A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field

Background : The COVID-19 pandemic led to severe health systems collapse, as well as logistics and supply delivery shortages across sectors. Delivery of PCR related healthcare supplies continue to be hindered. There is the need for a rapid and accessible SARS-CoV-2 molecular detection method in low resource settings. Objectives : To validate a novel isothermal amplification method for rapid detection of SARS-CoV-2 across seven sub-Sharan African countries. Study design : In this multi-country phase 2 diagnostic study, 3,231 clinical samples in seven African sites were tested with two reverse transcription Recombinase-Aided Amplification (RT-RAA) assays (based on SARS-CoV-2 Nucleocapsid (N) gene and RNA-dependent RNA polymerase (RdRP) gene). The test was performed in a mobile suitcase laboratory within 15 minutes. All results were compared to a real-time RT-PCR assay. Extraction kits based on silica gel or magnetic beads were applied. Results : Four sites demonstrated good to excellent agreement, while three sites showed fair to moderate results. The RdRP gene assay exhibited an overall PPV of 0.92 and a NPV of 0.88. The N gene assay exhibited an overall PPV of 0.93 and a NPV 0.88. The sensitivity of both RT-RAA assays varied depending on the sample Ct values. When comparing sensitivity between sites, values differed considerably. For high viral load samples, the RT-RAA assay sensitivity ranges were between 60.5 and 100% (RdRP assay) and 25 and 98.6 (N assay). Conclusion : Overall, the RdRP based RT-RAA test showed the best assay accuracy. This study highlights the challenges of implementing rapid molecular assays in field conditions. Factors that are important for successful deployment across countries include the implementation of standardized operation procedures, in-person continuous training for staff, and enhanced quality control measures.

Air pollution and mobility patterns in two Ugandan cities during COVID-19 mobility restrictions suggest the validity of air quality data as a measure for human mobility.

We explored the viability of using air quality as an alternative to aggregated location data from mobile phones in the two most populated cities in Uganda. We accessed air quality and Google mobility data collected from 15th February 2020 to 10th June 2021 and augmented them with mobility restrictions implemented during the COVID-19 lockdown. We determined whether air quality data depicted similar patterns to mobility data before, during, and after the lockdown and determined associations between air quality and mobility by computing Pearson correlation coefficients ([Formula: see text]), conducting multivariable regression with associated confidence intervals (CIs), and visualized the relationships using scatter plots. Residential mobility increased with the stringency of restrictions while both non-residential mobility and air pollution decreased with the stringency of restrictions. In Kampala, PM2.5 was positively correlated with non-residential mobility and negatively correlated with residential mobility. Only correlations between PM2.5 and movement in work and residential places were statistically significant in Wakiso. After controlling for stringency in restrictions, air quality in Kampala was independently correlated with movement in retail and recreation (- 0.55; 95% CI = - 1.01- - 0.10), parks (0.29; 95% CI = 0.03-0.54), transit stations (0.29; 95% CI = 0.16-0.42), work (- 0.25; 95% CI = - 0.43- - 0.08), and residential places (- 1.02; 95% CI = - 1.4- - 0.64). For Wakiso, only the correlation between air quality and residential mobility was statistically significant (- 0.99; 95% CI = - 1.34- - 0.65). These findings suggest that air quality is linked to mobility and thus could be used by public health programs in monitoring movement patterns and the spread of infectious diseases without compromising on individuals' privacy.

Respiratory Support Techniques for COVID-19-Related ARDS in a Sub-Saharan African Country: A Multicenter Observational Study.

