Higher livestock abortion burden in arid and semi-arid lands, Kenya, 2019-2020.

Tracking livestock abortion patterns over time and across factors such as species and agroecological zones (AEZs) could inform policies to mitigate disease emergence, zoonoses risk, and reproductive losses. We conducted a year-long population-based active surveillance of livestock abortion between 2019 and 2020, in administrative areas covering 52% of Kenya's landmass and home to 50% of Kenya's livestock. Surveillance sites were randomly selected to represent all AEZs in the country. Local animal health practitioners electronically transmitted weekly abortion reports from each ward, the smallest administrative unit, to a central server, using a simple short messaging service (SMS). Data were analyzed descriptively by administrative unit, species, and AEZ to reveal spatiotemporal patterns and relationships with rainfall and temperature. Of 23,766 abortions reported in all livestock species, sheep and goats contributed 77%, with goats alone contributing 53%. Seventy-seven per cent (n = 18,280) of these abortions occurred in arid and semi-arid lands (ASALs) that primarily practice pastoralism production systems. While spatiotemporal clustering of cases was observed in May-July 2019 in the ASALs, there was a substantial seasonal fluctuation across AEZs. Kenya experiences high livestock abortion rates, most of which go unreported. We recommend further research to document the national true burden of abortions. In ASALs, studies linking pathogen, climate, and environmental surveillance are needed to assign livestock abortions to infectious or non-infectious aetiologies and conducting human acute febrile illnesses surveillance to detect any links with the abortions.

Risk factors of adverse birth outcomes among a cohort of pregnant women in Coastal Kenya, 2017-2019.

INTRODUCTION: Adverse birth outcomes particularly preterm births and congenital anomalies, are the leading causes of infant mortality globally, and the burden is highest in developing countries. We set out to determine the frequency of adverse birth outcomes and the risk factors associated with such outcomes in a cohort of pregnant women in Kenya. METHODS: From October 2017 to July 2019, pregnant women < 28 weeks gestation were enrolled and followed up until delivery in three hospitals in coastal Kenya. Newborns were examined at delivery. Among women with birth outcome data, we assessed the frequency of congenital anomalies defined as gastroschisis, umbilical hernia, limb abnormalities and Trisomy 21, and adverse birth outcomes, defined as either stillbirth, miscarriage, preterm birth, small for gestational age, or microcephaly. We used log-binomial regression to identify maternal characteristics associated with the presence of at least one adverse outcome. RESULTS: Among the 2312 women enrolled, 1916 (82.9%) had birth outcome data. Overall, 402/1916 (20.9%; 95% confidence interval (CI): 19.1-22.8) pregnancies had adverse birth outcomes. Specifically, 66/1916 (3.4%; 95% CI: 2.7-4.4) were stillbirths, 34/1916 (1.8%; 95% CI: 1.2-2.4) were miscarriages and 23/1816 (1.2%; 95% CI: 0.8-1.9) had congenital anomalies. Among the participants with anthropometric measurements data, 142/1200 (11.8%; 95% CI: 10.1 - 13.8) were small for gestational age and among the participants with ultrasound records, 143/1711 (8.4%; 95% CI: 7.1-9.8) were preterm. Febrile illnesses in current pregnancy (adjusted risk ratio (aRR): 1.7; 95% CI: 1.1-2.8), a history of poor birth outcomes in prior pregnancy (aRR: 1.8; 95% CI: 1.3-2.4) and high blood pressure in pregnancy (aRR: 3.9, 95% CI: (1.7-9.2) were independently associated with adverse birth outcomes in a model that included age, education, human immunodeficiency virus status and high blood pressure at enrolment. CONCLUSION: We found similar rates of overall adverse birth outcomes, congenital anomalies, and small for gestational age but higher rates of stillbirths and lower rates of prematurity compared to the rates that have been reported in the sub-Saharan Africa region. However, the rates of adverse birth outcomes in this study were comparable to other studies conducted in Kenya. Febrile illnesses during the current pregnancy, previous history of poor birth outcomes and high blood pressure in pregnancy are predictive of an increased risk of adverse birth outcomes.

