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

• Published in: Euro surveillance : bulletin européen sur les maladies transmissibles 2021-03, Vol.26 (10), p.1
• Main Authors: Borges, Vítor, Sousa, Carlos, Menezes, Luís, Gonçalves, António Maia, Picão, Miguel, Almeida, José Pedro, Vieita, Margarida, Santos, Rafael, Silva, Ana Rita, Costa, Mariana, Carneiro, Luís, Casaca, Pedro, Pinto-Leite, Pedro, Peralta-Santos, André, Isidro, Joana, Duarte, Sílvia, Vieira, Luís, Guiomar, Raquel, Silva, Susana, Nunes, Baltazar, Gomes, João P
• Format: Article
• Language: English
• Subjects: Antibodies; COVID-19; COVID-19 - transmission; COVID-19 - virology; Disease prevention; Gene expression; Humans; Mutation; Portugal - epidemiology; Rapid Communication; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - genetics; Viral infections
• ISSN: 1560-7917; 1025-496X; 1560-7917
• DOI: 10.2807/1560-7917.ES.2021.26.10.2100130

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.