Prospective Clinical Surveillance for Severe Acute Respiratory Illness in Kenyan Hospitals during the COVID-19 pandemic (preprint)

There are limited data from sub-Saharan Africa describing the pattern of admissions to public hospitals with severe acute respiratory infections during the COVID-19 pandemic. We conducted a prospective longitudinal hospital-based sentinel surveillance between May 2020 and December 2022 at 16 public hospitals in Kenya. All patients aged above 18 years admitted to adult medical wards in the participating hospitals were included. Demographic and clinical characteristics, COVID-19 infection and vaccination status and outcome data were collected. Of the 52,714 patients included in the study, 18,001 (35%) were admitted with severe acute respiratory illness (SARI). The mean age was 51 years. Patients were equally distributed across sexes. Pneumonia was the most common diagnosis at discharge. Hypertension, HIV and diabetes mellitus were the most common comorbidities. COVID-19 test results were positive in 2,370 (28%) of the 8,517 (47%) patients that underwent testing. Overall inpatient case fatality for SARI was 21% (n=3,828). After adjusting for age, sex and presence of a comorbidity, SARI patients had higher inpatient mortality compared to non-SARI patients regardless of their COVID-19 status (aHR 1.31, 95% CI 1.19 - 1.46). COVID-19 positive SARI patients had a higher inpatient mortality rate compared to their negative counterparts (aHR 1.31, 95% CI 1.12 - 1.54, p value < 0.0001). COVID-19 vaccine effectiveness against mortality due to SARI after adjusting for age, sex and presence of a comorbidity was 34% (95% CI 11% - 51%). We have provided a comprehensive description of the pattern of admissions with respiratory illnesses in Kenyan hospitals during the COVID-19 pandemic period. We have demonstrated the utility of routine surveillance activities within public hospitals in low-income settings which if strengthened can enhance the response to emerging health threats.

The Impact Of COVID-19 on Health Financing in Kenya (preprint)

Background Sudden shocks to health systems, such as the COVID-19 pandemic may disrupt health system functions. Health system functions may also influence the health systems ability to deliver in the face of sudden shocks such as the COVID-19 pandemic. We examined the impact of COVID-19 on the health financing function in Kenya, and how specific health financing arrangements influenced the health systems capacity to deliver services during the COVID-19 pandemic. Methods We conducted a cross-sectional study in three purposively selected counties in Kenya using a qualitative approach. We collected data using in-depth interviews (n = 56) and relevant document reviews. We interviewed national level health financing stakeholders, county department of health managers, health facility managers and COVID-19 healthcare workers. We analysed data using a framework approach. Results Purchasing arrangements: COVID-19 services were partially subsidized by the national government, exposing individuals to out-of-pocket costs given the high costs of these services. The National Health Insurance Fund (NHIF) adapted its enhanced schemes benefit package targeting formal sector groups to include COVID-19 services but did not make any adaptations to its general scheme targeting the less well-off in society. This had potential equity implications. Public Finance Management (PFM) systems: Nationally, PFM processes were adaptable and partly flexible allowing shorter timelines for budget and procurement processes. At county level, PFM systems were partially flexible with some resource reallocation but maintained centralized purchasing arrangements. The flow of funds to counties and health facilities was delayed and the procurement processes were lengthy. Reproductive and child health services: Domestic and donor funds were reallocated towards the pandemic response resulting in postponement of program activities and affected family planning service delivery. Universal Health Coverage (UHC) plans: Prioritization of UHC related activities was negatively impacted due the shift of focus to the pandemic response. Contrarily the strategic investments in the health sector were found to be a beneficial approach in strengthening the health system. Conclusions Strengthening health systems to improve their resilience to cope with public health emergencies requires substantial investment of financial and non-financial resources. Health financing arrangements are integral in determining the extent of adaptability, flexibility, and responsiveness of health system to COVID-19 and future pandemics.

