Health research prioritization in Somalia: setting the agenda for context specific knowledge to advance universal health coverage.

Introduction: Despite recognition that health research is an imperative to progress toward universal health coverage, resources for health research are limited. Yet, especially in sub-Saharan Africa, more than 85% of the resources available for health research are spent on answering less relevant research questions. This misalignment is partially due to absence of locally determined health research priorities. In this study, we identified health research priorities which, if implemented, can inform local interventions required to accelerate progress toward universal health coverage in Somalia. Methods: We adapted the child health and nutrition research initiative method for research priority setting and applied it in 4 major phases: (1) establishment of an exercise management team, (2) a web-based survey among 84 respondents to identify health research questions; (3) categorization of identified health research questions; and (4) a workshop with 42 participants to score and rank the identified health research questions. Ethical approval was received from ethics review committee of the London School of Hygiene and Tropical Medicine (Ref:26524) and the Somali Research and Development Institute (Ref: EA0143). Results: Two hundred and thirty-one unique health research questions were identified and categorized under health systems, services and social determinants (77), communicable diseases (54), non-communicable diseases (41) and reproductive, maternal, new-born, child, adolescent health and nutrition (59). A priority score ranging from 1 to 9 was assigned to each of the questions. For each category, a list of 10 questions with the highest priority scores was developed. Across the four categories, an overall list of 10 questions with the highest priority scores was also developed. These related to bottlenecks to accessing essential health services, use of evidence in decision making, antimicrobial resistance, distribution and risk factors for non-communicable diseases, post-traumatic stress disorder and factors associated with low antenatal care attendance among others. Conclusion and recommendations: The developed priority research questions can be used to focus health research and to inform appropriation of health research resources to questions that contribute to generation of local health system knowledge which is required to accelerate progress toward universal health coverage in Somalia. The Somalia national institute of health should set up a consortium for provision of technical and financial support for research addressing the identified priority research questions, establish a mechanism to continuously monitor the extent to which new health interventions in Somalia are informed by knowledge generated through conducting prioritized health research and prioritize interventions aimed at strengthening the broader national health research system for Somalia.

Development of novel composite data quality scores to evaluate facility-level data quality in electronic data in Kenya: a nationwide retrospective cohort study.

BACKGROUND: In this evaluation, we aim to strengthen Routine Health Information Systems (RHIS) through the digitization of data quality assessment (DQA) processes. We leverage electronic data from the Kenya Health Information System (KHIS) which is based on the District Health Information System version 2 (DHIS2) to perform DQAs at scale. We provide a systematic guide to developing composite data quality scores and use these scores to assess data quality in Kenya. METHODS: We evaluated 187 HIV care facilities with electronic medical records across Kenya. Using quarterly, longitudinal KHIS data from January 2011 to June 2018 (total N = 30 quarters), we extracted indicators encompassing general HIV services including services to prevent mother-to-child transmission (PMTCT). We assessed the accuracy (the extent to which data were correct and free of error) of these data using three data-driven composite scores: 1) completeness score; 2) consistency score; and 3) discrepancy score. Completeness refers to the presence of the appropriate amount of data. Consistency refers to uniformity of data across multiple indicators. Discrepancy (measured on a Z-scale) refers to the degree of alignment (or lack thereof) of data with rules that defined the possible valid values for the data. RESULTS: A total of 5,610 unique facility-quarters were extracted from KHIS. The mean completeness score was 61.1% [standard deviation (SD) = 27%]. The mean consistency score was 80% (SD = 16.4%). The mean discrepancy score was 0.07 (SD = 0.22). A strong and positive correlation was identified between the consistency score and discrepancy score (correlation coefficient = 0.77), whereas the correlation of either score with the completeness score was low with a correlation coefficient of -0.12 (with consistency score) and -0.36 (with discrepancy score). General HIV indicators were more complete, but less consistent, and less plausible than PMTCT indicators. CONCLUSION: We observed a lack of correlation between the completeness score and the other two scores. As such, for a holistic DQA, completeness assessment should be paired with the measurement of either consistency or discrepancy to reflect distinct dimensions of data quality. Given the complexity of the discrepancy score, we recommend the simpler consistency score, since they were highly correlated. Routine use of composite scores on KHIS data could enhance efficiencies in DQA at scale as digitization of health information expands and could be applied to other health sectors beyondHIV clinics.

