Molecular epidemiology and evolutionary characteristics of dengue virus 2 in East Africa

Sindiso Nyathi (), Izabela M. Rezende, Katharine S. Walter, Panpim Thongsripong, Francis Mutuku, Bryson Ndenga, Joel O. Mbakaya, Peter Aswani, Peter S. Musunzaji, Philip K. Chebii, Priscilla W. Maina, Paul S. Mutuku, Charles M. Ng’ang’a, Said L. Malumbo, Zainab Jembe, David M. Vu, Erin A. Mordecai, Shannon Bennett, Jason R. Andrews and A. Desiree LaBeaud
Additional contact information
Sindiso Nyathi: Stanford University School of Medicine
Izabela M. Rezende: Stanford University School of Medicine
Katharine S. Walter: University of Utah
Panpim Thongsripong: University of Florida
Francis Mutuku: Technical University of Mombasa
Bryson Ndenga: Kenya Medical Research Institute
Joel O. Mbakaya: Kenya Medical Research Institute
Peter Aswani: Kenya Medical Research Institute
Peter S. Musunzaji: Msambweni Hospital
Philip K. Chebii: Msambweni Hospital
Priscilla W. Maina: Msambweni Hospital
Paul S. Mutuku: Msambweni Hospital
Charles M. Ng’ang’a: Msambweni Hospital
Said L. Malumbo: Msambweni Hospital
Zainab Jembe: Diani Health Center
David M. Vu: Stanford University
Erin A. Mordecai: Stanford University
Shannon Bennett: 55 Music Concourse Drive
Jason R. Andrews: Stanford University School of Medicine
A. Desiree LaBeaud: Stanford University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Despite the increasing burden of dengue, the regional emergence of the virus in Kenya has not been examined. This study investigates the genetic structure and regional spread of dengue virus-2 in Kenya. Viral RNA from acutely ill patients in Kenya was enriched and sequenced. Six new dengue-2 genomes were combined with 349 publicly available genomes and phylogenies used to infer gene flow between Kenya and other countries. Analyses indicate two dengue-2 Cosmopolitan genotype lineages circulating in Kenya, linked to recent outbreaks in coastal Kenya and Burkina Faso. Lineages circulating in Western, Southern, and Eastern Africa exhibiting similar evolutionary features are also reported. Phylogeography suggests importation of dengue-2 into Kenya from East and Southeast Asia and bidirectional geneflow. Additional lineages circulating in Africa are also imported from East and Southeast Asia. These findings underscore how intermittent importations from East and Southeast Asia drive dengue-2 circulation in Kenya and Africa more broadly.

Date: 2024
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DOI: 10.1038/s41467-024-51018-0

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