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Previously identified only in Sierra Leone, Guinea, and southeastern Kenya, Bombali virus-infected Mops condylurus bats were recently found approximate to 750 km away in western Kenya. This finding supports the role of M. condylurus bats as hosts and the potential for Bombali virus circulation across the bats range in sub-Saharan Africa.

Background: Maternal immunisation to boost respiratory syncytial virus (RSV) antibodies in pregnant women, is a strategy being considered to enhance infant protection from severe RSV associated disease. However, little is known about the efficiency of transplacental transfer of RSV-specific antibodies in a setting with a high burden of malaria and HIV, to guide the implementation of such a vaccination program. Methods: Using a plaque reduction neutralization assay, we screened 400 pairs of cord and maternal serum specimens from pregnant women for RSV-specific antibodies. Participants were pregnant women of two surveillance cohorts: 200 participants from a hospital cohort in Kilifi, Coastal Kenya and 200 participants from a surveillance cohort in Siaya, Western Kenya. Transplacental transfer efficiency was determined by the cord to maternal transfer ratio (CMTR). Logistic regression was used to determine independent predictors of impaired transplacental transfer of RSV-specific antibodies. Results: A total of 800 samples were screened from the 400 participants. At enrollment the median age was 25 years (Interquartile range (IQR): 21-31). Overall, transplacental transfer was efficient and did not differ between Kilifi and Siaya cohort (1.02 vs. 1.02; p=0.946) but was significantly reduced among HIV-infected mothers compared to HIV-uninfected mothers (mean CMTR: 0.98 vs 1.03; p=0.015). Prematurity Conclusions: Transplacental transfer of RSV-specific antibodies among pregnant women in Kenya is efficient. A consideration to integrate other preventive interventions with maternal RSV vaccination targeting infants born premature (

Background The impact of human immunodeficiency virus (HIV) on pregnancy outcomes for women on antiretroviral therapy (ART) in sub-Saharan Africa remains unclear. Methods Pregnant women in Kenya were enrolled in the second trimester and followed up to delivery. We estimated effects of treated HIV with 3 pregnancy outcomes: loss, premature birth, and low birth weight and factors associated with HIV-positive status. Results Of 2113 participants, 311 (15%) were HIV infected and on ART. Ninety-one of 1762 (5%) experienced a pregnancy loss, 169/1725 (10%) a premature birth ( Conclusions Currently treated HIV was not significantly associated with adverse pregnancy outcomes. HIV-infected women, however, had a higher prevalence of other factors associated with adverse pregnancy outcomes.

BackgroundMaternal immunisation to prevent respiratory syncytial virus (RSV) associated disease among infants is in focus. However, little is known about adverse birth outcomes and associated factors occurring in a setting with high morbidities of malaria, HIV infection and undernutrition. Quantifying these ahead of introduction of a maternal vaccine would assist in assessing an association between RSV vaccination and adverse birth outcomes. MethodsA cross-sectional survey was conducted to collect data on birth outcomes from women residents of the health and demographic surveillance systems (HDSS) of Siaya and Kilifi, Kenya and from the maternity wards of Siaya County referral hospital and Bondo sub-county hospital. Participants of the HDSS sites had pregnancies registered in the years 2017 to 2020 through census rounds and were traced at home for interview. All women had a birth outcome by the time of data collection. Multiple logistic regression was used to determine independent predictors of adverse birth outcomes. Results A total of 2219 women were interviewed. Median age during pregnancy was 27.7yrs (range: 22.7-32.4), 1857 (83.7%) attended antenatal care clinic (ANC), 1,979 (89.2%) delivered at a health facility and 2204 (99.3%) reported they would take up a new maternal vaccine. Adverse birth outcomes occurred in 781 (35%) of pregnancies; 490 (62.7%) were preterm, 247 (31.6%) low birth weight, 189 (24.2%) macrosomia and 42 (5.4%) still births. Predictors of adverse birth outcomes were, eclampsia (AOR 6.86 (1.40-33.60); p=0.017), gestational diabetes (AOR 3.01 (1.24-7.30; p=0.015), and home delivery (AOR 2.48 (1.20-5.13); p=0.014). Being multiparous (AOR 0.52 (0.33-0.81); p=0.004) was protective. Home delivery was significantly associated with older maternal age 40-49 years (p=0.001), multiparous >5 (p=0.001), level of formal education below primary (p=0.001) and Islamic religion (p=0.001). ConclusionsIn this maternal population, about a third of pregnancies have adverse birth outcomes. Recognizing this baseline prevalence will be important in validating safety of a new maternal vaccine. Monitoring of the actual safety outcomes of the maternal RSV vaccine, will require integrated initiatives to mitigate against factors affecting utilization of maternal healthcare services and individual factors associated with adverse birth outcomes.

