Development of New Rt-Pcr Assays for the Specific Detection of Ba.2.86 Sars-Cov-2 and its Descendent Sublineages

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 more than 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. 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. Our results confirmed that both PiroMet assays are highly specific, with a sensitivity of about 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. 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.

Note:

Funding Information: Statens Serum Institut was supported by co-funding from the EU's EU4Health programme (grant agreement number 101102733 DURABLE). Views and opinions expressed do not necessarily reflect those of the EU or European Health and Digital Executive Agency. Neither the EU nor the granting authority can be held responsible for them. The funder did not have any role in writing of the Manuscript or the decision to submit it for publication.

Declaration of Interests: The authors declare no competing interests.

Ethics Approval Statement: Exemption for review by the ethical committee system and informed consent were given by the Committee on Biomedical Research Ethics—Capital Region in accordance with Danish law on assay development projects.

Keywords: SARS-CoV-2, BA.2.86 sublineages, RT-PCR, digital RT-PCR, wastewater surveillance