Development of new RT-PCR assays for the specific detection of BA.2.86 SARS-CoV-2 and its descendent sublineages
Objectives
To develop and validate specific RT-PCR assays for the rapid identification of the SARS-CoV-2 BA.2.86 variant and its sublineages, thereby offering a quicker and cost-effective alternative to sequencing for monitoring the spread of these variants and enhancing SARS-CoV-2 wastewater surveillance.
Methods
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. 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 assay (which can universally recognize all SARS-CoV-2 variants), to quantify the proportion of BA.2.86 sublineages in the samples.
Results
Validation confirmed that both PiroMet assays are highly specific, with a sensitivity of 0.7 RNA copies/µl. In conjunction with the OmMet and JRC-CoV-UCE.2 assays, the PiroMet assays accurately quantified BA.2.86 sublineages in wastewater samples.
Conclusions
Our results 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.
SPIESS Katja;
PETRILLO Mauro;
PARACCHINI Valentina;
LEONI Gabriele;
LASSAUNIERE Maria Magdalena;
POLACEK STRANDH Charlotta;
MARVING Ellinor Lindberg;
LARSEN Nicolai Balle;
GUNALAN Vithiagaran;
RING Alexander;
BULL Maireid;
BUTTINGER Gerhard;
VENERI Carolina;
SUFFREDINI Elisabetta;
LA ROSA Giuseppina;
CORBISIER Philippe;
QUERCI Maddalena;
RASMUSSEN Morten;
MARCHINI Antonio;
2024-09-26
ELSEVIER
JRC137936
0048-9697 (online),
https://www.sciencedirect.com/science/article/pii/S0048969724065215,
https://publications.jrc.ec.europa.eu/repository/handle/JRC137936,
10.1016/j.scitotenv.2024.176365 (online),
Additional supporting files
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