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Previous efforts to estimate the travel time to comprehensive emergency obstetric care (CEmOC) in low- and middle-income countries (LMICs) have either been based on spatial models or self-reported travel time, both with known inaccuracies. The study objectives were to estimate more realistic travel times for pregnant women in emergency situations using Google Maps, determine system-level factors that influence travel time and use these estimates to assess CEmOC geographical accessibility and coverage in Lagos state, Nigeria. Data on demographics, obstetric history and travel to CEmOC facilities of pregnant women with an obstetric emergency, who presented between 1st November 2018 and 31st December 2019 at a public CEmOC facility were collected from hospital records. Estimated travel times were individually extracted from Google Maps for the period of the day of travel. Bivariate and multivariate analyses were used to test associations between travel and health system-related factors with reaching the facility >60 minutes. Mean travel times were compared and geographical coverage mapped to identify ‘hotspots’ of predominantly >60 minutes travel to facilities. For the 4005 pregnant women with traceable journeys, travel time ranges were 2–240 minutes (without referral) and 7–320 minutes (with referral). Total travel time was within the 60 and 120 minute benchmark for 80 and 96% of women, respectively. The period of the day of travel and having been referred were significantly associated with travelling >60 minutes. Many pregnant women living in the central cities and remote towns typically travelled to CEmOC facilities around them. We identified four hotspots from which pregnant women travelled >60 minutes to facilities. Mean travel time and distance to reach tertiary referral hospitals were significantly higher than the secondary facilities. Our findings suggest that actions taken to address gaps need to be contextualized. Our approach provides a useful guide for stakeholders seeking to comprehensively explore geographical inequities in CEmOC access within urban/peri-urban LMIC settings.

Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) exhibits a high mutations rate and monitoring its spread and evolution is essential for global control of the pandemic. This study determined the SARS-CoV-2 variants circulating in Lagos, from July 2021 to January 2022, when the nation experienced its third and fourth waves.The study utilised archived SARS-CoV-2 positive samples and Midnight whole-genome sequencing workflow from Oxford Nanopore Technologies. Six hundred and sixty-six archived SARS-CoV-2 positive samples, 488 community testing and 178 travellers were analysed. Three hundred forty-one sequences samples were assigned lineages, but 327 sequences with doubly verified collection dates recreated the timeline. 86.5% of the samples came from persons between 16 and 60 years old. Two infections with the Omicron variant (BA.1) among community testers were detected in August 2021 and from seven outbound travellers in September 2021. An inbound traveller also had the Omicron variant (BA.1) in September 2021. Thirteen lineages of the Delta variant and four lineages of the Omicron variant were detected.We show that the Omicron variant was in Nigeria before November 2021 and could have caused the short reprieve between the third and fourth waves. Several lineages detected suggest several introductions, highlighting the need for surveillance.

