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.