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 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.

An important step towards COVID-19 pandemic control is adequate knowledge and adherence to mitigation measures, including vaccination. We assessed the level of COVID-19 knowledge, attitudes, and practices (KAP) among residents from an urban informal settlement in the City of Nairobi (Kibera), and a rural community in western Kenya (Asembo). A cross-sectional survey was implemented from April to May 2021 among randomly selected adult residents from a population-based infectious diseases surveillance (PBIDS) cohort in Nairobi and Siaya Counties. KAP questions were adopted from previous studies. Factors associated with the level of COVID-19 KAP, were assessed using multivariable regression methods. COVID-19 vaccine acceptance was 83.6% for the participants from Asembo and 59.8% in Kibera. The reasons cited for vaccine hesitancy in Kibera were safety concerns (34%), insufficient information available to decide (18%), and a lack of belief in the vaccine (21%), while the reasons in Asembo were safety concerns (55%), insufficient information to decide (26%) and lack of belief in the vaccine (11%). Our study findings suggest the need for continued public education to enhance COVID-19 knowledge, attitudes, and practices to ensure adherence to mitigation measures. Urban informal settlements require targeted messaging to improve vaccine awareness, acceptability, and uptake.

Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and poultry workers in live bird markets and among wild migratory birds in various lakes that are resting sites during migration to assess introduction and circulation of avian influenza viruses in these populations. We tested 7464 specimens (oropharyngeal (OP) and cloacal specimens) from poultry and 6531 fresh fecal specimens from wild birds for influenza A viruses by real-time RT-PCR. Influenza was detected in 3.9% (n = 292) of specimens collected from poultry and 0.2% (n = 10) of fecal specimens from wild birds. On hemagglutinin subtyping, most of the influenza A positives from poultry (274/292, 93.8%) were H9. Of 34 H9 specimens randomly selected for further subtyping, all were H9N2. On phylogenetic analysis, these viruses were genetically similar to other H9 viruses detected in East Africa. Only two of the ten influenza A-positive specimens from the wild bird fecal specimens were successfully subtyped; sequencing analysis of one specimen collected in 2018 was identified as a low-pathogenicity avian influenza H5N2 virus of the Eurasian lineage, and the second specimen, collected in 2020, was subtyped as H11. A total of 18 OP and nasal specimens from poultry workers with acute respiratory illness (12%) were collected; none were positive for influenza A virus. We observed significant circulation of H9N2 influenza viruses in poultry in live bird markets in Kenya. During the same period, low-pathogenic H5N2 virus was detected in a fecal specimen collected in a site hosting a variety of migratory and resident birds. Although HPAI H5N8 was not detected in this survey, these results highlight the potential for the introduction and establishment of highly pathogenic avian influenza viruses in poultry populations and the associated risk of spillover to human populations.

Brucellosis remains a major zoonotic disease worldwide, with disproportionate burden in low- and middle-income countries where limited veterinary and healthcare infrastructure constrain effective control measures. However, its pathways of transmission are poorly understood. In pastoralist settings, we hypothesize that camels have a high burden of Brucella spp. and play a key role in spreading it to humans and other livestock. This manuscript presents a study protocol to quantify the relative contribution of various livestock species to brucellosis transmission and identify cost-effective control strategies in Kenya. Using probability-proportional-to-size sampling, we aimed to recruit a longitudinal cohort of 170 households and their herds per site in the Marsabit and Kajiado counties. Households rearing at least one livestock species (cattle, camels, goats, sheep) were eligible. Serum, milk, and vaginal swabs (from livestock), and serum (from humans) were collected for testing using Rose Bengal Test, ELISA, qPCR, and culture methods. Concurrently, surveillance for suspected brucellosis was conducted in study health facilities. A qualitative ethnographic study and livestock movement monitoring using GPS-collared animals were nested within the cohort. These data will be used to parameterize a multi-host, multi-species infectious disease model through Approximate Bayesian Computation. Through this One Health approach, our study will identify and optimize potential interventions and help inform the development of a comprehensive cost-effective national control program for brucellosis.

An important step towards COVID-19 pandemic control is adequate knowledge and adherence to mitigation measures, including vaccination. We assessed the level of COVID-19 knowledge, attitudes, and practices among residents from an urban informal settlement in the City of Nairobi (Kibera), and a rural community in western Kenya (Asembo). A cross-sectional survey was implemented from April to May 2021 among randomly selected adult residents from a population-based infectious diseases surveillance (PBIDS) cohort in Nairobi and Siaya Counties. Factors associated with the level of COVID-19 KAP, were assessed using multivariable regression methods. COVID-19 vaccine acceptance was 83.6% for the participants from Asembo and 59.8% in Kibera. The reasons cited for vaccine hesitancy in Kibera were safety concerns (34.0%), insufficient information available to decide (18.0%), and a lack of belief in the vaccine (21.0%), while the reasons in Asembo were safety concerns (55.0%), insufficient information to decide (26.0%) and lack of belief in the vaccine (11%). Our study findings suggest the need for continued public education to enhance COVID-19 knowledge, attitudes, and practices to ensure adherence to mitigation measures. Urban informal settlements require targeted messaging to improve vaccine awareness, acceptability, and uptake.

Following the detection of highly pathogenic avian influenza (HPAI) virus in countries bordering Kenya to the west, we conducted surveillance among domestic and wild birds along the shores of Lake Victoria. In addition, between 2018 and 2020, we conducted surveillance among poultry and poultry workers in live bird markets and among wild migratory birds in various lakes that are resting sites during migration to assess introduction and circulation of avian influenza viruses in these populations. We tested 7,464 specimens (oropharyngeal and cloacal swabs) from poultry and 6,531 fresh fecal specimens from wild birds for influenza A viruses by real-time RT-PCR. Influenza was detected in 3.9% (n=292) of specimens collected from poultry and 0.2% (n=10) of fecal specimens from wild birds. On hemagglutinin subtyping, most of the influenza A positives from poultry (274/292, 93.8%) were H9. Of 34 H9 specimens randomly selected for further subtyping, all were H9N2. On phylogenetic analysis, these viruses were genetically similar to other H9 viruses detected in East Africa. Only two of the ten influenza A positive specimens from the wild bird fecal specimens were successfully subtyped; sequencing analysis of one specimen collected in 2018 was identified as low pathogenicity avian influenza H5N2 virus of the Eurasian lineage and the second specimen, collected in 2020, was subtyped as H11. A total of 18 OP/NS swabs from poultry workers with ARI (12%) were collected; none were positive for influenza A virus. We observed significant circulation of H9N2 influenza viruses in poultry in live bird markets in Kenya. During the same period, low pathogenic H5N2 virus was detected in a fecal specimen collected in a site hosting a variety of migratory and resident birds. Although HPAI H5N8 was not detected in this survey, these results highlight the potential for introduction and establishment of highly pathogenic avian influenza viruses in poultry populations and the associated risk of spillover to human populations.