Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria

Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of den...

Full description

Saved in:
Bibliographic Details
Published in:Emerging microbes & infections 2024-12, Vol.13 (1), p.2307511
Main Authors: Onoja, Bernard Anyebe, Oguzie, Judith Uche, George, Uwem Etop, Asoh, Kaego Emmanuel, Ajayi, Philip, Omofaye, Toluwanimi Faithful, Igeleke, Imafidon Oluwatoyin, Eromon, Philomena, Harouna, Soumare, Parker, Edyth, Adeniji, Adekunle Johnson, Happi, Christian T
Format: Article
Language:English
Subjects:
Cross-Sectional Studies
Dengue
Dengue fever
Dengue Virus - genetics
Genetic diversity
Genomes
genomic sequencing
Humans
IgG
IgM
Malaria
Malaria - epidemiology
NGS
Nigeria - epidemiology
NS1
Phylogeny
Rainforest
Seroepidemiologic Studies
Surveillance
Tropical diseases
Whole Genome Sequencing
Citations: Items that this one cites
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Dengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.
ISSN:2222-1751
2222-1751
DOI:10.1080/22221751.2024.2307511