This collaborative meta-analysis was supported by the Swiss National Science Foundation and the Laura and John Arnold Foundation (grant supporting the post-doctoral fellowship at the Meta-Research Innovation Center at Stanford (METRICS), Stanford University). The funders had no role in the design of this collaborative meta-analysis; in the collection, analysis, and interpretation of data; or in the report writing., We would like to express our warm gratitude to all participating patients and convalescent plasma donors. We thank Katja Suter and Sina Ullrich, University of Basel, for their administrative assistance. For their helpful contribution to individual trials, we thank Erica Wood, Iain Gosbell, Richard Charlewood, Thomas Hills, Veronica Hoad, Kristina Kairaitis, Aikaj Jindal, John Gerrard, Hong Foo, Adam Stewart, and Nanette Trask (ASCOT trial); Amalia Bravo-Lindoro, Ral Carrillo-Esper, Karla Maldonado-Silva, Catalina Casillas-Suárez, Orlando Carrillo-Torres, Sandra Murrieta, Elizabeth Diaz-Padilla, Eli Omar Zavaleta, Yadira Bejar-Ramirez, and Evelyn Cortina-de la Rosa (CPC-SARS trial); Sheri Renaud, Roel Rolando-Almario, and Jacqueline Day (NCT04385199 trial); Sandra Tingsgrd, MD, Karen Brorup Heje Pedersen, MD, Michaela Tinggaard, MD, Louise Thorlacius-Ussing, MD, Clara Lundetoft Clausen, MD, Nichlas Hovmand, MD, Simone Bastrup Israelsen, MD, Cecilie Leding, MD, Katrine Iversen, MD, Maria Engel Miller, MD, Hkon Sandholdt, MSc biostatistician (CCAP-2 trial). On behalf of the IRCT20200310046736N1 trial, we thank the Khuzestan Blood Transfusion Organization for specialized assistance in the preparation and maintenance of plasma samples. On behalf of the NCT04332835 trial, we thank all the members of the "PC-COVID-19 Group" at the Clinica del Occidente and Hospital Universitario Mayor Mederi in Bogota, and Clinica CES in Medellin. On behalf of the NCT04403477 trial, we thank Miles Carroll for his support regarding the antibody testing in Bangladesh. The Co-CLARITY team would like to extend their gratitude to the Department of Science and Technology Philippine Council for Health Research and Development and the UP-Philippine General Hospital for all their support in the setting up and conduct of the trial. For helpfully communicating details of their trial, we thank members of the PlasmAr trial, NCT04359810 trial (Max O´Donnell), NCT04468009 trial, and CTRI/2020/05/025299 trial. Support for title page creation and format was provided by AuthorArranger, a tool developed at the National Cancer Institute (https://www.cancer.gov/)., During the conduct of the study, the following is reported: Dr. Berry reports being employee with ownership role at Berry Consultants (receives payments for statistical modeling and design of REMAP-CAP). Dr. Castillo reports grants from DOST PCHRD. Dr. Daly reports grants from Medical Research Future Fund (Australian Govt) and RBWH. Dr. Denkinger reports grants from German Ministry for Education and Research. Dr. Dumagay reports grants from Philippine Council for Health Research and Development. Dr. Dunachie reports grants from UK Department of Health and Social Care, grants from UK National Institute of Health Research. Dr. Gauiran reports grants from Department of Science and Technology—Philippine Council for Health Research and Development. Dr. Gordon reports grants from NIHR, grants from NIHR Research Professorship (RP-2015-06-18), and non-financial support from NIHR Clinical Research Network. Dr. Higgins reports grants from NHMRC and from the Minderoo Foundation. Dr. Hills reports grants from Health Research Council of New Zealand. Dr. Holm reports grants from Swedish Government Funds for Clinical Research (ALF). Dr. Janssen and Dr. Müller-Tidow report grants from the Federal Ministry of Education and Research in Germany (BMBF) to the RECOVER clinical trial. Dr. Krapp reports grants from Department of Foreign Affairs, Trade, and Development of Canada, grants from Fundación Telefónica del Perú. Dr. J. Lim reports grants from the Department of Science and Technology, Philippine Council for Health Research and Development. Dr. Lucero reports grants from Philippine Council for Health Research and Development. Dr Manrique reports economic support from Grupo ISA Intercolombia for the project development of trial NCT04332835. Drs. McQuilten and Wood report grants from Medical Research Future Fund. Dr. McVerry reports grants from The Pittsburgh Foundation, Translational Breast Cancer Research Consortium, and from UPMC Learning While Doing Program. Mr. Mouncey reports grants from National Institute for Health Research and from the European Union FP7: PREPARE. Dr. Najdovski reports payment from KUL Leuven to Belgian Red Cross for supply of convalescent plasma. Dr. Nichol reports grants from Health Research Board of Ireland. Dr. D. Roberts reports grants from the National Institute for Health (UKRIDHSC COVID-19 Rapid Response Rolling Call—Grant Reference Number COV19-RECPLAS) and the European Commission (SUPPORT-E #101015756). Dr. Rowan reports grants from the European Commission and from the UK National Institute for Health Research. Dr. Shankar-Hari reports grants from National Institute for Health Research UK, grants from UKRI-National Institute for Health Research UK. Dr. Turgeon reports grants from Canadian Institutes of Health Research. Dr. Venkatesh reports grants from Baxter. Dr. Webb reports grants from National Health and Medical Research Council, grants from Minderoo Foundation. Dr. Zacharowski reports grants from EU Horizon 2020. The ASCOT trial team (Drs Bowen, Daly, Davis, Denholm, Hammond, Jha, L. Lim, McQuilten, Molton, Morpeth, O’Sullivan, Paterson, Perry, Price, Rees, Roberts, Rogers, Sasadeusz, Snelling, Tong, Venkatesh, Wood) is funded by grants from from Royal Brisbane and Women’s Hospital Foundation, Pratt Foundation, Minderoo Foundation, BHP Foundation, Hospital Research Foundation, Macquarie Group Foundation, Health Research Council of New Zealand, Australian Partnership for Preparedness Research on Infectious Disease Emergencies (APPRISE), and the collection and supply of convalescent plasma was conducted within Lifeblood’s funding arrangements. The CONFIDENT trial is funded by the Belgian KCE (blood establishments received payment for the convalescent plasma supplied in the clinical trial). REMAP-CAP was supported in part by funding from UKRIDHSC COVID-19 Rapid Response Rolling Call (Grant Reference Number COV19-RECPLAS). Collection of convalescent plasma for REMAP-CAP was funded by the Department of Health and Social Care, UK. The IRCT20200310046736N1 trial was supported by the Ahvaz Jundishapur University of Medical Sciences (Grant No. R.AJUMS.REC.1399.003, Dr. Pouladzadeh). The PC-COVID-19 Group is supported by the Universidad del Rosario, IDCBIS, ISA Group and Suramericana (Colombia). Outside the submitted work, the following is reported: Dr. Axfors reports postdoctoral grants from the Knut and Alice Wallenberg Foundation, Uppsala University, the Swedish Society of Medicine, the Blanceflor Foundation, and the Sweden-America Foundation. Dr. Aomar reports personal fees from SOBI, GEDEON RICHTER, and GSK. Dr. Benfield reports grants from Novo Nordisk Foundation, Simonsen Foundation, Lundbeck Foundation, Kai Hansen Foundation, Erik and Susanna Olesen’s Charitable Fund; grants and personal fees from GSK, Pfizer, Gilead; and personal fees from Boehringer Ingelheim, MSD, and Pentabase ApS. Dr. Estcourt reports being an investigator on the RECOVERY trial. Dr. Gordon reports personal fees from GlaxoSmithKline, Bristol Myers Squibb, and 30 Respiratory. Dr. Jha reports grants and personal fees from Baxter Healthcare, personal fees from Astra Zeneca, grants from NephroPlus. Dr. Laterre reports personal fees from Adrenomed. Dr. McVerry reports grants from NIH/NHLBI and Bayer Pharmaceuticals, Inc. Dr. Mondragon reports financial activities outside the submitted work (employment at Johnson & Johnson). Dr. Perry reports partner being employed at CSL and owning shares in CSL. Dr. Paterson reports involvement with ALLIANCE trial of COVID-19 treatments. Dr. J. Roberts reports other COVID-19 related trials (in different patient groups): tocilizumab in ICU patients; hydroxychloroquine dosing in ICU patients; planned study of remdesivir pharmacokinetics in patients during expanded access program; and in silico evaluation of ivermectin dosing. Dr Sasadeusz reports grants from various Pharma companies including Gilead Sciences, Abvvie, Merck, and Takeda. Dr. Zacharowski reports personal fees from Biotest AG, CSL Behring, GE Heathcare, and is President of the ESAIC., Background: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, https://doi.org/10.17605/OSF.IO/GEHFX). Methods: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung–Knapp–Sidik–Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. Results: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. Conclusions: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care., Amalia Bravo-Lindoro, BHP Foundation, Blanceflor Foundation, Department of Foreign Affairs, Trade, and Development of Canada, Eli Omar Zavaleta, Erik and Susanna Olesen’s Charitable Fund, Federal Ministry of Education and Research in Germany, Fundación Telefónica del Perú, IDCBIS, ISA Group and Suramericana, Kai Hansen Foundation, Katja Suter and Sina Ullrich, Khuzestan Blood Transfusion Organization, Macquarie Group Foundation, Medical Research Future Fund, NephroPlus, RBWH, Roel Rolando-Almario NCT04385199, Royal Brisbane, Sheri Renaud, Simonsen Foundation, UKRI-National Institute for Health Research UK, UKRIDHSC COV19-RECPLAS, UP-Philippine General Hospital CTRI/2020/05/025299, NCT04359810, NCT04468009, Women’s Hospital Foundation, National Institutes of Health, National Heart, Lung, and Blood Institute, Pittsburgh Foundation, Pfizer, Baxter International, Stanford University, Gilead Sciences, National Institute on Handicapped Research RP-2015-06-18, Meso Scale Diagnostics, Universität Basel, Laura and John Arnold Foundation, Health Research Board, Pratt Foundation, Canadian Institutes of Health Research, National Institute for Health Research, Department of Health and Social Care, European Commission 101015756, National Health and Medical Research Council, Department of Science and Technology, Ministry of Science and Technology, India, Health Research Council of New Zealand, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Sweden-America Foundation, Bundesministerium für Bildung und Forschung, Lundbeckfonden, Knut och Alice Wallenbergs Stiftelse, Seventh Framework Programme, Ahvaz Jundishapur University of Medical Sciences, Université Pierre et Marie Curie, Uppsala Universitet, Horizon 2020, Svenska Läkaresällskapet, Universidad del Rosario, Pharmaceuticals Bayer, Novo Nordisk Fonden, Department of Science and Technology, Philippines, Philippine Council for Health Research and Development, Minderoo Foundation

