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Abstract
Genomic surveillance (GS) programmes were crucial in identifying and quantifying the mutating patterns of SARS-CoV-2 during the COVID-19 pandemic. In this work, we develop a Bayesian framework to quantify the relative transmissibility of different variants tailored for regions with limited GS. We use it to study the relative transmissibility of SARS-CoV-2 variants in Chile. Among the 3443 SARS-CoV-2 genomes collected between January and June 2021, where sampling was designed to be representative, the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. We found that Lambda and Gamma variants’ reproduction numbers were 5% (95% CI: [1%, 14%]) and 16% (95% CI: [11%, 21%]) larger than Alpha’s, respectively. Besides, we observed a systematic mutation enrichment in the Spike gene for all circulating variants, which strongly correlated with variants’ transmissibility during the studied period (r = 0.93, p-value = 0.025). We also characterised the mutational signatures of local samples and their evolution over time and with the progress of vaccination, comparing them with those of samples collected in other regions worldwide. Altogether, our work provides a reliable method for quantifying variant transmissibility under subsampling and emphasises the importance of continuous genomic surveillance.
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1 Universidad de Talca, Facultad de Medicina, Talca, Chile (GRID:grid.10999.38) (ISNI:0000 0001 0036 2536)
2 Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany (GRID:grid.419514.c) (ISNI:0000 0004 0491 5187); University of Göttingen, Institute for the Dynamics of Complex Systems, Göttingen, Germany (GRID:grid.7450.6) (ISNI:0000 0001 2364 4210)
3 Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany (GRID:grid.419514.c) (ISNI:0000 0004 0491 5187)
4 Universidad de Magallanes, Departamento de Ingeniería en Computación, Punta Arenas, Chile (GRID:grid.442242.6) (ISNI:0000 0001 2287 1761)
5 Institute of Public Health of Chile (ISP), Sub Department of Molecular Genetics, Santiago, Chile (GRID:grid.510309.e) (ISNI:0000 0001 2186 0462)
6 Universidad de Chile, Centre for Biotechnology and Bioengineering, Santiago, Chile (GRID:grid.443909.3) (ISNI:0000 0004 0385 4466)
7 Universidad de Talca, Facultad de Medicina, Talca, Chile (GRID:grid.10999.38) (ISNI:0000 0001 0036 2536); Universidad de Chile, Departamento de Oncología Básico-Clínica, Facultad de Medicina, Santiago, Chile (GRID:grid.443909.3) (ISNI:0000 0004 0385 4466)
8 Universidad de Chile, Centre for Biotechnology and Bioengineering, Santiago, Chile (GRID:grid.443909.3) (ISNI:0000 0004 0385 4466); Universidad de Chile, Department of Chemical Engineering, Biotechnology and Materials, Santiago, Chile (GRID:grid.443909.3) (ISNI:0000 0004 0385 4466)