Cost & Cost-Effectiveness of Implementing SD Biosensor Antigen Detecting SARs-CoV-2 Rapid Diagnostic Tests in Kenya (preprint)

The COVID-19 pandemic has created a need to rapidly scale-up testing services. In Kenya, services for SARS-CoV-2 nucleic acid amplifying test (NAAT) have often been unavailable or delayed, precluding the clinical utility of the results. The introduction of antigen-detecting rapid diagnostic tests (Ag-RDT) has had the potential to fill at least a portion of the testing gap. We, therefore, evaluated the cost-effectiveness of implementing SD Biosensor Antigen Detecting SARs-CoV-2 Rapid Diagnostic Tests in Kenya. We conducted a cost and cost-effectiveness of implementing SD biosensor antigen-detecting SARS-CoV-2 rapid diagnostic test using a decision tree model following the Consolidated Health Economic Evaluation Standards (CHEERS) guidelines under two scenarios. In the first scenario, we compared the use of Ag-RDT as a first-line diagnostic followed by using NAAT assay, to the use of NAAT only. In the second scenario, we compared the use of Ag-RDT to clinical judgement. We used a societal perspective and a time horizon of patient care episodes. Cost and outcomes data were obtained from primary and secondary data. We used one-way and probabilistic sensitivity analysis to assess the robustness of the results. At the point of care, Ag-RDT use for case management in settings with access to delayed confirmatory NAAT testing, the use of Ag-RDT was cost-effective (ICER = US$ 964.63 per DALY averted) when compared to Kenyas cost-effectiveness threshold (US$ 1003.4). In a scenario with no access to NAAT, comparing the Ag-RDT diagnostic strategy with the no-test approach, the results showed that Ag-RDT was a cost-saving and optimal strategy (ICER = US$ 1490.33 per DALY averted). At a higher prevalence level and resource-limited setting such as Kenya, implementing Ag-RDT to complement NAAT testing will be a cost-effective strategy in a scenario with delayed access to NAAT and a cost-saving strategy in a scenario with no access to NAAT assay.

Effects of the COVID-19 pandemic on hospital admissions and inpatient mortality in Kenya (preprint)

Background: The impact of COVID-19 in Africa remains poorly defined. We sought to describe trends in hospitalisation due to all medical causes, pneumonia-specific admissions, and inpatient mortality in Kenya before and during the first five waves of the COVID-19 pandemic in Kenya. Methods: We conducted a hospital-based observational study of patients admitted to 13 public referral facilities in Kenya from January 2018 to December 2021. The pre-COVID population included patients admitted before 1 March 2020. We fitted time series models to compare observed and predicted trends for each outcome. To estimate the impact of the COVID-19 pandemic we calculated incidence rate ratios (IRR) and corresponding 95% confidence intervals (CI) from negative binomial mixed-effects models. Results: Out of 302,703 patients (range 7453 to 27168) hospitalised across the 13 surveillance sites 84,337 (55.2%) were aged 15 years and older. Compared with the pre-COVID period, hospitalisations declined markedly among adult (IRR 0.68, 95% CI 0.63 to 0.73) and paediatric (IRR 0.67, 95% CI 0.62 to 0.73) patients. Adjusted in-hospital mortality also declined among both adult (IRR 0.83, 95% CI 0.77 to 0.89) and paediatric (IRR 0.85, 95% CI 0.77 to 0.94) admissions. Pneumonia-specific admissions among adults were higher during the pandemic (IRR 1.75, 95% CI 1.18 to 2.59), while the paediatric pneumonia cases were lower than pre-pandemic levels in the first year of the pandemic and elevated in late 2021 (IRR 0.78, 95% CI 0.51 to 1.20). Conclusions: Contrary to initial predictions, the COVID-19 pandemic was associated with lower rates of hospitalisation and in-hospital mortality, despite increased pneumonia admissions among adults. These trends were sustained after the withdrawal of containment measures that resulted in the disruption of essential health services, suggesting a role for additional factors that warrant further investigation.

Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study (preprint)

Background: There is uncertainty about the mortality impact of the COVID-19 pandemic in Africa because of poor ascertainment of cases and limited national civil vital registration. We analysed excess mortality from 1st January 2020-5th May 2022 in a Health and Demographic Surveillance Study in Coastal Kenya where the SARS-CoV-2 seroprevalence reached 75% among adults in March 2022 despite vaccine uptake of only 17%. Methods: We modelled expected mortality in 2020-2022 among a population of 306,000 from baseline surveillance data between 2010-2019. We calculated excess mortality as the ratio of observed/expected deaths in 5 age strata for each month and for each national wave of the pandemic. We estimated cumulative mortality risks as the total number of excess deaths in the pandemic per 100,000 population. We investigated observed deaths using verbal autopsy. Findings: We observed 16,236 deaths among 3,410,800 person years between 1st January 2010 and 5th May 2022. Across 5 waves of COVID-19 cases during 1st April 2020-16th April 2022, population excess mortality was 4.1% (95% PI -0.2%, 7.9%). Mortality was elevated among those aged [≥]65 years at 14.3% (95% PI 7.4%, 21.6%); excess deaths coincided with wave 2 (wild-type), wave 4 (Delta) and wave 5 (Omicron BA1). Among children aged 1-14 years there was negative excess mortality of -20.3% (95% PI -29.8%, -8.1%). Verbal autopsy data showed a transient reduction in deaths from acute respiratory infections in 2020 at all ages. For comparison with other studies, cumulative excess mortality risk for January 2020-December 2021, age-standardized to the Kenyan population, was 47.5/100,000. Interpretation: Net excess mortality during the pandemic was substantially lower in Coastal Kenya than in many high income countries. However, adults, aged [≥]65 years, experienced substantial excess mortality suggesting that targeted COVID-19 vaccination of older persons may limit further COVID-19 deaths by protecting the residual pool of naive individuals.

SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February-June 2022 (preprint)

Background Up-to-date SARS-CoV-2 antibody seroprevalence estimates are important for informing public health planning, including priorities for Coronavirus disease 2019 (COVID-19) vaccination programs. We sought to estimate infection- and vaccination-induced SARS-CoV-2 antibody seroprevalence within representative samples of the Kenyan population approximately two years into the COVID-19 pandemic and approximately one year after rollout of the national COVID-19 vaccination program. Methods We conducted cross-sectional serosurveys within random, age-stratified samples of Kilifi Health and Demographic Surveillance System (HDSS) and Nairobi Urban HDSS residents. Anti-spike (anti-S) immunoglobulin G (IgG) and anti-nucleoprotein (anti-N) IgG were measured using validated in-house ELISAs. Target-specific Bayesian population-weighted seroprevalence was calculated overall, by sex and by age, with adjustment for test performance as appropriate. Anti-S IgG concentrations were estimated with reference to the WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin and their reverse cumulative distributions plotted. Results Between February and June 2022, 852 and 851 individuals within the Kilifi HDSS and the Nairobi Urban HDSS, respectively, were sampled. Only 11.0% (95% confidence interval [CI] 9.0-13.3) of all Kilifi HDSS participants and 33.4% (95%CI 30.2-36.6) of all Nairobi Urban HDSS participants had received any doses of COVID-19 vaccine. Population-weighted anti-S IgG seroprevalence was 69.1% (95% credible interval [CrI] 65.8-72.3) within the Kilifi HDSS and 88.5% (95%CrI 86.1-90.6) within the Nairobi Urban HDSS. Among COVID-unvaccinated residents of the Kilifi HDSS and Nairobi Urban HDSS, it was 66.7% (95%CrI 63.3-70.0) and 85.3% (95%CrI 82.1-88.2), respectively. Population-weighted, test-adjusted anti-N IgG seroprevalence within the Kilifi HDSS was 53.5% (95%CrI 46.5-61.1) and 65.5% (95%CrI 56.0-75.6) within the Nairobi Urban HDSS. The prevalence of anti-N antibodies was similar in vaccinated and unvaccinated subgroups in both HDSS populations. Anti-S IgG concentrations were significantly lower among Kilifi HDSS residents than among Nairobi Urban HDSS residents (p< 0.001). Conclusions Approximately, 7 in 10 Kilifi residents and 9 in 10 Nairobi residents were seropositive for anti-S IgG by May 2022 and June 2022, respectively. Given COVID-19 vaccination coverage, anti-S IgG seropositivity among COVID-unvaccinated individuals, and anti-N IgG seroprevalence, population-level anti-S IgG seroprevalence was predominantly derived from infection. Interventions to improve COVID-19 vaccination uptake should be targeted to individuals in rural Kenya who are at high risk of severe COVID-19.

Essential Emergency and Critical Care as a health system response to critical illness and the COVID19 pandemic: What does it cost? (preprint)

