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Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexed RT-qPCR assay.
Borsová, Kristína; Paul, Evan D; Kovácová, Viera; Radvánszka, Monika; Hajdu, Roman; Cabanová, Viktória; Sláviková, Monika; Licková, Martina; Lukáciková, Lubomíra; Belák, Andrej; Roussier, Lucia; Kosticová, Michaela; Lísková, Anna; Madarová, Lucia; Stefkovicová, Mária; Reizigová, Lenka; Nováková, Elena; Sabaka, Peter; Koscálová, Alena; Brejová, Brona; Staronová, Edita; Misík, Matej; Vinar, Tomás; Nosek, Jozef; Cekan, Pavol; Klempa, Boris.
  • Borsová K; Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Paul ED; Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
  • Kovácová V; MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
  • Radvánszka M; MultiplexDX, Inc., One Research Court, Rockville, MD, USA.
  • Hajdu R; MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
  • Cabanová V; MultiplexDX, Inc., One Research Court, Rockville, MD, USA.
  • Sláviková M; MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
  • Licková M; MultiplexDX, Inc., One Research Court, Rockville, MD, USA.
  • Lukáciková L; MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia.
  • Belák A; MultiplexDX, Inc., One Research Court, Rockville, MD, USA.
  • Roussier L; School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
  • Kosticová M; Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Lísková A; Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Madarová L; Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Stefkovicová M; Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Reizigová L; Institute of Ethnology and Social Anthropology, Slovak Academy of Sciences, Bratislava, Slovakia.
  • Nováková E; Intervention Team, Ministry of Health, Bratislava, Slovakia.
  • Sabaka P; Intervention Team, Ministry of Health, Bratislava, Slovakia.
  • Koscálová A; Intervention Team, Ministry of Health, Bratislava, Slovakia.
  • Brejová B; Institute of Social Medicine and Medical Ethics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia.
  • Staronová E; Department of Clinical Microbiology, Nitra Faculty Hospital, Nitra, Slovakia.
  • Misík M; Regional Authority of Public Health, Banská Bystrica, Slovakia.
  • Vinar T; Regional Authority of Public Health, Trencín, Slovakia.
  • Nosek J; Faculty of Healthcare, Alexander Dubcek University of Trencín, Trencín, Slovakia.
  • Cekan P; Regional Authority of Public Health, Trencín, Slovakia.
  • Klempa B; Department of Laboratory Medicine, Faculty of Healthcare and Social Work, Trnava University, Trnava, Slovakia.
Sci Rep ; 11(1): 20494, 2021 10 14.
Article in English | MEDLINE | ID: covidwho-1469989
ABSTRACT
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 ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Multiplex Polymerase Chain Reaction / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-99661-7

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Multiplex Polymerase Chain Reaction / COVID-19 Nucleic Acid Testing / SARS-CoV-2 / COVID-19 Type of study: Diagnostic study / Observational study / Prognostic study Topics: Vaccines / Variants Limits: Humans Country/Region as subject: Europa Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-99661-7