SARS-CoV-2 genetic diversity in Venezuela: Predominance of D614G variants and analysis of one outbreak

Autor: Héctor R. Rangel, Rossana C. Jaspe, Marwan Aguilar, Mariangel Delgado, Flor H. Pujol, Víctor Alarcón, Domingo Garzaro, Pierina D´Angelo, José L. Zambrano, Lieska Rodríguez, Carmen L. Loureiro
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0301 basic medicine
RNA viruses
Protein Structure Comparison
Topography
Viral Diseases
Coronaviruses
viruses
Viral Nonstructural Proteins
Genome
Biochemistry
Geographical locations
Medical Conditions
Macromolecular Structure Analysis
Pathology and laboratory medicine
Phylogeny
Data Management
Genetics
Sanger sequencing
Islands
Multidisciplinary
virus diseases
Phylogenetic Analysis
Genomics
Medical microbiology
Phylogenetics
Infectious Diseases
Viruses
symbols
Medicine
SARS CoV 2
Pathogens
Research Article
Protein Structure
Computer and Information Sciences
Lineage (genetic)
SARS coronavirus
Science
030106 microbiology
Genome
Viral
Biology
Microbiology
03 medical and health sciences
symbols.namesake
Protein Domains
Genetic variation
Humans
Evolutionary Systematics
Gene
Molecular Biology
Taxonomy
Medicine and health sciences
Genetic diversity
Landforms
Evolutionary Biology
Biology and life sciences
SARS-CoV-2
Organisms
Viral pathogens
Outbreak
Proteins
COVID-19
Genetic Variation
Geomorphology
Covid 19
South America
Venezuela
Microbial pathogens
030104 developmental biology
Earth Sciences
People and places
Zdroj: PLoS ONE, Vol 16, Iss 2, p e0247196 (2021)
PLoS ONE
ISSN: 1932-6203
Popis: SARS-CoV-2 is the new coronavirus responsible for COVID-19 disease. The first two cases of COVID-19 were detected in Venezuela on March 13, 2020. The aim of this study was the genetic characterization of Venezuelan SARS-CoV-2 isolates. A total of 7 full SARS-CoV-2 genome sequences were obtained by Sanger sequencing, from patients of different regions of Venezuela, mainly from the beginning of the epidemic. Ten out of 11 isolates (6 complete genomes and 4 partial spike genomic regions) belonged to lineage B, bearing the D614G mutation in the Spike protein. Isolates from the first outbreak that occurred in the Margarita Island harbored an in-frame deletion in its sequence, without amino acids 83–85 of the NSP1 of the ORF1. The search for deletions in 48,635 sequences showed that the NSP1 gene exhibit the highest frequency of deletions along the whole genome. Structural analysis suggests a change in the N-terminal domain with the presence of this deletion. In contrast, isolates circulating later in this island lacked the deletion, suggesting new introductions to the island after this first outbreak. In conclusion, a high diversity of SARS-CoV-2 isolates were found circulating in Venezuela, with predominance of the D614G mutation. The first small outbreak in Margarita Island seemed to be associated with a strain carrying a small deletion in the NSP1 protein, but these isolates do not seem to be responsible for the larger outbreak which started in July.
Databáze: OpenAIRE
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