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

40 Pages Posted: 4 Jun 2024

See all articles by Katja Spiess

Katja Spiess

Statens Serum Institut

Mauro Petrillo

affiliation not provided to SSRN

Valentina Paracchini

affiliation not provided to SSRN

Gabriele Leoni

affiliation not provided to SSRN

Ria Lassauniere

Statens Serum Institut - Department of Virus and Microbiological Special Diagnostics

Charlotta Polacek Strandh

Statens Serum Institut - Department of Virus and Microbiological Special Diagnostics

Ellinor Marving

Statens Serum Institut

Nicolai Balle Larsen

Statens Serum Institut

Vithiagaran Gunalan

Statens Serum Institut - Virus Research & Development Laboratory

Aleksander Ring

Statens Serum Institut

Maireid Bull

Statens Serum Institut

Gerhard Buttinger

affiliation not provided to SSRN

Carolina Veneri

University of North Carolina (UNC) at Chapel Hill - National Institute of Health

Elisabetta Suffredini

University of North Carolina (UNC) at Chapel Hill - National Institute of Health

Giuseppina La Rosa

Istituto Superiore di Sanità

Philippe Corbisier

Joint Research Center of the European Commission

Maddalena Querci

affiliation not provided to SSRN

Morten Rasmussen

Statens Serum Institut - Virus Research & Development Laboratory

Antonio Marchini

affiliation not provided to SSRN

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

Suggested Citation

Spiess, Katja and Petrillo, Mauro and Paracchini, Valentina and Leoni, Gabriele and Lassauniere, Ria and Strandh, Charlotta Polacek and Marving, Ellinor and Larsen, Nicolai Balle and Gunalan, Vithiagaran and Ring, Aleksander and Bull, Maireid and Buttinger, Gerhard and Veneri, Carolina and Suffredini, Elisabetta and La Rosa, Giuseppina and Corbisier, Philippe and Querci, Maddalena and Rasmussen, Morten and Marchini, Antonio, Development of New Rt-Pcr Assays for the Specific Detection of Ba.2.86 Sars-Cov-2 and its Descendent Sublineages. Available at SSRN: https://ssrn.com/abstract=4824553 or http://dx.doi.org/10.2139/ssrn.4824553

Katja Spiess

Statens Serum Institut ( email )

Mauro Petrillo

affiliation not provided to SSRN ( email )

No Address Available

Valentina Paracchini

affiliation not provided to SSRN ( email )

No Address Available

Gabriele Leoni

affiliation not provided to SSRN ( email )

No Address Available

Ria Lassauniere

Statens Serum Institut - Department of Virus and Microbiological Special Diagnostics ( email )

Charlotta Polacek Strandh

Statens Serum Institut - Department of Virus and Microbiological Special Diagnostics ( email )

Ellinor Marving

Statens Serum Institut ( email )

Nicolai Balle Larsen

Statens Serum Institut ( email )

Vithiagaran Gunalan

Statens Serum Institut - Virus Research & Development Laboratory ( email )

Aleksander Ring

Statens Serum Institut ( email )

Denmark

Maireid Bull

Statens Serum Institut ( email )

Denmark

Gerhard Buttinger

affiliation not provided to SSRN ( email )

No Address Available

Carolina Veneri

University of North Carolina (UNC) at Chapel Hill - National Institute of Health ( email )

Elisabetta Suffredini

University of North Carolina (UNC) at Chapel Hill - National Institute of Health ( email )

Giuseppina La Rosa

Istituto Superiore di Sanità ( email )

Viale Regina Elena 299
Roma, 00161
Italy

Philippe Corbisier

Joint Research Center of the European Commission ( email )

Via E. Fermi 2749
Brussels, B-1049
Belgium

Maddalena Querci

affiliation not provided to SSRN ( email )

No Address Available

Morten Rasmussen

Statens Serum Institut - Virus Research & Development Laboratory ( email )

Copenhagen
Denmark

Antonio Marchini (Contact Author)

affiliation not provided to SSRN ( email )

No Address Available

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