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. 2024 Dec;16(4):449-457.
doi: 10.1007/s12560-024-09607-1. Epub 2024 Jun 25.

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

C Veneri  1 , D Brandtner  2 , P Mancini  1 , G Bonanno Ferraro  1 , M Iaconelli  1 , E Suffredini  3 , M Petrillo  4 , G Leoni  5 , V Paracchini  5 , B M Gawlik  5 , A Marchini  6 ; SARI Network; G La Rosa  7
Collaborators, Affiliations

Tracking the Spread of the BA.2.86 Lineage in Italy Through Wastewater Analysis

C Veneri et al. Food Environ Virol. 2024 Dec.

Abstract

The emergence of new SARS-CoV-2 variants poses challenges to global surveillance efforts, necessitating swift actions in their detection, evaluation, and management. Among the most recent variants, Omicron BA.2.86 and its sub-lineages have gained attention due to their potential immune evasion properties. This study describes the development of a digital PCR assay for the rapid detection of BA.2.86 and its descendant lineages, in wastewater samples. By using this assay, we analyzed wastewater samples collected in Italy from September 2023 to January 2024. Our analysis revealed the presence of BA.2.86 lineages already in October 2023 with a minimal detection rate of 2% which then rapidly increased, becoming dominant by January 2024, accounting for a prevalence of 62%. The findings emphasize the significance of wastewater-based surveillance in tracking emerging variants and underscore the efficacy of targeted digital PCR assays for environmental monitoring.

Keywords: BA.2.86; Digital PCR; JN.1; SARS-CoV-2; Wastewater surveillance.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Prevalence and trend of positivity for BA.2.86* over the study period for both environmental and clinical data
Fig. 2
Fig. 2
Box plot illustrating the distribution of BA.2.86 lineage normalized concentrations in positive samples across months. Dots indicate individual measurements; the lines of the box represent the 25th, 50th and 75th percentile (bottom, middle, and top lines, respectively); whiskers show the range from minimum to maximum values, not including outliers
Fig. 3
Fig. 3
Geographical distribution of BA.2.86 lineage prevalence over four months. The detection of the Omicron BA.2.86* is represented with increasing shades of blue based on its prevalence. Grey Regions/A.P. tested negative for the BA.2.86* variant. Regions/A.P. without any tested sample in a given month are shown in stripes
See this image and copyright information in PMC

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Supplementary concepts