Kristina Borsova, Evan D. Paul, Viera Kovacova, Monika Radvanszka, Roman Hajdu, Viktoria Cabanova, Monika Slavikova, Martina Lickova, Lubomira Lukacikova, Andrej Belak, Lucia Roussier, Michaela Kosticova, Anna Liskova, Lucia Madarova, Maria Stefkovicova, Lenka Reizigova, Elena Novakova, Peter Sabaka, Alena Koscalova, Brona Brejova, Edita Staronova, Matej Misik, Tomas Vinar, Jozef Nosek, Pavol Cekan, Boris Klempa. Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexedRT-qPCR assay. Scientific Reports, 11(1):20494. 2021.
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The emergence of a novel SARS-CoV-2 B.1.1.7 variant sparked global alarm due to increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack genomic surveillance programs and failed assays detect unrelated variants containing similar mutations as B.1.1.7, we used allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop an RT-qPCR test that accurately and rapidly differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing and conducted a country-wide surveillance study of B.1.1.7 prevalence in Slovakia. Our multiplexed RT-qPCR test showed 97% clinical sensitivity and retesting 6,886 SARS-CoV-2 positive samples obtained during three campaigns performed within one month, revealed pervasive spread of B.1.1.7 with an average prevalence of 82%. Labs can easily implement this test to rapidly scale B.1.1.7 surveillance efforts and it is particularly useful in countries with high prevalence of variants possessing only the DeltaH69/DeltaV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.