Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with pneumonia in Kilifi, Kenya

Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged &lt;5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one HCoV type. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection.  Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged &lt;1 year (66%, n=208), though there was no age-dependence in the proportion testing positive. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, with no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into the potential future burden and epidemiological characteristics of SARS-CoV-2.</ns4:p

Quantitative and quality losses caused by rodents in on-farm stored maize: a case study in the low land tropical zone of Kenya

Rodents are one of the major storage pests in on-farm maize storage in the tropics. However, information on actual magnitude of weight and quality losses caused by rodents in maize stores and species of rodent associated with the losses is scarce and if available would help to improve maize postharvest management. Maize stores of small-scale farmers in the lowland tropical zone of Kenya were monitored for actual weight losses caused by rodents and rodent trapping was conducted to determine species and estimate population of the rodents associated with the losses. Moulds and total aflatoxin contamination and nutritional value of rodent-damaged grain and non-damaged grain samples were also compared to evaluate the impact of rodent infestation on grain quality. In a sample of 20 farmers, we found that cumulative weight losses due to rodents ranged from 2.2 to 6.9% in shelled maize grain and from 5.2 to 18.3% in dehusked cobs after storage for 3 months. Rattus rattus was the only rodent species captured over the whole trapping period with a trap success rate of 0.6–10.0%. Total mould count, Fusarium spp. incidence and total aflatoxin contamination were significantly higher in rodent-damaged grains than in the non-damaged ones whereas no significant differences were observed for the incidence of Aspergillus spp. There were also significant decreases in dry-matter, fat, crude protein and fatty acid content in rodent-damaged grain compared to non-damaged grain. These findings show that rodents are a significant cause of postharvest losses in on-farm maize storage and impact negatively on food nutrition and safety. Mitigation strategies for postharvest losses should therefore include rodent control

Good immune restitution but unsatisfactory viral suppression in children on ART in a remote Western Kenya area

Mexico AIDS Conference 200

Technical efficiency and technology gaps of sorghum plots in Uganda: A gendered stochastic metafrontier analysis

Sorghum plot managers in different locations have varying levels of resource endowment that in turn influence technical efficiency (TE). Therefore, plot managers operate at different levels of technology. The present study applied a stochastic metafrontier approach to assess TE and technology gaps of female, male and jointly-managed sorghum plots. A two limit-Tobit model was subsequently applied to assess determinants of TE. Results indicate that male-managed sorghum plots had the highest metafrontier technical efficiencies (MTEs) (61%, 56% and 15%) and technology gap ratios (TGRs) (98%, 92% and 20%) for Lira, Serere and Kumi districts, respectively compared to female and jointly managed plots. However, jointly managed plots had higher TE and TGRs compared to female plot managers but lower than those of the male-managed plots. Age, distance to plot and farmer group membership influenced TE positively while household size, years of farming sorghum and access to credit had negative effects on efficiency

An intensive, active surveillance reveals continuous invasion and high diversity of rhinovirus in households

We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3–4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5–13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to <14 days. Individual repeat infections were frequent (range 1–7 over 6 months), decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection

Intermittent Preventive Treatment in Infants for the Prevention of Malaria in Rural Western Kenya: A Randomized, Double-Blind Placebo-Controlled Trial