The recent Ebola outbreak in West African is reported to have started in December 2013 in Guinea from where it spread to the neighboring countries of Sierra Leone, Liberia, Mali, Nigeria and Senegal (Abayomi et al., 2016). Consequently, this attracted a great attention from all quarters such as humanitarian NGOs, local and international health organisations, governmental agencies, research and development facilities as well as pharmaceutical companies. During the outbreak, a large number of patients were screened for the Ebola Virus (EBOV) with thousands of biomedical samples generated over a short period of time and in rapid succession. These samples were sent to laboratories including mobile laboratories hastily formed to manage the situation due to the absence of infrastructure to deal with such instance in West Africa. A good number of these samples were destroyed, exported out of the country of origin with the government’s consent and documentation and in other cases without such consent while the remaining samples were stored in facilities without adequate biosafety or biosecurity (Abayomi et al., 2016). Ebola virus along with other pathogens of high consequence requires specialized facilities such as Biosafety Level 3 (BSL3) and Biosafety Level 4 (BSL4) to handle during research and identification for surveillance. Similarly, facilities of such high infrastructure and security are needed to store and secure such samples and their products.

BackgroundThe current pandemic of coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown epidemiological and clinical characteristics that appear worsened in hypertensive patients. The morbidity and mortality of the disease among hypertensive patients in Africa have yet to be well described.MethodsIn this retrospective cohort study all confirmed COVID-19 adult patients (≥18 years of age) in Lagos between February 27 to July 62,020 were included. Demographic, clinical and outcome data were extracted from electronic medical records of patients admitted at the COVID-19 isolation centers in Lagos. Outcomes included dying, being discharged after recovery or being evacuated/transferred.Descriptive statistics considered proportions, means and medians. The Chi-square and Fisher’s exact tests were used in determining associations between variables. Kaplan–Meier survival analysis and Cox regression were performed to quantify the risk of worse outcomes among hypertensives with COVID-19 and adjust for confounders.P-value ≤0.05 was considered statistically significant.ResultsA total of 2075 adults with COVID-19 were included in this study. The prevalence of hypertension, the most common comorbidity, was 17.8% followed by diabetes (7.2%) and asthma (2.0%). Overall mortality was 4.2% while mortality among the hypertensives was 13.7%. Severe symptoms and mortality were significantly higher among the hypertensives and survival rates were significantly lowered by the presence of additional comorbidity to 50% from 91% for those with hypertension alone and from 98% for all other patients (P P = 0.001, 95%CI = 1.4–4.0, death: HR = 2.30,P = 0.001, 95%CI = 1.2–4.6, for those with hypertension only} {severe/critical illness: HR = 3.76,P = 0.001, 95%CI = 2.1–6.4, death: crude HR = 6.63,P = 0.001, 95%CI = 3.4–1.6, for those with additional comorbidities}. Hypertension posed an increased risk of severe morbidity (approx. 4-fold) and death (approx. 7-fold) from COVID-19 in the presence of multiple comorbidities.ConclusionThe potential morbidity and mortality risks of hypertension especially with other comorbidities in COVID-19 could help direct efforts towards prevention and prognostication. This provides the rationale for improving preventive caution for people with hypertension and other comorbidities and prioritizing them for future antiviral interventions.

