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Background Uganda is prone to Emerging Infectious Diseases (EIDs) which can cause serious epidemics and pandemics. Uganda’s capacity for EID research, surveillance and control is improving but still low partly due to inadequate highly knowledgeable and skilled human and animal health workers. To inform the design of training programs that can address Uganda’s health workforce capacity gaps, we conducted a training needs assessment. Methods A qualitative study involving a desk review, 25 key informant interviews and a 1-day consultative workshop to review study findings. Results The majority of infectious disease research, surveillance and control in Uganda focuses on HIV/AIDS, Tuberculosis, Malaria and viral hemorrhagic fevers e.g., Ebola and Marburg. Health workforce capacity for surveillance and control is robust compared to many other resource-constrained settings but research capacity and output are relatively low, especially for EIDs. Public and private tertiary institutions in Uganda predominantly offer training in primary health care and population studies through problem-based learning, community-based education and services, and Blended Learning (BL). There are several training programs in advanced clinical and epidemiological sciences, but few opportunities in biomedical sciences (e.g. virology, immunology, bioinformatics and predictive modeling), social sciences, One Health and leadership. To address the gaps, the following interventions were recommended: 1) advanced graduate and/or post-graduate training in basic biomedical sciences; 2) short-term training for continuous knowledge and skills development in multidisciplinary/One Health approaches; and 3) pedagogy and mentorship through BL, networking and experiential training programs that effectively leverage North-South collaborations. Training and mentorship should be achieved by (a) conducting most of the in-person didactic and experiential training at Southern tertiary and research institutions, (b) utilizing electronic-learning for didactic training and mentor-mentee interactions with subject-matter experts at Northern institutions, and (c) well-orchestrated placements at Northern institutions for hands-on experience using the latest advances in science and technology. Conclusion Inadequate health workforce capacity for EID research was identified as a priority gap that requires long and short-term multidisciplinary training interventions. Efficiently leveraging North-South collaborations for e-learning, short-term placements and mentorship will enable Uganda to remain abreast with latest advances in science and technology for EID research, surveillance and control.

IntroductionAccurate and affordable laboratory testing is key to timely diagnosis and appropriate management of patients with COVID-19. New laboratory test protocols are released into the market under emergency use authorisation with limited evidence on diagnostic test accuracy. As such, robust evidence on the diagnostic accuracy and the costs of available tests is urgently needed to inform policy and practice especially in resource-limited settings. We aim to determine the diagnostic test accuracy, cost-effectiveness and utility of laboratory test strategies for COVID-19 in low-income and middle-income countries.Methods and analysisThis will be a multistaged, protocol-driven systematic review conducted in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for diagnostic test accuracy studies. We will search for relevant literature in at least six public health databases, including PubMed, Google Scholar, MEDLINE, Scopus, Web of Science and the WHO Global Index Medicus. In addition, we will search Cochrane Library, COVID-END and grey literature databases to identify additional relevant articles before double-screening and abstraction of data. We will conduct a structured narrative and quantitative synthesis of the results guided by the Fryback and Thornbury framework for assessing a diagnostic test. The primary outcome is COVID-19 diagnostic test accuracy. Using the GRADE approach specific to diagnostic accuracy tests, we will appraise the overall quality of evidence and report the results following the original PRISMA statement. The protocol is registered with the International Prospective Register of Systematic Reviews (PROSPERO; https://www.crd.york.ac.uk/prospero/).Ethics and disseminationEthical review was done by the School of Biomedical Sciences Research Ethics Committee and the Uganda National Council for Science and Technology. The published article will be accessible to policy and decision makers. The findings of this review will guide clinical practice and policy decisions and highlight areas for future research.PROSPERO registration number CRD42020209528.

Background: Globally, health care workers continue to be infected, fall ill and die at the frontline of the Coronavirus Disease 2019 (COVID-19) fight, an indicator of inadequate safety in health facilities. This rapid evidence synthesis aims to highlight the impacts of COVID-19 on healthcare workers in low-and middle-income countries (LMICs) in terms of infections, illnesses and deaths. Methods: A systematic review will be done. Article search will be performed by an experienced librarian in PubMed, MEDLINE Ovid, Google Scholar, COVID-END, Cochrane library and targeted search from other relevant sources. MeSH terms and Boolean operators “AND” and “OR” will be used in the article search. Independent reviewers will screen the retrieved articles using a priori criteria. Data abstraction will be done using an excel based abstraction tool and synthesized using structured narratives and summary of findings tables. Discussion: This evidence synthesis seeks to analyze the impact of COVID-19 on the healthcare systems of low- and middle-income countries. Information on healthcare worker infections, illness, and deaths due to COVID-19, will be collated from published research articles. This will help guide decision makers in establishing low- cost high impact interventions to mitigate the effects of COVID-19 in the health work force.Protocol registration: PROSPERO CRD 42020204174 [1] [1] This protocol registration can be found at; https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42020204174

