Strategies for rapid scale up of laboratory capacity in a public health emergency in a resource-constrained setting: the SARS-CoV-2 Nigeria response experience (preprint)

Introduction: Sufficient laboratory capacity is vital to containing infectious diseases outbreaks. This study was conducted to assess SARS-CoV-2 testing performance, the strategies adopted to scale up laboratory testing capacity, and to highlight challenges and lessons learnt in Nigeria’s response to COVID-19 pandemic regarding testing strategies.Methods This cross-sectional descriptive study adopted a mixed method approach including desk reviews and key informant interviews (KIIs). The KIIs were conducted among actors of the COVID-19 response teams in states (SMoH) and the Federal Ministry of Health (FMoH) in Nigeria. Data extraction tools were populated from the relevant online resources and documents of the FMoH, SMoH and the Nigeria Centre for Disease Control.Results At the beginning of the pandemic in Nigeria, testing performance was poor, but this improved over time. To manage the demand for testing, Nigeria adopted targeted testing with a focus on symptomatic contacts and alerts, returning travelers from high-risk countries who were symptomatic during the quarantine period, among others groups. Strategies to enhance laboratory capacity and improve the turnaround time for results included leveraging on existing tuberculosis laboratory network or building new laboratories where none existed; decentralization of sample collection and testing; staff health workers repurposing and hiring of volunteers; training and retraining of laboratory personnel; adoption of rapid diagnostic testing; and strengthening public-private partnerships to leverage the private sector testing. From an initial three laboratories with capacity to test for SARS-CoV-2 in February, 2020, the number of laboratories increased to 158 by March, 2022. Although laboratory capacity increased, logistics and supply chain disruption was still a challenge.Conclusion Investment in local manufacturing capacities of laboratory consumables such as RDTs and reagents would promote self-reliance and sustainability for a country as populous as Nigeria.

A Collaborative Approach to the Analysis of the COVID-19 Response in Africa (preprint)

The COVID-19 crisis has emphasized the need for scientific methods such as machine learning to speed up the discovery of solutions to the pandemic. Harnessing machine learning techniques requires quality data, skilled personnel and advanced compute infrastructure. In Africa, however, machine learning competencies and compute infrastructures are limited. This paper demonstrates a cross-border collaborative capacity building approach to the application of machine learning techniques in discovering answers to COVID-19 questions.

Private Sector Engagement in the COVID-19 Response Experiences and Lessons from the Democratic Republic of Congo, Nigeria, Senegal and Uganda (preprint)

Background: Private entities play a major role in health globally. However, their contribution has not been fully optimized to strengthen delivery of public health services. The COVID-19 pandemic has overwhelmed health systems and precipitated coalitions between public and private sectors to address critical gaps in the response. We conducted a study to document the public and private sector partnerships and engagements to inform current and future responses to public health emergencies. Methods This was a multi-country cross-sectional study conducted in the Democratic Republic of Congo, Nigeria, Senegal and Uganda to assess responses to the COVID-19 pandemic. We conducted a scoping literature review and key informant interviews (KIIs) with private and public health sector stakeholders. The literature reviewed included COVID-19 country guidelines and response plans, program reports, websites and peer-reviewed and non-peer-reviewed publications. KIIs elicited information on country approaches and response strategies specifically the engagement of the private sector in any of the strategic response operations. Results Across the 4 countries, private sector strengthened laboratory systems, COVID-19 case management, risk communication and health service continuity. In the DRC and Nigeria, private entities supported contact tracing and surveillance activities. Across the 4 countries, the private sector supported expansion of access to testing services through establishing partnerships with the public health sector to provide COVID-19 testing albeit at unregulated fees. In Senegal and Uganda, governments established partnerships with private sector to manufacture COVID-19 rapid diagnostic tests. The private sector also contributed to treatment and management of COVID-19 cases. In addition, private entities provided personal protective equipment, conducted risk communication to promote adherence to safety procedures and health promotion for health service continuity. However, there were concerns related to reporting, quality and cost of services, calling for quality and price regulation in the provision of services. Conclusions The private sector greatly contributed to the COVID-19 response through engagement in COVID-19 surveillance and testing, management of COVID-19 cases, and health promotion to maintain health access. There is a need to develop regulatory frameworks that support sustainable public-private engagements including regulation of pricing, quality assurance and alignment with national plans, strategies and priorities during response to epidemics.

Unintended Socio-Economic and Health Consequences of COVID-19 among Slum Dwellers in Kampala, Uganda (preprint)