Kenya's experience implementing event-based surveillance during the COVID-19 pandemic.

Event-based surveillance (EBS) can be implemented in most settings for the detection of potential health threats by recognition and immediate reporting of predefined signals. Such a system complements existing case-based and sentinel surveillance systems. With the emergence of the COVID-19 pandemic in early 2020, the Kenya Ministry of Health (MOH) modified and expanded an EBS system in both community and health facility settings for the reporting of COVID-19-related signals. Using an electronic reporting tool, m-Dharura, MOH recorded 8790 signals reported, with 3002 (34.2%) verified as events, across both community and health facility sites from March 2020 to June 2021. A subsequent evaluation found that the EBS system was flexible enough to incorporate the addition of COVID-19-related signals during a pandemic and maintain high rates of reporting from participants. Inadequate resources for follow-up investigations to reported events, lack of supportive supervision for some community health volunteers and lack of data system interoperability were identified as challenges to be addressed as the EBS system in Kenya continues to expand to additional jurisdictions.

Comparing performance of year-round and campaign-mode influenza vaccination strategies among children aged 6-23 months in Kenya: 2019-2021.

INTRODUCTION: In 2016, the Kenya National Immunization Technical Advisory Group requested additional programmatic and cost effectiveness data to inform the choice of strategy for a national influenza vaccination program among children aged 6-23 months of age. In response, we conducted an influenza vaccine demonstration project to compare the performance of a year-round versus campaign-mode vaccination strategy. Findings from this demonstration project will help identify essential learning lessons for a national program. METHODS: We compared two vaccine delivery strategies: (i) a year-round vaccination strategy where influenza vaccines were administered throughout the year at health facilities. This strategy was implemented in Njoro sub-county in Nakuru (November 2019 to October 2021) and Jomvu sub-county in Mombasa (December 2019 to October 2021), (ii) a campaign-mode vaccination strategy where vaccines were available at health facilities over four months. This strategy was implemented in Nakuru North sub-county in Nakuru (June to September 2021) and Likoni sub-county in Mombasa (July to October 2021). We assessed differences in coverage, dropout rates, vaccine wastage, and operational needs. RESULTS: We observed similar performance between strategies in coverage of the first dose of influenza vaccine (year-round strategy 59.7 %, campaign strategy 63.2 %). The coverage obtained in the year-round sub-counties was similar (Njoro 57.4 %; Jomvu 63.1 %); however, more marked differences between campaign sub-counties were observed (Nakuru North 73.4 %; Likoni 55.2 %). The campaign-mode strategy exceeded the cold chain capacity of participating health facilities, requiring thrice monthly instead of once monthly deliveries, and was associated with a two-fold increase in workload compared to the year-round strategy (168 vaccines administered per day in the campaign strategy versus 83 vaccines administered per day in the year-round strategy). CONCLUSION: Although both strategies had similar coverage levels, the campaign-mode strategy was associated with considerable operational needs that could significantly impact the immunization program.

Costs of seasonal influenza vaccine delivery in a pediatric demonstration project for children aged 6-23 months - Nakuru and Mombasa Counties, Kenya, 2019-2021.