Background: Chronic lymphocytic leukaemia (CLL) is a common lymphoproliferative disorder in developed countries. However, this condition is rare in Africa and there is a paucity of information on CLL, specifically on the continent. Aim: This study described, retrospectively, the frequency, demographics and laboratory features of CLL cases diagnosed from 2011 to 2016. Setting: Department of Pathology, National Health Laboratory Service, Tygerberg Academic Hospital, Cape Town. Methods: A retrospective analysis was performed for all CLL diagnoses made between 01 January 2011 and 31 December 2016. Results: Eighty CLL cases were diagnosed between 2011 and 2016. Men and women presented with the disease equally (48.8% vs. 51.2%, p > 0.05). The mean age at diagnosis was 66.79 years (range of 37–95 years) and the modal age range (36.3%) was 60–69 years. Men presented with the disease at a significantly younger age than women (mean = 64 years vs. mean = 69.5 years, p < 0.05). There were three (3.75%) human immunodeficiency virus (HIV)-positive patients (age range 43–50 years). Chromosome 13q14 deletion was found in 6 out of 19 patients (31.6%). Trisomy 12 and deletion 11q22 were found in 5 out of 21 (24%) and 7 out of 21 (33.3%) patients, respectively. Deletions 13q34 and 17p were negative for 6 and 20 patients, respectively. Conclusion: Chronic lymphocytic leukaemia at our facility presented equally in men and women. Men presented with the disease at a younger age than women. Additionally, our findings suggested that HIV is uncommon amongst CLL patients tested for HIV.

Background Coronavirus disease once thought to be a respiratory infection is now recognised as a multi-system disease affecting the respiratory, cardiovascular, gastrointestinal, neurological, immune, and hematopoietic systems. An emerging body of evidence suggests the persistence of COVID-19 symptoms of varying patterns among some survivors. This study aimed to describe persistent symptoms in COVID-19 survivors and investigate possible risk factors for these persistent symptoms. Methods The study used a retrospective study design. The study population comprised of discharged COVID-19 patients. Demographic information, days since discharge, comorbidities, and persistent COVID-19 like symptoms were assessed in patients attending the COVID-19 outpatient clinic in Lagos State. Statistical analysis was done using STATA 15.0 software (StataCorp Texas) with significance placed at p-value Results A total of 274 patients were enrolled in the study. A majority were within the age group > 35 to ≤49 years (38.3%), and male (66.1%). More than one-third (40.9%) had persistent COVID-19 symptoms after discharge, and 19.7% had more than three persistent COVID-like symptoms. The most persistent COVID-like symptoms experienced were easy fatigability (12.8%), headaches (12.8%), and chest pain (9.8%). Symptomatic COVID-19 disease with moderate severity compared to mild severity was a predictor of persistent COVID-like symptoms after discharge (p Conclusion Findings from this study suggests that patients who recovered from COVID-19 disease may still experience COVID-19 like symptoms, particularly fatigue and headaches. Therefore, careful monitoring should be in place after discharge to help mitigate the effects of these symptoms and improve the quality of life of COVID-19 survivors.

Background The presence of COVID-19 has led to the disruption of health systems globally, including essential reproductive, maternal, newborn and child health (RMNCH) services. This study aimed to assess the challenges faced by women who used RMNCH services in Nigeria’s epicentre, their satisfaction with care received during the COVID-19 pandemic and the factors associated with their satisfaction. Methods This cross-sectional survey was conducted in Lagos, southwest Nigeria among 1,241 women of reproductive age who had just received RMNCH services at one of twenty-two health facilities across the primary, secondary and tertiary tiers of health care. The respondents were selected via multi-stage sampling and face to face exit interviews were conducted by trained interviewers. Client satisfaction was assessed across four sub-scales: health care delivery, health facility, interpersonal aspects of care and access to services. Bivariate and multivariate analyses were used to assess the relationship between personal characteristics and client satisfaction. Results About 43.51% of respondents had at least one challenge in accessing RMNCH services since the COVID-19 outbreak. Close to a third (31.91%) could not access service because they could not leave their houses during the lockdown and 18.13% could not access service because there was no transportation. The mean clients’ satisfaction score among the respondents was 43.25 (SD: 6.28) out of a possible score of 57. Satisfaction scores for the interpersonal aspects of care were statistically significantly lower in the PHCs and general hospitals compared to teaching hospitals. Being over 30 years of age was significantly associated with an increased clients’ satisfaction score (ß = 1.80, 95%CI: 1.10–2.50). Conclusion The COVID-19 lockdown posed challenges to accessing RMNCH services for a significant proportion of women surveyed. Although overall satisfaction with care was fairly high, there is a need to provide tailored COVID-19 sensitive inter-personal care to clients at all levels of care.

