Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile.
Karen Y Or��stica, Sebastian B Mohr, Jonas Dehning, Simon Bauer, David Medina-Ortiz, Emil N Iftekhar, Karen Mujica, Paulo C Covarrubias, Soledad Ulloa, Andr��s E Castillo, Anamar��a Daza-S��nchez, Ricardo A Verdugo, Jorge Fern��ndez, ��lvaro Olivera-Nappa, Viola Priesemann, Seba Contreras
Author Information
Karen Y Or��stica: Facultad de Medicina, Universidad de Talca, Talca, Chile.
Sebastian B Mohr: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany.
Jonas Dehning: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany.
Simon Bauer: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany.
David Medina-Ortiz: Departamento de Ingenier��a en Computaci��n, Universidad de Magallanes, Punta Arenas, Chile.
Emil N Iftekhar: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany.
Karen Mujica: Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile.
Paulo C Covarrubias: Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile.
Soledad Ulloa: Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile.
Andr��s E Castillo: Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile.
Anamar��a Daza-S��nchez: Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile.
Ricardo A Verdugo: Facultad de Medicina, Universidad de Talca, Talca, Chile.
Jorge Fern��ndez: Sub Department of Molecular Genetics, Institute of Public Health of Chile (ISP), Santiago, Chile.
��lvaro Olivera-Nappa: Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile.
Viola Priesemann: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany.
Seba Contreras: Max Planck Institute for Dynamics and Self-Organization, G��ttingen, Germany. seba.contreras@ds.mpg.de.
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.
