Evidence of circulation of Orthobunyaviruses in diverse mosquito species in Kwale County, Kenya.

BACKGROUND: Arbovirus surveillance and recurrence of outbreaks in Kenya continues to reveal the re-emergence of viruses of public health importance. This calls for sustained efforts in early detection and characterization of these agents to avert future potential outbreaks. METHODS: A larval survey was carried out in three different sites in Kwale County, Vanga, Jego and Lunga Lunga. All containers in every accessible household and compound were sampled for immature mosquitoes. In addition, adult mosquitoes were also sampled using CO2-baited CDC light traps and BG-Sentinel traps in the three sites and also in Tsuini. The mosquitoes were knocked down using trimethylamine and stored in a liquid nitrogen shipper for transportation to the laboratory where they were identified to species, pooled and homogenized ready for testing. RESULTS: A total of 366 houses and 1730 containers were inspected. The House Index (HI), Container Index (CI) and Breateau Index (BI) for Vanga Island were (3%: 0.66: 3.66) respectively. In Jego, a rural site, the HI, CI and BI were (2.4%: 0.48: 2.4) respectively. In Lunga Lunga, a site in an urban area, the HI, CI and BI were (22.03%: 3.97: 29.7) respectively. The indices suggest that this region is at risk of arbovirus transmission given they were above the WHO threshold (CI > 1, HI > 1% and BI > 5). The most productive containers were the concrete tanks (44.4%), plastic tank (22.2%), claypot (13.3%), plastic drums (8.9%), plastic basins (4%), jerricans (1.2%) and buckets (0.3%). Over 20,200 adult mosquitoes were collected using CDC light traps, and over 9,200 using BG- sentinel traps. These mosquitoes were screened for viruses by inoculating in Vero cells. Eleven Orthobunyavirus isolates were obtained from pools of Ae. pembaensis (4), Ae. tricholabis (1), Cx. quinquefasciatus (3), Culex spp. (1) and Cx. zombaensis (2). Five of the Orthobunyaviruses were sequenced and four of these were determined to be Bunyamwera viruses while one isolate was found to be Nyando virus. One isolate remained unidentified. CONCLUSIONS: These results indicate circulation of Orthobunyaviruses known to cause diverse grades of febrile illness with rash in humans in this region and highlights the need for continued monitoring and surveillance to avert outbreaks.

Probable contribution of Culex quinquefasciatus mosquitoes to the circulation of chikungunya virus during an outbreak in Mombasa County, Kenya, 2017-2018.

BACKGROUND: Chikungunya virus is an alphavirus, primarily transmitted by Aedes aegypti and Ae. albopictus. In late 2017-2018, an outbreak of chikungunya occurred in Mombasa county, Kenya, and investigations were conducted to establish associated entomological risk factors. METHODS: Homes were stratified and water-filled containers inspected for immature Ae. aegypti, and larval indices were calculated. Adult mosquitoes were collected in the same homesteads using BG-Sentinel and CDC light traps and screened for chikungunya virus. Experiments were also conducted to determine the ability of Culex quinquefasciatus to transmit chikungunya virus. RESULTS: One hundred thirty-one houses and 1637 containers were inspected; 48 and 128 of them, respectively, were positive for immature Ae. aegypti, with the house index (36.60), container index (7.82) and Breteau index (97.71) recorded. Jerry cans (n = 1232; 72.26%) and clay pots (n = 2; 0.12%) were the most and least inspected containers, respectively, while drums, the second most commonly sampled (n = 249; 15.21%), were highly positive (65.63%) and productive (60%). Tires and jerry cans demonstrated the highest and lowest breeding preference ratios, 11.36 and 0.2, respectively. Over 6900 adult mosquitoes were collected and identified into 15 species comprising Cx. quinquefasciatus (n = 4492; 65.04%), Aedes vittatus (n = 1137; 16.46%) and Ae. aegypti (n = 911; 13.19%) and 2 species groups. Simpson's dominance and Shannon-Wiener diversity indices of 0.4388 and 1.1942 were recorded, respectively. Chikungunya virus was isolated from pools of Ae. aegypti (1) and Cx. quinquefasciatus (4), two of which were males. Minimum infection rates of 3.0 and 0.8 were observed for female Ae. aegypti and Cx. quinquefasciatus, respectively. Between 25 and 31.3% of exposed mosquitoes became infected with CHIKV 7, 14 and 21 days post-exposure. For the experimentally infected Cx. quinquefasciatus mosquitoes, between 13 and 40% had the virus disseminated, with 100% transmission being observed among those with disseminated infection. CONCLUSIONS: These results demonstrated high risk of chikungunya transmission for residents in the sampled areas of Mombasa. Transmission data confirmed the probable role played by Cx. quinquefasciatus in the outbreak while the role of Ae. vittatus in the transmission of chikungunya virus remains unknown.