Background : The COVID-19 pandemic has been described to have significant effects on the mental health and emotional well-being of people all over the world generally. This study aimed at describing the set up and functions of the psychosocial support service for the COVID-19 response in Lagos South West Nigeria.Methods: A retrospective and descriptive overview of the psychosocial support for covid-19 patients supported in Lagos, Nigeria over a four-month period. Remote interventions given included Psychological first aid, counselling, psycho pharmacology, and virtual support group sessions. Results: The Psychosocial care provided was a part of the Covid-19 outbreak response strategy in Lagos State, Nigeria. Over 43,000 support calls were made to Covid-19 positive persons; 1,316 hospitalised patients were supported remotely during isolation and more than half declined admission, opting to self-isolate at home instead. Psychosocial home care support group sessions and discharge support groups held. Liaison with all other thematic pillars of the response was key. Conclusion: A comprehensive multidisciplinary mental health and psychosocial support service is an integral part of the management strategy during the pandemic response. The Psychosocial support by the Lagos Covid-19 response presents a practical reproducible approach.

Background: In April 2020, a community-based active case search surveillance system of coronavirus disease 2019 (COVID-19) was developed by the emergency outbreak committee in Lagos State. This followed the evidence of community transmission of coronavirus disease in the twenty Local Government Areas in Lagos State. This study assessed the value of respiratory and other symptoms in predicting positive SARS-CoV-2 using reverse transcription-polymerase chain reaction (RT-PCR). It is hoped that if symptoms are predictive, they can be used in screening before testing. Methods: Communities were included based on the alerts from community members through the rumour alert system set up by the state. All members of the households of the communities from where the alert came were eligible. Household members who declined to participate were excluded from the study. A standardised interviewer-administered electronic investigation form was used to collect sociodemographic information, clinical details and history for each possible case. Data was analysed to see the extent of agreement or correlation between reported symptoms and the results of PCR testing for SARS-COV-2. Results: A total of 12,739 persons were interviewed. The most common symptoms were fever, general weakness, cough and difficulty in breathing. Different symptoms recorded different levels of sensitivity as follows: fever, 28.9%; cough, 21.7%; general body weakness, 10.9%; and sore throat, 10.9%. Sensitivity and specificity for fever, the most common symptom, were 28.3% and 50.2%, respectively, while similar parameters for general body weakness, the next most common symptom, were 10.9% and 73.2%, respectively. Conclusion: From these findings, the predictive ability of symptoms for COVID-19 diagnosis was extremely weak. It is unlikely that symptoms alone will suffice to predict COVID-19 in a patient. An additional measure, such as confirmatory test by RT-PCR testing, is necessary to confirm the disease.

Background: The current pandemic of coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown epidemiological and clinical characteristics that appear worsened in hypertensive patients with COVID-19. The morbidity and mortality of the disease among hypertensive patients in Africa have yet to be well described.Methods: In this retrospective cohort study all confirmed COVID-19 adult patients (≥18 years of age) in Lagos between February 27 to July 6 2020 were included. Demographic, clinical and outcome data were extracted from electronic medical records of patients admitted at the COVID-19 isolation centers in Lagos. Outcomes included dying or being discharged by July 6, 2020. Variables were compared between hypertensive and non-hypertensives using univariable and multivariable logistic regression, cox regression and Kaplan Meier survival analysis methods to assess hypertension as a risk factor associated with worsened disease severity and death.Results: A total of 2075 adults with COVID-19 were included in this study. The prevalence of hypertension was 17.8% and it was the most common comorbidity followed by diabetes (7.2%) and asthma (2.0%). Overall mortality from COVID-19 was 4.2% while mortality among the hypertensives was 13.7%. Severe symptoms and mortality were significantly higher among the hypertensives and survival rates were significantly lowered by the presence of an additional comorbidity to 50% from 91% for those with hypertension alone and from 98% for all other patients (PConclusion: The potential morbidity and mortality risks of hypertension especially with other comorbidities in COVID-19 could help direct efforts towards prevention and prognostication. This provides the rationale for improving preventive caution for people with hypertension and other comorbidities and prioritizing them for future antiviral interventions.

Introduction Success in curtailing the pandemic coronavirus disease (COVID-19) depends largely on a sound understanding of the epidemiologic and clinical profile of cases in a population as well as the case management approach. This study documents the presenting characteristics, treatment modalities and outcomes of the first 32 COVID-19 patients in Nigeria. Methods This retrospective study used medical records of the first 32 patients admitted and discharged from the Mainland Hospital, Lagos State, southwest Nigeria between February 27 and April 6, 2020. The outcomes of interest were death, promptness of admission process and duration of hospitalization. Results The mean age of the patients was 38.1 years (SD: 15.5) and 66% were male. Three-quarters (75%) of the patients presented in moderately severe condition while 16% were asymptomatic. The most common presenting symptoms were fever (59%) and dry cough (44%). The mean time between a positive test result and admission was 1.63 days (SD: 1.31). Almost all (97%) the patients were treated with lopinavir-ritonavir with no recorded death. The median duration of hospital stay was 12 days (IQR: 9-13.5). Conclusion In this preliminary analysis of the first COVID-19 cases in Nigeria, clinical presentation was mild to moderate with no mortality. Processes to improve promptness of admission and reduce hospital stay are required to enhance the response to COVID-19 in Nigeria.

Genomic research and the biobanking capacity it requires are experiencing considerable growth on the continent of Africa. However genomic research and biobanking raise a range of legal, ethical, social, and cultural issues, including concerns about broad consent, confidentiality, community stigmatization, discrimination, indefinite storage, and long-term use. There is a need to establish governance frameworks that address these issues, and many international health research ethics and biobanking guidelines now recommend that the best way to do so is by involving potential research participants and key community stakeholders in the research development and the process of acquiring samples and data through active community engagement (CE). This article describes the experience and challenges in developing an educational tool as part of a CE initiative in South Africa and the commentaries reflect on how this process may be improved going forward.