BACKGROUND: Few data from low-income countries report on respiratory support techniques in COVID-19-associated ARDS. RESEARCH QUESTION: Which respiratory support techniques are used in patients with COVID-19-associated ARDS in Uganda? STUDY DESIGN AND METHODS: A multicenter, prospective, observational study was conducted at 13 Ugandan hospitals during the pandemic and included adults with COVID-19-associated ARDS. Patient characteristics, clinical and laboratory data, initial and most advanced respiratory support techniques, and 28-day mortality were recorded. Standard tests, log-rank tests, and logistic regression analyses were used for statistical analyses. RESULTS: Four hundred ninety-nine patients with COVID-19-associated ARDS (mild, n = 137; moderate, n = 247; and severe, n = 115) were included (ICU admission, 38.9%). Standard oxygen therapy (SOX), high-flow nasal oxygen (HFNO), CPAP, noninvasive ventilation (NIV), and invasive mechanical ventilation (IMV) was used as the first-line (most advanced) respiratory support technique in 37.3% (35.3%), 10% (9.4%), 11.6% (4.8%), 23.4% (14.4%), and 17.6% (36.6%) of patients, respectively. The first-line respiratory support technique was escalated in 19.8% of patients. Twenty-eight-day mortality was 51.9% (mild ARDS, 13.1%; moderate ARDS, 62.3%; severe ARDS, 75.7%; P < .001) and was associated with respiratory support techniques as follows: SOX, 19.9%; HFNO, 31.9%; CPAP, 58.3%; NIV 61.1%; and IMV, 83.9% (P < .001). Proning was used in 79 patients (15.8%; 59/79 awake) and was associated with lower mortality (40.5% vs 54%; P = .03). The oxygen saturation to Fio2 ratio (OR, 0.99; 95% CI, 0.98-0.99; P < .001) and respiratory rate (OR, 1.07; 95% CI, 1.03-1.12; P = .002) at admission and NIV (OR, 6.31; 95% CI, 2.29-17.37; P < .001) or IMV (OR, 8.08; 95% CI, 3.52-18.57; P < .001) use were independent risk factors for death. INTERPRETATION: SOX, HFNO, CPAP, NIV, and IMV were used as respiratory support techniques in patients with COVID-19-associated ARDS in Uganda. Although these data are observational, they suggest that the use of SOX and HFNO therapy as well as awake proning are associated with a lower mortality resulting from COVID-19-associated ARDS in a resource-limited setting.

Health Care Workers' Perceived Self-Efficacy to Manage COVID-19 Patients in Central Uganda: A Cross-Sectional Study.

Background: The novel coronavirus disease 2019 (COVID-19) pandemic placed health workers at the frontline of the emergency task force response; a duty that requires professional expertise and confidence to rapidly identify and treat patients with COVID-19. This study explored perceived self-efficacy (PSE) of health care workers (HCWs) in the management of patients with COVID-19 and associated factors in central Uganda. Methods: We recruited 418 HCWs from four national referral hospitals in Uganda. Multivariate linear regression analysis was utilized to determine factors associated with PSE. A p-value > 0.05 was considered statistically significant. Results: Majority of the participants were female, about half were nurses/midwives, and had 10 years of work experience on average. Overall, HCWs reported moderate PSE in managing COVID-19 patients which reduced with increasing severity of the COVID-19 illness. Having a PhD, being a medical doctor, agreeing or completely agreeing that one has knowledge about COVID-19 management, and having COVID-19 management training were significantly associated with increase in one's level of PSE. Conclusion: This study highlights an unsatisfactory, moderate level of PSE among HCWs in the management of patients with COVID-19 in central Uganda. The health sector should focus on improving HCWs' self-efficacy through continuous training of all HCWs in the clinical management of especially the severe and critically ill cases of COVID-19. Non-doctor HCWs should be given priority as they scored lower levels of PSE; yet they are the corner stone of the primary health care system and make majority of the health human resource in low- and middle-income countries. Interventions towards creating a safe working environment for HCWs through provision of adequate infection prevention and control strategies are essential in boosting HCWs confidence to manage COVID-19 patients.