Essential Emergency and Critical Care (EECC) is a novel approach to the care of critically ill patients, focusing on first-tier, low-cost care and designed to be feasible even in low-resourced and low-staffed settings. This is distinct from advanced critical care, usually conducted in ICUs with specialised staff, facilities and technologies. This paper estimates the incremental cost of EECC and advanced critical care for the planning of care for critically ill patients in low resource settings with Kenya and Tanzania as case studies.The incremental costing took a health systems perspective. A normative approach based on the ingredients defined through the recently published global consensus on EECC was used. The setting was a district hospital in which the patient is provided with the definitive care typically provided at that level for their condition. Quantification of resource use was based on COVID-19 as a tracer condition using clinical expertise. Local prices were used where available, and all costs were converted to USD2020.The costs per patient day of EECC is estimated to be 1.01 USD, 10.83 USD and 32.84 USD in Tanzania and 1.76 USD, 14.86 USD and 37.43 USD in Kenya, for moderate, severe and critical COVID-19 patients respectively. The cost per patient day of advanced critical care is estimated to be 13.11 USD and 17.33 USD for severe and 297.30 USD and 369.64 USD for critical COVID-19 patients in Tanzania and Kenya, respectively.EECC, an approach of providing the essential care to all critically ill patients, is low-cost. The components of EECC are basic and universal and, when assessed against the existing gaps in critical care coverage and costs of advanced critical care, suggest that it should be a priority area of investment for health systems around the globe.

Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya (preprint)

ABSTRACT Background Few studies have assessed the benefits of COVID-19 vaccines in settings where most of the population had been exposed to SARS-CoV-2 infection. Methods We conducted a cost-effectiveness analysis of COVID-19 vaccine in Kenya from a societal perspective over a 1.5-year time frame. An age-structured transmission model assumed at least 80% of the population to have prior natural immunity when an immune escape variant was introduced. We examine the effect of slow (18 months) or rapid (6 months) vaccine roll-out with vaccine coverage of 30%, 50% or 70% of the adult (> 18 years) population prioritizing roll-out in over 50-year olds (80% uptake in all scenarios). Cost data were obtained from primary analyses. We assumed vaccine procurement at $7 per dose and vaccine delivery costs of $3.90-$6.11 per dose. The cost-effectiveness threshold was USD 919. Findings Slow roll-out at 30% coverage largely targets over 50-year-olds and resulted in 54% fewer deaths (8,132(7,914 to 8,373)) than no vaccination and was cost-saving (ICER=US$-1,343 (-1,345 to - 1,341) per DALY averted). Increasing coverage to 50% and 70%, further reduced deaths by 12% (810 (757 to 872) and 5% (282 (251 to 317) but was not cost-effective, using Kenya’s cost-effectiveness threshold ($ 919.11). Rapid roll-out with 30% coverage averted 63% more deaths and was more cost-saving (ICER=$-1,607 (-1,609 to -1,604) per DALY averted) compared to slow roll-out at the same coverage level, but 50% and 70% coverage scenarios were not cost-effective. Interpretation With prior exposure partially protecting much of the Kenyan population, vaccination of young adults may no longer be cost-effective. KEY QUESTIONS What is already known? The COVID-19 pandemic has led to a substantial number of cases and deaths in low-and middle-income countries. COVID-19 vaccines are considered the main strategy of curtailing the pandemic. However, many African nations are still at the early phase of vaccination. Evidence on the cost-effectiveness of COVID-19 vaccines are useful in estimating value for money and illustrate opportunity costs. However, there is a need to balance these economic outcomes against the potential impact of vaccination. What are the new findings? In Kenya, a targeted vaccination strategy that prioritizes those of an older age and is deployed at a rapid rollout speed achieves greater marginal health impacts and is better value for money. Given the existing high-level population protection to COVID-19 due to prior exposure, vaccination of younger adults is less cost-effective in Kenya. What do the new findings imply? Rapid deployment of vaccines during a pandemic averts more cases, hospitalisations, and deaths and is more cost-effective. Against a context of constrained fiscal space for health, it is likely more prudent for Kenya to target those at severe risk of disease and possibly other vulnerable populations rather than to the whole population.

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. (preprint)

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.

Impact of the COVID-19 epidemic on mortality in rural coastal Kenya (preprint)

