Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023.

Espinosa-Gongora C, Berg C, Rehn M, Varg JE, Dillner L, Latorre-Margalef N, Székely AJ, Andersson E, Movert E

Euro Surveill 28 (46) - [2023-11-00; online 2023-11-17]

The SARS-CoV-2 BA.2.86 Omicron subvariant was first detected in wastewater in Sweden in week 31 2023, using 21 highly specific markers from the 50 investigated. We report BA.2.86's introduction and subsequent spread to all 14 regions performing wastewater sampling, and on 70 confirmed COVID-19 cases, along with the emergence of sublineages JN.1 and JN.2. Further, we investigated two novel mutations defining the unique BA.2.86 branching in Sweden. Our integrated approach enabled variant tracking, offering evidence for well-informed public health interventions.

Category: Genomics & transcriptomics

Category: Other

Funder: VR

Research Area: Environmental virus profiling

Type: Journal article

PubMed 37971659

DOI 10.2807/1560-7917.ES.2023.28.46.2300595

Crossref 10.2807/1560-7917.ES.2023.28.46.2300595

pmc: PMC10655203
Whole genome sequence data from individuals for all Swedish BA.2.86 cases is available on GISAID. The accession numbers are avilable in the supplementary materials (linked here).
The findings of the BA.2.86 marker specificity assessment are based on metadata associated with 13,513 sequences available on GISAID from 1 July to 19 October 2023
Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar.

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