Validity of air quality as a measure of human mobility. The COVID-19 context. (preprint)

Background: Mobility patterns are valuable in identifying transmission patterns for infectious diseases and in parametrizing mathematical models. Aggregated location data from mobile phones which have been the main means of measuring human mobility on a population level come with several limitations. Methods: We explored the viability of using ground monitored air quality data as an alternative to aggregated location data from mobile phones in two cities in Uganda. We determined associations between air quality and human mobility and the effect of mobility restrictions on mobility and air quality using Pearson correlation (R), multivariable regression and visualized relationships using scatter plots. Results: Fine particulate matter (PM 2.5 ) was negatively correlated with the government response stringency index for Kampala (R = -0.31, p<0.001) and Wakiso (R = -0.21, p<0.001). In Kampala, PM 2.5 was positively associated with movement in grocery and pharmacy (R = 0.24, p<0.001), parks (R = 0.25, p<0.001), retail and recreation (R = 0.24, p<0.001), transit stations (R = 0.3, p<0.001) and work places (R = 0.2, p<0.001); and negatively correlated with movement in residential places (R = -0.3, p<0.001). Only associations between PM 2.5 and movement in workplaces and residential places were statistically significant in Wakiso (R = 0.14, p<0.001 and R = -0.19, p = 0.003 respectively). Conclusions: These findings suggest that air quality data are linked to human mobility data and could thus be used to monitor human movement patterns. This is a pioneer study to assess the value of air quality as a surrogate for human mobility.

Whole-genome analysis to determine the rate and patterns of intra-subtype reassortment among influenza type-A viruses in Africa.

Influenza type-A viruses (IAVs) present a global burden of human respiratory infections and mortality. Genome reassortment is an important mechanism through which epidemiologically novel influenza viruses emerge and a core step in the safe reassortment-incompetent live-attenuated influenza vaccine development. Currently, there are no data on the rate, spatial and temporal distribution, and role of reassortment in the evolution and diversification of IAVs circulating in Africa. We aimed to detect intra-subtype reassortment among Africa pandemic H1N1pdm09 (2009-10), seasonal H1N1pdm09 (2011-20), and seasonal H3N2 viruses and characterize the genomic architecture and temporal and spatial distribution patterns of the resulting reassortants. Our study was nested within the Uganda National Influenza Surveillance Programme. Next-generation sequencing was used to generate whole genomes (WGs) from 234 H1N1pdm09 (n = 116) and H3N2 (n = 118) viruses sampled between 2010 and 2018 from seven districts in Uganda. We combined our newly generated WGs with 658 H1N1pdm09 and 1131 H3N2 WGs sampled between 1994 and 2020 across Africa and identified reassortants using an automated Graph Incompatibility Based Reassortment Finder software. Viral reassortment rates were estimated using a coalescent reassortant constant population model. Phylogenetic analysis was used to assess the effect of reassortment on viral genetic evolution. We observed a high frequency of intra-subtype reassortment events, 12 · 4 per cent (94/758) and 20 · 9 per cent (256/1,224), and reassortants, 13 · 3 per cent (101/758) and 38 · 6 per cent (472/1,224), among Africa H1N1pdm09 and H3N2 viruses, respectively. H1N1pdm09 reassorted at higher rates (0.1237-0.4255) than H3N2 viruses (0 · 00912-0.0355 events/lineage/year), a case unique to Uganda. Viral reassortants were sampled in 2009 through 2020, except in 2012. 78 · 2 per cent (79/101) of H1N1pdm09 reassortants acquired new non-structural, while 57 · 8 per cent (273/472) of the H3N2 reassortants had new hemagglutinin (H3) genes. Africa H3N2 viruses underwent more reassortment events involving larger reassortant sets than H1N1pdm09 viruses. Viruses with a specific reassortment architecture circulated for up to five consecutive years in specific countries and regions. The Eastern (Uganda and Kenya) and Western Africa harboured 84 · 2 per cent (85/101) and 55 · 9 per cent (264/472) of the continent's H1N1pdm09 and H3N2 reassortants, respectively. The frequent reassortment involving multi-genes observed among Africa IAVs showed the intracontinental viral evolution and diversification possibly sustained by viral importation from outside Africa and/or local viral genomic mixing and transmission. Novel reassortant viruses emerged every year, and some persisted in different countries and regions, thereby presenting a risk of influenza outbreaks in Africa. Our findings highlight Africa as part of the global influenza ecology and the advantage of implementing routine whole-over partial genome sequencing and analyses to monitor circulating and detect emerging viruses. Furthermore, this study provides evidence and heightens our knowledge on IAV evolution, which is integral in directing vaccine strain selection and the update of master donor viruses used in recombinant vaccine development.