BACKGROUND: During November 2019-October 2021, a pediatric influenza vaccination demonstration project was conducted in four sub-counties in Kenya. The demonstration piloted two different delivery strategies: year-round vaccination and a four-month vaccination campaign. Our objective was to compare the costs of both delivery strategies. METHODS: Cost data were collected using standardized questionnaires and extracted from government and project accounting records. We reported total costs and costs per vaccine dose administered by delivery strategy from the Kenyan government perspective in 2021 US$. Costs were separated into financial costs (monetary expenditures) and economic costs (financial costs plus the value of existing resources). We also separated costs by administrative level (national, regional, county, sub-county, and health facility) and program activity (advocacy and social mobilization; training; distribution, storage, and waste management; service delivery; monitoring; and supervision). RESULTS: The total estimated cost of the pediatric influenza demonstration project was US$ 225,269 (financial) and US$ 326,691 (economic) for the year-round delivery strategy (30,397 vaccine doses administered), compared with US$ 214,753 (financial) and US$ 242,385 (economic) for the campaign strategy (25,404 doses administered). Vaccine purchase represented the largest proportion of costs for both strategies. Excluding vaccine purchase, the cost per dose administered was US$ 1.58 (financial) and US$ 5.84 (economic) for the year-round strategy and US$ 2.89 (financial) and US$ 4.56 (economic) for the campaign strategy. CONCLUSIONS: The financial cost per dose was 83% higher for the campaign strategy than the year-round strategy due to larger expenditures for advocacy and social mobilization, training, and hiring of surge staff for service delivery. However, the economic cost per dose was more comparable for both strategies (year-round 22% higher than campaign), balanced by higher costs of operating equipment and monitoring activities for the year-round strategy. These delivery cost data provide real-world evidence to inform pediatric influenza vaccine introduction in Kenya.

Resilience of routine childhood immunization services in two counties in Kenya in the face of the COVID-19 pandemic.

The recently emerged coronavirus disease 2019 (COVID-19) has caused considerable morbidity and mortality worldwide and disrupted health services. We describe the effect of the COVID-19 pandemic on utilization of childhood vaccination services during the pandemic. Using a mixed methods approach combining retrospective data review, a cross-sectional survey, focus group discussions among care givers and key informant interviews among nurses, we collected data between May and September 2021 in Mombasa and Nakuru counties. Overall, there was a <2 % decline in the number of vaccine doses administered during the pandemic period compared to the pre-pandemic period but this was statistically insignificant, both for the pentavalent-1 vaccine (ß = -0.013, p = 0.505) and the pentavalent-3 vaccine (ß = -0.012, p = 0.440). In government health facilities, there was 7.7 % reduction in the number of pentavalent-1 (ß = -0.08, p = 0.010) and 10.4 % reduction in the number of pentavalent-3 (ß = -0.11, p < 0.001) vaccine doses that were administered during the pandemic period. In non-government facilities, there was a 25.8 % increase in the number of pentavalent-1 (ß=0.23, p < 0.001) and 31.0 % increase in the number of pentavalent-3 (ß = -0.27, p < 0.001) vaccine doses that were administered facilities during the pandemic period. The strategies implemented to maintain immunization services during the pandemic period included providing messaging on the availability and importance of staying current with routine vaccination and conducting catch-up vaccinations and vaccination outreaches. Our findings suggest that the COVID-19 pandemic did not impact childhood vaccination services in Mombasa and Nakuru counties in Kenya. The private health facilities cushioned vaccination services against the effects of the pandemic and the strategies that were put in place by the ministry of health ensured continuation of vaccination services and encouraged uptake of the services during the pandemic period in the two counties in Kenya. These findings provide useful information to safeguard vaccination services during future pandemics.

Prevalence and functional profile of SARS-CoV-2 T cells in asymptomatic Kenyan adults.