Background: The impact of COVID-19 on all-cause mortality in sub-Saharan Africa remains unknown. Methods: We monitored mortality among 306,000 residents of Kilifi Health and Demographic Surveillance System, Kenya, through four COVID-19 waves from April 2020-September 2021. We calculated expected deaths using negative binomial regression fitted to baseline mortality data (2010-2019) and calculated excess mortality as observed-minus-expected deaths. We excluded deaths in infancy because of under-ascertainment of births during lockdown. In February 2021, after two waves of wild-type COVID-19, adult seroprevalence of anti-SARS-CoV-2 was 25.1%. We predicted COVID-19-attributable deaths as the product of age-specific seroprevalence, population size and global infection fatality ratios (IFR). We examined changes in cause of death by Verbal Autopsy (VA). Results: Between April 2020 and February 2021, we observed 1,000 deaths against 1,012 expected deaths (excess mortality -1.2%, 95% PI -6.6%, 5.8%). Based on SARS-CoV-2 seroprevalence, we predicted 306 COVID-19-attributable deaths (a predicted excess mortality of 30.6%) within this period. Monthly mortality analyses showed a significant excess among adults aged [≥]45 years in only two months, July-August 2021, coinciding with the fourth (Delta) wave of COVID-19. By September 2021, overall excess mortality was 3.2% (95% PI -0.6%, 8.1%) and cumulative excess mortality risk was 18.7/100,000. By VA, there was a transient reduction in deaths attributable to acute respiratory infections in 2020. Conclusions: Normal mortality rates during extensive transmission of wild-type SARS-CoV-2 through February 2021 suggests that the IFR for this variant is lower in Kenya than elsewhere. We found excess mortality associated with the Delta variant but the cumulative excess mortality risk remains low in coastal Kenya compared to global estimates.

SARS-CoV-2 Seroprevalence in three Kenyan Health and Demographic Surveillance Sites, December 2020-May 2021 (preprint)

Importance Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. Objective To determine the cumulative incidence of infection with SARS-CoV-2, from a randomly selected sample of individuals normally resident at three Health and Demographic Surveillance Systems (HDSSs) in Kenya. Design This was a cross-sectional population-based serosurvey conducted at Kilifi HDSS, Nairobi Urban HDSS, and Manyatta HDSS in Kenya. We selected age-stratified samples at HDSSs in Kilifi, Kisumu and Nairobi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. Setting Kilifi HDSS comprises a predominantly rural population, Manyatta HDSS comprises a predominantly semi-urban population, while Nairobi Urban HDSS comprises an urban population. The total population under regular surveillance at the three sites is ~470,000. Exposure We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally validated assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. Main Outcome and Measures The primary outcome measure was cumulative incidence of infection with SARS-COV-2 virus as evidenced by seropositivity to SARS-CoV-2 whole spike protein. We adjusted our estimates using classical methods and Bayesian modelling to account for assay performance. We performed multivariable logistic regression to test associations between seropositivity and age category, time period and sex. Results We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27years (10-78) and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kilifi, Kisumu and Nairobi, seroprevalences at the beginning of the study were 14.5 % (9.1-21), 36.0 (28.2-44.4) and 32.4 % (23.1-42.4) respectively; at the end they were 27.6 % (21.4-33.9), 42.0 % (34.7-50.0) and 50.2 % (39.7-61.1), respectively. In multivariable logistic regression models that adjusted for sex and period of sample collections, age category was strongly associated with seroprevalence (p<0.001), with the highest seroprevalences being observed in the 35-44 and [≥]65 year age categories. Conclusion There has been substantial unobserved transmission of SARS-CoV-2 in the general population in Kenya. There is wide variation in cumulative incidence by location and age category.

Examining the Unit Costs of COVID-19 Vaccine Delivery in Kenya (preprint)

ABSTRACT Introduction Vaccines are considered the path out of the COVID-19 pandemic. The government of Kenya is implementing a phased strategy to vaccinate the Kenyan population, initially targeting populations at high risk of severe disease and infection. We estimated the financial and economic unit costs of procuring and delivering the COVID-19 vaccine in Kenya across various vaccination strategies. Methods We used an activity-based costing approach to estimate the incremental costs of COVID-19 vaccine delivery, from a health systems perspective. Document reviews and key informant interviews (n=12) were done to inform the activities, assumptions and the resources required. Unit prices were derived from document reviews or from market prices. Both financial and economic vaccine procurement costs per person vaccinated with 2-doses, and the vaccine delivery costs per person vaccinated with 2-doses were estimated and reported in 2021USD. Results The financial costs of vaccine procurement per person vaccinated with 2-doses ranged from $2.89-$13.09 in the 30% and 100% coverage levels respectively, however, the economic cost was $17.34 across all strategies. Financial vaccine delivery costs per person vaccinated with 2-doses, ranged from $4.28-$3.29 in the 30% and 100% coverage strategies: While the economic delivery costs were two to three times higher than the financial costs. The total procurement and delivery costs per person vaccinated with 2-doses ranged from $7.34-$16.47 for the financial costs and $29.7-$24.68 for the economic costs for the 30% and 100% coverage respectively. With the exception of procurement costs, the main cost driver of financial and economic delivery costs was supply chain costs (47-59%) and advocacy, communication and social mobilization (29-35%) respectively. Conclusion This analysis presents cost estimates that can be used to inform local policy and may further inform parameters used in cost-effectiveness models. The results could potentially be adapted and adjusted to country-specific assumptions to enhance applicability in similar low-and middle-income settings.