Background Maternal immunisation to boost respiratory syncytial virus (RSV) specific antibodies in pregnant women is a strategy to enhance infant protection. The timing of maternal vaccination during pregnancy may be critical for its effectiveness. However, Kenya has no documented published data on gestational age distribution of pregnant women attending antenatal care (ANC), or the proportion of women attending ANC during the proposed window period for vaccination, to inform appropriate timing for delivery or estimate potential uptake of this vaccine. Methods A cross-sectional survey was conducted within the Kilifi Health and Demographic Surveillance System (KHDSS), coastal Kenya. A simple random sample of 1000 women who had registered pregnant in 2017 to 2018 and with a birth outcome by the time of data collection was taken. The selected women were followed at their homes, and individually written informed consent was obtained. Records of their antenatal attendance during pregnancy were abstracted from their ANC booklet. The proportion of all pregnant women from KHDSS (55%) who attended for one or more ANC in 2018 was used to estimate vaccine coverage. Results Of the 1000 women selected, 935 were traced with 607/935 (64.9%) available for interview, among whom 470/607 (77.4%) had antenatal care booklets. The median maternal age during pregnancy was 28.6 years. The median (interquartile range) gestational age in weeks at the first to fifth ANC attendance was 26 (21–28), 29 (26–32), 32 (28–34), 34 (32–36) and 36 (34–38), respectively. The proportion of women attending for ANC during a gestational age window for vaccination of 28–32 weeks (recommended), 26–33 weeks and 24–36 weeks was 76.6% (360/470), 84.5% (397/470) and 96.2% (452/470), respectively. Estimated vaccine coverage was 42.1, 46.5 and 52.9% within the narrow, wide and wider gestational age windows, respectively. Conclusions In a random sample of pregnant women from Kilifi HDSS, Coastal Kenya with card-confirmed ANC clinic attendance, 76.6% would be reached for maternal RSV vaccination within the gestational age window of 28–32 weeks. Widening the vaccination window (26–33 weeks) or (24–36 weeks) would not dramatically increase vaccine coverage and would require consideration of antibody kinetics data that could affect vaccine efficacy.

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 summary Dengue 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–Taveta, where no dengue has been reported before. Genetic analysis of the virus suggests it to be most likely of Indian origin. This Indian origin DENV-2 was detected in the Mombasa outbreak in 2013, in Kilifi in 2014, in Taita–Taveta in 2016 (our study samples) and again in the Malindi outbreak in 2017. The results suggest that dengue is unrecognized in rural Kenya and more studies are needed for local risk assessment. Our findings of virus transmission between epidemics contribute to better understanding of the epidemiological situation and origins of DENV in Kenya.

Development of next-generation sequencing and metagenomics has revolutionized detection of novel viruses. Among these viruses are 3 human protoparvoviruses: bufavirus, tusavirus, and cutavirus. These viruses have been detected in feces of children with diarrhea. In addition, cutavirus has been detected in skin biopsy specimens of cutaneous T-cell lymphoma patients in France and in 1 melanoma patient in Denmark. We studied seroprevalences of IgG against bufavirus, tusavirus, and cutavirus in various populations (n = 840), and found a striking geographic difference in prevalence of bufavirus IgG. Although prevalence was low in adult populations in Finland (1.9%) and the United States (3.6%), bufavirus IgG was highly prevalent in populations in Iraq (84.8%), Iran (56.1%), and Kenya (72.3%). Conversely, cutavirus IgG showed evenly low prevalences (0%-5.6%) in all cohorts, and tusavirus IgG was not detected. These results provide new insights on the global distribution and endemic areas of protoparvoviruses.

Introduction: The commonly expected causative agents associated with flu-like symptoms in Kenya are the classical viral pathogens identifiable as influenza virus, adenovirus, parainfluenza virus, enteroviruses, respiratory syncytial virus (RSV) and rhinovirus. However, newer agents have been identified globally that present with illnesses clinically indistinguishable from those caused by the classical pathogens; one of them is human bocavirus. Methodology: A total of 384 specimens were analyzed, primarily to determine if the emerging human bocavirus (HBoV) infections exist in Kenya as coinfections with other respiratory viruses and to describe the genotype of the virus in circulation. In brief, viral nucleic acids were extracted from culture supernatants, amplified by PCR, and sequenced. Results: HBoV DNA was amplified from 1.8% of screened specimens. Coinfection with parainfluenza virus, adenovirus, and enterovirus was 2.5%, 2%, and 1.4%, respectively. Multiple coinfections consisting of HBoV plus two other viruses were found in 3% of specimens. Isolation occurred in the months of January, March, April, August, and November. Retrospective review of clinical parameters indicated that all the individuals complained of non-specific symptoms, mainly fever, coughs, nasal stuffiness, runny noses, and vomiting. Phylogenetically, the GenBank deposited sequences of this study’s isolates cluster closely to the reference strain NC_07455 (HBoV1). Conclusion: Coinfections with human bocavirus (HBoV1) occur in Kenya, and high incidence might primarily be during the early stages of children’s lives.

