Monitoring the rise of the SARS-CoV-2 lineage B.1.1.7 in Tenerife (Spain) since mid-December 2020
Authors: Julia Alcoba-Florez, Jose M. Lorenzo-Salazar, Helena Gil-Campesino, Antonio Íñigo-Campos, Diego García Martínez de Artola, Victor García-Olivares, Oscar Díez-Gil, Agustín Valenzuela-Fernández, Laura Ciuffreda, Rafaela González-Montelongo, Carlos Flores
Journal: Journal of Infection (2021)

•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 of B.1.1.7 lineage since mid-December 2020. In this Journal, Tang and colleagues recently discussed the emergence of a new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant in the UK and the necessity to determine its impact on society and healthcare capacity.1Tang J.W. Tambyah P.A. Hui D.S. Emergence of a new SARS-CoV-2 variant in the UK.J Infect. 2021; 82: e27-e28Abstract Full Text Full Text PDF PubMed Scopus (191) Google Scholar Tenerife (Canary Islands, Spain) is one of the top destinations for UK travelers all year long and was an air corridor until late 20202Department for Transport and Foreign, Commonwealth & Development Office, Government of UK. Canary Islands, Denmark, Maldives and Mykonos added to travel corridor 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 Scholar as the coronavirus disease 2019 (COVID-19) had <50 cases of accumulated incidence per 100,000 inhabitants in the last 14 days (AI14) until late September, retaining one of the lowest case levels among all Spanish communities since the decrease of the first wave during April 2020. Starting in December 2020, Tenerife faced an unexplained rapid increase of COVID-19 cases compared to the rest of the Archipelago as AI14 jumped from <130 cases between August and late November 2020 to 248 cases by the 23rd of December 2020. As a consequence, border restrictions and mobility limitations between municipalities from the 19th of December 2020 until the 2nd of January 2021 were imposed. The emergence of novel SARS-CoV-2 variants is generating widespread concern, as they harbor a constellation of mutations that might lead to increased transmissibility3Kirby T. New variant of SARS-CoV-2 in UK causes surge of COVID-19.Lancet Respir Med. 2021; 9: E20-E21Abstract Full Text Full Text PDF PubMed Scopus (243) Google Scholar and/or immune evasion from 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 by mRNA-1273 vaccine — preliminary report.N Engl J Med. 2021; 384: 1468-1470Crossref PubMed Scopus (287) Google Scholar The lineage B.1.1.7 (variant of concern [VOC]−202012/01; also known as clade 20I/501Y.V1), firstly identified in the UK in December 2020,1Tang J.W. Tambyah P.A. Hui D.S. Emergence of a new SARS-CoV-2 variant in the UK.J Infect. 2021; 82: e27-e28Abstract Full Text Full Text PDF PubMed Scopus (191) Google Scholar,5O'Toole A.O. Hill V. Pybus O.G. Watts A. Bogoch I.I. Khan K. et al.Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and 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 Scholar has rapidly spread worldwide (https://cov-lineages.org/global_report_B.1.1.7.html). By mid-January 2021, this VOC had an accumulated prevalence over 76% among all UK sequences despite restrictions in many of the affected areas.5O'Toole A.O. Hill V. Pybus O.G. Watts A. Bogoch I.I. Khan K. et al.Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and 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 Scholar Among the mutations characterizing this lineage, the deletion predicting the loss of the amino acids 69 and 70 (Δ69/70) in the S protein has been associated with a "Spike gene target failure" (SGTF) for two commercial RT-qPCR kits for COVID-19 diagnosis.6FDA COVID-19 UpdateGenetic variants of SARS-CoV-2 may lead to false negative results with molecular tests for detection of SARS-CoV-2 - letter to clinical laboratory staff and healthcare 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 Scholar Here we aimed to monitor the SARS-CoV-2 B.1.1.7 lineage cases in Tenerife by leveraging the SGTF during the RT-qPCR followed by viral genome sequencing of the prioritized samples. The study was conducted at the University Hospital Nuestra Señora de Candelaria (Santa Cruz de Tenerife, Spain) and its review board approved the study (CHUNSC_2020_24). We assessed nasopharyngeal swabs from COVID-19/SARS-CoV-2 patients corresponding to independent outbreaks declared from 18th of December 2020 to 25th of February 2021. Routine COVID-19 diagnosis was conducted as described elsewhere.7Alcoba-Florez J. Gil-Campesino H. García-Martínez de Artola D. González-Montelongo R. Valenzuela-Fernández A. Ciuffreda L. et al.Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection.Int J Infect Dis. 2020; 99: 190-192Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar We first used the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific) to monitor the SGTF in the COVID-19 positive patients as it has been suggested to occur by the presence of the Δ69/70 deletion6FDA COVID-19 UpdateGenetic variants of SARS-CoV-2 may lead to false negative results with molecular tests for detection of SARS-CoV-2 - letter to clinical laboratory staff and healthcare 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 Scholar that is known to have arisen in multiple lineages.8Davies N.G. Abbott S. Barnard R.C. Jarvis C.I. Kucharski A.J. Munday J.D. et al.Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.Science. 