Assessment of COVID-19 pandemic responses in African countries: thematic synthesis of WHO intra-action review reports.

OBJECTIVES: We conducted a review of intra-action review (IAR) reports of the national response to the COVID-19 pandemic in Africa. We highlight best practices and challenges and offer perspectives for the future. DESIGN: A thematic analysis across 10 preparedness and response domains, namely, governance, leadership, and coordination; planning and monitoring; risk communication and community engagement; surveillance, rapid response, and case investigation; infection prevention and control; case management; screening and monitoring at points of entry; national laboratory system; logistics and supply chain management; and maintaining essential health services during the COVID-19 pandemic. SETTING: All countries in the WHO African Region were eligible for inclusion in the study. National IAR reports submitted by March 2021 were analysed. RESULTS: We retrieved IAR reports from 18 African countries. The COVID-19 pandemic response in African countries has relied on many existing response systems such as laboratory systems, surveillance systems for previous outbreaks of highly infectious diseases and a logistics management information system. These best practices were backed by strong political will. The key challenges included low public confidence in governments, inadequate adherence to infection prevention and control measures, shortages of personal protective equipment, inadequate laboratory capacity, inadequate contact tracing, poor supply chain and logistics management systems, and lack of training of key personnel at national and subnational levels. CONCLUSION: These findings suggest that African countries' response to the COVID-19 pandemic was prompt and may have contributed to the lower cases and deaths in the region compared with countries in other regions. The IARs demonstrate that many technical areas still require immediate improvement to guide decisions in subsequent waves or future outbreaks.

Health trends, inequalities and opportunities in South Africa's provinces, 1990-2019: findings from the Global Burden of Disease 2019 Study.

BACKGROUND: Over the last 30 years, South Africa has experienced four 'colliding epidemics' of HIV and tuberculosis, chronic illness and mental health, injury and violence, and maternal, neonatal, and child mortality, which have had substantial effects on health and well-being. Using data from the 2019 Global Burden of Diseases, Injuries and Risk Factors Study (GBD 2019), we evaluated national and provincial health trends and progress towards important Sustainable Development Goal targets from 1990 to 2019. METHODS: We analysed GBD 2019 estimates of mortality, non-fatal health loss, summary health measures and risk factor burden, comparing trends over 1990-2007 and 2007-2019. Additionally, we decomposed changes in life expectancy by cause of death and assessed healthcare system performance. RESULTS: Across the nine provinces, inequalities in mortality and life expectancy increased over 1990-2007, largely due to differences in HIV/AIDS, then decreased over 2007-2019. Demographic change and increases in non-communicable diseases nearly doubled the number of years lived with disability between 1990 and 2019. From 1990 to 2019, risk factor burdens generally shifted from communicable and nutritional disease risks to non-communicable disease and injury risks; unsafe sex remained the top risk factor. Despite widespread improvements in healthcare system performance, the greatest gains were generally in economically advantaged provinces. CONCLUSIONS: Reductions in HIV/AIDS and related conditions have led to improved health since 2007, though most provinces still lag in key areas. To achieve health targets, provincial governments should enhance health investments and exchange of knowledge, resources and best practices alongside populations that have been left behind, especially following the COVID-19 pandemic.

The occurrence of long COVID: a rapid review.

The long-term effects of the severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) are not well understood. This rapid review was aimed at synthesizing evidence on the long-term effects of the SARS-CoV-2 infection among survivors. We considered both randomised controlled trials and non-randomised studies eligible for inclusion in this review. The following databases were searched: PubMed, Scopus, Cochrane library, Google Scholar, and the World Health Organization (WHO) COVID-19 database. The reference lists of all the included studies were also searched. Two authors independently screened the search outputs and reviewed full texts of potentially eligible articles. Data extraction was done by one author and checked by a second author. A meta-analysis was not conducted due to heterogeneity among the included studies. Results are presented narratively. Eleven studies met our inclusion criteria. All these studies were conducted in high-income countries. Study findings demonstrate that COVID-19 survivors can experience persistent symptoms after recovering from their initial illness, especially among previously hospitalized persons. The majority of symptoms reported were fatigue, shortness of breath, cough, and sleep disorders. Mental conditions, such as depression and anxiety disorders, were also reported. In conclusion, this study showed that COVID-19 survivors can experience persistent symptoms after recovering from their initial illness. Therefore, there is a need for a long-term follow-up of COVID-19 patients and rehabilitation services for survivors. More research is needed in this area, especially in Africa.