Background: Human TP53 is the gatekeeper for generation of human cells and is highly conserved. Any alteration/mutation to TP53 adversely affects the regulatory function of the protein, potentially resulting in cancer. This study investigated mutations in codons 7 and 249 of TP53, among patients with hepatocellular carcinoma (HCC) and chronic hepatitis B virus (HBV) infection at the Moi Teaching and Referral Hospital (MTRH), Eldoret, Kenya. Methods: In total, 33 HBV-positive patients attending MTRH hospital between September 2013 and July 2017 were purposely selected from medical records for the study; those with HCC were confirmed from the cancer registry. The patients were aged between 25-67 years, with a male-to-female ratio of 1.1:1. Blood samples were collected from the patients. DNA was extracted, amplified and sequenced using TP53 forward and reverse primers. Gene mutation detection and analysis was done on exons 4 and 7 Results: Of the 33 patients, 75.8% were chronically infected with HBV and had HCC; the rest were HBsAg positive without HCC. Homozygous proline was prevalent (54.5%) at exon 4 codon 72, followed by heterozygous Arg/Pro (33.3%) and lastly homozygous Arg/Arg (12.1%,). Pro/Pro allele was frequent in HCC group while Arg/Arg allele was common in patients without HCC. There was no significant association between the HCC and codon polymorphisms (p=0.12). In exon 7, codon 249, 24.2% of patients had an Arg-Ser mutation of which, 75.0% had HCC and 25.0% did not. There was no significant association between HCC patients and codon 249 mutation (p=0.15). Conclusion: TP53 is a gene gate keeper, the mutations under study may dependently play a role in HCC development. This study did not find any association or clear mutational pattern between P53 mutations and HCC development. Therefore, TP53 mutation is a poor indicator for prognosis and a tumor’s biological behavior among HBV-positive subjects in Kenya.

Performances of serological parallel and serial testing algorithms were analyzed using a combination of three ELISA and three rapid tests for the confirmation of HIV infection. Each was assessed individually for their sensitivity and specificity on a blinded panel of 769 retrospective sera of known HIV status. Western blot was used as a confirmatory assay for discordant results. Subsequently, one parallel and one serial testing algorithm were assessed on a new panel of 912 HIV-positive and negative samples. Individual evaluation of the ELISAs and rapid tests indicated a sensitivity of 100% for all assays except Uni-Gold with 99.7%. The specificities ranged from 99.1% to 99.4% for rapid assays and from 97.5% to 99.1% for ELISAs. A parallel and serial testing algorithms using Enzygnost and Vironostika, and Determine followed by Uni-Gold respectively, showed 100% sensitivity and specificity. The cost for testing 912 samples was US$4.74 and US$ 1.9 per sample in parallel and serial testing respectively. Parallel or serial testing algorithm yielded a sensitivity and specificity of 100%. This alternative algorithm is reliable and reduces the occurrence of both false negatives and positives. The serial testing algorithm was more cost effective for diagnosing HIV infections in this population.

Diachasmimorpha longicaudata entomopoxvirus (DlEPV) is a symbiotic entomopoxvirus (EPV) of the parasitic wasp Diachasmimorpha longicaudata. It has a double-stranded DNA genome of 250–300 kb and is >60% A-T rich. We describe ten ORFs (RI-35-1 to -10) contained within a 5.64 kb clone, RI-35, from a DlEPV EcoRI genomic library. Our goal was to identify unique motifs and compare them with others in the database, particularly those of poxviruses. Two ORFs (RI-35-1 and RI-35-7, respectively) encode putative proteins (113 aa and 219 aa) that are probably involved in regulating gene expression based on their predicted nuclear localization and the presence of SPxx motifs, leucine-zipper like sequences (113 aa), and a basic domain (219 aa). The largest gene (RI-35-3) is under the control of an intermediate/late promoter and is presumed to encode a cytoplasmic 480 aa DNA-dependent DNA helicase with conserved motifs that are characteristic of DExH helicases. Amino acid analysis of the DNA helicase sequence showed that DlEPV is close to but distinct from the Genus B EPVs. The DlEPV helicase is also distinct from that of the Diadromus pulchellus ascovirus 1a from the D. pulchellus parasitic wasp, with less than 10% amino acid identity. DlEPV encodes a 207 aa oligoribonuclease (RI-35-8) of the DEDDh family of exoribonucleases. The second largest ORF (RI-35-9) is under the control of a poxvirus early promoter and encodes a protein of 329 aa that is likely DlEPV-specific. Three ORFs (RI-35-4, -5, and -6) overlap (in the anti-sense strand) with ORFs encoding putatively important virus replication proteins (which were also under the control of intermediate promoters) and are presumably not expressed in DlEPV. These results support earlier reports that DlEPV is a member of the sub-family Entomopoxvirinae, most likely in Group C, and is the first symbiotic EPV described to date from a parasitic wasp.

