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

• Author(s): 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.
• Date: 2021
• Persistent ID: http://hdl.handle.net/10400.18/8056
• Origin: Repositório Científico do Instituto Nacional de Saúde
• Subject(s): 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); Infecções Respiratórias; Estados de Saúde e de Doença; Portugal
• Document Type: Journal article
• Language: English
• Contributor(s): Repositório Científico do Instituto Nacional de Saúde

Description

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.