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Veterinary sciences2022; 9(6); 258; doi: 10.3390/vetsci9060258

Phylogenetic and Mutation Analysis of the Venezuelan Equine Encephalitis Virus Sequence Isolated in Costa Rica from a Mare with Encephalitis.

Abstract: Venezuelan Equine Encephalitis virus (VEEV) is an arboviral pathogen in tropical America that causes lethal encephalitis in horses and humans. VEEV is classified into six subtypes (I to VI). Subtype I viruses are divided into epizootic (IAB and IC) and endemic strains (ID and IE) that can produce outbreaks or sporadic diseases, respectively. The objective of this study was to reconstruct the phylogeny and the molecular clock of sequences of VEEV subtype I complex and identify mutations within sequences belonging to epizootic or enzootic subtypes focusing on a sequence isolated from a mare in Costa Rica. Bayesian phylogeny of the VEEV subtype I complex tree with 110 VEEV complete genomes was analyzed. Evidence of positive selection was evaluated with Datamonkey server algorithms. The putative effects of mutations on the 3D protein structure in the Costa Rica sequence were evaluated. The phylogenetic analysis showed that Subtype IE-VEEV diverged earlier than other subtypes, Costa Rican VEEV-IE ancestors came from Nicaragua in 1963 and Guatemala in 1907. Among the observed non-synonymous mutations, only 17 amino acids changed lateral chain groups. Fourteen mutations located in the NSP3, E1, and E2 genes are unique in this sequence, highlighting the importance of E1-E2 genes in VEEV evolution.
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Publication Date: 2022-05-28 PubMed ID: 35737310PubMed Central: PMC9229380DOI: 10.3390/vetsci9060258Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The research attempts to understand the phylogeny and molecular clock of Venezuelan Equine Encephalitis Virus (VEEV) subtype I complex and identify mutations in specific sequences. Particular focus was given to a sequence isolated from a mare in Costa Rica. The findings show the evolution and divergence of the virus over time while identifying specific non-synonymous mutations in certain genes unique to this sequence.

Objective of the Study

  • The main aim of the study was to understand the evolution and mutation patterns of the Venezuelan Equine Encephalitis Virus (VEEV) subtype I complex. This involved analyzing the phylogeny and molecular clock of the virus.
  • A key focus of the research was an examination of a sequence of the virus that was isolated from a mare in Costa Rica. The researchers aimed to identify any mutations in this sequence.

Methods and Analysis

  • The researchers reconstructed the Bayesien phylogeny of the VEEV subtype I complex tree using 110 complete VEEV genomes.
  • Positive selection, which is a key process in evolution, was evaluated using Datamonkey server algorithms.
  • The putative effects of the identified mutations on the 3D protein structure within the Costa Rican sequence were also evaluated. This helped to understand how these mutations might impact the functionality of the virus.

Research Findings

  • The phylogenetic analysis revealed that the Subtype IE-VEEV diverged earlier than the other subtypes, with the Costa Rican VEEV-IE ancestors traced back to Nicaragua in 1963 and Guatemala in 1907.
  • The researchers found non-synonymous mutations (mutations that alter the amino acid sequence of a protein) with only 17 amino acids changing their lateral chain groups.
  • Out of these, 14 mutations were unique to the sequence isolated from the mare in Costa Rica. These mutations were located in the NSP3, E1 and E2 genes, underscoring the role these genes might play in VEEV evolution.

Implications of the Study

  • This kind of genetic and phylogenetic understanding can play a fundamental role in predicting the possible evolution and spread of the virus.
  • The identification of unique mutations in specific genes also provides potential targets for diagnostics, treatment, and vaccines for this pathogen.

Cite This Article

APA
León B, González G, Nicoli A, Rojas A, Pizio AD, Ramirez-Carvajal L, Jimenez C. (2022). Phylogenetic and Mutation Analysis of the Venezuelan Equine Encephalitis Virus Sequence Isolated in Costa Rica from a Mare with Encephalitis. Vet Sci, 9(6), 258. https://doi.org/10.3390/vetsci9060258

Publication

Veterinary sciences
ISSN: 2306-7381
NlmUniqueID: 101680127
Country: Switzerland
Language: English
Volume: 9
Issue: 6
PII: 258

Researcher Affiliations

León, Bernal
  • LSE Laboratory, Veterinary Service National Laboratory, Animal Health National Service, Ministry of Agriculture and Cattle, Heredia 40104, Costa Rica.
  • Virology, Universidad Técnica Nacional (UTN), Atenas 20505, Costa Rica.
González, Gabriel
  • National Virus Reference Laboratory, College Dublin, D04 V1W8 Belfield, Ireland.
Nicoli, Alessandro
  • Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany.
Rojas, Alicia
  • Laboratory of Helminthology, Centro de Investigación en Enfermedades Tropicales, University of Costa Rica, San José 11501, Costa Rica.
Pizio, Antonella Di
  • Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany.
Ramirez-Carvajal, Lisbeth
  • Veterinary Medicine Infection and Immunity, Virology, University of Utrecht, 3584 CS Utrecht, The Netherlands.
Jimenez, Carlos
  • Laboratory of Virology, Tropical Diseases Research Program (PIET), School of Veterinary Medicine, Universidad Nacional, Heredia 40101, Costa Rica.

Conflict of Interest Statement

The authors declare no conflict of interest.

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