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. 2022 Apr;27(16):2200257.
doi: 10.2807/1560-7917.ES.2022.27.16.2200257.

Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022

Erika Lindh  1 , Teemu Smura  2   3 , Soile Blomqvist  1 , Kirsi Liitsola  1 , Hanna Vauhkonen  2 , Laura Savolainen  4 , Jaana Ikonen  5 , Jukka Ronkainen  6 , Jyri Taskila  7 , Tea Taskila  8 , Pertti Sakaranaho  9 , Carita Savolainen-Kopra  1 , Olli Vapalahti  10   2   3 , Niina Ikonen  1
Affiliations

Genomic and epidemiological report of the recombinant XJ lineage SARS-CoV-2 variant, detected in northern Finland, January 2022

Erika Lindh et al. Euro Surveill. 2022 Apr.

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.

Keywords: SARS-CoV-2; XJ-lineage; omicron; recombinant; variant.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Schematic representation of the SARS-CoV-2 BA.1/BA.2 recombinant genome arrangement
Figure 2
Figure 2
Phylogenetic trees of all SARS-CoV-2 lineage XJ recombinant genomes that had fewer than 1,000 ambiguous nucleotides, Finland, January–February 2022 (n = 96)
Figure 3
Figure 3
Potential parental genomes of SARS-CoV-2 lineage XJ recombinants, Länsi-Pohja district, Finland, January–February 2022 (n = 19)
Figure 4
Figure 4
SARS-CoV-2 variant distribution, Länsi-Pohja hospital district, Finland, week 1–11/2022 (n = 191 XJ among 1,094 sequences)
See this image and copyright information in PMC

References

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Supplementary concepts