T he most recent SARS-CoV-2 variant of concern, Omicron (Pango lineage B.1.1.529), was first detected in South Africa (1), although it might have emerged elsewhere, and has since spread globally at an unforeseen speed. Notable examples include a superspreading event in Norway (2) and the rapid increase in incidence in Denmark (3) despite high vaccination coverage (83% of infected persons had received 2-3 vaccine doses). This rapid spread indicates the novel variant's exceptional transmissibility, as well as its potential for reinfection and vaccination breakthrough. We describe the genotypes of cases of Omicron entering Finland from their early spread up to established community transmission through the first week of January 2022. No ethics approval was needed because this study was based on routine CO-VID-19 surveillance data. The study regarding Helsinki University Hospital (HUH) samples was approved by the local ethical and research committee (Helsinki and Uusimaa Hospital District [HUS]; Clinical microbiology of COVID-19: diagnostics, laboratory findings and biorisks; HUS/244/2021). The StudyA total of 99,988 samples found positive for SARS-CoV-2 by reverse transcription PCR, 12.1% of 825,006 total samples tested, were detected in Finland during the study period, November 29, 2021-January 6, 2022 (Figure 1). Weekly positivity rates among persons tested rose from 6.1% of 156,077 in week 48 to 25.6% of 172,451 (3.1% of the Finnish population) in week 52 (https://sampo.thl.fi). In HUS, test positivity increased from 5.0% to 36.7% over the corresponding weeks 48-52. After a change in testing strategy favoring home antigen testing, the number of registered SARS-CoV-2 cases dropped (Appendix, https://wwwnc.cdc.gov/ EID/article/28/6/22-0515-App1.pdf).We estimated the proportions of Omicron variant lineages BA.1 and BA.1.1 within HUS by comparing PCR-based data on S-gene target failure (SGTF) to that of other circulating lineages (Figure 1; Appendix). The results showed a decrease in SGTF rates from week 24, when the proportion of the Alpha variant (B.1.1.7) was declining, to near 0 when the Delta variant (B.1.617.2) was dominant. This decrease aligns well with sequence-confirmed lineage turnover

No abstract

Recombinant sequences of the SARS-CoV-2 Omicron variant were detected in surveillance samples collected in north-western Finland in January 2022. We detected 191 samples with an identical genome arrangement in weeks 3 to 11, indicating sustained community transmission. The recombinant lineage has a 5’-end of BA.1, a recombination breakpoint between orf1a and orf1b (nucleotide position 13,296–15,240) and a 3’-end of BA.2 including the S gene. We describe the available genomic and epidemiological data about this currently circulating recombinant XJ lineage.

Two SARS-CoV-2 Variants of Concern, Alpha (~ 80%) and Beta (~ 23%) rapidly became dominant in Finland in the spring of 2021 but diminished near summer. To assess their temporal epidemiological dynamics among Finnish cases, we began large-scale sequencing efforts to identify spreading events and sources via phylogenetic clustering analyses. The results show the majority belonged to clusters spreading in the community while few sequenced samples were singletons. The results highlight the importance of surveillance and preventative policies in controlling the epidemic.