Response to the coronavirus disease 2019 (COVID-19) pandemic at private retail pharmacies in Kenya: a mixed methods study (preprint)

Background: Private retail pharmacies in developing countries present a unique channel for COVID-19 prevention. We assessed the response to the COVID-19 pandemic by pharmacies in Kenya, aiming to identify strategies for maximising their contribution to the national response. Methods: We conducted a prospective mixed-methods study, consisting of a questionnaire survey (n=195), a simulated client survey (n=103), and in-depth interviews (n=18). Data collection started approximately seven months after the pandemic reached Kenya. Quantitative data were summarized using measures of central tendency and multivariable modelling done using logistic regression. Qualitative analysis followed a thematic approach. Results: The initial weeks of the pandemic were characterized by fear and panic among service providers and a surge in client flow. Subsequently, 61% of pharmacies experienced a dip in demand to below pre-pandemic levels and 31% reported challenges with unavailability, high price, and poor-quality of products. Almost all pharmacies were actively providing preventive materials and therapies; educating clients on prevention measures; counselling anxious clients; and handling and referring suspect cases. Fifty-nine pharmacies (55% [95% CI 45-65%]) reported ever receiving a client asking for COVID-19 testing and a similar proportion supported pharmacy-based testing. For treatment, most pharmacies (71%) recommended alternative therapies and nutritional supplements such as vitamin C; only 27% recommended conventional therapies such as antibiotics. While 48% had at least one staff member trained on COVID-19, a general feeling of disconnection from the national program prevailed. Conclusions: Private pharmacies in Kenya were actively contributing to the COVID-19 response, but more deliberate engagement, support and linkages are required. Notably, there is an urgent need to develop guidelines for pharmacy-based COVID-19 testing, a service that is clearly needed and which could greatly increase test coverage. Roll-out of this and other pharmacy-based COVID-19 programs should be accompanied with implementation research in order to inform current and future pandemic responses.

Level and determinants of willingness to pay for rapid COVID-19 testing delivered through private retail pharmacies in Kenya (preprint)

Introduction To support the government response to the coronavirus disease 2019 (COVID-19) pandemic, accessible and sustainable testing approaches are needed. Private retail pharmacies are a key channel through which communities can access COVID-19 testing. We examined the level and determinants of the willingness to pay (WTP) for rapid COVID-19 testing delivered through private retail pharmacies in Kenya. Methods Data was collected following a cross-sectional double-bounded dichotomous choice contingent valuation survey across 341 clients visiting five private retail pharmacies in Nairobi, Kisumu and Siaya counties. Results Our findings indicate mean and median WTP levels of KES 611 (US$ 5.59) and KES 506 (US$ 4.63), respectively. Estimated WTP varied across counties and increased with household income and self-reported interest in pharmacy-based COVID-19 rapid testing. Conclusion These findings can inform price setting, price differentiation, price subsidization and other program design features geared towards enhancing affordability, equity, and uptake. Key Questions What is already known? The Coronavirus disease 2019 (COVID-19) global pandemic continues to cause great morbidity, mortality, social and economic burden. Pharmacies in Kenya have been involved in the delivery of several health interventions, such as malaria rapid testing, HIV self-testing, and other disease screening services. While COVID-19 testing remains an important response strategy to the ongoing COVID-19 pandemic, it is not clear how much pharmacy clients in Kenya and similar settings would be willing to pay (WTP) to obtain rapid COVID-19 testing at pharmacies What are the new findings? The mean and median willingness to pay (WTP) for a rapid test delivered at a private retail pharmacy was KES 611 (US$ 5.59) and KES 506 (US$ 4.63), respectively. WTP varied by county, hence, the need for county-specific price-setting for pharmacy-based COVID-19 testing. WTP increased with household income and interest in getting the COVID-19 test at a private retail pharmacy. What do the new findings imply? A better understanding of the user’s willingness to pay price that can guide price setting, price differentiation, price subsidization and other program design features geared towards enhancing affordability, equity, and uptake.

