Emerging & Re-emerging Arboviral Infections in Patients With Acute Febrile Illness in Two Counties in Kenya

Abstract

Background Covid-19 has demonstrated the impact that emerging infections can have on our health, social and economic wellbeing. About three-quarters of emerging infections have a zoonotic origin, and are transmitted to humans by arthropod vectors and vertebrate hosts such as bats and rodents. The incidence of arthropod-borne viruses has increased in recent decades mainly due to globalization, international travel and climate change. They have the potential to emerge and re-emerge in most parts of the globe posing a substantial threat to public health. Diagnosis of emerging pathogens remains a challenge due to the non-specific clinical presentation and lack of point-of-care diagnostic assays in many regions where these infections are frequent. This means that emerging infections are often not identified at all, or in time to contain an outbreak before it spreads to other areas. Objectives To determine the prevalence of emerging and re-emerging arboviral infections in patients with acute febrile illness in Kibera informal settlement and Taita-Taveta County. Methods This was a cross-sectional study on patients with acute febrile illness presenting at selected health facilities in Taita-Taveta County (3 health facilities) and Kibera informal settlement, Nairobi (3 health facilities). A clinician-administered questionnaire to collect demographic and clinical information was used. Blood samples were analyzed for infection or exposure to arboviruses as well as the presence of other viral pathogens using ELISA and immunofluorescence assays to screen for IgG and IgM antibodies against flaviviruses and alphaviruses which are the commonest arboviruses in the country. Where sufficient sample volume was available, antibody-positive samples were analyzed using plaque reduction neutralizing tests (PRNT). Reverse-transcription PCR with degenerate group-consensus primers was used to screen for alphavirus and flavivirus nucleic acid. Samples that were PCR-positive were further analyzed using Sanger sequencing to identify the specific virus. High-throughput sequencing using Illumina MiSeq™ was used to analyze PCR-positive samples as well as 110 randomly selected samples (in 22 pools of 5 samples each) and screened for novel or unexpected viral pathogens in the samples. Both clinical and laboratory data were analyzed using IBM SPSS Statistics 22. Data on prevalence of arboviruses were summarized using frequencies and percentages. Associations were tested using logistic regression. A p-value of <0.05 was considered significant. Findings A total of 557 samples from individual patients were analyzed; 326 serum samples from Taita-Taveta and 231 plasma samples from Kibera. The prevalence of current flavivirus infection (IgM antibodies, NS1 antigen or PCR positive) was 1.5 % (2.1% in Taita- Taveta and 0.4% in Nairobi). Previous exposure to flaviviruses (IgG antibody) was 9% (13% in Taita-Taveta and 3% in Nairobi). Four patients (0.2%) had alphavirus IgM antibodies on both ELISA and PRNT. Of all samples, 49 (8.8%) were IgG positive on IFA; 22 (6.7%) in Taita-Taveta and 27 (11.7%) in Kibera. Most of the samples tested on alphavirus PRNT had higher titers (2 to 8-fold) against ONNV than CHIKV and a few with higher titers for CHIKV than for ONNV. Five samples (1%) tested positive for flavivirus and only one for alphavirus on PCR. Dengue virus was isolated from two samples in culture. Three complete coding sequences and one dengue env gene sequence were retrieved. All dengue sequences were identified as dengue type 2 and formed a single monophyletic cluster that was closely related to other dengue sequences recovered from coastal Kenya between 2014 and 2017. Human pegiviruses, HIV, Enterovirus A and Torquetenoviruses were also detected in sample pools that were analyzed using Illumina MiSeq™ high-throughput sequencing. Conclusion Arboviruses are associated with acute febrile illness even during inter-epidemic periods. Exposure to both alphaviruses and flaviviruses is moderate in both Taita-Taveta and Nairobi which are geographically disparate areas in the country. Emerging and reemerging disease surveillance systems in Kenya should include arboviruses even in areas where arbovirus outbreaks have not yet been reported.