Complete Coding Sequences of Dengue Virus Type 2 Strains from Febrile Patients Seen in Malindi District Hospital, Kenya, during the 2017 Dengue Fever Outbreak

Gathii, Kimita; Nyataya, Josphat; Mutai, Beth; Awinda, George; Waitumbi, John N.

doi:10.1128/genomea.00076-18

Cited by 10 publications

(13 citation statements)

References 6 publications

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“…Our sequence data from Taita-Taveta, located inland approximately 150 kilometres from the coast, is from the year 2016 and thus timed between the two large dengue outbreaks of the coastal cities of Mombasa in 2013 and Malindi in 2017. The findings are in line with previous work, which used complete genomic data and concluded that the 2017 Malindi outbreak strains were clonally derived and closely related to strains from India [11]. Our analysis further estimated the timing of the introduction of this lineage to Kenya a year before the 2013 Mombasa outbreak.…”

Section: Discussionsupporting

confidence: 91%

“…The IgG IFA titres ranged from 10 to 2560. 12 samples had low titres (10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20), 31 samples had intermediate titers and 7 samples had high titers (640-2560). For one sample, the titre could not be determined after the initial screening dilution due to a lack of sample volume.…”

Section: Diagnostic Assay Resultsmentioning

confidence: 99%

“…The currently available data suggest, that after the 2013 Mombasa outbreak the virus spread towards the northeast along the coast. The virus was detected from febrile patients in Kilifi in 2014 [10] and later caused the Malindi 2017 outbreak [11] (Fig 1). In our analysis, the sister group to all the Kenyan cosmopolitan DENV-2 strains included Indian strains and interestingly also a strain originating from Djibouti or Ethiopia in 2016 from a traveller patient.…”

Section: Discussionmentioning

confidence: 99%

“…From this outbreak three DENV-2 isolates were obtained and sequenced [9], followed by ten strains of cosmopolitan genotype DENV-2 obtained from patient samples collected in 2014-2015 in Kilifi [10]. Again in 2017 an outbreak occurred in Malindi, where ten strains of related cosmopolitan genotype DENV-2 were isolated [11] demonstrating sustained DENV-2 circulation in Kenya.…”

Section: Introductionmentioning

confidence: 99%

“…Maps of study areas in Kenya. The smaller map shows the locations of the study sites in Nairobi and the Taita Hills, as well as the dengue endemic coastal cities with reported dengue virus (DENV) -2 outbreaks (Mombasa 2013 and Malindi 2017)[11,15]) and the town of Kilifi where DENV-2 was detected in febrile patients in 2014[10]. The larger map shows more detailed sample collection locations in Voi, Wundanyi and Mwatate in Taita-Taveta County.…”

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confidence: 99%

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Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

et al. 2020

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Dengue virus (DENV) has caused recent outbreaks in coastal cities of Kenya, but the epidemiological situation in other areas of Kenya is largely unknown. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. Altogether, 560 patients were sampled in 2016-2017 in rural Taita-Taveta County (n = 327) and urban slums of Kibera, Nairobi (n = 233). The samples were studied for DENV IgM, IgG, NS1 antigen and flaviviral RNA. IgG seroprevalence was found to be higher in Taita-Taveta (14%) than in Nairobi (3%). Five Taita-Taveta patients were positive for flaviviral RNA, all identified as DENV-2, cosmopolitan genotype. Local transmission in Taita-Taveta was suspected in a patient without travel history. The sequence analysis suggested that DENV-2 strains circulating in coastal and southern Kenya likely arose from a single introduction from India. The molecular clock analyses dated the most recent ancestor to the Kenyan strains a year before the large 2013 outbreak in Mombasa. After this, the virus has been detected in Kilifi in 2014, from our patients in Taita-Taveta in 2016, and in an outbreak in Malindi in 2017. The results highlight that silent transmission occurs between epidemics and also affects rural areas. More information is needed to understand the local epidemiological characteristics and future risks of dengue in Kenya. Author summaryDengue virus (DENV) is an emerging mosquito-borne global health threat in the tropics and subtropics. The majority of the world's population live in areas at risk of dengue that can cause a wide variety of symptoms from febrile illness to haemorrhagic fever. Information of DENV in Africa is limited and fragmented. In Kenya, dengue is a recognized disease in coastal cities that have experienced recent outbreaks. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. We found DENV-2 in five febrile patients from rural Taita-

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Section: Discussionsupporting

confidence: 91%

Section: Diagnostic Assay Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

et al. 2020

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The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications

Pollett

Gathii

Figueroa

et al. 2021

Infection, Genetics and Evolution

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Evolution, heterogeneity and global dispersal of cosmopolitan genotype of Dengue virus type 2

Yenamandra

Koo

Chiang

et al. 2021

Sci Rep

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Dengue virus type 2 (DENV-2) contributes substantially to the dengue burden and dengue-related mortality in the tropics and sub-tropics. DENV-2 includes six genotypes, among which cosmopolitan genotype is the most widespread. The present study investigated the evolution, intra-genotype heterogeneity and dispersal of cosmopolitan genotype to understand unique genetic characteristics that have shaped the molecular epidemiology and distribution of cosmopolitan lineages. The spatial analysis demonstrated a wide geo-distribution of cosmopolitan genotype through an extensive inter-continental network, anchored in Southeast Asia and Indian sub-continent. Intra-genotype analyses using 3367 envelope gene sequences revealed six distinct lineages within the cosmopolitan genotype, namely the Indian sub-continent lineage and five other lineages. Indian sub-continent lineage was the most diverged among six lineages and has almost reached the nucleotide divergence threshold of 6% within E gene to qualify as a separate genotype. Genome wide amino acid signatures and selection pressure analyses further suggested differences in evolutionary characteristics between the Indian sub-continent lineage and other lineages. The present study narrates a comprehensive genomic analysis of cosmopolitan genotype and presents notable genetic characteristics that occurred during its evolution and global expansion. Whether those characteristics conferred a fitness advantage to cosmopolitan genotype in different geographies warrant further investigations.

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Complete Coding Sequences of Dengue Virus Type 2 Strains from Febrile Patients Seen in Malindi District Hospital, Kenya, during the 2017 Dengue Fever Outbreak

Cited by 10 publications

References 6 publications

Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

Detection of dengue virus type 2 of Indian origin in acute febrile patients in rural Kenya

The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications

Evolution, heterogeneity and global dispersal of cosmopolitan genotype of Dengue virus type 2

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