Modelling the cost-effectiveness of essential and advanced critical care for COVID-19 patients in Kenya (preprint)

BackgroundCase management of symptomatic COVID-19 patients is a key health system intervention. The Kenyan government embarked to fill capacity gaps in essential and advanced critical care needed for the management of severe and critical COVID-19. However, given scarce resources, gaps in both essential and advanced critical care persist. This study assessed the cost-effectiveness of investments in essential and advanced critical care to inform the prioritization of investment decisions. MethodsWe employed a decision tree model to assess the incremental cost-effectiveness of investment in essential care (EC) and investment in both essential and advanced critical care (EC+ACC) compared to current health care provision capacity (status quo) for COVID-19 patients in Kenya. We used a health system perspective, and an inpatient care episode time horizon. Cost data was obtained from primary empirical analysis while outcomes data was obtained from epidemiological model estimates. We used univariate and probabilistic sensitivity analysis (PSA) to assess the robustness of the results. ResultsThe status quo option is more costly and less effective compared to investment in essential care and is thus dominated by the later. The incremental cost effectiveness ratio (ICER) of Investment in essential and advanced critical care (EC+ACC) was US $1,378.21 per DALY averted and hence not a cost-effective strategy when compared to Kenyas cost-effectiveness threshold (USD 908). ConclusionWhen the criterion of cost-effectiveness is considered, and within the context of resource scarcity, Kenya will achieve better value for money if it prioritizes investments in essential care before investments in advanced critical care. This information on cost-effectiveness will however need to be considered as part of a multi-criteria decision-making framework that uses a range of criteria that reflect societal values of the Kenyan society. Key questionsO_ST_ABSWhat is already known?C_ST_ABSO_LIThe COVID-19 pandemic is responsible for substantial health effects in low- and middle-income countries C_LIO_LIThe case management of COVID-19 is one of the key control interventions deployed by country health systems. C_LIO_LISimilar to other low- and middle-income countries, Kenya had substantial gaps in both essential and advanced critical care at the beginning of the pandemic. C_LI What are the new findings?O_LIProvision of essential care and advanced critical care for COVID-19 at the current health system capacity (status quo) was costly and the least effective strategy. C_LIO_LIInvestment in both essential care and advanced critical care for COVID-19 is not cost-effective in Kenya when compared to investment in essential care. C_LI What do the new findings imply?O_LIPrioritizing investments in filling capacity gaps in essential care before investing in filling capacity gaps in advanced critical care for COVID-19 is more cost-effective in Kenya C_LIO_LIThese findings are intended to inform the sequencing of investments in case management rather than the selection of either strategy, within a context of substantial resource constraint, and capacity gaps in both essential and advanced critical care or COVID-19 C_LIO_LIKenya will need to consider these findings on cost-effectiveness within a multi-criteria decision-making framework that use a range of criteria that reflect societal values. C_LI

Assessing equity and the determinants of socio-economic impacts of COVID-19: results from a cross-sectional survey in three counties in Kenya (preprint)

Background: COVID-19 mitigation measures have major ramifications on all aspects of people’s livelihoods. Based on data collected in February 2021, we present an analysis of the socio-economic impacts of COVID-19 mitigation measures in three counties in Kenya. Methods: : We conducted a cross-sectional phone-based survey in three counties in Kenya to assess the level of disruption across seven domains: income, food insecurity, schooling, domestic tension/violence, communal violence, mental health, and decision-making. An overall disruption index was computed from the seven domains using principal component analysis. We used a linear regression model to examine the determinants of vulnerability to disruptions as measured by the index. We used concentration curves and indices to assess inequality in the disruption domains and the overall disruption index. Results: : The level of disruption in income was the highest (74%), while the level of disruption for domestic tension/violence was the lowest (30%). Factors associated with increased vulnerability to the overall disruption index included: older age, being married, belonging in the lowest socio-economic tertile and receiving COVID-19 related assistance. The concentration curves showed that all the seven domains of disruption were disproportionately concentrated among households in the lowest socio-economic tertile, a finding that was supported by the concentration index of the overall disruption index (CI = - 0.022; p = 0.074). Conclusion: The COVID-19 mitigation measures resulted in unintended socio-economic effects that unfairly affected certain vulnerable groups, including those in the lowest socio-economic group and the elderly. Measures to protect households against the adverse socio-economic effects of the pandemic should be scaled up and targeted to the most vulnerable, with attention to the constantly evolving nature of the pandemic.

