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

Viruses. 2023. Vol. 15. No. 7. Article 1415.

Klink G. V., Danilenko D., Komissarov A., Yolshin N., Shneider O., Shcherbak S., Nabieva E., Shvyrev N., Konovalova N., Zheltukhina A., Fadeev A., Komissarova K., Ksenafontov A., Musaeva T., Eder V., Pisareva M., Nekrasov P., Shchur V., Bazykin G., Lioznov D.

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: Россия, Russia, SARS-CoV-2, SARS-CoV-2, founder effect, BA.1.1, superspreading, outbreak, эффект основателя, BA.1.1, суперраспространение, вспышка инфекции

Publication based on the results of: Statistical analysis of population genetic diversity (2023)