Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages

The SARS-CoV-2 BA.2.86 variant, also known as Pirola, has acquired over 30 amino acid changes in the Spike protein, evolving into >150 sublineages within ten months of its emergence. Among these, the JN.1, has been rapidly increasing globally becoming the most prevalent variant. To facilitate the identification of BA.2.86 sublineages, we designed the PiroMet-1 and PiroMet-2 assays in silico and validated them using BA.2.86 viral RNA and clinical samples to ascertain analytical specificity and sensitivity. Both assays resulted very specific with limit of detection of about 1-2 RNA copies/μL. The assays were then applied in a digital RT-PCR format to wastewater samples, combined with the OmMet assay (which identifies Omicron sublineages except BA.2.86 and its descendants) and the JRC-UCE.2 assay (which can universally recognize all SARS-CoV-2 variants). When used together with the OmMet and JRC-CoV-UCE.2 assays, the PiroMet assays accurately quantified BA.2.86 sublineages in wastewater samples. Our findings support the integration of these assays into routine SARS-CoV-2 wastewater surveillance as a timely and cost-effective complement to sequencing for monitoring the prevalence and spread of BA.2.86 sublineages within communities.

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Publication Details

Journal
The Science of The Total Environment
Published
2024-09-17
DOI
https://doi.org/10.1016/j.scitotenv.2024.176365
Citations
1
Primary Topic
SARS-CoV-2 detection and testing
Type
article
Field-Weighted Citation Impact
0.39

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article

Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages

Giuseppina La Rosa, Mauro Petrillo, Antonio Marchini, Gabriele Leoni et al.
1 citations
The Science of The Total Environment
SARS-CoV-2 detection and testing
0.39
article

Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages

Giuseppina La Rosa, Mauro Petrillo, Antonio Marchini, Gabriele Leoni, Maddalena Querci, Ria Lassaunière, Valentina Paracchini, Carolina Veneri, Ellinor Marving, Morten Rasmussen, Vithiagaran Gunalan, Gerhard Buttinger, Maireid Bull, Nicolai Balle Larsen, Philippe Corbisier, Charlotta Polacek, Katja Spieß, Elisabetta Suffredini, Aleksander Ring
article en
1 citations

Abstract

The SARS-CoV-2 BA.2.86 variant, also known as Pirola, has acquired over 30 amino acid changes in the Spike protein, evolving into >150 sublineages within ten months of its emergence. Among these, the JN.1, has been rapidly increasing globally becoming the most prevalent variant. To facilitate the identification of BA.2.86 sublineages, we designed the PiroMet-1 and PiroMet-2 assays in silico and validated them using BA.2.86 viral RNA and clinical samples to ascertain analytical specificity and sensitivity. Both assays resulted very specific with limit of detection of about 1-2 RNA copies/μL. The assays were then applied in a digital RT-PCR format to wastewater samples, combined with the OmMet assay (which identifies Omicron sublineages except BA.2.86 and its descendants) and the JRC-UCE.2 assay (which can universally recognize all SARS-CoV-2 variants). When used together with the OmMet and JRC-CoV-UCE.2 assays, the PiroMet assays accurately quantified BA.2.86 sublineages in wastewater samples. Our findings support the integration of these assays into routine SARS-CoV-2 wastewater surveillance as a timely and cost-effective complement to sequencing for monitoring the prevalence and spread of BA.2.86 sublineages within communities.

The Science of The Total EnvironmentVol. 954
Statens Serum Institut (DK), Istituto Superiore di Sanità (IT), European Commission (BE), Joint Research Centre (IT)
European Commission
Openalex Percentile: Top 37%
SARS-CoV-2 detection and testing
0.39
DOIOpen Access PDFOpenAlex
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