The Omicron variant of SARS-CoV-2 has rapidly spread globally in late 2021 - early 2022, displacing the previously prevalent Delta variant. Before December 16, 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 December 16 - 29, 2021, which was the earliest known instance of 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 has been tested by whole-genome sequencing, 111 (94.1%) carried the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported previous COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sublineage of Omicron. 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 other countries. The rapid spread of Omicron in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.

The authors have declared no competing interest.

Samples acquisition and sequencing were supported by the Ministry of Health of Russian Federation as a research work of the state assignment #121110800170-8 (2022). Bioinformatic analysis was funded by the Russian Science Foundation (project no. 21-74-20160 to G.A.B.)

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Samples used in this study were collected as part of approved ongoing surveillance conducted by the Smorodintsev Research Institute of Influenza. Written informed consent was obtained from all subjects. All samples were deidentified prior to receipt by the study team. The study was presented to the Local Ethics Committee at the Smorodintsev Research Institute of Influenza. The Committee concluded (protocol #177) that the study does not make use of new identifiable biological samples and does not bring forward any new sensitive data. Therefore, according to the rules of the Committee and national regulations this project does not require ethical approval.

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