BackgroundSARS-CoV-2 infection in Africa has been characterized by a less severe disease profile than what has been observed elsewhere, but the profile of SARS-CoV-2-specific adaptive immunity in these mainly asymptomatic patients has not, to our knowledge, been analyzed.MethodsWe collected blood samples from residents of rural Kenya (n = 80), who had not experienced any respiratory symptoms or had contact with individuals with COVID-19 and had not received COVID-19 vaccines. We analyzed spike-specific antibodies and T cells specific for SARS-CoV-2 structural (membrane, nucleocapsid, and spike) and accessory (ORF3a, ORF7, ORF8) proteins. Pre-pandemic blood samples collected in Nairobi (n = 13) and blood samples from mild-to-moderately symptomatic COVID-19 convalescent patients (n = 36) living in the urban environment of Singapore were also studied.ResultsAmong asymptomatic Africans, we detected anti-spike antibodies in 41.0% of the samples and T cell responses against 2 or more SARS-CoV-2 proteins in 82.5% of samples examined. Such a pattern was absent in the pre-pandemic samples. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, we observed strong T cell immunogenicity against viral accessory proteins (ORF3a, ORF8) but not structural proteins, as well as a higher IL-10/IFN-γ cytokine ratio profile.ConclusionsThe high incidence of T cell responses against different SARS-CoV-2 proteins in seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. The functional and antigen-specific profile of SARS-CoV-2-specific T cells in African individuals suggests that environmental factors can play a role in the development of protective antiviral immunity.FundingUS Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health's National Medical Research Council (COVID19RF3-0060, COVID19RF-001, COVID19RF-008, MOH-StaR17Nov-0001).

Mapping of cholera hotspots in Kenya using epidemiologic and water, sanitation, and hygiene (WASH) indicators as part of Kenya's new 2022-2030 cholera elimination plan.

Cholera is an issue of major public health importance. It was first reported in Kenya in 1971, with the country experiencing outbreaks through the years, most recently in 2021. Factors associated with the outbreaks in Kenya include open defecation, population growth with inadequate expansion of safe drinking water and sanitation infrastructure, population movement from neighboring countries, crowded settings such as refugee camps coupled with massive displacement of persons, mass gathering events, and changes in rainfall patterns. The Ministry of Health, together with other ministries and partners, revised the national cholera control plan to a multisectoral cholera elimination plan that is aligned with the Global Roadmap for Ending Cholera. One of the key features in the revised plan is the identification of hotspots. The hotspot identification exercise followed guidance and tools provided by the Global Task Force on Cholera Control (GTFCC). Two epidemiological indicators were used to identify the sub-counties with the highest cholera burden: incidence per population and persistence. Additionally, two indicators were used to identify sub-counties with poor WASH coverage due to low proportions of households accessing improved water sources and improved sanitation facilities. The country reported over 25,000 cholera cases between 2015 and 2019. Of 290 sub-counties, 25 (8.6%) sub-counties were identified as a high epidemiological priority; 78 (26.9%) sub-counties were identified as high WASH priority; and 30 (10.3%) sub-counties were considered high priority based on a combination of epidemiological and WASH indicators. About 10% of the Kenyan population (4.89 million) is living in these 30-combination high-priority sub-counties. The novel method used to identify cholera hotspots in Kenya provides useful information to better target interventions in smaller geographical areas given resource constraints. Kenya plans to deploy oral cholera vaccines in addition to WASH interventions to the populations living in cholera hotspots as it targets cholera elimination by 2030.

Healthcare-seeking behavior for respiratory illnesses in Kenya: implications for burden of disease estimation.

BACKGROUND: Understanding healthcare-seeking patterns for respiratory illness can help improve estimation of disease burden and target public health interventions to control acute respiratory disease in Kenya. METHODS: We conducted a cross-sectional survey to determine healthcare utilization patterns for acute respiratory illness (ARI) and severe pneumonia in four diverse counties representing urban, peri-urban, rural mixed farmers, and rural pastoralist communities in Kenya using a two-stage (sub-locations then households) cluster sampling procedure. Healthcare seeking behavior for ARI episodes in the last 14 days, and severe pneumonia in the last 12 months was evaluated. Severe pneumonia was defined as reported cough and difficulty breathing for > 2 days and report of hospitalization or recommendation for hospitalization, or a danger sign (unable to breastfeed/drink, vomiting everything, convulsions, unconscious) for children < 5 years, or report of inability to perform routine chores. RESULTS: From August through September 2018, we interviewed 28,072 individuals from 5,407 households. Of those surveyed, 9.2% (95% Confidence Interval [CI] 7.9-10.7) reported an episode of ARI, and 4.2% (95% CI 3.8-4.6) reported an episode of severe pneumonia. Of the reported ARI cases, 40.0% (95% CI 36.8-43.3) sought care at a health facility. Of the74.2% (95% CI 70.2-77.9) who reported severe pneumonia and visited a medical health facility, 28.9% (95% CI 25.6-32.6) were hospitalized and 7.0% (95% CI 5.4-9.1) were referred by a clinician to the hospital but not hospitalized. 21% (95% CI 18.2-23.6) of self-reported severe pneumonias were hospitalized. Children aged < 5 years and persons in households with a higher socio-economic status were more likely to seek care for respiratory illness at a health facility. CONCLUSION: Our findings suggest that hospital-based surveillance captures less than one quarter of severe pneumonia in the community. Multipliers from community household surveys can account for underutilization of healthcare resources and under-ascertainment of severe pneumonia at hospitals.