Cochrane corner: digital contact tracing technologies in epidemics.

Contact tracing is a public health measure implemented to control the spread and break the chains of transmission of an infectious disease. It is done by identifying, assessing, and managing people who have been exposed to an infectious disease to prevent onward transmission. We summarize findings from a rapid Cochrane review that included cohort and modelling studies to assess the benefits and harms of digital solutions for identifying contacts of confirmed positive cases of an infectious disease. The review included 12 studies, which assessed digital contact tracing for the following infectious diseases: Ebola, tuberculosis, pertussis and coronavirus disease 2019 (COVID-19). This review revealed low-certainty evidence of a decrease in secondary cases of the targeted infectious disease, if digital contact tracing was used. However, it is uncertain from the currently available evidence whether digital contact tracing would produce more reliable counts of contacts and reduce the time taken to complete contact tracing. Therefore, implementation of digital contact tracing in the context of the ongoing coronavirus pandemic in African countries should be accompanied by a robust monitoring and evaluation framework. There should be an evaluation and documentation of the benefits, cost-effectiveness, acceptability, feasibility, equity impacts, and unintended consequences of the intervention.

'Any and every cure for COVID-19': an imminent epidemic of alternative remedies amidst the pandemic?

The magnitude of the COVID-19 pandemic is unprecedented, causing lots of apprehension among scientists, industry actors, politicians, and the general populace. Adverse health, social and economic effects of the pandemic have triggered an urgency among policy makers to seek an effective panacea. In this commentary, we examine the covert outbreak of a demand for alternative remedies with limited scientific evidence on their effectiveness to manage COVID-19 in Africa. Similar demands have been displayed in previous epidemics, though the ubiquity of social media in this current clime fuels such demands even more. We describe the attendant consequences of this demand surge on ongoing public health efforts to mitigate the spread of COVID-19 and highlight its future repercussions which may continue to plague health systems beyond the present outbreak. Going forward, governments must be proactive in surveillance of this covert epidemic, actively engage community influencers in knowledge transfer and implement targeted health promotion interventions.

Treatment of COVID-19: implications for antimicrobial resistance in Africa.

There is currently no approved pharmaceutical product for the treatment of COVID-19. However, antibiotics are currently being used for the management of COVID-19 patients in many settings either treat to co-infections or for the treatment of COVID-19 itself. In this commentary, we highlight that the increased rates of antimicrobial prescribing for COVID-19 patients could further worsen the burden of antimicrobial resistance (AMR). We also highlight that though AMR is a global threat, Africa tends to suffer most from the consequences. We, therefore, call on African countries not to lose sight of the possible implications of the treatment of COVID-19 on AMR and a need to redouble efforts towards the fight against AMR while dealing with the pandemic.

Understanding the underlying drivers of obesity in Africa: a scoping review protocol.

INTRODUCTION: The worldwide prevalence of obesity and overweight has doubled since 1980, such that approximately a third of the world's population is reported as obese or overweight. Obesity rates have increased in all ages and both sexes irrespective of geographical area, ethnicity or socioeconomic status. Due to the high prevalence, related health consequences and costs of childhood and adult obesity, there is a need to comprehensively identify and assess the major underlying drivers of obesity and overweight in the African context. METHODS AND ANALYSIS: This scoping review will be carried out as per the methodological outline by Arksey and O'Malley. The search strategy will be developed and search performed in the Scopus and PubMed electronic databases. In the first search, we will identify concepts that are used as an equivalent to obesity and overweight. Subsequently, we will search for studies comprising of search terms on the underlying factors that drive the development of obesity and overweight. Lastly, we will check reference lists for additional publications. Abstracts and full-text studies will independently be screened by two authors. ETHICS AND DISSEMINATION: The proposed study will generate evidence from published data and hence does not require ethics approval. Evidence generated from this review will be disseminated through journal publications and conference presentations.

Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infection with HIV: clinical case series analysis in North Central Nigeria.