The importance of community health workers as frontline responders during the COVID-19 pandemic, Somalia, 2020-2021.

Introduction: We examined the contribution of community health workers as frontline responders for the community-based surveillance in Somalia during the first year of the COVID-19 pandemic for detection of COVID-19 cases and identification of contacts. Methods: We retrieved COVID-19 surveillance data from 16 March 2020 to 31 March 2021 from the health ministry's central database. These data were collected through community health workers, health facilities or at the points of entry. We compared the number of suspected COVID-19 cases detected by the three surveillance systems and the proportion that tested positive using the chi-squared test. We used logistic regression analysis to assess association between COVID-19 infection and selected variables. Results: During the study period, 154,004 suspected cases of COVID-19 were detected and tested, of which 10,182 (6.6%) were positive. Of the notified cases, 32.7% were identified through the community-based surveillance system, 54.0% through the facility-based surveillance system, and 13.2% at points of entry. The positivity rate of cases detected by the community health workers was higher than that among those detected at health facilities (8.6% versus 6.4%; p < 0.001). The community health workers also identified more contacts than those identified through the facility-based surveillance (13,279 versus 1,937; p < 0.001). The odds of COVID-19 detection generally increased by age. Community-based surveillance and health facility-based surveillance had similar odds of detecting COVID-19 cases compared with the points-of-entry surveillance (aOR: 7.0 (95% CI: 6.4, 7.8) and aOR: 7.5 (95% CI: 6.8, 8.3), respectively). Conclusion: The community health workers proved their value as first responders to COVID-19. They can be effective in countries with weak health systems for targeted community surveillance in rural and remote areas which are not covered by the facility-based surveillance system.

Value of Verbal Autopsy in a Fragile Setting: Reported versus Estimated Community Deaths Associated with COVID-19, Banadir, Somalia.

BACKGROUND: Accurate mortality data associated with infectious diseases such as coronavirus disease 2019 (COVID-19) are often unavailable in countries with fragile health systems such as Somalia. We compared officially reported COVID-19 deaths in Somalia with COVID-19 deaths estimated using verbal autopsy. METHODS: We interviewed relatives of deceased persons to collect information on symptoms, cause, and place of death. We compared these data with officially reported data and estimated the positive and negative predictive values of verbal autopsy. RESULTS: We identified 530 deaths during March-October 2020. We classified 176 (33.2%) as probable COVID-19 deaths. Most deaths (78.5%; 416/530) occurred at home and 144 (34.6%) of these were attributed to COVID-19. The positive predictive value of verbal autopsy was lower for home deaths (22.3%; 95% CI: 15.7-30.1%) than for hospital deaths (32.3%; 95% CI: 16.7-51.4%). The negative predictive value was higher: 97.8% (95% CI: 95.0-99.3%) for home deaths and 98.4% (95% CI: 91.5-100%) for hospital deaths. Conclusions Verbal autopsy has acceptable predictive value to estimate COVID-19 deaths where disease prevalence is high and can provide data on the COVID-19 burden in countries with low testing and weak mortality surveillance where home deaths may be missed.

All-cause and cause-specific mortality rates for Kisumu County: a comparison with Kenya, low-and middle-income countries.

