ABSTRACT
Worldwide concern about the novel coronavirus (2019-nCoV) as a global threat to public health is the reason for the exponential growth of phylogenetic analyses. The purpose of this review was to describe the mode of operation and advantages of the tool Nextstrain, as well as the sequencing of the SARS-CoV-2 virus worldwide. The interface of the Nextstrain page was used to show its functions and data visualization modes. These were downloaded from the website GISAID to show the number of SARS-CoV-2 sequencing processes performed so far. Nextstrain is an open code project created by bioinformatics biologists to make good use of the scientific and public health potential of data about genomes of pathogens. Nextstrain consists in a set of tools operating with unprocessed sequences (in FASTA format). Nextstrain performs a sequence alignment of the input data into a multiple sequence alignment based on fast Fourier transform. Its use is based on two software applications: Augur and Auspice. Nextstrain is an efficient tool by which lay people may obtain epidemiological data in a simple manner. It may be used in the public health sector, since it shows real time data about epidemics and their geographic distribution. It may also be used to follow-up outbreaks, as is the case with COVID-19. © 2021, Centro Nacional de Informacion de Ciencias Medicas. All rights reserved.
ABSTRACT
Introduction: Genomic analysis of samples from documented COVID-19 cases can be used successfully to help track sources of Sars-Cov-2 infection, which can be quarantined to prevent the recurrent spread of the disease around the world. Objectives: To describe the SARS-CoV-2 sequences isolated from Peruvian patients. Methods: All genomes published up to March 2021, uploaded in the GISAID and Nextstrain repository, were selected. All data is on the web in a public way;In addition, the information was filtered by continent, country, region, clade, lineage, and sex from March 2020 to February 2021. Results: It was evidenced that the region with the most isolated genomes was Lima, the most frequent clade is GR, the viral lineage B.1.1 is the most frequent and persistent in time and most of the genomes were isolated from people of the female sex. Conclusions: The clade GR is common to all South American countries and the European and Asian continents, followed by clades G and GH with greater frequency;on the other hand, the most persistent viral lineage in Peru is B.1.1, this being not common with other countries.