Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2021 Mar;26(10):2100131.
doi: 10.2807/1560-7917.ES.2021.26.10.2100130.

Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021

Vítor Borges  1   2 , Carlos Sousa  2   3 , Luís Menezes  4 , António Maia Gonçalves  5 , Miguel Picão  6 , José Pedro Almeida  7 , Margarida Vieita  7 , Rafael Santos  7 , Ana Rita Silva  3 , Mariana Costa  3 , Luís Carneiro  3 , Pedro Casaca  8 , Pedro Pinto-Leite  8 , André Peralta-Santos  8 , Joana Isidro  1 , Sílvia Duarte  9 , Luís Vieira  9 , Raquel Guiomar  10 , Susana Silva  11 , Baltazar Nunes  11 , João P Gomes  1
Affiliations

Tracking SARS-CoV-2 lineage B.1.1.7 dissemination: insights from nationwide spike gene target failure (SGTF) and spike gene late detection (SGTL) data, Portugal, week 49 2020 to week 3 2021

Vítor Borges et al. Euro Surveill. 2021 Mar.

Abstract

We show that the SARS-CoV-2 B.1.1.7 lineage is highly disseminated in Portugal, with the odds of B.1.1.7 proportion increasing at an estimated 89% (95% confidence interval: 83-95%) per week until week 3 2021. RT-PCR spike gene target late detection (SGTL) can constitute a useful surrogate to track B.1.1.7 spread, besides the spike gene target failure (SGTF) proxy. SGTL/SGTF samples were associated with statistically significant higher viral loads, but not with substantial shift in age distribution compared to non-SGTF/SGTL cases.

Keywords: B.1.1.7 lineage; RT-PCR; SARS-CoV-2; genome sequencing; laboratory surveillance; spike gene target failure (SGTF); spike gene target late detection (SGTL).

PubMed Disclaimer

Conflict of interest statement

Conflict of interest: CS, LM, AMG, MP, JPA, MV, RS, ARS, MC and LC are employees of the private laboratory Unilabs as technicians, bioinformatics or executive manager (LM) and do not have any influence on the decisions made by the health authorities or government.

Figures

Figure 1
Figure 1
Proportion of spike gene target failure and spike gene late detection positive samples among all TaqPath COVID-19 positive samples, Portugal, week 49 2020–week 3 2021
Figure 2
Figure 2
Estimated weekly frequency time trend of spike gene target failure/spike gene target late detection and B.1.1.7 cases using a binomial logistic model with 95% prediction interval, Portugal, week 3–week 6 2021
Figure 3
Figure 3
Scatter, violin and box plots of the (A) N-gene and (B) ORF1ab cycle threshold values obtained for spike gene target failure and spike gene late detection samples compared with non-SGTF/SGTL positive samples, Portugal, week 49 2020–week 3 2021 (n = 30,407)
Figure 4
Figure 4
Distribution of spike gene target failure/spike gene target late detection positive cases compared with non-spike gene target failure/spike gene target late detection positive cases by (A) age groups (histogram) and (B) age (Violin and box plot), Portugal, week 49 2020–week 3 2021 (n = 30,407)
See this image and copyright information in PMC

References

    1. Public Health England (PHE). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01: Technical briefing document on novel SARS-CoV-2 variant. London: PHE; 2020. Available from: https://www.gov.uk/government/publications/investigation-of-novel-sars-c...
    1. European Centre for Disease Prevention and Control (ECDC). Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA – 29 December 2020. ECDC: Stockholm; 2020. Available from: https://www.ecdc.europa.eu/sites/default/files/documents/COVID-19-risk-r...
    1. Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Transmission of SARS-CoV-2 Lineage B. 1.1. 7 in England: Insights from linking epidemiological and genetic data; medRxiv 2021. 10.1101/2020.12.30.20249034 - DOI
    1. Galloway SE, Paul P, MacCannell DR, Johansson MA, Brooks JT, MacNeil A, et al. Emergence of SARS-CoV-2 B.1.1.7 Lineage - United States, December 29, 2020-January 12, 2021. MMWR Morb Mortal Wkly Rep. 2021;70(3):95-9. 10.15585/mmwr.mm7003e2 - DOI - PMC - PubMed
    1. Rambaut A, Loman N, Pybus O, Barclay W, Barrett J, Carabelli A, et al. Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological.org; 2020. Available from: https://virological.org/t/preliminary-genomic-characterisation-of-an-eme...

Substances

LinkOut - more resources