Emergence of a novel chikungunya virus strain bearing the E1:V80A substitution, out of the Mombasa, Kenya 2017-2018 outbreak.

Between late 2017 and mid-2018, a chikungunya fever outbreak occurred in Mombasa, Kenya that followed an earlier outbreak in mid-2016 in Mandera County on the border with Somalia. Using targeted Next Generation Sequencing, we obtained genomes from clinical samples collected during the 2017/2018 Mombasa outbreak. We compared data from the 2016 Mandera outbreak with the 2017/2018 Mombasa outbreak, and found that both had the Aedes aegypti adapting mutations, E1:K211E and E2:V264A. Further to the above two mutations, 11 of 15 CHIKV genomes from the Mombasa outbreak showed a novel triple mutation signature of E1:V80A, E1:T82I and E1:V84D. These novel mutations are estimated to have arisen in Mombasa by mid-2017 (2017.58, 95% HPD: 2017.23, 2017.84). The MRCA for the Mombasa outbreak genomes is estimated to have been present in early 2017 (2017.22, 95% HPD: 2016.68, 2017.63). Interestingly some of the earliest genomes from the Mombasa outbreak lacked the E1:V80A, E1:T82I and E1:V84D substitutions. Previous laboratory experiments have indicated that a substitution at position E1:80 in the CHIKV genome may lead to increased CHIKV transmissibility by Ae. albopictus. Genbank investigation of all available CHIKV genomes revealed that E1:V80A was not present; therefore, our data constitutes the first report of the E1:V80A mutation occurring in nature. To date, chikungunya outbreaks in the Northern and Western Hemispheres have occurred in Ae. aegypti inhabited tropical regions. Notwithstanding, it has been suggested that an Ae. albopictus adaptable ECSA or IOL strain could easily be introduced in these regions leading to a new wave of outbreaks. Our data on the recent Mombasa CHIKV outbreak has shown that a potential Ae. albopictus adapting mutation may be evolving within the East African region. It is even more worrisome that there exists potential for emergence of a CHIKV strain more adapted to efficient transmission by both Ae. albopictus and Ae.aegypti simultaneously. In view of the present data and history of chikungunya outbreaks, pandemic potential for such a strain is now a likely possibility in the future. Thus, continued surveillance of chikungunya backed by molecular epidemiologic capacity should be sustained to understand the evolving public health threat and inform prevention and control measures including the ongoing vaccine development efforts.

Epidemiological Investigation of a Rift Valley Fever Outbreak in Humans and Livestock in Kenya, 2018.