Background Intermittent preventive treatment in infants (IPTi) with sulphadoxine-pyrimethamine (SP) for the prevention of malaria has shown promising results in six trials. However, resistance to SP is rising and alternative drug combinations need to be evaluated to better understand the role of treatment versus prophylactic effects. Methods Between March 2004 and March 2008, in an area of western Kenya with year round malaria transmission with high seasonal intensity and high usage of insecticide-treated nets, we conducted a randomized, double-blind placebo-controlled trial with SP plus 3 days of artesunate (SP-AS3), 3 days of amodiaquine-artesunate (AQ3-AS3), or 3 days of short-acting chlorproguanil-dapsone (CD3) administered at routine expanded programme of immunization visits (10 weeks, 14 weeks and 9 months). Principal Findings 1,365 subjects were included in the analysis. The incidence of first or only episode of clinical malaria during the first year of life (primary endpoint) was 0.98 episodes/person-year in the placebo group, 0.74 in the SP-AS3 group, 0.76 in the AQ3-AS3 group, and 0.82 in the CD3 group. The protective efficacy (PE) and 95% confidence intervals against the primary endpoint were: 25.7% (6.3, 41.1); 25.9% (6.8, 41.0); and 16.3% (−5.2, 33.5) in the SP-AS3, AQ3-AS3, and CD3 groups, respectively. The PEs for moderate-to-severe anaemia were: 27.5% (−6.9, 50.8); 23.1% (−11.9, 47.2); and 11.4% (−28.6, 39.0). The duration of the protective effect remained significant for up to 5 to 8 weeks for SP-AS3 and AQ3-AS3. There was no evidence for a sustained beneficial or rebound effect in the second year of life. All regimens were well tolerated. Conclusions These results support the view that IPTi with long-acting regimens provide protection against clinical malaria for up to 8 weeks even in the presence of high ITN coverage, and that the prophylactic rather than the treatment effect of IPTi appears central to its protective efficacy

Water, sanitation and hygiene at sex work venues to support menstrual needs

Introduction: Adequate menstrual health and hygiene (MHH) is necessary for women’s health and equity of all menstruators. Female sex workers (FSW) require good MHH to prevent discomfort and exposure to pathogens. No studies have evaluated water, sanitation, and hygiene (WASH) conditions of FSW. We report on a cross-sectional WASH assessment at FSW venues in Kisumu, western Kenya. Methods: Stakeholders identified 77 FSW venues in Kisumu, of which 47 were randomly sampled and visited between April-May 2023. A standardized structured survey of WASH conditions was deployed by trained research staff using Android tablets after proprietor’s consent. WASH scores ranging 0 – 3 were computed based on point each for direct observation of water available, soap available, and acceptable latrine. MHH scores ranging between 0-4 were computed (one point each) for direct observation of: currently available soap and water, locking door on a usable latrine, functional lighting, and a private area for changing clothes or menstrual materials, separate from the latrine(s). WASH and MHH scores were compared by venue type using non-parametric Kruskal-Wallis tests, and non-parametric Spearman rank tests. Results: Full WASH criteria was met by 29.8% of venues; 34.0% had no adequate WASH facilities; 46.8% had no female latrine, and 25.5% provided soap and water in private spaces for women. While 76.6% had menstrual waste disposal only 14 (29.8%) had covered bins. One in 10 venues provided adequate MHM facilities. Poorest WASH facilities were in brothels and in bars, and three-quarters of bars with accommodation had no MHH facilities. Discussion: WASH and MHH services were sub-optimal in the majority of FSW venues, preventing menstrual management safely, effectively, with dignity and privacy. This study highlights the unmet need for MHH support for this population. Poor MHH can deleteriously impact FSW health and wellbeing and compound the stigma and shame associated with their work and ability to stay clean. Acceptable and cost-effective solutions to sustainably improve WASH facilities for these populations are needed

Surveillance of endemic human coronaviruses (HCoV-NL63, OC43 and 229E) associated with childhood pneumonia in Kilifi, Kenya.