Human brucellosis in Baringo County, Kenya: Evaluating the diagnostic kits used and identifying infecting Brucella species.

Human brucellosis diagnosis has been a challenge in Brucella-endemic areas. In Kenya, diagnosis is usually carried out using Febrile Brucella Antigen agglutination test (FBAT) whose performance is not well documented. This paper reports on the sensitivity and specificity of the FBAT used for brucellosis diagnosis on blood samples/serum collected in three healthcare facilities in Baringo County, Kenya, and on Brucella species present in the study area. The FBAT test results at the hospitals were used to guide patient management. Patients who visited the hospital's laboratory with a clinician's request for brucellosis testing also filled a questionnaire to assess knowledge and attitudes associated with transmission of the disease in the study area. The remaining serum samples were tested again using FBAT and Rose Bengal Plate Test (RBPT) within a month of blood collection at the University Nairobi Laboratory. The two rapid tests were then compared, with respect to brucellosis diagnostic sensitivity and specificity. To identify infecting Brucella species, a proportion 43% (71/166) of the blood clots were analyzed by multiplex polymerase chain reaction (PCR) using specific primers for B. abortus, B. melitensis, B. ovis and B. suis. Out of 166 serum samples tested, 26.5% (44/166) were positive using FBAT and 10.2% (17/166) positive using RBPT. The sensitivity and specificity of FBAT compared to RBPT was 76.47% and 71.19%, respectively while the positive and negative predictive values were 29.55% and 96.72%, respectively. The FBAT showed higher positivity then RBPT. The difference in sensitivity and specificity of FBAT and RBPTs was relatively low. The high FBAT positivity rate would be indication of misdiagnosis; this would lead to incorrect treatment. Brucella abortus was detected from 9.9% (7/71) of the blood clots tested; no other Brucella species were detected. Thus human brucellosis, in Baringo was mainly caused by B. abortus.

Characterization of COVID-19 cases in the early phase (March to July 2020) of the pandemic in Kenya.