On the last week of May of 2018, a community-based syndromic surveillance system detected mass abortions and deaths of young livestock in northeastern Kenya. Two weeks later, Rift Valley fever (RVF) was confirmed in humans presenting with febrile illness and hemorrhagic syndrome in the same region. A joint animal and human response team carried out an investigation to characterize the outbreak and identify drivers of disease transmission. Here, we describe the outbreak investigation and findings. A total of 106 human cases were identified in the months of May and June 2018: 92% (98) and 8% (8) of these cases occurring in the northern and western regions of Kenya, respectively. Seventy-six (72%) were probable cases, and 30 (28%) were laboratory confirmed by ELISA and/or PCR. Among the confirmed cases, the median age was 27.5 years (interquartile range = 20), and 60% (18) were males. Overall, the case fatality rate was 7% (n = 8). The majority of the confirmed cases, 19 (63%), reported contact with livestock during slaughter and consumption of meat from sick animals. All confirmed cases had fever, 40% (12) presented with hemorrhagic syndrome, and 23% (7) presented with jaundice. Forty-three livestock herds with at least one suspect and/or confirmed animal case were identified. Death of young animals was reported in 93% (40) and abortions in 84% (36) of livestock herds. The outbreak is indicative of the emergence potential of RVF in traditionally high- and low-risk areas and the risk posed by zoonosis to livestock keepers.

Serological Evidence of Chikungunya Virus Infection Among Suspected Measles Cases in Selected Regions of Kenya: 2008-2014.

Chikungunya virus (family Togavirdae and genus Alphavirus) is an emerging and reemerging virus of public health importance both regionally and globally. In Kenya, about 50-60% of the suspected measles cases remain undiagnosed once measles and rubella is ruled out by immunoglobulin M (IgM) ELISA thus prompted the need to do differential diagnosis on the measles/rubella negative samples. Nothing is known about the role played by chikungunya infection among these suspected measles cases. Febrile rash illness is a common clinical presentation of arboviruses, including chikungunya. In this study, we conducted a serosurvey to explore the possible role of chikungunya infections among suspected measles cases in Kenya that had tested negative for measles and rubella. Sera were tested by commercially available ELISA for the presence of IgG and IgM antibodies against the chikungunya virus. All positive samples for chikungunya by ELISA were confirmed by plaque reduction neutralization test (PRNT), and to rule out cross-reactivity with other alphaviruses a panel of viruses was used, namely o' nyong' nyong, Semliki Forest, and Sindbis viruses. Of the 392 serum samples screened, 0.3% (n = 1) tested positive for IgM antibodies, while 4.6% (n = 18) tested positive for IgG antibodies against the chikungunya virus. PRNT results indicated 2 (11%) chikungunya positives and 7 (38.9%) o' nyong' nyong positives. We recommend awareness among health care providers and improved surveillance for these arboviruses by both serology and molecular testing. Testing for other pathogens should also be done to improve disease detection and diagnosis.

Origin and evolution of dengue virus type 2 causing outbreaks in Kenya: Evidence of circulation of two cosmopolitan genotype lineages.

Dengue fever (DF) is an arboviral disease caused by dengue virus serotypes 1-4 (DENV 1-4). Globally, DF incidence and disease burden have increased in the recent past. Initially implicated in a 1982 outbreak, DENV-2 recently reemerged in Kenya causing outbreaks between 2011 and 2014 and more recently 2017-8. The origin and the evolutionary patterns that may explain the epidemiological expansion and increasing impact of DENV-2 in Kenya remain poorly understood. Using whole-genome sequencing, samples collected during the 2011-4 and 2017-8 dengue outbreaks were analyzed. Additional DENV-2 genomes were downloaded and pooled together with the fourteen genomes generated in this study. Bioinformatic methods were used to analyze phylogenetic relationships and evolutionary patterns of DENV-2 causing outbreaks in Kenya. The findings from this study have shown the first evidence of circulation of two different Cosmopolitan genotype lineages of DENV-2; Cosmopolitan-I (C-I) and Cosmopolitan-II (C-II), in Kenya. Our results put the origin location of C-I lineage in India in 2011, and C-II lineage in Burkina Faso between 1979 and 2013. C-I lineage was the most isolated during recent outbreaks, thus showing the contribution of this newly emerged strain to the increased DENV epidemics in the region. Our findings, backed by evidence of recent local epidemics that have been associated with C-I in Kenya and C-II in Burkina Faso, add to the growing evidence of expanding circulation and the impact of multiple strains of DENV in the region as well as globally. Thus, continued surveillance efforts on DENV activity and its evolutionary trends in the region, would contribute toward effective control and the current vaccine development efforts.

Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak.

In 2016, a chikungunya virus (CHIKV) outbreak was reported in Mandera, Kenya. This was the first major CHIKV outbreak in the country since the global reemergence of this virus in Kenya in 2004. We collected samples and sequenced viral genomes from this outbreak. All Kenyan genomes contained two mutations, E1:K211E and E2:V264A, recently reported to have an association with increased infectivity, dissemination, and transmission in the Aedes aegypti vector. Phylogeographic inference of temporal and spatial virus relationships showed that this variant emerged within the East, Central, and South African lineage between 2005 and 2008, most probably in India. It was also in India where the first large outbreak caused by this virus appeared, in New Delhi, 2010. More importantly, our results also showed that this variant is no longer contained to India. We found it present in several major outbreaks, including the 2016 outbreaks in Pakistan and Kenya, and the 2017 outbreak in Bangladesh. Thus, this variant may have a capability of driving large CHIKV outbreaks in different regions of the world. Our results point to the importance of continued genomic-based surveillance and prompt urgent vector competence studies to assess the level of vector susceptibility and virus transmission, and the impact this might have on this variant's epidemic potential and global spread.

Human and entomologic investigations of chikungunya outbreak in Mandera, Northeastern Kenya, 2016.

Chikungunya is a reemerging vector borne pathogen associated with severe morbidity in affected populations. Lamu, along the Kenyan coast was affected by a major chikungunya outbreak in 2004. Twelve years later, we report on entomologic investigations and laboratory confirmed chikungunya cases in northeastern Kenya. Patient blood samples were received at the Kenya Medical Research Institute (KEMRI) viral hemorrhagic fever laboratory and the immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against chikungunya and dengue. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus, alphavirus and chikungunya specific primers were used to detect acute infections and representative PCR positive samples sequenced to confirm the circulating strain. Immature mosquitoes were collected from water-holding containers indoors and outdoors in the affected areas in northeastern Kenya. A total of 189 human samples were tested; 126 from Kenya and 63 from Somalia. 52.9% (100/189) tested positive for Chikungunya virus (CHIKV) by either IgM ELISA or RT-PCR. Sequence analysis of selected samples revealed that the virus was closely related to that from China (2010). 29% (55/189) of the samples, almost all from northeastern Kenya or with a history of travel to northern Kenya, tested positive for dengue IgM antibodies. Entomologic risk assessment revealed high house, container and Breteau indices of, 14.5, 41.9 and 17.1% respectively. Underground water storage tanks were the most abundant, 30.1%, of which 77.4% were infested with Aedes aegypti mosquitoes. These findings confirm the presence of active chikungunya infections in the northeastern parts of Kenya. The detection of dengue IgM antibodies concurrently with chikungunya virus circulation emphasizes on the need for improved surveillance systems and diagnostic algorithms with the capacity to capture multiple causes of arbovirus infections as these two viruses share common vectors and eco-systems. In addition sustained entomological surveillance and vector control programs targeting most productive containers are needed to monitor changes in vector densities, for early detection of the viruses and initiate vector control efforts to prevent possible outbreaks.

Investigation of laboratory confirmed Dengue outbreak in North-eastern Kenya, 2011.