Validity of Air Quality as a Measure of Human Mobility in Uganda. The COVID-19 Context. (preprint)

Background: Mobility patterns are valuable in identifying transmission patterns for infectious diseases and in deriving contact matrices that are used to parametrize mathematical models. Aggregated location data from mobile phones have been the main means of measuring human mobility on a population level. However, these data come with several limitations related to individual privacy, access and restriction of the GPS location by the user that limit their use. Methods We explored the viability of using ground monitored air quality data as an alternative to aggregated location data from mobile phones, as a measure of human mobility in two cities in Uganda. We determined associations between air quality and human mobility; and the effect of mobility restrictions on mobility and air quality using Pearson correlation (R), multivariate regression and visualized these relationships using scatter plots. Results Daily mean levels for PM 2.5 in both cities were consistently higher than the WHO guideline limit, with a mean of 77.0µg/m 3 (Range = 22.0–309) for Kampala and 60.0µg/m 3 (Range = 18.2–331) for Wakiso. PM 10 levels had a mean of 84.6µg/m 3 (Range = 25.0–318) in Kampala and 67.9µg/m 3 (Range = 21.0–340) in Wakiso. PM 2.5 was negatively correlated with the government response stringency index for Kampala (R = -0.31, p 

Biobanking: Strengthening Uganda's Rapid Response to COVID-19 and Other Epidemics.

Introduction: SARS-CoV-2 is a fatal disease of global public health concern. Measures to reduce its spread critically depend on timely and accurate diagnosis of virus-infected individuals. Biobanks can have a pivotal role in elucidating disease etiology, translation, and advancing public health. In this article, we show how a biobank has been a critical resource in the rapid response to coronavirus disease of 2019 (COVID-19) in Uganda. Materials and Methods: The Integrated Biorepository of H3Africa Uganda established a COVID-19 biobank. Standard Operating Procedures for sample and data collection, sample processing, and storage were developed. An e-questionnaire data tool was used to collect sociodemographic factors. Samples were collected at 7-day intervals from patients, analyzed for key parameters, processed, annotated, characterized, and stored at appropriate temperatures. Results: Stored samples have been used in validation of 17 diagnostic kits, the Cepheid Xpert Xpress SARS-CoV-2 assay, as well as a sample pooling technique for mass screening and polymerase chain reaction assay validation. Kits that passed validation were deployed for mass screening boosting early detection, isolation, and treatment of COVID-19 cases. Also, 10 applications from researchers and biotech companies have been received and approved and 4 grants have been awarded Conclusion: The CoV-Bank has proven to be an invaluable resource in the fight against the COVID-19 pandemic in Uganda, as samples have been resources in the validation and development of COVID-19 diagnostic tools, which are important in tracing and isolation of infected cases to confront, delay, and stop the spread of the SARS-CoV-2 virus.

Sustained Dysregulation of the Plasma Renin-angiotensin System in Acute COVID-19 (preprint)

SARS-CoV-2 enters cells by binding to angiotensin-converting enzyme 2 (ACE2), and COVID-19 infection may therefore induce changes in the renin-angiotensin system (RAS). To determine the effects of COVID-19 on plasma RAS components, we measured plasma ACE, ACE2, and angiotensins I, (1-7), and II in 46 adults with COVID-19 at hospital admission and on days 2, 4, 7 and 14, compared to 50 blood donors (controls). We compared survivors vs. non-survivors, males vs. females, ventilated vs. not ventilated, and angiotensin receptor blocker (ARB) and angiotensin-converting enzyme (ACE) inhibitor-exposed vs. not exposed. At admission, COVID-19 patients had higher plasma levels of ACE (p=0.012), ACE2 (p=0.001) and angiotensin-(1-7) (p<0.001) than controls. Plasma ACE and ACE2 remained elevated for 14 days in COVID-19 patients, while plasma angiotensin-(1-7) decreased after 7 days. In adjusted analyses, plasma ACE was higher in males vs. females (p=0.042), and plasma angiotensin I was significantly lower in ventilated vs. non-ventilated patients (p=0.001). In summary, plasma ACE and ACE2 are increased for at least 14 days in patients with COVID-19 infection. Angiotensin-(1-7) levels are also elevated, but decline after 7 days. The results indicate dysregulation of the RAS with COVID-19, with increased circulating ACE2 throughout the course of infection.Clinical Trial Registration: https://clinicaltrials.gov/ Unique Identifier: NCT04510623

