Levels of genetic diversity of SARS-CoV-2 virus: reducing speculations about the genetic variability of the virus in South America

Filho, Cícero Batista do Nascimento; Ramos, Raquel de Souza; Paulino, Antônio João; Venâncio, Dallynne Bárbara Ramos; Felix, Pierre Teodosio

doi:10.1101/2020.09.14.296491

Cited by 4 publications

(2 citation statements)

References 6 publications

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“…This suggests that molecular diversity may be due to non-synonymous substitutions as the main components of variations. All analyses supported that the data are a confirmation that there is no consensus in the conservation of the SARS-CoV-2 genome in Brazil, corroborating what was described by FELIX et al , 2020a, for the Countries of South America, and it is therefore safe to affirm that the genetic variability of the Virus is different in different subsets for other Brazilian regions.…”

Section: Discussionsupporting

confidence: 77%

“…Part of this expansion is mainly due to the lack of infrastructure in the public health system (due to lack of personnel, medical equipment, diagnostic and/or therapeutic material) and misuse or even “non-use” of personal protective equipment (MILLER et al , 2020). With rapid dissemination and a diversified expansion in specific regions of Brazil, usually marked by insufficient sanitation and hygiene measures, SARS-CoV-2 has been establishing itself as the pandemic whose efforts in the use of protocols are by far the most inefficient since colonization (FELIX et al , 2020a).…”

Section: Introductionmentioning

confidence: 99%

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SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, São Paulo, Paraná and Tocantins

Albuquerque¹,

Silva²,

Venâncio³

et al. 2020

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In this work, 18 sequences of the SARS-CoV-2 virus were used, from four Brazilian states (Rio de Janeiro, São Paulo, Paraná and Tocantins) with 09, 04, 04, 8 and 01 haplotypes, respectively, with lengths ranging from 234 to 29,903 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform and were previously aligned with the MEGA X software, where all gaps and ambiguous sites were extracted for the construction of the phylogenetic tree. Of the 301 sites analyzed, 68% varied, 131 of which were parsimonium-informative sites. Phylogenetic analyses revealed the presence of two distinct subgroups, corroborated by the high FST (80%). The high degree of polymorphism found among these samples helped to establish a clear pattern of non-genetic structuring, based on the time of divergence between the groups. All molecular variance estimators confirmed that there was no consensus in the conservation of the studied sequences, also indicating a high variation for the protein products of the virus. In a highly miscegenational and diverse population such as the Brazilian population, this observation draws our attention to the need for an urgent increase in public health actions, awareness strategies, hygiene and distancing practices and not the other way around.

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Section: Discussionsupporting

confidence: 77%

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, São Paulo, Paraná and Tocantins

Albuquerque¹,

Silva²,

Venâncio³

et al. 2020

Preprint

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Genetic diversity analysis of the D614G mutation in SARS-CoV-2

Felix¹,

Dbr²,

Edab³

et al. 2020

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In this work, we evaluated the levels of genetic diversity in 18 genomes of SARS-CoV-2 carrying the D614G mutation, coming from Malaysia and Venezuela and publicly available at the National Center of Biotechnology and Information (NCBI). These haplotypes were previously used for phylogenetic analysis, following the LaBECom protocols. All gaps and unconserved sites were extracted for the construction of a phylogenetic tree. As specific methodologies for paired FST estimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, 20,000 random permutations were always used. The results revealed the presence of only 57 sites of polymorphic and parsimonium-informative among the 29,827bp analyzed and the analyses based on FST values confirmed the presence of two distinct genetic entities with fixation index of 22% and with a higher component of population variation (78.14%). Tau variations revealed a significant time of divergence, supported by mismatch analysis of the observed distribution (τ = 42%). It is safe to say that the small number of existing polymorphisms should not reflect major changes in the protein products of viral populations in both countries and this consideration provides the safety that, although there are differences in the haplotypes studied, these differences are minimal for both regions analyzed geographically and, therefore, it seems safe to extrapolate the levels of polymorphism and molecular diversity found in the samples for other mutant genomes of SARS-CoV-2 in other countries. This reduces speculation about the possibility of large differences between mutant strains of SARS-CoV-2 (D614G) and wild strains, at least at the level of their protein products, although the mutant form has higher transmission speed and infection. The analyses suggest that possible variations in protein products, of the wild virus in relation to its mutant form, should be minimal, bringing peace of mind as to the increased risk of death from the new form of the virus, as well as possible problems of gradual adjustments in some molecular targets for vaccines.

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The new Coronavirus (SARS-CoV-2) in Central America: Demographic-spatial simulations, Analyses of Molecular Variance (AMOVA) and Neutrality Tests in complete genomes from Belize, Guatemala, Cuba, Jamaica and Puerto Rico

Felix¹,

Ramos²,

Venâncio³

et al. 2021

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In this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2 from five Central American countries (Belize, Guatemala, Cuba, Jamaica and Puerto Rico) with 04, 10, 2, 8 and 14 haplotypes, respectively, with an extension of up to 29,885 bp. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform. Using specific methodologies for paired FST, AMOVA, mismatch, demographic-spatial expansion, molecular diversity and for the time of evolutionary divergence, it was possible to notice that only 79 sites remained conserved and that the high number of polymorphisms found helped to establish a clear pattern of genetic non-structuring, based on the time of divergence between the groups. The analyses also showed that significant evolutionary divergences within and between the five countries corroborate the fact that possible rapid and silent mutations are responsible for the increase in genetic variability of the Virus, a fact that would hinder the work with molecular targets for vaccines and medications in general.

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Levels of genetic diversity of SARS-CoV-2 virus: reducing speculations about the genetic variability of the virus in South America

Cited by 4 publications

References 6 publications

SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, São Paulo, Paraná and Tocantins

SARS-CoV-2 in Brazil: analysis of molecular variance and genetic diversity in viral haplotypes found in the states of Rio de Janeiro, São Paulo, Paraná and Tocantins

Genetic diversity analysis of the D614G mutation in SARS-CoV-2

The new Coronavirus (SARS-CoV-2) in Central America: Demographic-spatial simulations, Analyses of Molecular Variance (AMOVA) and Neutrality Tests in complete genomes from Belize, Guatemala, Cuba, Jamaica and Puerto Rico

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