The first laboratory confirmed dengue outbreak in Kenya was reported in coastal towns of Malindi and Kilifi in 1982. Since then, no other outbreak had been confirmed in Kenya. Dengue outbreak was confirmed among African Mission soldiers in Somalia (AMISOM) between May to October 2011. From September 2011, an upsurge of febrile patients who were negative for malaria on microscopy were reported in several health facilities in Mandera town, an adjacent area to Somalia in northern Kenya. We investigated a suspected dengue outbreak in Mandera town from 26th September 2011 to 5th October 2011. A suspected case was defined as acute onset of fever with two or more of the following: headache, arthralgia, myalgia, rash and hemorrhages and negative malaria microscopy results in a person presenting to a health facility in Mandera town from 1st August to 2nd October 2011. We prospectively identified new cases meeting the suspect case definition from 2nd October to 5th October 2011 and we collected blood samples from consenting patients. Blood was collected into plastic vacutainers and stored in dry shipper at -80oc to laboratory for dengue virus testing using real time reverse transcriptase polymerase chain reaction (rRT-PCR). We administered a standardized form to obtain clinical information. We calculated descriptive statistics to describe the outbreak. A total of 1,332 patients had been line listed by the district surveillance team, of which 381 (29%) met our suspect case definition of dengue. Cases peaked between 10th September and 1st October 2011 and thereafter declined. We prospectively identified 33 cases meeting the suspect case definition, of whom 30 (91%) were positive for dengue virus serotype 3 by PCR. Among the 30 laboratory confirmed patients, 20 (67%) required hospitalization (Median hospitalization period, two days with a range: 1-4 days)). And of these, 26 (86%) patients reported aches and pain, 16 (53%) reported vomiting, and four (13%) gingival bleeding. Twenty-three (77%) received anti-malarial therapy. Among laboratory-confirmed dengue patients, seven (23%) had malaria co-infection. This was the second confirmed Dengue outbreak in Kenya, and highlighted the need for improved surveillance to better define disease burden and continuous education to medical personnel to improve detection and clinical management. We also recommended enhanced community education for disease prevention.

Detection of dengue virus serotypes 1, 2 and 3 in selected regions of Kenya: 2011-2014.

BACKGROUND: Dengue fever, a mosquito-borne disease, is associated with illness of varying severity in countries in the tropics and sub tropics. Dengue cases continue to be detected more frequently and its geographic range continues to expand. We report the largest documented laboratory confirmed circulation of dengue virus in parts of Kenya since 1982. METHODS: From September 2011 to December 2014, 868 samples from febrile patients were received from hospitals in Nairobi, northern and coastal Kenya. The immunoglobulin M enzyme linked immunosorbent assay (IgM ELISA) was used to test for the presence of IgM antibodies against dengue, yellow fever, West Nile and Zika. Reverse transcription polymerase chain reaction (RT-PCR) utilizing flavivirus family, yellow fever, West Nile, consensus and sero type dengue primers were used to detect acute arbovirus infections and determine the infecting serotypes. Representative samples of PCR positive samples for each of the three dengue serotypes detected were sequenced to confirm circulation of the various dengue serotypes. RESULTS: Forty percent (345/868) of the samples tested positive for dengue by either IgM ELISA (14.6 %) or by RT-PCR (25.1 %). Three dengue serotypes 1-3 (DENV1-3) were detected by serotype specific RT-PCR and sequencing with their numbers varying from year to year and by region. The overall predominant serotype detected from 2011-2014 was DENV1 accounting for 44 % (96/218) of all the serotypes detected, followed by DENV2 accounting for 38.5 % (84/218) and then DENV3 which accounted for 17.4 % (38/218). Yellow fever, West Nile and Zika was not detected in any of the samples tested. CONCLUSION: From 2011-2014 serotypes 1, 2 and 3 were detected in the Northern and Coastal parts of Kenya. This confirmed the occurrence of cases and active circulation of dengue in parts of Kenya. These results have documented three circulating serotypes and highlight the need for the establishment of active dengue surveillance to continuously detect cases, circulating serotypes, and determine dengue fever disease burden in the country and region.

A household serosurvey to estimate the magnitude of a dengue outbreak in Mombasa, Kenya, 2013.