Introduction: Human coronaviruses (HCoVs) circulate endemically in human populations, often with seasonal variation. We describe the long-term patterns of paediatric disease associated with three of these viruses, HCoV-NL63, OC43 and 229E, in coastal Kenya. Methods: Continuous surveillance of pneumonia admissions was conducted at the Kilifi county hospital (KCH) located in the northern coastal region of Kenya. Children aged <5 years admitted to KCH with clinically defined syndromic severe or very severe pneumonia were recruited. Respiratory samples were taken and tested for 15 virus targets, using real-time polymerase chain reaction. Unadjusted odds ratios were used to estimate the association between demographic and clinical characteristics and HCoV positivity. Results: From 2007 to 2019, we observed 11,445 pneumonia admissions, of which 314 (3.9%) tested positive for at least one of the HCoV types surveyed in the study. There were 129 (41.1%) OC43, 99 (31.5%) 229E, 74 (23.6%) NL63 positive cases and 12 (3.8%) cases of HCoV to HCoV coinfection.  Among HCoV positive cases, 47% (n=147) were coinfected with other respiratory virus pathogens. The majority of HCoV cases were among children aged <1 year (66%, n=208), though there was was no change in the proportion infected by age. HCoV-OC43 was predominant of the three HCoV types throughout the surveillance period. Evidence for seasonality was not identified. Conclusions: Overall, 4% of paediatric pneumonia admissions were associated with three endemic HCoVs, with a high proportion of cases co-occurring with another respiratory virus, no clear seasonal pattern, and with the age-distribution of cases following that of pneumonia admissions (i.e. highest in infants). These observations suggest, at most, a small severe disease contribution of endemic HCoVs in this tropical setting and offer insight into their potential future burden and epidemiological characteristics

Maternal Malaria and Perinatal HIV Transmission, Western Kenya1,2

To determine whether maternal placental malaria is associated with an increased risk for perinatal mother-to-child HIV transmission (MTCT), we studied HIV-positive women in western Kenya. We enrolled 512 mother-infant pairs; 128 (25.0%) women had malaria, and 102 (19.9%) infants acquired HIV perinatally. Log10 HIV viral load and episiotomy or perineal tear were associated with increased perinatal HIV transmission, whereas low-density malaria (<10,000 parasites/μL) was associated with reduced risk (adjusted relative risk [ARR] 0.4). Among women dually infected with malaria and HIV, high-density malaria (>10,000 parasites/μL) was associated with increased risk for perinatal MTCT (ARR 2.0), compared to low-density malaria. The interaction between placental malaria and MTCT appears to be variable and complex: placental malaria that is controlled at low density may cause an increase in broad-based immune responses that protect against MTCT; uncontrolled, high-density malaria may simultaneously disrupt placental architecture and generate substantial antigen stimulus to HIV replication and increase risk for MTCT

Enteric permeability, systemic inflammation, and post-discharge growth among a cohort of hospitalized children in Kenya and Pakistan

Objectives: To determine whether gut permeability is associated with post-discharge growth and systemic inflammation among hospitalized children in low- and middle-income countries. Methods: Children aged 2–23 months being discharged from Civil Hospital Karachi (Pakistan) and Migori County Referral Hospital (Kenya) underwent lactulose-rhamnose ratio (LRR) permeability testing and were compared to age-matched children from their home communities. Linear mixed effect models estimated the associations between LRR among discharged children with change in length-for-age (LAZ) and weight-for-age z score (WAZ) at 45, 90, and 180 days after discharge. Linear regression tested if relationships between LRR, systemic inflammation [C-reative protein (CRP), Cluster of Differentiation 14 (CD14), Tumour Necrosis Factor Alpha (TNFα), Interleukin-6 (IL-6)], and enterocyte damage [Intestinal Fatty-Acid Binding protein (I-FABP)] differed between the hospitalized and community groups. Results: One hundred thirty-seven hospitalized and 84 community participants were included. The hospitalized group had higher log-LRR [0.43, 95% confidence interval (CI): 0.15–0.71, P = 0.003] than the community children. Adjustment for weight-for-length z score at discharge attenuated this association (0.31, 95% CI: 0.00–0.62, P = 0.049). LRR was not associated with changes in WAZ or LAZ in the post-discharge period. Associations between LRR and CRP (interaction P = 0.036), TNFα (P = 0.017), CD14 (P = 0.078), and IL-6 (P = 0.243) differed between community and hospitalized groups. LRR was associated with TNFα (P = 0.004) and approached significance with CD14 (P = 0.078) and IL-6 (P = 0.062) in community children, but there was no evidence of these associations among hospitalized children. Conclusions: Although increased enteric permeability is more prevalent among children being discharged from hospital compared to children in the community, it does not appear to be an important determinant of systemic inflammation or post-discharge growth among hospitalized children