Background: Kenya detected the first case of COVID-19 on March 13, 2020, and as of July 30, 2020, 17 975 cases with 285 deaths (case fatality rate (CFR) = 1.6%) had been reported. This study described the cases during the early phase of the pandemic to provide information for monitoring and response planning in the local context. Methods: We reviewed COVID-19 case records from isolation centres while considering national representation and the WHO sampling guideline for clinical characterization of the COVID-19 pandemic within a country. Socio-demographic, clinical, and exposure data were summarized using median and mean for continuous variables and proportions for categorical variables. We assigned exposure variables to socio-demographics, exposure, and contact data, while the clinical spectrum was assigned outcome variables and their associations were assessed. Results: A total of 2796 case records were reviewed including 2049 (73.3%) male, 852 (30.5%) aged 30-39 years, 2730 (97.6%) Kenyans, 636 (22.7%) transporters, and 743 (26.6%) residents of Nairobi City County. Up to 609 (21.8%) cases had underlying medical conditions, including hypertension (n = 285 (46.8%)), diabetes (n = 211 (34.6%)), and multiple conditions (n = 129 (21.2%)). Out of 1893 (67.7%) cases with likely sources of exposure, 601 (31.8%) were due to international travel. There were 2340 contacts listed for 577 (20.6%) cases, with 632 contacts (27.0%) being traced. The odds of developing COVID-19 symptoms were higher among case who were aged above 60 years (odds ratio (OR) = 1.99, P = 0.007) or had underlying conditions (OR = 2.73, P < 0.001) and lower among transport sector employees (OR = 0.31, P < 0.001). The odds of developing severe COVID-19 disease were higher among cases who had underlying medical conditions (OR = 1.56, P < 0.001) and lower among cases exposed through community gatherings (OR = 0.27, P < 0.001). The odds of survival of cases from COVID-19 disease were higher among transport sector employees (OR = 3.35, P = 0.004); but lower among cases who were aged ≥60 years (OR = 0.58, P = 0.034) and those with underlying conditions (OR = 0.58, P = 0.025). Conclusion: The early phase of the COVID-19 pandemic demonstrated a need to target the elderly and comorbid cases with prevention and control strategies while closely monitoring asymptomatic cases.

Anthrax hotspot mapping in Kenya support establishing a sustainable two-phase elimination program targeting less than 6% of the country landmass.

Using data collected from previous (n = 86) and prospective (n = 132) anthrax outbreaks, we enhanced prior ecological niche models (ENM) and added kernel density estimation (KDE) approaches to identify anthrax hotspots in Kenya. Local indicators of spatial autocorrelation (LISA) identified clusters of administrative wards with a relatively high or low anthrax reporting rate to determine areas of greatest outbreak intensity. Subsequently, we modeled the impact of vaccinating livestock in the identified hotspots as a national control measure. Anthrax suitable areas included high agriculture zones concentrated in the western, southwestern and central highland regions, consisting of 1043 of 1450 administrative wards, covering 18.5% country landmass, and hosting 30% of the approximately 13 million cattle population in the country. Of these, 79 wards covering 5.5% landmass and hosting 9% of the cattle population fell in identified anthrax hotspots. The rest of the 407 administrative wards covering 81.5% of the country landmass, were classified as low anthrax risk areas and consisted of the expansive low agricultural arid and semi-arid regions of the country that hosted 70% of the cattle population, reared under the nomadic pastoralism. Modelling targeted annual vaccination of 90% cattle population in hotspot administrative wards reduced > 23,000 human exposures. These findings support an economically viable first phase of anthrax control program in low-income countries where the disease is endemic, that is focused on enhanced animal and human surveillance in burden hotspots, followed by rapid response to outbreaks anchored on public education, detection and treatment of infected humans, and ring vaccination of livestock. Subsequently, the global anthrax elimination program focused on sustained vaccination and surveillance in livestock in the remaining few hotspots for a prolonged period (> 10 years) may be implemented.

Prevalence of microcephaly and Zika virus infection in a pregnancy cohort in Kenya, 2017-2019.