Diagnostic methods allowing for rapid identification of pathogens are crucial for controlling and preventing dissemination after disease outbreaks as well as for use in surveillance programs. For arboviruses, detection of the presence of virus in their arthropod hosts is important for monitoring of viral activity and quantitative information is useful for modeling of transmission dynamics. In this study, molecular detection of Rift Valley fever virus (RVFV) in mosquito samples from the 2006 to 2007 East African outbreaks was performed using quantitative real-time PCR assay (qRT-PCR). Specific RVFV sequence-based primer/fluorogenic (TaqMan) probe sets were derived from the L and S RNA segments of the virus. Both primer-probe L and S segment-based combinations detected genomic RVFV sequences, with generally comparable levels of sensitivity. Viral loads from three mosquito species, Aedes mcintoshi, Aedes ochraceus and Mansonia uniformis were estimated and significant differences of between 5- and 1000-fold were detected between Ae. mcintoshi and M. uniformis using both the L and S primer-probe-based assays. The genetic relationships of the viral sequences in mosquito samples were established by partial M segment sequencing and assigned to the two previously described viral lineages defined by analysis of livestock isolates obtained during the 2006-2007 outbreak, confirming that similar viruses were present in both the vector and mammalian host. The data confirms the utility of qRT-PCR for identification and initial quantification of virus in mosquito samples during RVFV outbreaks. © 2012 Elsevier B.V.

OBJECTIVES: To estimate HIV prevalence and characterize risk factors among young adults in Asembo, rural western Kenya. DESIGN: Community-based cross-sectional survey. METHODS: From a demographic surveillance system, we selected a random sample of residents aged 13-34 years, who were contacted at home and invited to a nearby mobile study site. Consent procedures for non-emancipated minors required assent and parental consent. From October 2003 - April 2004, consenting participants were interviewed on risk behavior and tested for HIV and HSV-2. HIV voluntary counseling and testing was offered. RESULTS: Of 2606 eligible residents, 1822 (70%) enrolled. Primary reasons for refusal included not wanting blood taken, not wanting to learn HIV status, and partner/parental objection. Females comprised 53% of 1762 participants providing blood. Adjusted HIV prevalence was 15.4% overall: 20.5% among females and 10.2% among males. HIV prevalence was highest in women aged 25-29 years (36.5%) and men aged 30-34 years (41.1%). HSV-2 prevalence was 40.0% overall: 53% among females, 25.8% among males. In multivariate models stratified by gender and marital status, HIV infection was strongly associated with age, higher number of sex partners, widowhood, and HSV-2 seropositivity. CONCLUSIONS: Asembo has extremely high HIV and HSV-2 prevalence, and probable high incidence, among young adults. Further research on circumstances around HIV acquisition in young women and novel prevention strategies (vaccines, microbicides, pre-exposure prophylaxis, HSV-2 prevention, etc.) are urgently needed.

Background: There is need for locally-derived age-specific clinical laboratory reference ranges of healthy Africans in subSaharan Africa. Reference values from North American and European populations are being used for African subjects despite previous studies showing significant differences. Our aim was to establish clinical laboratory reference values for African adolescents and young adults that can be used in clinical trials and for patient management. Methods and Findings: A panel of 298, HIV-seronegative individuals aged 13–34 years was randomly selected from participants in two population-based cross-sectional surveys assessing HIV prevalence and other sexually transmitted infections in western Kenya. The adolescent (,18 years)-to-adults ($18 years) ratio and the male-to-female ratio was 1:1. Median and 95% reference ranges were calculated for immunohematological and biochemistry values. Compared with U.Sderived reference ranges, we detected lower hemoglobin (HB), hematocrit (HCT), red blood cells (RBC), mean corpuscular volume (MCV), neutrophil, glucose, and blood urea nitrogen values but elevated eosinophil and total bilirubin values. Significant gender variation was observed in hematological parameters in addition to T-bilirubin and creatinine indices in all age groups, AST in the younger and neutrophil, platelet and CD4 indices among the older age group. Age variation was also observed, mainly in hematological parameters among males. Applying U.S. NIH Division of AIDS (DAIDS) toxicity grading to our results, 40% of otherwise healthy study participants were classified as having an abnormal laboratory parameter (grade 1–4) which would exclude them from participating in clinical trials. Conclusion: Hematological and biochemistry reference values from African population differ from those derived from a North American population, showing the need to develop region-specific reference values. Our data also show variations in hematological indices between adolescent and adult males which should be considered when developing reference ranges. This study provides the first locally-derived clinical laboratory reference ranges for adolescents and young adults in western Kenya.