Dengue appears to be endemic in Africa with a number of reported outbreaks. In February 2013, several individuals with dengue-like illnesses and negative malaria blood smears were identified in Mombasa, Kenya. Dengue was laboratory confirmed and an investigation was conducted to estimate the magnitude of local transmission including a serologic survey to determine incident dengue virus (DENV) infections. Consenting household members provided serum and were questioned regarding exposures and medical history. RT-PCR was used to identify current DENV infections and IgM anti-DENV ELISA to identify recent infections. Of 1,500 participants from 701 households, 210 (13%) had evidence of current or recent DENV infection. Among those infected, 93 (44%) reported fever in the past month. Most (68, 73%) febrile infected participants were seen by a clinician and all but one of 32 participants who reportedly received a diagnosis were clinically diagnosed as having malaria. Having open windows at night (OR = 2.3; CI: 1.1-4.8), not using daily mosquito repellent (OR = 1.6; CI: 1.0-2.8), and recent travel outside of Kenya (OR = 2.5; CI: 1.1-5.4) were associated with increased risk of DENV infection. This survey provided a robust measure of incident DENV infections in a setting where cases were often unrecognized and misdiagnosed.

Dengue expansion in Africa-not recognized or not happening?

An expert conference on Dengue in Africa was held in Accra, Ghana, in February 2013 to consider key questions regarding the possible expansion of dengue in Africa. Four key action points were highlighted to advance our understanding of the epidemiology of dengue in Africa. First, dengue diagnostic tools must be made more widely available in the healthcare setting in Africa. Second, representative data need to be collected across Africa to uncover the true burden of dengue. Third, established networks should collaborate to produce these types of data. Fourth, policy needs to be informed so the necessary steps can be taken to provide dengue vector control and health services.

Detection of avian influenza viruses in wild waterbirds in the Rift Valley of Kenya using fecal sampling.

Highly pathogenic avian influenza virus A/H5N1 has been reported in 11 African countries. Migratory waterbirds have the potential of introducing A/H5N1 into east Africa through the Rift Valley of Kenya. We present the results of a wild bird surveillance system for A/H5N1 and other avian influenza viruses based on avian fecal sampling in Kenya. We collected 2630 fecal samples in 2008. Viral RNA was extracted from pools of 3-5 fecal samples and analyzed for presence of avian influenza virus RNA by real-time RT-PCR. Twelve (2.3%) of the 516 sample pools were positive for avian influenza virus RNA, 2 of which were subtyped as H4N6 viruses. This is the first report of avian influenza virus in wild birds in Kenya. This study demonstrates the success of this approach in detecting avian influenza virus in wild birds and represents an efficient surveillance system for avian influenza virus in regions with limited resources.

Seroprevalence and distribution of arboviral infections among rural Kenyan adults: a cross-sectional study.

BACKGROUND: Arthorpod-borne viruses (arboviruses) cause wide-spread morbidity in sub-Saharan Africa, but little research has documented the burden and distribution of these pathogens. METHODS: Using a population-based, cross-sectional study design, we administered a detailed questionnaire and used ELISA to test the blood of 1,141 healthy Kenyan adults from three districts for the presence of anti-viral Immunoglobulin G (IgG) antibodies to the following viruses: dengue (DENV), West Nile (WNV), yellow fever (YFV), Chikungunya (CHIKV), and Rift Valley fever (RVFV). RESULTS: Of these, 14.4% were positive for DENV, 9.5% were WNV positive, 9.2% were YFV positive, 34.0% were positive for CHIKV and 0.7% were RVFV positive. In total, 46.6% had antibodies to at least one of these arboviruses. CONCLUSIONS: For all arboviruses, district of residence was strongly associated with seropositivity. Seroprevalence to YFV, DENV and WNV increased with age, while there was no correlation between age and seropositivity for CHIKV, suggesting that much of the seropositivity to CHIKV is due to sporadic epidemics. Paradoxically, literacy was associated with increased seropositivity of CHIKV and DENV.

A growing global network's role in outbreak response: AFHSC-GEIS 2008-2009.

