Juliette R. Ongus

Differing Burden and Epidemiology of Non-Typhi Salmonella Bacteremia in Rural and Urban Kenya, 2006–2009

Background The epidemiology of non-Typhi Salmonella (NTS) bacteremia in Africa will likely evolve as potential co-factors, such as HIV, malaria, and urbanization, also change. Methods As part of population-based surveillance among 55,000 persons in malaria-endemic, rural and malaria-nonendemic, urban Kenya from 2006–2009, blood cultures were obtained from patients presenting to referral clinics with fever ≥38.0°C or severe acute respiratory infection. Incidence rates were adjusted based on persons with compatible illnesses, but whose blood was not cultured. Results NTS accounted for 60/155 (39%) of blood culture isolates in the rural and 7/230 (3%) in the urban sites. The adjusted incidence in the rural site was 568/100,000 person-years, and the urban site was 51/100,000 person-years. In both sites, the incidence was highest in children <5 years old. The NTS-to-typhoid bacteremia ratio in the rural site was 4.6 and in the urban site was 0.05. S. Typhimurium represented >85% of blood NTS isolates in both sites, but only 21% (urban) and 64% (rural) of stool NTS isolates. Overall, 76% of S. Typhimurium blood isolates were multi-drug resistant, most of which had an identical profile in Pulse Field Gel Electrophoresis. In the rural site, the incidence of NTS bacteremia increased during the study period, concomitant with rising malaria prevalence (monthly correlation of malaria positive blood smears and NTS bacteremia cases, Spearmans correlation, p = 0.018 for children, p = 0.16 adults). In the rural site, 80% of adults with NTS bacteremia were HIV-infected. Six of 7 deaths within 90 days of NTS bacteremia had HIV/AIDS as the primary cause of death assigned on verbal autopsy. Conclusions NTS caused the majority of bacteremias in rural Kenya, but typhoid predominated in urban Kenya, which most likely reflects differences in malaria endemicity. Control measures for malaria, as well as HIV, will likely decrease the burden of NTS bacteremia in Africa.

Blood Meal Analysis and Virus Detection in Blood-Fed Mosquitoes Collected During the 2006–2007 Rift Valley Fever Outbreak in Kenya

BACKGROUND Rift Valley fever (RVF) is a zoonosis of domestic ruminants in Africa. Blood-fed mosquitoes collected during the 2006-2007 RVF outbreak in Kenya were analyzed to determine the virus infection status and animal source of the blood meals. MATERIALS AND METHODS Blood meals from individual mosquito abdomens were screened for viruses using Vero cells and RT-PCR. DNA was also extracted and the cytochrome c oxidase 1 (CO1) and cytochrome b (cytb) genes amplified by PCR. Purified amplicons were sequenced and queried in GenBank and Barcode of Life Database (BOLD) to identify the putative blood meal sources. RESULTS The predominant species in Garissa were Aedes ochraceus, (n=561, 76%) and Ae. mcintoshi, (n=176, 24%), and Mansonia uniformis, (n=24, 72.7%) in Baringo. Ae. ochraceus fed on goats (37.6%), cattle (16.4%), donkeys (10.7%), sheep (5.9%), and humans (5.3%). Ae. mcintoshi fed on the same animals in almost equal proportions. RVFV was isolated from Ae. ochraceus that had fed on sheep (4), goats (3), human (1), cattle (1), and unidentified host (1), with infection and dissemination rates of 1.8% (10/561) and 50% (5/10), respectively, and 0.56% (1/176) and 100% (1/1) in Ae. mcintoshi. In Baringo, Ma. uniformis fed on sheep (38%), frogs (13%), duikers (8%), cattle (4%), goats (4%), and unidentified hosts (29%), with infection and dissemination rates of 25% (6/24) and 83.3% (5/6), respectively. Ndumu virus (NDUV) was also isolated from Ae. ochraceus with infection and dissemination rates of 2.3% (13/561) and 76.9% (10/13), and Ae. mcintoshi, 2.8% (5/176) and 80% (4/5), respectively. Ten of the infected Ae. ochraceus had fed on goats, sheep (1), and unidentified hosts (2), and Ae. mcintoshi on goats (3), camel (1), and donkey (1). CONCLUSION This study has demonstrated that RVFV and NDUV were concurrently circulating during the outbreak, and sheep and goats were the main amplifiers of these viruses respectively.

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Human rhinoviruses (HRVs) are a well‐established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized.