Biorepositories in Africa need significant infrastructural support to meet International Society for Biological and Environmental Repositories (ISBER) Best Practices to support population-based genomics research. ISBER recommends a biorepository information management system which can manage workflows from biospecimen receipt to distribution. The H3Africa Initiative set out to develop regional African biorepositories where Uganda, Nigeria, and South Africa were successfully awarded grants to develop the state-of-the-art biorepositories. The biorepositories carried out an elaborate process to evaluate and choose a laboratory information management system (LIMS) with the aim of integrating the three geographically distinct sites. In this article, we review the processes, African experience, lessons learned, and make recommendations for choosing a biorepository LIMS in the African context.

The challenges Africa is facing include, among others, the increasing incidence of emerging Infectious diseases (EIDs) which are worsened by Africa’s inadequate health care facilities, expanding population demographics and shortage of human capacity in medical and allied sciences. The convergence of the above four pose threats of the magnitude that we experienced with the Ebola outbreak in West Africa (Kamradt-Scott A, Third World Q 37:401–418, 2016), the ongoing outbreak in the Democratic Republic of Congo and many other current infectious disease outbreaks, like yellow fever, meningitis, Lassa fever, to name a few. There is therefore an urgent need for harnessing and deploying science, technology and innovation to address some of these challenges. This need has been the subject of major policy and academic debates of late, and Africa, like the rest of the world, has taken some steps towards realising this (Abuja Declaration). The Global Emerging Pathogens Treatment Consortium (GET) is made up of African experts who had assembled to set up interventions to address, in the first instance, the West African Ebola outbreak, and subsequently to address biosecurity issues on the Continent.

The 2014 Ebola outbreak in West Africa, which started on December 2013, but commonly known as the 2014 Ebola outbreak led to an urgent need for effective and affordable treatment options for Ebola Virus Disease (EVD). While there are a number of experimental drugs for the treatment of EVD, there is also a parallel interest in the use of human convalescent blood or plasma for the treatment of EVD as well as a post-exposure prophylaxis. The use of human convalescent plasma as a form of therapy in an epidemic situation has its challenges and raises a number of socio-cultural issues that need to be taken into consideration when planning interventions. In this chapter, we discuss these socio-cultural concerns and challenges. We also suggest that the successful use of convalescent plasma for therapy or as a post exposure prophylaxis, would require: active community engagement; effective public education; collaborations that are equitable; and building trust between the general public and other stakeholders (researchers, funders, civil societies, healthcare workers and humanitarian organizations) involved in trials on human convalescent therapy.

Sub-Saharan Africa is heavily endowed with natural and human resources. Yet, these same resources appear to be the bane of its poor development. “Until the rotten tooth is pulled out, the mouth must chew with caution”, says a Nigerian proverb. Despite being surrounded by wealth, several existing challenges deter African populations from taking full advantage as others have in other regions of the globe. Crucial among these challenges is the health of the population and nature of healthcare accessible to them. African populations cannot enjoy the benefits of their great resource endowment until their health and wellbeing receive considerable attention. By ‘Africa’, we refer to countries south of the Sahara that largely represent the World Health Organisation’s Africa Region (World Health Organisation 2017). The Sub-Saharan Africa region consists of several independent states, with varying geographical landscapes and diverse social and cultural outlooks. Yet, there are underlying commonalities that cut across the region.

Background Data on the comorbidities that result in negative outcomes for people with COVID-19 are currently scarce for African populations. This study identifies comorbidities that predict death among a large sample of COVID-19 patients from Nigeria. Methods This was a retrospective analysis of medical records for 2184 laboratory confirmed cases of COVID-19 in Lagos, southwest Nigeria. Extracted data included age, sex, severity of condition at presentation and self-reported comorbidities. The outcomes of interest were death or discharge from facility. Results Most of the cases were male (65.8%) and the median age was 43 years (IQR: 33–55). Four hundred and ninety-two patients (22.5%) had at least one comorbidity and the most common amongst them were hypertension (74.2%) and diabetes (30.3%). The mortality rate was 3.3% and a significantly higher proportion of patients with comorbidities died compared to those with none. The comorbidities that predicted death were hypertension (OR: 2.21, 95%CI: 1.22–4.01), diabetes (OR: 3.69, 95% CI: 1.99–6.85), renal disease (OR: 12.53, 95%CI: 1.97–79.56), cancer (OR: 14.12, 95% CI: 2.03–98.19) and HIV (OR: 1.77–84.15]. Conclusion Comorbidities are prevalent and the associated risk of death is high among COVID-19 patients in Lagos, Nigeria. Public enlightenment, early identification and targeted care for COVID-19 cases with comorbidities are recommended as the pandemic evolves.

In the aftermath of the 2014–2016 West Africa Ebola outbreak, there are a multitude of Ebola samples that are unaccounted for as well as virus samples stored in facilities that do not have an appropriate level of biosecurity and biosafety, creating serious threats to public health and security. In this article, we review the existing global governance mechanisms for addressing this biosafety and biosecurity concern. We also describe an ongoing effort to support the Government of Sierra Leone to find and secure Ebola samples as foreign labs are shut down, and institute systems for biosafety and biosecurity. We describe the challenges of tracking all Ebola samples and their associated data, and efforts to place these samples in suitable inventoried repositories by local health authorities. We recommend that governments around the world ensure that plans, procedures and regulations are in place prior to the chaos of an emergency in order to ensure that dangerous pathogens are handled in safe and secu...

