{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/mutational-signatures-and-transmissibility-of","title":"Mutational signatures and transmissibility of SARS-CoV-2 Gamma and Lambda variants","arxiv_id":"2108.10018","date":"2021-08-23","proceeding":null,"authors":["Karen Y. Oróstica","Sebastian Contreras","Sebastian B. Mohr","Jonas Dehning","Simon Bauer","David Medina-Ortiz","Emil N. Iftekhar","Karen Mujica","Paulo C. Covarrubias","Soledad Ulloa","Andrés E. Castillo","Ricardo A. Verdugo","Jorge Fernández","Álvaro Olivera-Nappa","Viola Priesemann"],"abstract":"The emergence of SARS-CoV-2 variants of concern endangers the long-term control of COVID-19, especially in countries with limited genomic surveillance. In this work, we explored genomic drivers of contagion in Chile. We sequenced 3443 SARS-CoV-2 genomes collected between January and July 2021, where the Gamma (P.1), Lambda (C.37), Alpha (B.1.1.7), B.1.1.348, and B.1.1 lineages were predominant. Using a Bayesian model tailored for limited genomic surveillance, we found that Lambda and Gamma variants' reproduction numbers were about 5% and 16% larger than Alpha's, respectively. We observed an overabundance of mutations in the Spike gene, strongly correlated with the variant's transmissibility. Furthermore, the variants' mutational signatures featured a breakpoint concurrent with the beginning of vaccination (mostly CoronaVac, an inactivated virus vaccine), indicating an additional putative selective pressure. Thus, our work provides a reliable method for quantifying novel variants' transmissibility under subsampling (as newly-reported Delta, B.1.617.2) and highlights the importance of continuous genomic surveillance.","url_abs":"https://arxiv.org/abs/2108.10018v1","url_pdf":"https://arxiv.org/pdf/2108.10018v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"mutational-signatures-and-transmissibility-of","repo_url":"https://github.com/Priesemann-Group/covid19_inference","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}