ArticleScientific reports2024
Early mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants in Chile.
Article in Scientific reports, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Overview of SARS-CoV-2 genomic surveillance in Central America and the Dominican Republic from February 2020 to January 2023: the impact of PAHO and COMISCA's collaborative efforts.Frontiers in public health · 2026Article
- Molecular Epidemiology of SARS-CoV-2 during Five COVID-19 Waves and the Significance of Low-Frequency Lineages.Viruses · 2023Article
- The role of machine learning in health policies during the COVID-19 pandemic and in long COVID management.Frontiers in public health · 2023Review
- Spike protein of SARS-CoV-2 variants: a brief review and practical implications.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2022Review
- Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences.Vaccines · 2022Review
- New year, new SARS-CoV-2 variant: Resolutions on genomic surveillance protocols to face Omicron.Lancet regional health. Americas · 2022Article
- Has Omicron Changed the Evolution of the Pandemic?JMIR public health and surveillance · 2022Article
- Describing a landscape we are yet discovering.Advances in statistical analysis : AStA : a journal of the German Statistical Society · 2022Review
- Identification of the Gamma variant in an outbreak of COVID-19 at a prison in Peru.Revista espanola de sanidad penitenciariaArticle
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Authors and funding
16 authors.
Funding
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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