The clinical spectrum of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is still evolving. This study describes the clinical characteristics and investigates factors that predict symptomatic presentation and duration of hospitalisation in a cohort of coronavirus disease 2019 (COVID-19) patients managed in Lagos, Nigeria.This was a retrospective assessment of patients hospitalised with COVID-19 disease in six dedicated facilities in Lagos, Nigeria, between April 1A total of 632 cases were analysed. The median age was 40 years (IQR: 30.5-49); male patients accounted for 60.1%. About 63% of patients were asymptomatic at presentation. Among the symptomatic, the most common symptoms were cough (47.4%) and fever (39.7%). The most common comorbidities were hypertension (16.8%) and diabetes (5.2%). The median duration of hospitalisation was 10 days (IQR: 8-14). Comorbidities increased the odds of presenting with symptoms 1.6-fold (P = 0.025) for one comorbidity and 3.2-fold (P = 0.005) for ≥2 comorbidities. Individuals aged ≥50 years were twice as likely to be hospitalised for more than 14 days compared to individuals aged50 years (P = 0.016).Most individuals had no symptoms with comorbidities increasing the likelihood of symptoms. Older age was associated with longer duration of hospitalisation. Age and comorbidities should be used for COVID-19 triaging for efficient resource allocation.

The incidence of HIV-related lymphomas (HRLs) is increased by 60-100 times in patients with HIV. When compared to the general population, patients with HRLs often present with extranodal lymphoid proliferation, most frequently of the gastrointestinal tract, central nervous system, liver and bone marrow. MicroRNAs (miRs) are non-coding double-stranded RNA molecules of 18-25 nucleotides that regulate post-translational gene expression by inhibiting translation or promoting degradation of messenger RNA complementary sequences. Before their discovery, tumorigenesis was thought to have been caused by the alteration of protein-coding oncogenes and tumor-suppressor genes, but once identified in B-cell chronic lymphocytic leukemia, miRs function as either oncogenes or tumor-suppressor genes was confirmed in different types of malignancies. Since miRs are clearly involved in tumorigenesis in many cancers, their role in HRLs is now receiving attention. A few studies have been conducted thus far in some HRLs on the involvement of miR in the pathogenesis of lymphoid malignancies. Since B-cell lymphomas arise from various stages of B-cell development in both HIV-infected and HIV-naïve patients, investigators have tried to determine the different miR signatures in B-cell development. As classic immunohistochemistry staining is sometimes not enough for the differential diagnosis of HRLs, in the present review, we have described the potential use of miRs in the prognosis and diagnosis of these diseases.

Background: Biospecimen shipping and handling challenges in Africa include climates that can potentially jeopardize sample integrity, and infrastructure and regulation limitations that affect courier reliability, access, and costs. There is a lack of investigations reporting on validation of standardized processes for biospecimen exchange among African countries and regions. The Human Heredity and Health in Africa (H3Africa) Initiative funded four African biorepositories (BR) to pilot test operations, and assess effectiveness of trans-African shipment of high-quality DNA, and other biospecimens for genomics research. Pilot studies tested the following: workflows and forms related to biospecimen exchange, transport logistics, and comparability and confirmation of quality control (QC) methods. Methods: Ethical and legal requirements for biospecimen, and data transfer were acquired before shipment. Biospecimens were collected and subjected to QC by the BR of origin before shipment, and by the recipient BR on...

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.

The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth and public health development. Increased SA research on these diseases and syndromes and the collection of associated biospecimens has ensured a plethora of biobanks created by individuals, albeit without the foresight of prospective and collective use by other local and international researchers. As the need for access to high-quality specimens in statistically relevant numbers has increased, so has the necessity for the development of national human biobanks in SA and across the Continent. The prospects of achieving sustainable centralized biobanks are still an emerging and evolving concept, primarily and recently driven by the launch of the H3Africa consortium, which includes the development of harmonized and standardized biobanking operating procedures. This process is hindered by a myriad of complex societal considerations and ethico-legal challenges. Efforts to consolidate and standardize biological sample collections are further compromised by the lack of full appreciation by national stakeholders of the biological value inherent in these collections, and the availability of high quality human samples with well-annotated data for future scientific research and development. Inadequate or nonexistent legislative structures that specifically regulate the storage, use, dispersal, and disposal of human biological samples are common phenomena and pose further challenges. Furthermore, concerns relating to consent for unspecified future uses, as well as access to information and data protection, are all new paradigms that require further consideration and public engagement. This article reviews important fundamental issues such as governance, ethics, infrastructure, and bioinformatics that are important foundational prerequisites for the establishment and evolution of successful human biobanking in South Africa.

Human Heredity and Health in Africa (H3Africa) research seeks to promote fair collaboration between scientists in Africa and those from elsewhere. Here, we outline how concerns over inequality and exploitation led to a policy framework that places a firm focus on African leadership and capacity building as guiding principles for African genomics research.