BACKGROUND: Zika virus (ZIKV), first discovered in Uganda in 1947, re-emerged globally in 2013 and was later associated with microcephaly and other birth defects. We determined the incidence of ZIKV infection and its association with adverse pregnancy and fetal outcomes in a pregnancy cohort in Kenya. METHODS: From October 2017 to July 2019, we recruited and followed up women aged ≥ 15 years and ≤ 28 weeks pregnant in three hospitals in coastal Mombasa. Monthly follow-up included risk factor questions and a blood sample collected for ZIKV serology. We collected anthropometric measures (including head circumference), cord blood, venous blood from newborns, and any evidence of birth defects. Microcephaly was defined as a head circumference (HC) < 2 standard deviations (SD) for sex and gestational age. Severe microcephaly was defined as HC < 3 SD for sex and age. We tested sera for anti-ZIKV IgM antibodies using capture enzyme-linked immunosorbent assay (ELISA) and confirmed positives using the plaque reduction neutralization test (PRNT90) for ZIKV and for dengue (DENV) on the samples that were ZIKV neutralizing antibody positive. We collected blood and urine from participants reporting fever or rash for ZIKV testing. RESULTS: Of 2889 pregnant women screened for eligibility, 2312 (80%) were enrolled. Of 1916 recorded deliveries, 1816 (94.6%) were live births and 100 (5.2%) were either stillbirths or spontaneous abortions (< 22 weeks of gestation). Among 1236 newborns with complete anthropometric measures, 11 (0.9%) had microcephaly and 3 (0.2%) had severe microcephaly. A total of 166 (7.2%) participants were positive for anti-ZIKV IgM, 136 of whom became seropositive during follow-up. Among the 166 anti-ZIKV IgM positive, 3 and 18 participants were further seropositive for ZIKV and DENV neutralizing antibodies, respectively. Of these 3 and 18 pregnant women, one and 13 (72.2%) seroconverted with antibodies to ZIKV and DENV, respectively. All 308 samples (serum and urine samples collected during sick visits and samples that were anti-ZIKV IgM positive) tested by RT-PCR were negative for ZIKV. No adverse pregnancy or neonatal outcomes were reported among the three participants with confirmed ZIKV exposure. Among newborns from pregnant women with DENV exposure, four (22.2%) were small for gestational age and one (5.6%) had microcephaly. CONCLUSIONS: The prevalence of severe microcephaly among newborns in coastal Kenya was high relative to published estimates from facility-based studies in Europe and Latin America, but little evidence of ZIKV transmission. There is a need for improved surveillance for microcephaly and other congenital malformations in Kenya.

Outbreak of Middle East Respiratory Syndrome Coronavirus in Camels and Probable Spillover Infection to Humans in Kenya.

The majority of Kenya's > 3 million camels have antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV), although human infection in Africa is rare. We enrolled 243 camels aged 0−24 months from 33 homesteads in Northern Kenya and followed them between April 2018 to March 2020. We collected and tested camel nasal swabs for MERS-CoV RNA by RT-PCR followed by virus isolation and whole genome sequencing of positive samples. We also documented illnesses (respiratory or other) among the camels. Human camel handlers were also swabbed, screened for respiratory signs, and samples were tested for MERS-CoV by RT-PCR. We recorded 68 illnesses among 58 camels, of which 76.5% (52/68) were respiratory signs and the majority of illnesses (73.5% or 50/68) were recorded in 2019. Overall, 124/4692 (2.6%) camel swabs collected from 83 (34.2%) calves in 15 (45.5%) homesteads between April−September 2019 screened positive, while 22 calves (26.5%) recorded reinfections (second positive swab following ≥ 2 consecutive negative tests). Sequencing revealed a distinct Clade C2 virus that lacked the signature ORF4b deletions of other Clade C viruses. Three previously reported human PCR positive cases clustered with the camel infections in time and place, strongly suggesting sporadic transmission to humans during intense camel outbreaks in Northern Kenya.

Point-prevalence survey of antibiotic use at three public referral hospitals in Kenya.