BACKGROUND: Understanding the magnitude and causes of mortality at national and sub-national levels for countries is critical in facilitating evidence-based prioritization of public health response. We provide comparable cause of death data from Kisumu County, a high HIV and malaria-endemic county in Kenya, and compared them with Kenya and low-and-middle income countries (LMICs). METHODS: We analyzed data from a mortuary-based study at two of the largest hospital mortuaries in Kisumu. Mortality data through 2019 for Kenya and all LMICs were downloaded from the Global Health Data Exchange. We provided age-standardized rates for comparisons of all-cause and cause-specific mortality rates, and distribution of deaths by demographics and Global Burden of Disease (GBD) classifications. RESULTS: The all-cause age-standardized mortality rate (SMR) was significantly higher in Kisumu compared to Kenya and LMICs (1118 vs. 659 vs. 547 per 100,000 population, respectively). Among women, the all-cause SMR in Kisumu was almost twice that of Kenya and double the LMICs rate (1150 vs. 606 vs. 518 per 100,000 population respectively). Among men, the all-cause SMR in Kisumu was approximately one and a half times higher than in Kenya and nearly double that of LMICs (1089 vs. 713 vs. 574 per 100,000 population). In Kisumu and LMICs non-communicable diseases accounted for most (48.0 and 58.1% respectively) deaths, while in Kenya infectious diseases accounted for the majority (49.9%) of deaths. From age 10, mortality rates increased with age across all geographies. The age-specific mortality rate among those under 1 in Kisumu was nearly twice that of Kenya and LMICs (6058 vs. 3157 and 3485 per 100,000 population, respectively). Mortality from injuries among men was at least one and half times that of women in all geographies. CONCLUSION: There is a notable difference in the patterns of mortality rates across the three geographical areas. The double burden of mortality from GBD Group I and Group II diseases with high infant mortality in Kisumu can guide prioritization of public health interventions in the county. This study demonstrates the importance of establishing reliable vital registry systems at sub-national levels as the mortality dynamics and trends are not homogeneous.

Leading causes of death and high mortality rates in an HIV endemic setting (Kisumu county, Kenya, 2019).

BACKGROUND: In resource-limited settings, underlying causes of death (UCOD) often are not ascertained systematically, leading to unreliable mortality statistics. We reviewed medical charts to establish UCOD for decedents at two high volume mortuaries in Kisumu County, Kenya, and compared ascertained UCOD to those notified to the civil registry. METHODS: Medical experts trained in COD certification examined medical charts and ascertained causes of death for 456 decedents admitted to the mortuaries from April 16 through July 12, 2019. Decedents with unknown HIV status or who had tested HIV-negative >90 days before the date of death were tested for HIV. We calculated annualized all-cause and cause-specific mortality rates grouped according to global burden of disease (GBD) categories and separately for deaths due to HIV/AIDS and expressed estimated deaths per 100,000 population. We compared notified to ascertained UCOD using Cohen's Kappa (κ) and assessed for the independence of proportions using Pearson's chi-squared test. FINDINGS: The four leading UCOD were HIV/AIDS (102/442 [23.1%]), hypertensive disease (41/442 [9.3%]), other cardiovascular diseases (23/442 [5.2%]), and cancer (20/442 [4.5%]). The all-cause mortality rate was 1,086/100,000 population. The highest cause-specific mortality was in GBD category II (noncommunicable diseases; 516/100,000), followed by GBD I (communicable, perinatal, maternal, and nutritional; 513/100,000), and III (injuries; 56/100,000). The HIV/AIDS mortality rate was 251/100,000 population. The proportion of deaths due to GBD II causes was higher among females (51.9%) than male decedents (42.1%; p = 0.039). Conversely, more men/boys (8.6%) than women/girls (2.1%) died of GBD III causes (p = 0.002). Most of the records with available recorded and ascertained UCOD (n = 236), 167 (70.8%) had incorrectly recorded UCOD, and agreement between notified and ascertained UCOD was poor (29.2%; κ = 0.26). CONCLUSIONS: Mortality from infectious diseases, especially HIV/AIDS, is high in Kisumu County, but there is a shift toward higher mortality from noncommunicable diseases, possibly reflecting an epidemiologic transition and improving HIV outcomes. The epidemiologic transition suggests the need for increased focus on controlling noncommunicable conditions despite the high communicable disease burden. The weak agreement between notified and ascertained UCOD could lead to substantial inaccuracies in mortality statistics, which wholly depend on death notifications.

