The quiet circulation of dengue virus across Africa poses a growing threat that scientists are just beginning to understand
Imagine a virus that has flown under the radar for decades, silently circulating and evolving, until it explodes into outbreaks that overwhelm health systems.
This is the story of dengue in Africa, a neglected health crisis that scientists are now racing to understand through the lens of genetic sequencing and field surveillance. For years, much of Africa's dengue burden remained invisible, with limited surveillance systems and diagnostic capabilities obscuring the true scale of transmission. Recent advances in genomic technology are finally revealing the complex dynamics of this mosquito-borne threat.
The virus is primarily transmitted to humans through the bites of infected Aedes mosquitoes, particularly Aedes aegypti and, to a lesser extent, Aedes albopictus 2 .
Nucleotide RNA genome
Distinct serotypes
Encoded proteins
These viruses contain a single-stranded RNA genome of approximately 10,700 nucleotides that encodes three structural proteins (capsid, precursor membrane, and envelope) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) 2 .
The lack of proofreading activity during replication means the virus constantly accumulates mutations, leading to significant genetic diversity and enabling its adaptation to new environments and hosts 6 .
Infection with one serotype provides lifelong immunity against that specific serotype but only partial and temporary protection against the others. This phenomenon sets the stage for a potentially more severe outcome upon secondary infection with a different serotype, through a process called antibody-dependent enhancement (ADE) 7 9 .
For decades, Africa's dengue story remained largely untold, but recent data reveals an alarming upward trajectory.
Suspected dengue cases (2013-2023)
Confirmed cases
Reported deaths
The distribution of cases shows striking regional disparities. West Africa has emerged as the epicenter, contributing to over 80% of confirmed cases . Burkina Faso has been particularly heavily affected, reporting over 500 cases per 100,000 population .
West Africa's share of confirmed cases
Annual increase in West Africa cases
Cases per 100,000 in Burkina Faso
These numbers likely represent just the tip of the iceberg due to limited surveillance and diagnostic capabilities across much of the continent.
In 2023, a team of Kenyan and international scientists seized an opportunity to unravel the mysteries of dengue transmission in Africa. Their investigation, centered on an outbreak in Mombasa, aimed to answer a critical question: were Kenya's dengue cases seeded through international importation or driven by local transmission cycles that had escaped detection? 4
They collected 406 blood samples from patients presenting with symptoms consistent with arboviral infection at healthcare facilities in Mombasa between March and July 2023 4
Using the QIAamp Viral RNA Mini Kit, they extracted viral RNA from serum samples, then screened them with flavivirus genus-wide primers before conducting serotype-specific testing 4
The extracted RNA underwent library preparation using NEBNext Ultra II RNA Library Prep Kit, followed by sequencing on Illumina platforms 4
The team generated 38 whole genome sequences (24 from the 2023 outbreak and 14 from cases identified between 2020-2025) and compared them with globally circulating strains to determine evolutionary relationships 4
The results provided unprecedented insights into dengue's silent circulation in Kenya:
Transmission Pattern: Recent introduction, widespread
Geographical Links: Regional circulation in Eastern and Western Africa
Transmission Pattern: Long-term local circulation
Geographical Links: Evidence of local evolution in Kenya
Transmission Pattern: Recent introduction
Geographical Links: Connected to outbreaks in other African regions
This groundbreaking work demonstrated that Kenya, like other African nations, faces a dual challenge: managing both the introduction of new strains from other regions and the silent local circulation of established lineages.
The Kenyan study exemplifies how modern molecular techniques are revolutionizing our understanding of dengue epidemiology. These tools have become essential in the fight against this emerging threat.
Function: Isolate viral genetic material from patient samples
Application: First step in molecular detection and sequencing
Function: Convert RNA to DNA and amplify target sequences
Application: Detect and serotype dengue virus in patient samples
Function: Determine complete genetic code of viral samples
Application: Track mutations, understand evolution, and trace outbreaks
Function: Map evolutionary relationships between virus strains
Application: Reveal patterns of local circulation vs. new introductions
Beyond these core tools, scientists are also developing innovative cell culture systems to study the virus. Researchers have recently established stable cell lines capable of supporting continuous infection with all four dengue serotypes, enabling more detailed studies of immune responses and potential treatments 7 .
The standard CDC DENV-1-4 Real-Time RT-PCR Assay represents another critical tool, allowing for precise detection and serotyping of dengue viruses during the first 7 days of illness when nucleic acid amplification tests are most effective 1 .
The revelations from genetic studies in Kenya and epidemiological data from across Africa highlight an urgent need for strengthened surveillance systems capable of detecting and monitoring dengue transmission.
The silent, long-term circulation of viruses like DENV-2 in Kenya underscores how easily dengue can fly under the radar in regions with limited diagnostic resources.
The complex patterns of serotype circulation—with different serotypes dominating in different regions and at different times—demand a coordinated, continent-wide approach to dengue control.
The close link between transmission and rainy seasons provides opportunities for targeted, seasonal interventions that could disrupt the transmission cycle before outbreaks spiral out of control.
As one team of researchers concluded, "integrated strategies to curb dengue in Kenya, such as measures to disrupt local transmission as well as importation of new strains" are essential 4 . These strategies must combine enhanced laboratory capabilities, vector control programs, and community engagement to effectively reduce Africa's growing dengue burden.
The genetic insights now emerging from laboratories across Africa represent more than academic exercises—they provide the roadmap for smarter public health interventions that could ultimately break the cycle of silent transmission and prevent the devastating outbreaks that follow.