used to prevent the spread of this kind of infection.

Keywords: COVID-19; Omicron BA.1; Omicron BA.2; Russia; SARS-CoV-2.

Figure 1

Viral lineage dynamics in Pulkovo Airport arrivals with a confirmed COVID-19 diagnosis. Weekly dynamics of SARS-CoV-2 sublineages in arrivals (29 November 2021 to 27 February 2022) are shown.

Figure 2

Viral lineage dynamics in outpatients with a confirmed COVID-19 diagnosis. Weekly dynamics of SARS-CoV-2 sublineages in outpatients, and COVID-19 morbidity in St. Petersburg (3 January 2022 to 1 May 2022), are shown.

Figure 3

Viral lineage dynamics in hospitalized patients with a confirmed COVID-19 diagnosis. Weekly dynamics of SARS-CoV-2 sublineages in inpatients, and COVID-19 morbidity in St. Petersburg (3 January 2022 to 1 May 2022), are shown.

Figure 4

SARS-CoV-2 phylogenetic tree reconstruction of Omicron branches based on Nextclade tools. Strains obtained within this work are in red; strains from Nextstrain database are gray. The scale is in substitutions per site compared to the Wuhan-Hu-1/2019 reference sequence (GenBank: MN908947). 21K in Nextstrain lineage corresponds to BA.1 Pangolin lineage, 22 L lineage corresponds BA.2, 22A lineage corresponds BA.4, 22 B lineage corresponds BA.5, 22C lineage corresponds BA.2.12.1.

Figure 5

Phylogenetic network of SARS-CoV-2 Omicron BA.1 S gene sequences. Circle areas are proportional to the number of taxa, whereas each tick on the links represents a mutated nucleotide position. The median-joining network algorithm (epsilon parameter set to 10) was employed. Clusters are named by one of the sequences forming it. The node pie chart coloring illustrates the proportion of each group in the node. Key: strains introduced to St. Petersburg by Pulkovo Airport arrivals—green; strains from outpatients—orange; strains from inpatients—blue; and South African reference strain (EPI_ISL_6913991)—black.