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URL: https://dx.doi.org/DOI:10.17504/protocols.io.bmbvk2n6

Authors: Pierre Teodosio Felix, Robson da Silva Ramos, Dallynne Bárbara Ramos Venâncio, Cícero Batista do Nascimento Filho, Antônio João Paulino

Group: Coronavirus Method Development Community, LaBECom

Summary: In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2, publicly available on the National Center for Biotechnology Information (NCBI) platform and from six countries in South America (Brazil, Chile, Peru, Colombia, Uruguay and Venezuela with 16, 11, 1, 1, 1, 7 haplotypes, respectively), all with an extension of 29,906 bp and Phred values ≥ 40. These haplotypes were previously used for phylogenetic analyses, following the alignment protocols of the MEGA X software; where all gaps and unconserved sites were extracted for the construction of phylogenetic trees. The specific methodologies for Paired FSTestimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, were obtained using 20,000 random permutation.

Affiliations: Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA

Version: 1

Publication Date: 2020

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