Background: To reduce the spread of COVID-19, several countries in Africa instituted countrywide lockdowns and other public health measures. Whereas lockdowns contributed to the control of the pandemic, there were concerns about the unintended consequences of these measures especially in the most vulnerable populations. We assessed unintended socio-economic and health consequences due to the COVID-19 pandemic and the mitigation measures in slums in Kampala to inform the on-going and future pandemic response strategies. Methods: This was a mixed methods cross-sectional study conducted in Bwaise I and Bwaise III slums of Kawempe division, Kampala Uganda from October to December 2020. We used systematic sampling to randomly select 425 household heads for the face-to-face quantitative interviews. We also conducted six focus group discussions (FGDs) with slum dwellers and used photovoice among eight Community Health Workers (CHWs) to document unintended socio-economic and health consequences. Quantitative data were imported into STATA version 14.0 for analysis, while qualitative data were analysed thematically using NVivo version 12. Modified Poisson regression analysis was conducted to establish factors associated with impact on access to food. Results: Most respondents reported limited access to food (71.1%; 302/425); disruption in education (77.1%; 270/350); drop in daily income and wages (86.1%; 329/382) and loss of employment (63.1; 125/198). Twenty five percent of the respondents (25.4%; 86/338) reported domestic violence as one of the challenges. Seven themes emerged from the qualitative findings on the impact of COVID-19 including: limited access to food; negative impact on children’s rights (child labour and early pregnancies) and education; poor housing and lack of accommodation; negative social behaviours; negative impact on family and child care; reduced income and employment; and negative impact on health and access to health care services. Conclusion: The slum dwellers of Bwaise I and Bwaise III experienced several negative socio-economic consequences of COVID-19 and its prevention measures that severely affected their wellbeing. Children experienced severe consequences such as child labour and early pregnancies among the girls. Response activities should be contextualised to different settings and protocols to protect the vulnerable groups in the community such as children and women should be developed and mainstreamed in response activities.

The Ugandan Severe Acute Respiratory Syndrome -Coronavirus 2 (SARS-CoV-2) Model: A Data Driven Approach to Estimate Risk (preprint)

Objectives The first case of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) was identified on March 21, 2020, in Uganda. The number of cases increased to 8,287 by September 30, 2020. By May throughout June, most of the cases were predominantly imported cases of truck drivers from neighbouring countries. Uganda responded with various restrictions and interventions including lockdown, physical distancing, hand hygiene, and use of face masks in public, to control the growth rate of the outbreak. By end of September 2020, Uganda had transitioned into community transmissions and most of the reported cases were locals contacts and alerts. This study assessed risks associated with SARS-CoV-2 in Uganda, and presents estimates of the reproduction ratio in real time. An optimal control analysis was performed to determine how long the current mitigation measures such as controlling the exposure in communities, rapid detection, confirmation and contact tracing, partial lockdown of the vulnerable groups and control at the porous boarders, could be implemented and at what cost. Methods The daily confirmed cases of SARS-CoV-2 in Uganda were extracted from publicly available sources. Using the data, relative risks for age, gender, and geographical location were determined. Four approaches were used to forecast SARS-CoV-2 in Uganda namely linear exponential, nonlinear exponential, logistic and a deterministic model. The discrete logistic model and the next generation matrix method were used to estimate the effective reproduction number. Results Results: showed that women were at a higher risk of acquiring SARS-CoV-2 than the men, and the population attributable risk of SARS-CoV-2 to women was 42.22%. Most of the women affected by SARS-CoV-2 were likely contacts of cargo truck drivers at the boarders, where high infection rates were reported. Although most deaths in Uganda were in the age group of 60-69, the highest case fatality rate per 1000 was attributable the age group of 80-89, followed by 70-79. Geographically, Amuru had the highest relative risk compared to the national risk to SARS-CoV-2. For the case of mitigation scenarios, washing hands with 70% com pliance and regular hand washing of 6 times a day, was the most effective and sustainable to reduce SARS- CoV-2 exposure. This was followed by public wearing of face masks if at least 60% of the population complied, and physical distancing by 60% of the population. If schools, bars and churches were opened without compliance, i.e., no distancing, no handwashing and no public wearing of face masks, to mitigation measures, the highest incidence was observed, leading to a big replacement number. If mitigation measures are not followed by the population, then there will be high incidences and prevalence of the virus in the population.

Violence and Discrimination Among Ugandan Residents During the COVID-19 Lockdown (preprint)

Background: In March 2020, the World Health Organization (WHO) declared COVID-19 a pandemic. Many countries in Sub Saharan Africa, Uganda inclusive, implemented lockdowns, curfew, banning of both private and public transport systems and mass gatherings to minimize spread. Media reports indicated that cases of violence and discrimination had increased in Uganda’s communities following the lockdown. We estimated the incidence and factors associated with experiencing violence and discrimination among Ugandans during the COVID-19 lockdown to inform control and prevention measures. Methods: : In April 2020, we conducted a cross-sectional study under the International Citizen Project (ICP) to assess adherence to public health measures and their impact on the COVID-19 outbreak in Uganda. We abstracted and analyzed data on violence and discrimination from the ICP study. We performed descriptive statistics for all the participants’ characteristics and created a binary outcome variable called experiencing violence and/or discrimination. We performed logistic regression analysis to identify the factors associated with experiencing violence and discrimination. Results: : Of the 1,726 ICP study participants, 1,051 (58.8%) were males, 841 (48.7%) were currently living with a spouse or partner, and 376 (21.8%) had physically attended work for more than 3 days in the past week. Overall, 145 (8.4%) experienced any form of violence and/or discrimination by any perpetrator, and 46 (31.7%) of the 145 reported that it was perpetrated by a law enforcement officer. Factors associated with experiencing violence or discrimination were: being male (AOR= 1.60 CI:1.10-2.33), having attended work physically for more than 3 days in the past week (AOR=1.52 CI:1.03-2.23), and inability to access social or essential health services since the epidemic started (AOR=3.10 CI:2.14-4.50). Conclusion: A substantial proportion of Ugandan residents experienced violence and/or discrimination during the COVID-19 lockdown, mostly perpetrated by law enforcement officers. Mitigation of violence and/or discrimination, as well as increased access to health and social services should be integrated into control measures in large-scale public health emergencies.