Perspectives on perioperative management of children’s surgical conditions during the COVID-19 pandemic in low-income and middle-income countries: a global survey

BACKGROUND: Many organizations have issued recommendations to limit elective surgery during the coronavirus disease 2019 (COVID-19) pandemic. We surveyed providers of children’s surgical care working in low-income and middle-income countries (LMICs) to understand their perspectives on surgical management in the wake of the COVID-19 pandemic and how they were subsequently modifying their surgical care practices. METHODS: A survey of children’s surgery providers in LMICs was performed. Respondents reported how their perioperative practice had changed in response to COVID-19. They were also presented with 26 specific procedures and asked which of these procedures they were allowed to perform and which they felt they should be allowed to perform. Changes in surgical practice reported by respondents were analyzed thematically. RESULTS: A total of 132 responses were obtained from 120 unique institutions across 30 LMICs. 117/120 institutions (97.5%) had issued formal guidance on delaying or limiting elective children’s surgical procedures. Facilities in LICs were less likely to have issued guidance on elective surgery compared with middle-income facilities (82% in LICs vs 99% in lower middle-income countries and 100% in upper middle-income countries, p=0.036). Although 122 (97%) providers believed cases should be limited during a global pandemic, there was no procedure where more than 61% of providers agreed cases should be delayed or canceled. CONCLUSIONS: There is little consensus on which procedures should be limited or delayed among LMIC providers. Expansion of testing capacity and local, context-specific guidelines may be a better strategy than international consensus, given the disparities in availability of preoperative testing and the lack of consensus towards which procedures should be delayed.

Characteristics and outcomes of admitted patients infected with SARS-CoV-2 in Uganda.

RATIONALE: Detailed data on the characteristics and outcomes of patients with COVID-19 in sub-Saharan Africa are limited. OBJECTIVE: We determined the clinical characteristics and treatment outcomes of patients diagnosed with COVID-19 in Uganda. MEASUREMENTS: As of the 16 May 2020, a total of 203 cases had been confirmed. We report on the first 56 patients; 29 received hydroxychloroquine (HCQ) and 27 did not. Endpoints included admission to intensive care, mechanical ventilation or death during hospitalisation. MAIN RESULTS: The median age was 34.2 years; 67.9% were male; and 14.6% were <18 years. Up 57.1% of the patients were asymptomatic. The most common symptoms were fever (21.4%), cough (19.6%), rhinorrhea (16.1%), headache (12.5%), muscle ache (7.1%) and fatigue (7.1%). Rates of comorbidities were 10.7% (pre-existing hypertension), 10.7% (diabetes) and 7.1% (HIV), Body Mass Index (BMI) of ≥30 36.6%. 37.0% had a blood pressure (BP) of >130/90 mm Hg, and 27.8% had BP of >140/90 mm Hg. Laboratory derangements were leucopenia (10.6%), lymphopenia (11.1%) and thrombocytopenia (26.3%). Abnormal chest X-ray was observed in 14.3%. No patients reached the primary endpoint. Time to clinical recovery was shorter among patients who received HCQ, but this difference did not reach statistical significance. CONCLUSION: Most of the patients with COVID-19 presented with mild disease and exhibited a clinical trajectory not similar to other countries. Outcomes did not differ by HCQ treatment status in line with other concluded studies on the benefit of using HCQ in the treatment of COVID-19.