2021; 372 (eabg3055)Crossref PubMed Scopus (1558) Google Scholar We used this assay to assess all RNA extracts (Zymo Quick DNA/RNA kit, Zymo) from COVID-19 positives in the period. Thermocycling was conducted on a 7500 Fast Real-Time PCR System (Thermo Fisher Scientific) following manufacturers recommendations. Then, samples were selected for sequencing when categorized as SGTF and if they showed a cycle threshold (Ct)<30 for any of the targets assessed. The libraries were obtained using the COVIDSeq Test (Illumina, Inc.), covering the whole SARS-CoV-2 genome and including internal controls consisting of 11 human mRNA targets. The procedure followed the manufacturers recommendations and quality control steps. Sequencing was conducted on a NextSeq 550 (Illumina) instrument on High Output mode with 36 bp single end reads. Per sample consensus sequences and variants against the reference (NC_045512.2) were obtained based on the DRAGEN COVIDSeq Test v1.2.2 pipeline (Illumina, Inc.). Positive and negative amplification controls were included in each run. To be able to recover the FASTA sequences that were not automatically provided by DRAGEN COVIDSeq Test, the fastq files were reprocessed with DRAGEN Lineage v3.5.0 with the following specifications: coverage threshold of 20, virus detection threshold of 5, virus negative threshold of 5, and a human control threshold of 3. The PANGOLIN software suite v2.1.7 (https://github.com/cov-lineages/pangolin) was then used for lineage and clade classification following the nomenclature of Rambaut et al.9Rambaut A. Holmes E.C. O'Toole Á. Hill V. McCrone J.T. Ruis C. et al.A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.Nat Microbiol. 2020; 5: 1403-1407Crossref PubMed Scopus (1557) Google Scholar Nextclade v.0.12.0 was used for variant calling and functional predictions. The AI14 data was retrieved from the COVID-19 data hub from Gobierno de Canarias (https://www.gobiernodecanarias.org/principal/coronavirus/acceso_datos.html; accessed March 6th, 2021). In the analysis period, a total of 2091 COVID-19 positive samples were assessed, resulting in 226 SGTF samples identified and reaching a maximum of 10.7% at the end of the period under study. Remarkably, we detected a rapid increase in the prevalence of SGTF over this period, rising sharply during the Christmas season and steadily after December 28th, 2020 (Fig. 1A). We were able to sequence 147 (mean depth of coverage ± SD: 48X ± 9) out of the 226 SGTF samples in the period. The sequenced genomes of SARS-CoV-2 with SGTF were assigned to five different lineages where B.1.1.7 (VOC-202012/01) was the predominant (93.2%). Eleven of these had lower sequence quality (based on the aggregation of four metrics: missing data, mixed sites, private mutations, mutation clusters) and were not included in downstream analysis. Among those classified as B.1.1.7 lineage, the sequences carried between nine and 17 of the lineage-defining mutations,8Davies N.G. Abbott S. Barnard R.C. Jarvis C.I. Kucharski A.J. Munday J.D. et al.Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England.Science. 2021; 372 (eabg3055)Crossref PubMed Scopus (1558) Google Scholar with 93.4% of the sequences including ≥15 (Fig. 1B). Other lineages that were linked to the SGTF in this study were classified as B.1.258 (5), B.1.177 (3), B.1.221 (1), and B.1.1.222 (1). Based on RT-qPCR SGTF and viral genome sequencing, this study supports the local transmission of SARS-CoV-2 B.1.1.7 lineage in Tenerife since late December 2020. Despite vaccination campaign started in Spain on the 27th of December 2020 and given that it has not reached a large fraction of the population yet, the possibility that the B.1.1.7 lineage is also responsible for increased transmission in the rest of the Archipelago is high. Although neglecting a protective effect from vaccination, the models for some major cities in Europe indicate that the B.1.1.7 lineage will be the dominant by mid-March 2021 even if accounting for non-pharmaceutical interventions.10Gozzi N. Chinazzi M. Davis J.T. Mu K. Pastore y Piontti A. Ajelli M. et al.Estimating the spreading and dominance of SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) across Europe. medRxiv, 2021https://doi.org/10.1101/2021.02.22.21252235Crossref Google Scholar We anticipate that the data reported here should be taken as an underestimate as there will be genomes of the B.1.1.7 lineage that escape detection by RT-qPCR SGTF. We also assume that there is potential that some of the samples may derive from non-resident travelers that could have introduced an upward bias in the estimated AI14. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. We deeply acknowledge the University Hospital Nuestra Señora de Candelaria and the Instituto Tecnológico y de Energías Renovables board of directors for their strong support and assistance in accessing diverse resources used in the study. This work was supported by Cabildo Insular de Tenerife [grants CGIEU0000219140 and "Apuestas científicas del ITER para colaborar en la lucha contra la COVID-19″]; the agreement with Instituto Tecnológico y de Energías Renovables (ITER) to strengthen scientific and technological education, training research, development and innovation in Genomics, Personalized Medicine and Biotechnology [grant number OA17/008]; Ministerio de Ciencia e Innovación [grant numbers RTI2018-093747-B-100 and RTC-2017-6471-1], co-funded by the European Regional Development Fund (ERDF); Lab P2+ facility [grant number UNLL10-3E-783], co-funded by the ERDF and "Fundación CajaCanarias"; and the Spanish HIV/AIDS Research Network [grant number RIS-RETIC, RD16/0025/0011], co-funded by Instituto de Salud Carlos III and by the ERDF; and RIS-3 Canarias Strategy - "María del Carmen Betancourt y Molina" Program, "Consejería de Economía, Conocimiento y Empleo, Gobierno de Canarias" [grant number ProID2020010093]. The funders had no role in the study design, collection, analysis and interpretation of data, in the writing of the manuscript or in the decision to submit the manuscript for publication.