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. 2023 Jun 22;15(7):1415.
doi: 10.3390/v15071415.

An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia

Galya V Klink  1 , Daria Danilenko  2 , Andrey B Komissarov  2 , Nikita Yolshin  2 , Olga Shneider  2   3 , Sergey Shcherbak  3 , Elena Nabieva  1 , Nikita Shvyrev  4 , Nadezhda Konovalova  2 , Alyona Zheltukhina  2 , Artem Fadeev  2 , Kseniya Komissarova  2 , Andrey Ksenafontov  2 , Tamila Musaeva  2 , Veronika Eder  2 , Maria Pisareva  2 , Petr Nekrasov  2 , Vladimir Shchur  4 , Georgii A Bazykin  1   5 , Dmitry Lioznov  2   6
Affiliations

An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint Petersburg, Russia

Galya V Klink et al. Viruses. .

Abstract

The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021-early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between 16-29 December 2021, which was the earliest known instance of a large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR-positive. Among the 118 residents for whom the variant had been tested by whole-genome sequencing, 111 (94.1%) were found to carry the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported a previous infection of COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sub-lineage of the Omicron variant. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint Petersburg and has spread to other regions of Russia and even to other countries. The rapid spread of the Omicron variant in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.

Keywords: BA.1.1; Russia; SARS-CoV-2; founder effect; outbreak; public facility; superspreading.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
The Russian samples obtained between 3‒30 December 2021 and the Saint Petersburg dormitory outbreak on the global tree of BA.1.1. All 13 non-dormitory GISAID samples from Russia are shown (in red), together with a random sample of 400 (out of 8396) GISAID Omicron samples obtained in other countries (depicted in grey). Clade A, which is defined by the presence of the C5812T mutation, is shown in blue colour with yellow background. A zoom in of clade A including the outbreak samples (blue) is shown on the right, together with 51 descendant non-dormitory samples from Russia (red). Branch lengths are measured in number of mutations.
Figure 2
Figure 2
Skyline plots for the effective reproductive number Re for different values of the molecular clock rate.
Figure 3
Figure 3
The mean phylogenetic distance m between two samples obtained from the same room (A,B) or floor (C) (red), compared to the expected distributions obtained by reshuffling the room labels independent of the floor (A), within the floor (B), or by reshuffling yhr floor labels (C) of the samples. P represents the fraction of reshuffling trials with a mean phylogenetic distance below m. The Y-axis represents the number of reshufflings.
Figure 4
Figure 4
The fraction of clade A, BA.1.1, and Omicron samples among the Russian (A) and Saint Petersburg (B) samples obtained from the GISAID included in the UShER phylogenetic tree downloaded on 26 May 2022. Samples from the dormitory are not included.
Figure 5
Figure 5
Clade A samples (orange) among all BA.1.1 samples across all regions of Russia. Numbers on bars are the percentage of clade A samples in each region; 95% Wilson CIs are shown as bars. Dormitory samples are not included.
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