Evaluation of the Performance of OraQuick Rapid HIV-1/2 Test Among Decedents in Kisumu, Kenya.

BACKGROUND: Estimating cause-related mortality among the dead is not common, yet for clinical and public health purposes, a lot can be learnt from the dead. HIV/AIDS accounted for the third most frequent cause of deaths in Kenya; 39.7 deaths per 100,000 population in 2019. OraQuick Rapid HIV-1/2 has previously been validated on oral fluid and implemented as a screening assay for HIV self-testing in Kenya among living subjects. We assessed the feasibility and diagnostic accuracy of OraQuick Rapid HIV-1/2 for HIV screening among decedents. METHODS: Trained morticians collected oral fluid from 132 preembalmed and postembalmed decedents aged >18 months at Jaramogi Oginga Odinga Teaching and Referral Hospital mortuary in western Kenya and tested for HIV using OraQuick Rapid HIV-1/2. Test results were compared with those obtained using the national HIV Testing Services algorithm on matched preembalming whole blood specimens as a gold standard (Determine HIV and First Response HIV 1-2-O). We calculated positive predictive values, negative predictive values, area under the curve, and sensitivity and specificity of OraQuick Rapid HIV-1/2 compared with the national HTS algorithm. RESULTS: OraQuick Rapid HIV-1/2 had similar sensitivity of 92.6% [95% confidence interval (CI): 75.7 to 99.1] on preembalmed and postembalmed samples compared with the gold standard. Specificity was 97.1% (95% CI: 91.9 to 99.4) and 95.2% (95% CI: 89.2 to 98.4) preembalming and postembalming, respectively. Preembalming and postembalming positive predictive value was 89.3% (95% CI: 71.8 to 97.7) and 83.3% (95% CI: 65.3 to 94.4), respectively. The area under the curve preembalming and postembalming was 94.9% (95% CI: 89.6 to 100) and 93.9% (95% CI: 88.5 to 99.4), respectively. CONCLUSIONS: The study showed a relatively high-performance sensitivity and specificity of OraQuick Rapid HIV-1/2 test among decedents, similar to those observed among living subjects. OraQuick Rapid HIV-1/2 presents a convenient and less invasive screening test for surveillance of HIV among decedents within a mortuary setting.

A review of completeness, correctness, and order of cause of death statements among decedents with documented causes of death and HIV status at two major mortuaries in Kenya, 2015.

BACKGROUND: The cause of death (COD) statement is a vital statistic that refers to the disease(s) and process(es) that lead to death. Obtaining accurate COD is valuable for mortality prevention priorities. The statements are formulated using International Classification of Diseases and related health problems, version 10 (ICD-10) system. However, physicians may be unfamiliar with these standards or fail to use them and instead refer to mechanisms or manner of death when stating COD. We present results of an of assessment of quality of COD statements in decedent cases reviewed during a one-month mortuary-based surveillance at Kenyatta National Hospital (KNH) and the City mortuaries in Nairobi, Kenya in 2015. METHODS: Quality elements reviewed were completeness, correctness and order of stating the immediate (ICOD), antecedent, underlying (UCOD), and other significant causes (OSCs) as per the ICD 10 standards, in all deaths reported among adolescents and adults aged 15 years or older at the two mortuaries. COD were assessed for correct sequencing from immediate, antecedent, to underlying compared with autopsy pathology and clinical findings where available. Errors in COD statements were classified as missing or containing incomplete information such as: lack of underlying cause of an injury; incorrect words or statements; presence of more than one competing COD; use of the mechanism of death or anatomic and physiologic processes or signs and symptoms, and or laboratory results as CODs. Pearson's χ-squared test was used to compare proportions. RESULTS: Out of 810, 610 (75.3%) deaths having HIV statuses were abstracted and 356 had at least one COD documented; 114 (32%) females and 242 (68%) males; 239 (67.1%) from KNH and 117 (32.9%) City mortuary. The cases from City mortuary had higher rates of correct statements on 116 (99.1%) ICOD, 90 (89.1%) UCOD, and 40 (81.6%) OSCs, compared to KNH Mortuary; 50 (20.9%), 200 (90.1%) and 62 (76.5%) respectively, p < 0.001. The most common type of errors was incomplete information and citing mechanisms of death as the COD. CONCLUSIONS: In addition to revising national forms to conform to ICD-10, there is a need for periodic training of individuals responsible for completing death certificates. This will improve correctness and completeness of COD in order to provide reliable mortality data in Kenya.