Background In 2011, the World Health Organization recommended injectable artesunate as the first-line therapy for severe malaria (SM) due to its superiority in reducing mortality compared to quinine. There are limited data on long-term clinical and neurobehavioral outcomes after artemisinin use for treatment of SM. Methods From 2008 to 2013, 502 Ugandan children with two common forms of SM, cerebral malaria and severe malarial anemia, were enrolled in a prospective observational study assessing long-term neurobehavioral and cognitive outcomes following SM. Children were evaluated a week after hospital discharge, and 6, 12, and 24 months of follow-up, and returned to hospital for any illness. In this study, we evaluated the impact of artemisinin derivatives on survival, post-discharge hospital readmission or death, and neurocognitive and behavioral outcomes over 2 years of follow-up. Results 346 children received quinine and 156 received parenteral artemisinin therapy (artemether or artesunate). After adjustment for disease severity, artemisinin derivatives were associated with a 78% reduction in in-hospital mortality (adjusted odds ratio, 0.22; 95% CI, 0.07–0.67). Among cerebral malaria survivors, children treated with artemisinin derivatives also had reduced neurologic deficits at discharge (quinine, 41.7%; artemisinin derivatives, 23.7%, p=0.007). Over a 2-year follow-up, artemisinin derivatives as compared to quinine were associated with better adjusted scores (negative scores better) in internalizing behavior and executive function in children irrespective of the age at severe malaria episode. After adjusting for multiple comparisons, artemisinin derivatives were associated with better adjusted scores in behavior and executive function in children Conclusions Treatment of severe malaria with artemisinin derivatives, particularly artesunate, results in reduced in-hospital mortality and neurologic deficits in children of all ages, reduced inflammation following recovery, and better long-term behavioral outcomes. These findings suggest artesunate has long-term beneficial effects in children surviving severe malaria.

Globally, even though improvements have been made to effective surveillance and response, communicable diseases such as cholera remain high priorities for national health programs, especially in Africa. High-quality surveillance information coupled with adequate laboratory facilities are effective in curbing outbreaks from such diseases, ultimately reducing morbidity and mortality. One way of building this capacity is through simulation of response to such health events. This case study based on a cholera outbreak investigated by FETP trainees in October 2015 in Uganda can be used to reinforce skills of frontline FETP trainees and other novice public health practitioners through a practical simulation approach. This activity should be completed in 2.5 hours.

Cholera is a bacterial diarrheal disease caused by Vibrio cholerae. On 15 October 2015, a cholera outbreak involving dozens of cases and 2 deaths was reported in Kaiso, a lakeshore fishing village. The district health department responded by setting up a treatment center and sensitizing the community. Despite initial response, the outbreak persisted, prompting a detailed epidemiological investigation to identify the source and mode of transmission and recommend evidence-based interventions to stop the epidemic. We defined a suspected case as onset of acute watery diarrhoea in a Kaiso Village resident from 1 st October 2015 onward; a confirmed case was a suspected case with Vibrio cholerae isolated from stool. We performed descriptive epidemiology to generate a hypothesis, and conducted a case-control study to compare exposure histories of 61 cases and 126 controls randomly selected among village residents (age ≥ 4 years in both groups). We conducted environmental assessment and obtained meteorological data from a local weather station. 123 suspected cases (2 deaths) were line-listed at the village’s cholera clinic. The initial 2 deceased cases had onset on 2 nd and 10 th October. Heavy rainfall occurred during 7–11 th . October, setting in a point-source outbreak which started on 12 th and peaked on 13 th October. Three water collection points (WCP) A, B and C were associated with the outbreak. 9.8% (6/61) of case-persons and 31% (39/126) of control-persons usually collected water from WCP A. In comparison, 21% (13/61) of case-persons and 37% (46/126) of control-persons usually collected water from WCP B (OR= 1.8, 95%CI: 0.64-5.3) and 69% (42/61) of case-persons and 33% (41/126) of control-persons from WCP C (OR=6.7; 95%CI=2.5-17). 100% (61/61) of case-persons and 93% (117/126) of control-persons never treated/boiled drinking water (OR=∞, 95%CI Fisher =1.0-∞). A gully channel from a hillside open defecation area washed down feces to the lakeshore at WCP C. This outbreak was caused by drinking lakeshore water contaminated by feces washed down a gully from the village. We recommended water boiling and treatment, fixing the broken piped-water system and constructing latrines. The outbreak was stopped by implementing treatment and boiling of drinking water at household level.