Genomic surveillance reveals the spread patterns of SARS-CoV-2 in coastal Kenya during the first two waves (preprint)

The transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. We analyzed 684 genomes from samples collected across six counties in coastal Kenya during the first two waves (March 2020 - February 2021). Up to 32 Pango lineages were detected in the local sample with six accounting for 88.0% of the sequenced infections: B.1 (60.4%), B.1.1 (8.9%), B.1.549 (7.9%), B.1.530 (6.4%), N.8 (4.4%) and A (3.1%). In a contemporaneous global sample, 571 lineages were identified, 247 for Africa and 88 for East Africa. We detected 262 location transition events comprising: 64 viral imports into Coastal Kenya; 26 viral exports from coastal Kenya; and 172 inter-county import/export events. Most international viral imports (61%) and exports (88%) occurred through Mombasa, a key coastal touristic and commercial center; and many occurred prior to June 2020, when stringent local COVID-19 restriction measures were enforced. After this period, local transmission dominated, and distinct local phylogenies were seen. Our analysis supports moving control strategies from a focus on international travel to local transmission.

Prevalence of SARS-CoV-2 Antibodies from a one-year National Serosurveillance of Kenyan Blood Transfusion Donors (preprint)

In tropical Africa, SARS-CoV-2 epidemiology is poorly described because of lack of access to testing and weak surveillance systems. Since April 2020, we followed SARS-CoV-2 seroprevalence in plasma samples across the Kenya National Blood Transfusion Service. We developed an IgG ELISA against full length spike protein. Validated in locally-observed, PCR-positive COVID-19 cases and in pre-pandemic sera, sensitivity was 92.7% and sensitivity was 99.0%. Using sera from 9,922 donors, we estimated national seroprevalence of SARS-CoV-2 antibodies at 4.3% in April-June 2020 and 9.1% in August-September 2020. The second COVID-19 wave peaked in November 2020. Here we estimate national seroprevalence in early 2021. Between January 3 and March 15, 2021, we collected 3,062 samples from donors aged 16-64 years. Among 3,018 samples that met our study criteria 1,333 were seropositive (crude seroprevalence 44.2%, 95% CI 42.4-46.0%). After Bayesian test-performance adjustment and population weighting to represent the national population distribution, the national estimate of seroprevalence was 48.5% (95% CI 45.2-52.1%). Seroprevalence varied little by age or sex but was higher in Nairobi, the capital city, and lower in two rural regions. Almost half of Kenyan adult donors had evidence of past SARS-CoV-2 infection by March 2021. Although high, the estimate is corroborated by other population-specific estimates in country. Between March and June, 2% of the population were vaccinated against COVID-19 and the country experienced a third epidemic wave. Natural infection is outpacing vaccine delivery substantially in Africa, and this reality needs to be considered as objectives of the vaccine programme are set.

COVID-19 Transmission Dynamics Underlying Epidemic Waves in Kenya (preprint)

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of SARS-CoV-2 transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or when infection spreads to susceptible sub-populations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of a new higher-transmissibility variant. Reopening schools led to a minor increase in transmission between the second and third waves. Our predictions of current population exposure in Kenya (∼75% June 1st) have implications for a fourth wave and future control strategies. One Sentence Summary COVID-19 spread in Kenya is explained by mixing heterogeneity and a variant less constrained by high population exposure

Assessing the level and determinants of COVID-19 Vaccine Confidence in Kenya (preprint)

ABSTRACT The government of Kenya has launched a phased rollout of COVID-19 vaccination. A major barrier is vaccine hesitancy; the refusal or delay of accepting vaccination. This study evaluated the level and determinants of vaccine hesitancy in Kenya. We conducted a cross-sectional study administered through a phone-based survey in February 2021 in four counties of Kenya. Multivariate logistic regression was used to identify individual perceived risks and influences, context-specific factors, and vaccine-specific issues associated with COVID-19 vaccine hesitancy. COVID-19 vaccine hesitancy in Kenya was high: 60.1%. Factors associated with vaccine hesitancy included: older age, lower education level, perceived difficulty in adhering to government regulations on COVID-19 prevention, less adherence to wearing of face masks, not having ever been tested for COVID-19, no reported socio-economic loss as a result of COVID public-health restriction measures, and concerns regarding vaccine safety and effectiveness. There is a need for the prioritization of interventions to address vaccine hesitancy and improve vaccine confidence as part of the vaccine roll-out plan. These messaging and/or interventions should be holistic to include the value of other public health measures, be focused and targeted to specific groups, raise awareness on the risks of COVID-19 and effectively communicate the benefits and risks of vaccines.