Full-Length Genome and Partial Viral Genes Phylogenetic and Geographical Analysis of Dengue Serotype 3 Isolates.

Muhammad Amir,Hina Alam,Abrar Hussain,Muhammad Asif,Luigi Marceanu,Marius Alexandru Moga,Sagheer Ahmed,Alexandru Blidaru,Maria Elena Cocuz

doi:10.3390/microorganisms9020323

Abstract

Dengue fever is among the most common vector-borne diseases. Dengue virus (DENV), responsible for dengue fever as well as dengue hemorrhagic fever, belongs to the genus flavivirus and family Flaviviridae. Flaviviruses infect various vertebrate species and arthropods and are also responsible for diseases in birds, wild animals, and primates. DENV consists of a single-stranded, positive-sense RNA genome ~11 kb in size. Complete genome and partial gene sequences of geographically distinct DENV-3 strains were retrieved from the GenBank database. The evolutionary divergence of the 33 whole-genome and individual gene sequences of the nucleotides and amino acids of DENV-3 strains were generated with the maximum likelihood (ML) and Bayesian phylogenetic study (BEAST) methods using the MEGA 7 software. The genome size varied from 10,484 to 10,724 nucleotides among the strains with distinct geographical backgrounds belonging to Central America, South-Central Asia, and Eastern Asia. A phylogenetic analysis of the nucleotide and amino acid sequences of these DENV-3 isolates revealed extensive differences in the topologies due to PrM/M, NS1, NS2B, and NS3 genes. These results suggest substantial variation in the evolutionary pathways of the studied genes and genomes.

Highlights

Dengue fever (DF) is one of the most common vector-borne diseases in the world, mostly found in tropical as well as in subtropical regions
The 33 complete genome Dengue virus (DENV)-3 strains ranged in size from 10,484 to 10,724 nucleotides with various topographical backgrounds, including Central America, South
Previous studies have employed individual gene sequences of DENV-3 for phylogenetic investigations and classified them into various genotypes [18]. Most of such studies use E gene sequences for the genotyping of DENV-3 [19], other genes have been used by some investigators [20]

Summary

Introduction

Dengue fever (DF) is one of the most common vector-borne diseases in the world, mostly found in tropical as well as in subtropical regions. Dengue virus (DENV), the causative microorganism of DF and dengue hemorrhagic fever (DHF), is a member of the Flavivirus genus and belongs to the Flaviviridae family. Infection with flaviviruses varies from asymptomatic to lethal, and more than 50% of viruses may cause human diseases. Influenza-like illness with sudden onset of fever, arthralgia, myalgia, retro-orbital headaches, maculopapular rash, leukopenia, vascular leakage, and encephalitis are mostly associated with flaviviruses infections [2]. The genus flavivirus contains several important disease-causing viruses such as yellow fever virus (YFV), West Nile virus (WNV), and Japanese encephalitis virus (JEV), as well as tick-borne encephalitis virus (TBEV), associated with tick-borne diseases [3]

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Conclusion