Genetic divergence of Chikungunya virus plaque variants from the Comoros Island (2005)

Chikungunya virus (CHIKV) from a human sample collected during the 2005 Chikungunya outbreak in the Comoros Island, showed distinct and reproducible large (L2) and small (S7) plaques which were characterized in this study. The parent strain and plaque variants were analysed by in vitro growth kinetics in different cell lines and their genetic similarity assessed by whole genome sequencing, comparative sequence alignment and phylogenetic analysis. In vitro growth kinetic assays showed similar growth patterns of both plaque variants in Vero cells but higher viral titres of S7 compared to L2 in C6/36 cells. Amino acids (AA) alignments of the CHIKV plaque variants and S27 African prototype strain, showed 30 AA changes in the non-structural proteins (nsP) and 22 AA changes in the structural proteins. Between L2 and S7, only two AAs differences were observed. A missense substitution (C642Y) of L2 in the nsP2, involving a conservative AA substitution and a nonsense substitution (R524X) of S7 in the nsP3, which has been shown to enhance O’nyong-nyong virus infectivity and dissemination in Anopheles mosquitoes. The phenotypic difference observed in plaque size could be attributed to one of these AA substitutions. Phylogenetic analysis showed that the parent strain and its variants clustered closely together with each other and with Indian Ocean CHIKV strains indicating circulation of isolates with close evolutionary relatedness in the same outbreak. These observations pave way for important functional studies to understand the significance of the identified genetic changes in virulence and viral transmission in mosquito and mammalian hosts.

Natural Vertical Transmission of Ndumu Virus in Culex pipiens (Diptera: Culicidae) Mosquitoes Collected as Larvae

ABSTRACT Ndumu virus (NDUV) is a member of the family Togaviridae and genus Alphavirus. In Kenya, the virus has been isolated from a range of mosquito species but has not been associated with human or animal morbidity. Little is know about the transmission dynamics or vertebrate reservoirs of this virus. NDUV was isolated from two pools of female Culex pipiens mosquitoes, IJR37 (n = 18) and IJR73 (n = 3), which were collected as larvae on 15 April 2013 from two dambos near the village of Marey, Ijara District, Garissa County, Kenya, and reared to adults and identified to species. These results represent the first field evidence of vertical transmission of NDUV among mosquitoes.

The viral aetiology of influenza-like illnesses in Kampala and Entebbe, Uganda, 2008

Background As the threat of zoonoses and the emergence of pandemic-prone respiratory viruses increases, there is a need to establish baseline information on the incidence of endemic pathogens in countries worldwide. Objectives To investigate the presence of viruses associated with influenza-like illnesses (ILI) in Uganda. Methods A cross-sectional study was conducted in which nasopharyngeal swab specimens were collected from patients diagnosed with ILI in Kampala and Entebbe between 14 August 2008 – 15 December 2008. A multiplex polymerase chain reaction assay for detecting 12 respiratory viruses was used. Results A total of 369 patients (52.3% females) was enrolled; the median age was 6 years (range 1–70). One or more respiratory viruses were detected in 172 (46.6%) cases and their prevalence were influenza A virus (19.2%), adenovirus (8.7%), human rhinovirus A (7.9%), coronavirus OC43 (4.3%), parainfluenza virus 1 (2.7%), parainfluenza virus 3 (2.7%), influenza B virus (2.2%), respiratory syncytial virus B (2.2%), human metapneumovirus (1.4%), respiratory syncytial virus A (1.1%), parainfluenza virus 2 (0.5%) and coronavirus 229E (0.5%). There were 24 (14.0%) mixed infections. Conclusions This study identified some of the respiratory viruses associated with ILI in Uganda. The circulation of some of the viruses was previously unknown in the study population. These results are useful in order to guide future surveillance and case management strategies involving respiratory illnesses in Uganda.

Development and Evaluation of an in-House IgM-Capture ELISA for the Detection of Chikungunya and Its Application to a Dengue Outbreak Situation in Kenya in 2013

Chikungunya (CHIK) is a mosquito-borne viral disease. In the 2004 CHIK outbreak in Kenya, diagnosis was delayed because of the lack of accurate diagnostics. Therefore, this study aimed to develop and evaluate an in-house IgM-capture enzyme linked immunosorbent assay (ELISA) (in-house ELISA) for the detection of chikungunya virus (CHIKV) infections. Anti-CHIKV antibodies were raised in rabbits, purified and conjugated to horseradish peroxidase. These anti-CHIKV antibodies and cell-culture derived antigen were used to develop the ELISA. To validate the in-house ELISA, 148 patient sera from the 2005 Comoros CHIK outbreak were tested with centers for disease control and prevention (CDC) IgM-capture ELISA (CDC ELISA) and focus reduction neutralization test (FRNT) as reference assays. The in-house ELISA had a sensitivity of 97.6% and specificity of 81.3% compared to the CDC ELISA and a sensitivity of 91.1% and specificity of 96.7% compared to FRNT. Furthermore, 254 clinically suspected dengue patient samples from Eastern Kenya, collected in 2013, were tested for CHIKV IgM using the in-house ELISA. Out of the 254 samples, 26 (10.2%) were IgM positive, and of these 26 samples, 17 were further analyzed by FRNT and 14 (82.4%) were positive. The in-house ELISA was able to diagnose CHIKV infection among suspected dengue cases in the 2013 outbreak.