A cornerstone of effective disease surveillance programs comprises the early identification of infectious threats and the subsequent rapid response to prevent further spread. Effectively identifying, tracking and responding to these threats is often difficult and requires international cooperation due to the rapidity with which diseases cross national borders and spread throughout the global community as a result of travel and migration by humans and animals. From Oct.1, 2008 to Sept. 30, 2009, the United States Department of Defense's (DoD) Armed Forces Health Surveillance Center Global Emerging Infections Surveillance and Response System (AFHSC-GEIS) identified 76 outbreaks in 53 countries. Emerging infectious disease outbreaks were identified by the global network and included a wide spectrum of support activities in collaboration with host country partners, several of which were in direct support of the World Health Organization's (WHO) International Health Regulations (IHR) (2005). The network also supported military forces around the world affected by the novel influenza A/H1N1 pandemic of 2009. With IHR (2005) as the guiding framework for action, the AFHSC-GEIS network of international partners and overseas research laboratories continues to develop into a far-reaching system for identifying, analyzing and responding to emerging disease threats.

Seroprevalence of Chikungunya virus (CHIKV) infection on Lamu Island, Kenya, October 2004.

An outbreak of Chikungunya virus (CHIKV) disease associated with high fever and severe protracted arthralgias was detected in Lamu, Kenya, peaking in July 2004. At least 1,300 cases were documented. We conducted a seroprevalence study to define the magnitude of transmission on Lamu Island. We conducted a systematic cross-sectional survey. We administered questionnaires and tested 288 sera from Lamu residents for IgM and IgG antibodies to CHIKV. Chikungunya virus infection (seropositivity) was defined as a person with IgG and/or IgM antibodies to CHIKV. IgM antibodies to CHIKV were detected in 18% (53/288) and IgG antibodies in 72% (206/288); IgM and/or IgG antibodies were present in 75% (215/288). The seroprevalence findings suggested that the outbreak was widespread, affecting 75% of the Lamu population; extrapolating the findings to the entire population, 13,500 (95% CI, 12,458-14328) were affected. Vector control strategies are needed to control the spread of this mosquito-borne infection.

Genetic analysis of H3N2 influenza A viruses isolated in 2006-2007 in Nairobi, Kenya.

BACKGROUND: Minimal influenza surveillance has been carried out in sub-Saharan Africa to provide information on circulating influenza subtypes for the purpose of vaccine production and monitoring trends in virus spread and mutations. OBJECTIVE: The aim of this study was to investigate a surveillance program in Kenya to isolate and characterize influenza viruses. RESULTS: In the 2006-2007 influenza season, nine influenza A viruses were isolated. All were of H3N2 subtype with key amino acid (aa) changes indicating that they were more closely related to recent World Health Organization recommended vaccine strains than to older vaccine strains, and mirroring the evolution of circulating influenza A globally. Hemagglutination inhibition data showed that the 2006 Kenya isolates had titers identical to the 2005-2006 H3N2 vaccine strain but two- to threefold lower titers to the 2006-2007 vaccine strain, suggesting that the isolates were antigenic variants of the 2006-2007 vaccine strains. Analysis of aa substitutions of hemagglutinin-1 (HA1) protein of the 2006 Kenyan viruses revealed unique genetic variations with several aa substitutions located at immunodominant epitopes of the HA1 protein. These mutations included the V112I change at site E, the K 173 E substitution at site D and N 278 K change at site C, mutations that may result in conformational change on the HA molecule to expose novel epitopes thus abrogating binding of pre-existing antibodies at these sites. CONCLUSION: Characterization of these important genetic variations in influenza A viruses isolated from Kenya highlights the importance of continuing surveillance and characterization of emerging influenza drift variants in sub-Saharan Africa.

Laboratory diagnosis of Ebola hemorrhagic fever during an outbreak in Yambio, Sudan, 2004.

