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.
Publisher
University of Nairobi
Rights
Attribution-NonCommercial-NoDerivs 3.0 United StatesUsage Rights
http://creativecommons.org/licenses/by-nc-nd/3.0/us/Collections
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