Introduction : in September 2015, a cholera outbreak occurred in a village in Hoima District, western Uganda. The Ministry of Health assembled a rapid response team, with support by CDC, UNICEF and WHO, to investigate the outbreak, establish the Kaiso Cholera Treatment Center (KCTC), and implement control measures. The team identified 120 cholera cases (with 5 deaths) and determined that drinking contaminated water from the lakeshore caused this outbreak. We sought to determine the cost of investigating and controlling this outbreak, and compare it to a would-be simple preventive measure, constructing deep wells to provide cleaner water. Methods : we collected cost data, including personnel and material costs at KCTC, health facilities, Hoima District Health Office, Uganda Public Health Fellowship Program, UNICEF, CDC, and WHO. We defined direct cost of responding to this outbreak as expenditure on medications, medical equipment and supplies, utilities, and allowances and transport for responders; indirect cost included salary and other compensations for responders. We did not include difficult-to-measure costs such as vehicle depreciation, building maintenance, and loss of productivity to case-persons due to illness and deaths. The cost of constructing deep wells was quoted by a U.S.-based NGO. Results : the total cost incurred in investigating and controlling this outbreak was $71,769, including $21,059 in direct cost ($19,225 for allowances and transportation, $1,774 for medical equipment and supplies, and $60 for utilities), and $50,620 in indirect cost (74,484 person-hours of salary and other compensations for responders). Conversely, constructing a deep well to provide cleaner water would cost approximately $2500. Essentially, the total cost incurred in this outbreak would have been enough to construct 28 (=71769/2500) deep wells; even the direct cost only would have been enough to construct 8 (=21059/2500) deep wells. One such deep well would have prevented this outbreak and averted future waterborne outbreaks. Conclusion : a simple prevention measure such as constructing deep wells for village residents can be substantially cost-effective for preventing waterborne diseases such as cholera. We recommend that the government should proactively implement prevention measures for waterborne outbreaks whenever possible, instead of passively responding to these outbreaks.

A malaria epidemic has been confirmed in ten former IRS districts. Given the recent malaria control interventions, a sustained decline in the malaria cases would have been expected. Thus the need for a descriptive analysis on the trends in malaria morbidity in these districts among under 5yr olds for the past 3 financial years to help inform the Ministry of Health and predict future malaria epidemics. The objective of the analysis was to describe annual seasonal trends and peaks in prevalence in malaria morbidity among under 5yr olds over the past three financial years in former IRS districts. Describe the difference in incidence of malaria for the under 5yr olds among all the districts under study for the given period. A desk review of all under 5yr old malaria cases and malaria control interventions for the past three financial years in the given districts were conducted. There are two malaria seasons each year from April to July and September to November which coincides with the rainy seasons. The peaks in prevalence for all the districts were in June 2015. For the past three financial years, 7/9 districts each had a higher malaria incidence than Lamwo district which has 100% coverage of iCCM (P < 0.001). The rainy seasons present an opportunity for malaria epidemics, iCCM seems to have an effect in reducing the incidence of malaria among fewer than 5yr olds at health facilities. We recommended surveillance and monitoring of trends in malaria cases especially during the rainy season for early detection of epidemics; and assessment of the actual impact of iCCM on the reduction of malaria incidence.

Introduction : in 2012, Tororo was a high malaria endemic district in Uganda with community Plasmodium prevalence of 71%. The Ministry of Health introduced universal distribution of long lasting insecticide-treated nets (LLINs) in 2013 and indoor residual spraying (IRS) in 2014 to control malaria in the district. We assessed malaria incidence, test positivity rates and outpatient department (OPD) attendance due to malaria before and after vector control interventions. Methods : this study was based on analysis of health management information system, secondary malaria surveillance data from 2,727,850 people who were assessed for malaria at OPD in 61 health facilities from 2012-2015. We estimated monthly malaria incidence for the entire population and also separately for Results : in 2014 when LLINs were used alone, the annual mean monthly malaria incidence fell from 95 in 2013 to 76 cases per 1000 with no significant monthly reduction trend (OR = 0.99, 95% CI = 0.96-1.01, P=0.37). Among children Conclusion : malaria incidence in Tororo District declined rapidly following introduction of integrated vector control interventions. Universal distribution of LLINs alone was not associated with significant reduction in malaria incidence in the district.