Antimicrobial stewardship encourages appropriate antibiotic use, the specific activities of which will vary by institutional context. We investigated regional variation in antibiotic use by surveying three regional public hospitals in Kenya. Hospital-level data for antimicrobial stewardship activities, infection prevention and control, and laboratory diagnostic capacities were collected from hospital administrators, heads of infection prevention and control units, and laboratory directors, respectively. Patient-level antibiotic use data were abstracted from medical records using a modified World Health Organization point-prevalence survey form. Altogether, 1,071 consenting patients were surveyed at Kenyatta National Hospital (KNH, n = 579), Coast Provincial General Hospital (CPGH, n = 229) and Moi Teaching and Referral Hospital (MTRH, n = 263). The majority (67%, 722/1071) were ≥18 years and 53% (563/1071) were female. Forty-six percent (46%, 489/1071) were receiving at least one antibiotic. Antibiotic use was higher among children <5 years (70%, 150/224) than among other age groups (40%, 339/847; P < 0.001). Critical care (82%, 14/17 patients) and pediatric wards (59%, 155/265) had the highest proportion of antibiotic users. Amoxicillin/clavulanate was the most frequently used antibiotic at KNH (17%, 64/383 antibiotic doses), and ceftriaxone was most used at CPGH (29%, 55/189) and MTRH (31%, 57/184). Forty-three percent (326/756) of all antibiotic prescriptions had at least one missed dose recorded. Forty-six percent (204/489) of patients on antibiotics had a specific infectious disease diagnosis, of which 18% (37/204) had soft-tissue infections, 17% (35/204) had clinical sepsis, 15% (31/204) had pneumonia, 13% (27/204) had central nervous system infections and 10% (20/204) had obstetric or gynecological infections. Of these, 27% (56/204) had bacterial culture tests ordered, with culture results available for 68% (38/56) of tests. Missed antibiotic doses, low use of specimen cultures to guide therapy, high rates of antibiotic use, particularly in the pediatric and surgical population, and preference for broad-spectrum antibiotics suggest antibiotic use in these tertiary care hospitals is not optimal. Antimicrobial stewardship programs, policies, and guidelines should be tailored to address these areas.

Comparable Pregnancy Outcomes for HIV-Uninfected and HIV-Infected Women on Antiretroviral Treatment in Kenya.

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 (<37 weeks), and 74/1317 (6%) had a low-birth-weight newborn (<2500 g). There was no evidence of associations between treated HIV infection and pregnancy loss (adjusted relative risk [aRR], 1.19; 95% confidence interval [CI], .65-2.16; P = .57), prematurity (aRR, 1.09; 95% CI, .70-1.70; P = .69), and low birth weight (aRR, 1.36; 95% CI, .77-2.40; P = .27). Factors associated with an HIV-positive status included older age, food insecurity, lower education level, higher parity, lower gestation at first antenatal clinic, anemia, and syphilis. Women who were overweight or underweight were less likely to be HIV infected compared to those with normal weight. 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.

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic.

Background: Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods: SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Results: Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. Conclusions: The emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

Near-Complete SARS-CoV-2 Seroprevalence among Rural and Urban Kenyans despite Significant Vaccine Hesitancy and Refusal.

Considering the early inequity in global COVID-19 vaccine distribution, we compared the level of population immunity to SARS-CoV-2 with vaccine uptake and refusal between rural and urban Kenya two years after the pandemic onset. A population-based seroprevalence study was conducted in the city of Nairobi (n = 781) and a rural western county (n = 810) between January and February 2022. The overall SARS-CoV-2 seroprevalence was 90.2% (95% CI, 88.6−91.2%), including 96.7% (95% CI, 95.2−97.9%) among urban and 83.6% (95% CI, 80.6−86.0%) among rural populations. A comparison of immunity profiles showed that >50% of the rural population were strongly immunoreactive compared to <20% of the urban population, suggesting more recent infections or vaccinations in the rural population. More than 45% of the vaccine-eligible (≥18 years old) persons had not taken a single dose of the vaccine (hesitancy), including 47.6% and 46.9% of urban and rural participants, respectively. Vaccine refusal was reported in 19.6% of urban and 15.6% of rural participants, attributed to concern about vaccine safety (>75%), inadequate information (26%), and concern about vaccine effectiveness (9%). Less than 2% of vaccine refusers cited religious or cultural beliefs. These findings indicate that despite vaccine inequity, hesitancy, and refusal, herd immunity had been achieved in Kenya and likely other African countries by early 2022, with natural infections likely contributing to most of this immunity. However, vaccine campaigns should be sustained due to the need for repeat boosters associated with waning of SARS-CoV-2 immunity and emergence of immune-evading virus variants.