This paper describes the formation of a civil society consortium, spurred to action by frustration over the Ebola crises, to facilitate the development of infrastructure and frameworks including policy development to support a harmonized, African approach to health crises on the continent. The Global Emerging Pathogens Treatment Consortium, or GET, is an important example of how African academics, scientists, clinicians and civil society have come together to initiate policy research, multilevel advocacy and implementation of initiatives aimed at building African capacity for timely and effective mitigations strategies against emerging infectious and neglected pathogens, with a focus on biobanking and biosecurity. The consortium has been able to establish it self as a leading voice, drawing attention to scientific infrastructure gaps, the importance of cultural sensitivities, and the power of community engagement. The GET consortium demonstrates how civil society can work together, encourage government engagement and strengthen national and regional efforts to build capacity.The Pan African Medical Journal 2016;24

Ebola virus is categorized as one of the most dangerous pathogens in the world. Although there is no known cure for Ebola virus, there is some evidence that the severity of the disease can be curtailed using plasma from survivors. Although there is a general consensus on the importance of research, methodological and ethical challenges for conducting research in an emergency situation have been identified. Performing clinical trials is important, especially for health conditions that are of public health significance (including rare epidemics) to develop new therapies as well as to test the efficacy and effectiveness of new interventions. However, routine clinical trial procedures can be difficult to apply in emergency public health crises hence require a consideration of alternative approaches on how therapies in these situations are tested and brought to the market. This paper examines some of the ethical issues that arise when conducting clinical trials during a highly dangerous pathogen outbreak, with a special focus on the Ebola virus outbreak in West Africa. The issues presented here come from a review of a protocol that was submitted to the Global Emerging Pathogens Treatment Consortium (GET). In reviewing the proposal, which was about conducting a clinical trial to evaluate the safety and efficacy of using convalescent plasma in the management of Ebola virus disease, the authors deliberated on various issues, which were documented as minutes and later used as a basis for this paper. The experiences and reflections shared by the authors, who came from different regions and disciplines across Africa, present wide-ranging perspectives on the conduct of clinical trials during a dangerous disease outbreak in a resource-poor setting.

Biobanking for clinical or research purposes includes the collection, processing, storage, and analysis of biological specimens. It is now well recognized that biobanking involves a complex array of technical and ethical/regulatory considerations. Biobanking policies and procedures are often documented by best practices that are usually voluntary but may be supplemented and reinforced by strict rules and regulations that govern informed consent, privacy, QC, and other critical issues. As biobanking has emerged as a global endeavor, with national networks and international collaboration becoming the norm, it has become even more critical that practices are coordinated and that quality standards are developed. Biobanking is also often a business endeavor, in that formal strategic and business plans need to be developed to ensure the long-term survival of the associated research programs. As new technologies are developed for using biospecimens to diagnose and treat disease, as well as to evaluate genetic risks, patients are becoming more aware of the importance and benefits of biobanking as part of the medical infrastructure. As a result, patients who donate biospecimens are becoming more interested in learning more about their own sample's use and in seeing the actual results of the research. One of the aspects of these evolving attitudes toward biobanking was addressed in a previous QA Clin Chem 57:540–4). From the broad array of issues that could be addressed, this Q&A focuses on a few critical issues that many biobanks are facing today: quality management, biobank network design, long-term sustainability, conveying the importance of biobanking to the public, and the return of research results to biospecimen donors. Five experts who are engaged in national and international biobanking programs discuss these complex issues here. What are some of the important issues related to …

Background: The rise of genomic studies in Africa – not least due to projects funded under H3Africa – is associated with the development of a small number of biorepositories across Africa. For the ultimate success of these biorepositories, the creation of cell lines including those from selected H3Africa samples would be beneficial. In this paper, we map ethical challenges in the creation of cell lines. Discussion: The first challenge we identified relates to the moral status of cells living in culture. There is no doubt that cells in culture are alive, and the question is how this characteristic is relevant to ethical decision-making. The second challenge relates to the fact that cells in culture are a source of cell products and mitochondrial DNA. In combination with other technologies, cells in culture could also be used to grow human tissue. Whilst on the one hand, this feature increases the potential utility of the sample and promotes science, on the other it also enables further scientific work that may not have been specifically consented to or approved. The third challenge relates to ownership over samples, particularly in cases where cell lines are created by a biobank, and in a different country than where samples were collected. Relevant questions here concern the export of samples, approval of secondary use and the acceptability of commercialisation. A fourth challenge relates to perceptions of blood and bodily integrity, which may be particularly relevant for African research participants from certain cultures or backgrounds. Finally, we discuss challenges around informed consent and ethical review. Summary: In this paper, we sought to map the myriad of ethical challenges that need to be considered prior to making cell line creation a reality in the H3Africa project. Considering the relative novelty of this practice in Africa, such challenges will need to be considered, discussed and potentially be resolved before cell line creation in Africa becomes financially feasible and sustainable. We suggest that discussions need to be undertaken between stakeholders internationally, considering the international character of the H3Africa project. We also map out avenues for empirical research.

H3Africa is developing capacity for health-related genomics research in Africa

There is a race against time for millions in the world today. Both the technology and the manpower are currently available to deliver the services that are required to meet the needs of the 40 million people currently living with HIV/AIDS, but at what price? The reality is therefore that we are a long shot away from this realization. What are the facts and why have we not achieved even the simplest deadlines set by the World Health Organization (WHO)? Are these objectives realistic? What role does hard science have to play in the search for cost-effective solutions and futuristic effective options? To stem this unrelenting epidemic and convert the natural history of the disorder in those already living with the virus into one of chronicity, rather than one characterized by a dehumanizing and stigmatized death, requires a global commitment at all levels. This discussion examines the reality and offers a snapshot of capacity and experiences in the developing world. Crucially, it looks at the immediate and long term role of flow cytometry in the expanded care and treatment programs for developing nations.