HIV-Related Deaths in Nairobi, Kenya: Results From a HIV Mortuary Surveillance Study, 2015.

BACKGROUND: Death is an important but often unmeasured endpoint in public health HIV surveillance. We sought to describe HIV among deaths using a novel mortuary-based approach in Nairobi, Kenya. METHODS: Cadavers aged 15 years and older at death at Kenyatta National Hospital (KNH) and City Mortuaries were screened consecutively from January 29 to March 3, 2015. Cause of death was abstracted from medical files and death notification forms. Cardiac blood was drawn and tested for HIV infection using the national HIV testing algorithm followed by viral load testing of HIV-positive samples. RESULTS: Of 807 eligible cadavers, 610 (75.6%) had an HIV test result available. Cadavers from KNH had significantly higher HIV positivity at 23.2% (95% CI: 19.3 to 27.7) compared with City Mortuary at 12.6% (95% CI: 8.8 to 17.8), P < 0.001. HIV prevalence was significantly higher among women than men at both City (33.3% vs. 9.2%, P = 0.008) and KNH Mortuary (28.8% vs. 19.0%, P = 0.025). Half (53.3%) of HIV-infected cadavers had no diagnosis before death, and an additional 22.2% were only diagnosed during hospitalization leading to death. Although not statistically significant, 61.9% of males had no previous diagnosis compared with 45.8% of females (P = 0.144). Half (52.3%) of 44 cadavers at KNH with HIV diagnosis before death were on treatment, and 1 in 5 (22.7%) with a previous diagnosis had achieved viral suppression. CONCLUSIONS: HIV prevalence was high among deaths in Nairobi, especially among women, and previous diagnosis among cadavers was low. Establishing routine mortuary surveillance can contribute to monitoring HIV-associated deaths among cadavers sent to mortuaries.

Where No Universal Health Care Identifier Exists: Comparison and Determination of the Utility of Score-Based Persons Matching Algorithms Using Demographic Data.