Background On 12 October 2015, a cholera outbreak involving 65 cases and two deaths was reported in a fishing village in Hoima District, Western Uganda. Despite initial response by the local health department, the outbreak persisted. We conducted an investigation to identify the source and mode of transmission, and recommend evidence-led interventions to control and prevent cholera outbreaks in this area. Methods We defined a suspected case as the onset of acute watery diarrhoea from 1 October to 2 November 2015 in a resident of Kaiso Village. A confirmed case was a suspected case who had Vibrio cholerae isolated from stool. We found cases by record review and active community case finding. We performed descriptive epidemiologic analysis for hypothesis generation. In an unmatched case-control study, we compared exposure histories of 61 cases and 126 controls randomly selected among asymptomatic village residents. We also conducted an environmental assessment and obtained meteorological data from a weather station. Results We identified 122 suspected cases, of which six were culture-confirmed, 47 were confirmed positive with a rapid diagnostic test and two died. The two deceased cases had onset of the disease on 2 October and 10 October, respectively. Heavy rainfall occurred on 7–11 October; a point-source outbreak occurred on 12–15 October, followed by continuous community transmission for two weeks. Village residents usually collected drinking water from three lakeshore points – A, B and C: 9.8% (6/61) of case-persons and 31% (39/126) of control-persons were found to usually use point A, 21% (13/61) of case-persons and 37% (46/126) of control-persons were found to usually use point B (OR = 1.8, 95% CI: 0.64–5.3), and 69% (42/61) of case-persons and 33% (41/126) of control-persons were found to usually use point C (OR = 6.7; 95% CI: 2.5–17) for water collection. All case-persons (61/61) and 93% (117/126) of control-persons reportedly never treated/boiled drinking water (OR = ∞, 95% CI Fisher: 1.0 – ∞). The village’s piped water system had been vandalised and open defecation was common due to a lack of latrines. The lake water was found to be contiminated due to a gully channel that washed the faeces into the lake at point C. Conclusions This outbreak was likely caused by drinking lake water contaminated by faeces from a gully channel. We recommend treatment of drinking water, fixing the vandalised piped-water system and constructing latrines. Electronic supplementary material The online version of this article (10.1186/s40249-017-0359-2) contains supplementary material, which is available to authorized users.

Background In June 2015, a malaria epidemic was confirmed in ten districts of Northern Uganda; after cessation of indoor residual spraying (IRS). Epidemic was defined as an increase in incidence per month beyond one standard deviation above mean incidence of previous 5 years. Trends in malaria incidence among children-under-5-years were analysed so as to describe the extent of change in incidence prior to and after cessation of IRS. Methods Secondary data on out-patient malaria case numbers for children-under-5-years July 2012 to June 2015 was electronically extracted from the district health management information software2 (DHIS2) for ten districts that had IRS and ten control districts that didn’t have IRS. Data was adjusted by reporting rates, cleaned by smoothing and interpolation and incidence of malaria per 1000 population derived. Population data obtained from 2002 and 2014 census reports. Data on interventions obtained from malaria programme reports, rainfall data obtained from Uganda National Meteorological Authority. Three groups of districts were created; two based on when IRS ended, the third not having IRS. Line graphs were plotted showing malaria incidence vis-à-vis implementation of IRS, mass net distribution and rainfall. Changes in incidence after withdrawal of IRS were obtained using incidence rate ratios (IRR). IRR was calculated as incidence for each month after the last IRS divided by incidence of the IRS month. Poisson regression was used to test statistical significance. Results Incidence of malaria declined between spray activities in districts that had IRS. Decline in IRR for 4 months after last IRS month was greater in the sprayed than control districts. On the seventh month following cessation of IRS, incidence in sprayed districts rose above that of the last spray month [1.74: 95% CI (1.40–2.15); and 1.26: 95% CI (1.05–1.51)]. Rise in IRR continued from 1.26 to 2.62 (95% CI 2.21–3.12) in June 2015 for districts that ended IRS in April 2014. Peak in rainfall occurred in May 2015. Conclusion There was sustained control of malaria incidence during IRS implementation. Following withdrawal and peak in rainfall, incidence rose to epidemic proportions. This suggests a plausible link between the malaria epidemic, peak in rainfall and cessation of IRS.

