Monitoring the rise of the SARS-CoV-2 lineage B.1.1.7 in Tenerife (Spain) since mid-December 2020

•COVID-19 positives (n = 2091) were assessed for spike gene target failure (SGTF).•The B.1.1.7 lineage was found in 93.2% of the 226 SGTF samples.•The results support local transmission since mid-December 2020. In this Journal, Tang and colleagues recently discussed emergence a new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant UK necessity to determine its impact on society healthcare capacity.1Tang J.W. Tambyah P.A. Hui D.S. Emergence SARS-CoV-2 UK.J Infect. 2021; 82: e27-e28Abstract Full Text PDF PubMed Scopus (174) Google Scholar Tenerife (Canary Islands, Spain) is one top destinations travelers all year long an air corridor until late 20202Department Transport Foreign, Commonwealth & Development Office, Government UK. Canary Denmark, Maldives Mykonos added travel exempt list; 2020 Oct 22. Available from: https://www.gov.uk/government/news/canary-islands-denmark-maldives-and-mykonos-added-to-travel-corridor-exempt-list.Google as coronavirus disease 2019 (COVID-19) had <50 cases accumulated incidence per 100,000 inhabitants last 14 days (AI14) September, retaining lowest case levels among Spanish communities decrease first wave during April Starting December 2020, faced unexplained rapid increase COVID-19 compared rest Archipelago AI14 jumped from <130 between August November 248 by 23rd As consequence, border restrictions mobility limitations municipalities 19th 2nd January 2021 imposed. The novel variants generating widespread concern, they harbor constellation mutations that might lead increased transmissibility3Kirby T. New causes surge COVID-19.Lancet Respir Med. 9: E20-E21Abstract (223) and/or immune evasion previous infection or vaccination.4Wu K. Werner A.P. Koch M. Choi A. Narayanan E. Stewart-Jones G.B.E. et al.Serum neutralizing activity elicited mRNA-1273 vaccine — preliminary report.N Engl J 384: 1468-1470Crossref (269) (variant concern [VOC]−202012/01; also known clade 20I/501Y.V1), firstly identified 2020,1Tang Scholar,5O'Toole A.O. Hill V. Pybus O.G. Watts Bogoch I.I. Khan al.Tracking international spread lineages B.1.351/501Y-V2.2021https://virological.org/t/tracking-the-international-spread-of-sars-cov-2-lineages-b-1-1-7-and-b-1-351-501y-v2/592Google has rapidly worldwide (https://cov-lineages.org/global_report_B.1.1.7.html). By mid-January 2021, VOC prevalence over 76% sequences despite many affected areas.5O'Toole Among characterizing lineage, deletion predicting loss amino acids 69 70 (Δ69/70) S protein been associated with “Spike failure” (SGTF) two commercial RT-qPCR kits diagnosis.6FDA UpdateGenetic may false negative molecular tests detection - letter clinical laboratory staff providers.2021https://www.fda.gov/medical-devices/letters-health-care-providers/genetic-variants-sars-cov-2-may-lead-false-negative-results-molecular-tests-detection-sars-cov-2Google Here we aimed monitor leveraging followed viral genome sequencing prioritized samples. study conducted at University Hospital Nuestra Señora de Candelaria (Santa Cruz Tenerife, review board approved (CHUNSC_2020_24). We nasopharyngeal swabs COVID-19/SARS-CoV-2 patients corresponding independent outbreaks declared 18th 25th February 2021. Routine diagnosis described elsewhere.7Alcoba-Florez J. Gil-Campesino H. García-Martínez Artola D. González-Montelongo R. Valenzuela-Fernández Ciuffreda L. al.Sensitivity different solutions detection.Int Infect Dis. 2020; 99: 190-192Abstract (44) used TaqPath Combo Kit (Thermo Fisher Scientific) positive it suggested occur presence Δ69/70 deletion6FDA have arisen multiple lineages.8Davies N.G. Abbott S. Barnard R.C. Jarvis C.I. Kucharski A.J. Munday J.D. al.Estimated transmissibility England.Science. 372 (eabg3055)Crossref (22) assay assess RNA extracts (Zymo Quick DNA/RNA kit, Zymo) period. Thermocycling 7500 Fast Real-Time PCR System following manufacturers recommendations. Then, samples selected when categorized if showed cycle threshold (Ct)<30 any targets assessed. libraries obtained using COVIDSeq Test (Illumina, Inc.), covering whole including internal controls consisting 11 human mRNA targets. procedure recommendations quality control steps. Sequencing NextSeq 550 (Illumina) instrument High Output mode 36 bp single end reads. Per sample consensus against reference (NC_045512.2) based DRAGEN v1.2.2 pipeline Inc.). Positive amplification included each run. To be able recover FASTA not automatically provided Test, fastq files reprocessed Lineage v3.5.0 specifications: coverage 20, virus 5, 3. PANGOLIN software suite v2.1.7 (https://github.com/cov-lineages/pangolin) then classification nomenclature Rambaut al.9Rambaut Holmes E.C. O'Toole Á. McCrone J.T. Ruis C. al.A dynamic proposal assist genomic epidemiology.Nat Microbiol. 5: 1403-1407Crossref (1313) Nextclade v.0.12.0 calling functional predictions. data retrieved hub Gobierno Canarias (https://www.gobiernodecanarias.org/principal/coronavirus/acceso_datos.html; accessed March 6th, 2021). analysis period, total 2091 assessed, resulting reaching maximum 10.7% period under study. Remarkably, detected rising sharply Christmas season steadily after 28th, (Fig. 1A). sequence 147 (mean depth ± SD: 48X 9) out sequenced genomes assigned five where (VOC-202012/01) predominant (93.2%). Eleven these lower (based aggregation four metrics: missing data, mixed sites, private mutations, mutation clusters) downstream analysis. those classified carried nine 17 lineage-defining mutations,8Davies 93.4% ≥15 1B). Other linked B.1.258 (5), B.1.177 (3), B.1.221 (1), B.1.1.222 (1). Based sequencing, supports Despite vaccination campaign started Spain 27th given reached large fraction population yet, possibility responsible high. Although neglecting protective effect vaccination, models some major cities Europe indicate will dominant mid-March even accounting non-pharmaceutical interventions.10Gozzi N. Chinazzi Davis Mu Pastore y Piontti Ajelli al.Estimating spreading dominance 202012/01 (lineage B.1.1.7) across Europe. medRxiv, 2021https://doi.org/10.1101/2021.02.22.21252235Crossref anticipate reported here should taken underestimate there escape SGTF. assume potential derive non-resident could introduced upward bias estimated AI14. authors declare no competing financial interests personal relationships appeared influence work paper. deeply acknowledge Instituto Tecnológico Energías Renovables directors their strong assistance accessing diverse resources This supported Cabildo Insular [grants CGIEU0000219140 “Apuestas científicas del ITER para colaborar en la lucha contra COVID-19″]; agreement (ITER) strengthen scientific technological education, training research, development innovation Genomics, Personalized Medicine Biotechnology [grant number OA17/008]; Ministerio Ciencia e Innovación numbers RTI2018-093747-B-100 RTC-2017-6471-1], co-funded European Regional Fund (ERDF); Lab P2+ facility UNLL10-3E-783], ERDF “Fundación CajaCanarias”; HIV/AIDS Research Network RIS-RETIC, RD16/0025/0011], Salud Carlos III ERDF; RIS-3 Strategy “María Carmen Betancourt Molina” Program, “Consejería Economía, Conocimiento Empleo, Canarias” ProID2020010093]. funders role design, collection, interpretation writing manuscript decision submit publication.