BACKGROUND: A universal health care identifier (UHID) facilitates the development of longitudinal medical records in health care settings where follow up and tracking of persons across health care sectors are needed. HIV case-based surveillance (CBS) entails longitudinal follow up of HIV cases from diagnosis, linkage to care and treatment, and is recommended for second generation HIV surveillance. In the absence of a UHID, records matching, linking, and deduplication may be done using score-based persons matching algorithms. We present a stepwise process of score-based persons matching algorithms based on demographic data to improve HIV CBS and other longitudinal data systems. OBJECTIVE: The aim of this study is to compare deterministic and score-based persons matching algorithms in records linkage and matching using demographic data in settings without a UHID. METHODS: We used HIV CBS pilot data from 124 facilities in 2 high HIV-burden counties (Siaya and Kisumu) in western Kenya. For efficient processing, data were grouped into 3 scenarios within (1) HIV testing services (HTS), (2) HTS-care, and (3) within care. In deterministic matching, we directly compared identifiers and pseudo-identifiers from medical records to determine matches. We used R stringdist package for Jaro, Jaro-Winkler score-based matching and Levenshtein, and Damerau-Levenshtein string edit distance calculation methods. For the Jaro-Winkler method, we used a penalty (р)=0.1 and applied 4 weights (ω) to Levenshtein and Damerau-Levenshtein: deletion ω=0.8, insertion ω=0.8, substitutions ω=1, and transposition ω=0.5. RESULTS: We abstracted 12,157 cases of which 4073/12,157 (33.5%) were from HTS, 1091/12,157 (9.0%) from HTS-care, and 6993/12,157 (57.5%) within care. Using the deterministic process 435/12,157 (3.6%) duplicate records were identified, yielding 96.4% (11,722/12,157) unique cases. Overall, of the score-based methods, Jaro-Winkler yielded the most duplicate records (686/12,157, 5.6%) while Jaro yielded the least duplicates (546/12,157, 4.5%), and Levenshtein and Damerau-Levenshtein yielded 4.6% (563/12,157) duplicates. Specifically, duplicate records yielded by method were: (1) Jaro 5.7% (234/4073) within HTS, 0.4% (4/1091) in HTS-care, and 4.4% (308/6993) within care, (2) Jaro-Winkler 7.4% (302/4073) within HTS, 0.5% (6/1091) in HTS-care, and 5.4% (378/6993) within care, (3) Levenshtein 6.4% (262/4073) within HTS, 0.4% (4/1091) in HTS-care, and 4.2% (297/6993) within care, and (4) Damerau-Levenshtein 6.4% (262/4073) within HTS, 0.4% (4/1091) in HTS-care, and 4.2% (297/6993) within care. CONCLUSIONS: Without deduplication, over reporting occurs across the care and treatment cascade. Jaro-Winkler score-based matching performed the best in identifying matches. A pragmatic estimate of duplicates in health care settings can provide a corrective factor for modeled estimates, for targeting and program planning. We propose that even without a UHID, standard national deduplication and persons-matching algorithm that utilizes demographic data would improve accuracy in monitoring HIV care clinical cascades.

HIV-associated mortality in the era of antiretroviral therapy scale-up - Nairobi, Kenya, 2015.

BACKGROUND: Declines in HIV prevalence and increases in antiretroviral treatment coverage have been documented in Kenya, but population-level mortality associated with HIV has not been directly measured. In urban areas where a majority of deaths pass through mortuaries, mortuary-based studies have the potential to contribute to our understanding of excess mortality among HIV-infected persons. We used results from a cross-sectional mortuary-based HIV surveillance study to estimate the association between HIV and mortality for Nairobi, the capital city of Kenya. METHODS AND FINDINGS: HIV seropositivity in cadavers measured at the two largest mortuaries in Nairobi was used to estimate HIV prevalence in adult deaths. Model-based estimates of the HIV-infected and uninfected population for Nairobi were used to calculate a standardized mortality ratio and population-attributable fraction for mortality among the infected versus uninfected population. Monte Carlo simulation was used to assess sensitivity to epidemiological assumptions. When standardized to the age and sex distribution of expected deaths, the estimated HIV positivity among adult deaths aged 15 years and above in Nairobi was 20.9% (95% CI 17.7-24.6%). The standardized mortality ratio of deaths among HIV-infected versus uninfected adults was 4.35 (95% CI 3.67-5.15), while the risk difference was 0.016 (95% CI 0.013-0.019). The HIV population attributable mortality fraction was 0.161 (95% CI 0.131-0.190). Sensitivity analyses demonstrated robustness of results. CONCLUSIONS: Although 73.6% of adult PLHIV receive antiretrovirals in Nairobi, their risk of death is four-fold greater than in the uninfected, while 16.1% of all adult deaths in the city can be attributed to HIV infection. In order to further reduce HIV-associated mortality, high-burden countries may need to reach very high levels of diagnosis, treatment coverage, retention in care, and viral suppression.