Between the months of April and June 2004, an Ebola hemorrhagic fever (EHF) outbreak was reported in Yambio county, southern Sudan. Blood samples were collected from a total of 36 patients with suspected EHF and were tested by enzyme-linked immunosorbent assay (ELISA) for immunoglobulin G and M antibodies, antigen ELISA, and reverse-transcription polymerase chain reaction (PCR) of a segment of the Ebolavirus (EBOV) polymerase gene. A total of 13 patients were confirmed to be infected with EBOV. In addition, 4 fatal cases were classified as probable cases, because no samples were collected. Another 12 patients were confirmed to have acute measles infection during the same period that EBOV was circulating. Genetic analysis of PCR-positive samples indicated that the virus was similar to but distinct from Sudan EBOV Maleo 1979. In response, case management, social mobilization, and follow-up of contacts were set up as means of surveillance. The outbreak was declared to be over on 7 August 2004.

Seroprevalence of Chikungunya virus infection on Grande Comore Island, union of the Comoros, 2005.

An outbreak of Chikungunya virus (CHIKV) illness associated with high fever combined with prolonged and severe arthralgias occurred on Grande Comore Island from January through May 2005; 5,202 cases were reported. A seroprevalence study was conducted to define the extent of transmission on the island. We conducted a cross-sectional survey using a multistage sampling technique. A total of 481 households were sampled. In each household, one resident was selected randomly for interview and blood collection. We administered questionnaires and tested 331 sera for CHIKV-specific IgM and IgG antibodies by capture enzyme-linked immunosorbent assay. Infection with CHIKV infection (seropositivity) was defined as presence of IgG and/or IgM antibodies to CHIKV. A total of 331 (69%) of 481 survey participants consented to blood collection. Antibodies to CHIKV were detected in 63% of sera; IgM antibodies were found in 60% of specimens and IgG antibodies were detected in 27% of specimens. Extrapolation of the findings to the entire Grande Comore population suggested that nearly 215,000 people were infected with CHIKV during the outbreak. A total of 79% of the seropositive persons were hospitalized or stayed at home in bed for a mean of 6 days (range = 1-30 days); 52% missed work or school for a mean of 7 days (range = 1-40 days). The findings suggest that CHIKV was broadly transmitted during the outbreak with a high attack rate. Although not fatal during this outbreak, CHIKV infection caused significant morbidity and decreased economic productivity.

Literacy and recent history of diarrhoea are predictive of Plasmodium falciparum parasitaemia in Kenyan adults.

BACKGROUND: Malaria is one of the most serious health problems in Kenya. In 2004, the Kenya Medical Research Institute and the US Army Medical Research Unit--Kenya surveyed adults in Samburu, Malindi, and Busia districts to determine socioeconomic risk factors for infection. METHODS: Sociodemographic, health, and antimalarial data were collected along with blood for malaria testing. A smear was considered negative only if no Plasmodium falciparum parasites were observed in 100 high-powered fields. Univariate analysis was performed with Pearson's Chi-square test and univariate logistic regression. A multivariate logistic regression model was then created which included only variables found to be at least marginally significant in univariate analysis. RESULTS: A total of 1,141 subjects were recruited: 238 from Samburu, 442 from Malindi, and 461 from Busia. Smear positivities for P. falciparum were 1.7% in Samburu, 7.2% in Malindi and 22.3% in Busia. Interdistrict differences were statistically significant (p < 0.001) in univariate analysis and in a multivariate logistic regression model which included district, literacy, occupation, and recent illness as independent variables. In the model, literacy and recent diarrhoeal illness were positively and at least marginally significantly associated with parasitaemia (p = 0.023 and p = 0.067, respectively). Neither age, sex, occupation, history of malaria in the previous three months, nor use of antimalarials in the previous four weeks were significantly associated with parasitaemia. CONCLUSION: While district of residence was the variable most highly predictive for parasitaemia among Kenyan adults surveyed, both a recent history of diarrhoeal illness and literacy were at least marginally statistically significant predictors.