Molecular diagnosis of arboviruses (dengue, Chikungunya, yellow fever, Rift Valley fever, Mayaro, West Nile, and Zika viruses) in non-malaria acute febrile illnesses in Kenya’s Garissa County, July 2023, and Mombasa County, July 2024

Abstract Background Viral haemorrhagic fever outbreaks can have a devastating impact on local populations. In Mombasa County, and also remote Kenyan areas, such as Garissa County, where health centres have limited diagnostic capacity, the causes of non-malaria, febrile illnesses are often unknown. In particular mosquito-borne, arboviral infections, which can lead to severe disease manifestations, are difficult to detect without molecular diagnostics. The present study aimed to establish the prevalence of selected arboviral agents in blood samples from patients presenting with non-malarial febrile illness at health facilities in Garissa and Mombasa County. Methods Following the long rainy seasons and during peak-transmission season for mosquito-borne diseases, the National Public Health Laboratory, Ministry of Health, Kenya, deployed a mobile laboratory with molecular testing capacity to the remote Garissa County Referral Hospital (GCRH) in July 2023 and to Mvita Sub-County Hospital in Mombasa County in July 2024. With the help of this mobile laboratory, a prospective arboviral surveillance mission was conducted for the first time in Garissa County in north eastern Kenya bordering Somalia, as well as in the coastal region of Kenya’s Mombasa County. These, and neighbouring counties reported arboviral infections before. Results A total of 326 febrile patients from Garissa, for which malaria microscopy was negative, received differential diagnosis for risk group 3 arboviruses using the Altona Diagnostics Real Star RT-PCR kits for dengue, Chikungunya, Rift Valley, yellow fever viruses. We found four dengue virus PCR-positive patients and therefore 1.23% (CI95%: 0.36%-3.23%, modified Wald method) of non-malaria febrile illnesses were due to this virus. In Mombasa County, 289 non-malaria, febrile patients cases were screened with the VIASURE Tropical Panel I Real Time PCR Detection Kit for dengue, Chikungunya, yellow fever, Zika, Mayaro, West Nile viruses. We found 26 PCR-positive patients for dengue virus or a dengue prevalence of 9.00% (CI95%: 6.17%-12.90%). We did not detect any of the other mosquito-borne arboviruses, however we cannot exclude their role in future outbreaks in the region following rainy and mosquito seasons. Conclusions Although molecular diagnostics exist at the central NPHL, our findings show that in peripheral health centres in both counties, scaling-up of arboviral diagnostics in general, and dengue diagnostic capacity (rapid tests, PCR, serology) in particular, for patients presenting with febrile illness is urgently needed. As one of the novel dengue vaccine regulations recommend that only previously infected patients receive the vaccine in order to prevent severe forms of the disease, increased surveillance, serotyping of isolates and host serology is essential as well. The mobile laboratory demonstrated its added value to provide diagnostic services to remote cross-border areas.