Full-genome sequencing and analysis of DENV-3 serotype isolated from Yemen

Sayed Sartaj Sohrab; Tariq Ahmed Madani; Sherif Ali El- Kafrawy; Hussein Mohamed Al-Bar; Altayeb Mohamed Abo Elzein; Suha Abdulaal Ali Farraj; Norah Abdulhamed Uthman; Ahmed Mohamed Sharif Hassan; Leena Hussein Bajrai; Esam Ibraheem Azhar

doi:10.1016/j.jiph.2021.03.014

Full-genome sequencing and analysis of DENV-3 serotype isolated from Yemen

J Infect Public Health. 2021 Jun;14(6):803-810. doi: 10.1016/j.jiph.2021.03.014. Epub 2021 Apr 14.

Affiliations

¹ Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
² Department of Medicine, Faculty of Medicine, Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia; Scientific Chair of Sheikh Mohammad Hussein Al-Amoudi for Viral Hemorrhagic Fever, King Abdulaziz University, Jeddah, Saudi Arabia.
³ Department of Family and Community Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
⁴ Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Scientific Chair of Sheikh Mohammad Hussein Al-Amoudi for Viral Hemorrhagic Fever, King Abdulaziz University, Jeddah, Saudi Arabia.
⁵ Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
⁶ Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.
⁷ Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. Electronic address: eazhar@kau.edu.sa.

PMID: 34044250
DOI: 10.1016/j.jiph.2021.03.014

Abstract

Background: Dengue virus causes the dengue fever as well as hemorrhagic fever in tropical and sub-tropical countries. It is now endemic in most parts of the South East Asia. Full-genome information of dengue virus 3 is not available from Yemen.

Methods: In this study, the dengue virus 3 was detected by diagnostic tools like serology and RT-PCR in the samples isolated from a patient in Yemen. The full-genome was sequenced, and the identity, phylogenetic relationship and recombination analysis was performed by using BioEdit, MEGA X and RDP4 softwares.

Results: The full-genome of the Yemen isolate was found to be 10,643 nt long with 3390 amino acids. The Yemen dengue virus 3 isolate showed the sequence similarity (98.5-92.4%) with dengue virus 3 isolates from China, Pakistan, India and Bangladesh respectively. The significant non-synonymous substitutions of amino acid in Yemen isolate were observed with selected isolates. The phylogenetic tree of Yemen isolate formed a unique clade within genotype III and sub-clade into lineage III. The Dengue virus isolate from Jeddah formed separated cluster with lineage IV.

Conclusions: This reveals the unique genetic variability among DENV-3 serotypes from Jeddah and earlier reported isolates from other regions.

Keywords: Dengue virus; Genetic variation; Genome; Recombination; Yemen.

MeSH terms

Bangladesh
China
Dengue Virus* / genetics
Dengue* / epidemiology
Genotype
Humans
India
Pakistan
Phylogeny
RNA, Viral / genetics
Serogroup
Yemen / epidemiology

Substances

RNA, Viral