Background In 2012, Tororo District had the highest malaria burden in Uganda with community Plasmodium prevalence of 48%. To control malaria in the district, the Ministry of Health introduced universal distribution of long lasting insecticide-treated nets (LLINs) in 2013 and added indoor residual spraying (IRS) in 2014. This study assessed malaria incidence, test positivity rates and outpatient (OPD) attendance due to malaria before and after vector control interventions. Methods This study was based on analysis of Health Management Information System (HMIS) secondary malaria surveillance data of 2,727,850 patient records in OPD registers of 61 health facilities from 2012 to 2015. The analysis estimated monthly malaria incidence for the entire population and also separately for

Background In the midst of success with malaria reduction in Uganda, there are areas that still have high prevalence of malaria parasitaemia. This project aimed at investigating factors associated with this prevalence and its relationship with anaemia. Methods This is a secondary data analysis of the 2014 Malaria Indicator Survey dataset of children under 5 years. All had a blood sample taken by finger or heel prick for determination of malaria parasitaemia and estimation of haemoglobin level for anaemia status. The main outcome was the presence of malaria parasitaemia by microscopy and independent variables included: age, gender, residence (urban vs rural), use of a long-lasting, insecticidal-treated net, indoor residual spraying (IRS) of household in the past 6 months, mother’s highest education level, mother heard malaria prevention message in the past 6 months, and household wealth status. Results The analysis included 4930 children and of these, 938 (19.04%: 95% CI 16.63–21.71) tested positive for malaria parasites. Malaria parasite prevalence significantly increased from 11.08 (95% CI 9.12–13.40) among children with no anaemia to 50.99% (95% CI 39.13–62.74) with severe anaemia (Chi-square p-value = 0.001). Additionally, prevalence significantly rose from the youngest age group (under 6 months) by 1.62 times (95% CI 1.04–2.52, p = 0.033) among the age group of 7–12 months and to four times (95% CI 2.57–6.45, p = 0.001) among those who were between 49 and 59 months. The following were associated with reduced parasitaemia: IRS use (AOR 0.23 [0.08–0.61], p = 0.004), educated mothers (primary AOR 0.75 [0.59–0.96], p = 0.023 to tertiary AOR 0.11 [0.02–0.53], 0.006), mother heard malaria message (AOR 0.78 [0.62–0.99], p = 0.037), and wealthier households (richest AOR 0.17 [0.08–0.36], p = 0.001). Conclusions Increasing malaria parasite prevalence among children under 5 years is still related to increasing age and severity of anaemia even in the context of decreasing malaria prevalence. Designing interventions that include the use of IRS and behaviour change communication tailored to include older children, especially in areas with high malaria prevalence, could be of added value. All this should be done in an environment that improves the socio-economic status and equity of such populations.

Background The Uganda National Malaria Control Programme recommends the use of intermittent preventive therapy in pregnancy with sulfadoxine/pyrimethamine (SP) to prevent malaria, however, there is overwhelming evidence of low uptake of this intervention. This study, therefore, sought to examine the factors associated with taking two or more doses of therapy among women who had had the most recent live birth. Methods This was a secondary data analysis of the 2014 Malaria Indicator Survey dataset. The outcome was the use of two or more doses of SP for the most recent live birth while independent variables included; age, highest education attained, residence (rural and urban), use of radio and community health teams for malaria related messages, knowledge of taking SP and use of LLINS to prevent malaria, household wealth, skilled attendant seen at ANC and number of children the woman has. Results Of the 1820 women included in the final analysis, 822 (45.16 %) women took two or more doses of SP. Women who knew that this therapy was used to prevent malaria and those who had been seen by a skilled attendant were 10.72 times [Adjusted OR (95 % CI): 10.72 (7.62–15.08), p-value = 0.001] and 3.19 times [Adjusted OR (95 % CI): 3.19 (1.26–8.07), p-value = 0.015] more likely to take at least two doses as compared to those who did not know about this therapy and those seen by unskilled attendants, respectively. Conclusion This study shows that knowledge among women that SP is a medication used for malaria prevention during pregnancy increases the uptake of two or more doses of this therapy among pregnant women. This highlights the importance of behaviour change communication focused on IPTp uptake that can be complemented by having skilled personnel attending to pregnant women at the antenatal clinic.