Albuquerque, R. M. d. | Search bioRxiv

bioRxiv2020

Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China

In this work, 37 haplotypes of spike glycoprotein of SARS-CoV-2 from Hong Kong, China, were used. All sequences were publicly available on the Platform of the National Center for Biotechnology Information (NCBI) and were analyzed for their Molecular Variance (AMOVA), haplotypic diversity, mismatch, demographic and spatial expansion, molecular diversity and time of evolutionary divergence. The results suggested that there was a low diversity among haplotypes, with very low numbers of transitions, transversions, indels-type mutations and with total absence of population expansion perceived in the neutrality tests. The estimators used in this study supported the uniformity among all the results found and confirm the evolutionary conservation of the gene, as well as its protein product, a fact that stimulates the use of therapies based on neutralizing antibodies, such as vaccines based on protein S.

bioinformatics↗

bioRxiv2020

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

In this work, 18 sequences of the SARS-CoV-2 virus were used, from four Brazilian states (Rio de Janeiro, Sao Paulo, Parana 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.

bioinformatics↗