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. 2023 Nov;28(46):2300595.
doi: 10.2807/1560-7917.ES.2023.28.46.2300595.

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

Carmen Espinosa-Gongora  1   2 , Carlo Berg  1 , Moa Rehn  1 , Javier Edo Varg  3 , Lena Dillner  1 , Neus Latorre-Margalef  1 , Anna J Székely  3 , Emmi Andersson  1 , Elin Movert  1
Affiliations

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

Carmen Espinosa-Gongora et al. Euro Surveill. 2023 Nov.

Abstract

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.

Keywords: BA.2.86; Freyja; SARS-CoV-2; Sweden; wastewater surveillance; whole genome sequencing.

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Conflict of interest statement

Conflict of interest: None declared.

Figures

Figure 1
Figure 1
Relative abundance of SARS-CoV-2 BA.2.86 and other circulating variant groups in wastewater samples collected at 18 wastewater treatment plants in 14 of 21 regions, Sweden, weeks 31–38 2023 (n = 91 samples)
Figure 2
Figure 2
Relative abundance of SARS-CoV-2 BA.2.86 and other circulating variant groups in samples collected from COVID-19 cases in 19 of 21 regions, Sweden, weeks 31–38 2023 (n = 2,529 samples)
Figure 3
Figure 3
BA.2.86 spread in samples from wastewater treatment plants and COVID-19 cases, Sweden, weeks 31–38 2023
See this image and copyright information in PMC

References

    1. Rothstein AP, Qiu X, Robison K, Collins S, Muir G, Lu B, et al. Bayesian phylogenetics on globally emerging SARS-CoV-2 variant BA.2.86 suggest global distribution and rapid evolution. bioRxiv. 2023:2023.09.08.556912. Preprint . 10.1101/2023.09.08.556912 - DOI
    1. Rasmussen M, Møller FT, Gunalan V, Baig S, Bennedbæk M, Christiansen LE, et al. First cases of SARS-CoV-2 BA.2.86 in Denmark, 2023. Euro Surveill. 2023;28(36):2300460. 10.2807/1560-7917.ES.2023.28.36.2300460 - DOI - PMC - PubMed
    1. Bladh O, Greilert-Norin N, Havervall S, Marking U, Aguilera K, Alm JJ, et al. Mucosal and serum antibodies 3 weeks after symptomatic BA.2.86 infection. N Engl J Med. 2023;389(17):1626-8. 10.1056/NEJMc2310347 - DOI - PubMed
    1. World Health Organization (WHO). Tracking SARS-CoV-2 variants. Geneve: WHO. [Accessed: 17 Oct 2023]. Available from: https://www.who.int/activities/tracking-SARS-CoV-2-variants
    1. European Centre for Disease Prevention and Control (ECDC). SARS-CoV-2 variants of concern. Stockholm: ECDC. [Accessed: 17 Oct 2023]. Available from: https://www.ecdc.europa.eu/en/covid-19/variants-concern