SARS-CoV-2 has created a global public health emergency with significant mortality and morbidity for people living with HIV (PLWH). Preliminary data reveals persons with immune-compromised status are at risk of developing adverse clinical outcomes from SARS-CoV-2. We aimed to characterise clinical outcomes of HIV patients co-infected with SARS-CoV-2 infection in Nasarawa State, North Central Nigeria. We followed four (4) hospitalised HIV patients that tested positive to SARS-CoV-2 in Nasarawa State and characterised their laboratory findings and clinical outcomes. The consent of the cases was sought and they agreed that their clinical data be published. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 nucleic acid were performed using nasopharyngeal swabs (novel coronavirus PCR fluorescence diagnostic kit, BioGerm medical biotechnology) at the Nigeria Centre for Disease Control (NCDC) in Abuja, Nigeria. Our study reveals mild clinical outcome among HIV patients with SARS-CoV-2 co-infection. There is need for a syndemic framework to be used to conceptualise SARS-CoV-2 impact among HIV patients and an urgent need to strengthen healthcare programmes within Nigeria.

A systematic review of vaccine availability at the national, district, and health facility level in the WHO African Region.

INTRODUCTION: To describe vaccine stock-outs at national, district, and health facility levels in the WHO African region. AREAS COVERED: We conducted a systematic review to identify studies reporting on vaccine stock-outs at national, district, and health facility levels in 47 African countries. We searched both published and unpublished literature, including the WHO/UNICEF Joint Reporting Form (JRF), for eligible studies. EXPERT OPINION: Countries within the WHO African region continue to face the challenge of vaccine stock-outs at national, district, and health facility levels and this impacts on the delivery of immunization services. The frequency and the proportion of stock-outs vary between countries and between regions within a country. Countries need to put more efforts toward finding lasting solutions to vaccine shortages. We look forward to having more countries reporting vaccine stock-outs especially at the health facility level. Furthermore, countries are currently exploring different approaches for improving vaccine stock management. It is expected that in half a decade from now, more well-designed studies will be available that will inform decision-making.

Vaccine stock management in primary health care facilities in OR Tambo District, Eastern Cape, South Africa.

BACKGROUND: Poor stock management has been identified as one of the causes of vaccine stock-outs in health facilities. This study assessed the occurrence of vaccine stock-outs and vaccine stock management practices in primary health care facilities in OR Tambo district of the Eastern Cape province, South Africa. METHODS: Descriptive cross-sectional study design was used in this study to assess both the stock management practices and the availability of vaccines in the facilities. The study was conducted in 64 primary health care facilities across all sub-districts in OR Tambo. Data were collected using a questionnaire administered by the researcher, record checks and through observation. The occurrence of stock-outs of six tracer vaccines on the day of the visit and in the preceding 24 months were assessed. The data were captured into REDCap tool and analysed using STATA version 14. RESULTS: Most standard stock management procedures were not adhered to, as these procedures were mostly handled by health care workers who either required formal training or refresher training on vaccine management. Cold chain capacity was not adequate and some vaccines were exposed to freezing. Both stock cards and the stock visibility solution (SVS) device were used in all the facilities for vaccine stock management. Less than half of the facilities visited 27 (44%) filled their stock cards regularly. Delays in receiving supplies from the pharmaceutical depot were commonly reported by facilities, which contributed to stock-outs. A total of 49 (77%) health facilities had at least one stockout for at least one vaccine on the day of the visit. Furthermore, BCG and OPV were the most affected vaccines in 37 (58%) and 28 (44%) of facilities, respectively. CONCLUSION: Interventions for improving vaccine availability should be considered, especially those targeting human resources and the entire stock management system.

Mobile reporting of vaccine stock-levels in primary health care facilities in the Eastern Cape Province of South Africa: perceptions and experiences of health care workers.

The use of mobile and wireless digital technologies - mobile health (mhealth)- is increasingly been adopted in low- and middle-income countries (LMICs) to improve data visibility, improve decision-making, and consequently help ensure availability of health commodities in health facilities. In a bid to improve availability of medicines in primary health care facilities, the South African department of Health launched the Stock Visibility Solution (SVS), a mobile application developed for the purpose of capturing and monitoring stock levels of medicines including vaccines using mobile phones. The stock levels of medicines in facilities are usually uploaded to the central stock management system so that managers can act promptly to address stock-out situations. Pilot studies show that the SVS has the potential to reduce stock-outs from occurring. This study aimed to explore the perceptions and experiences of the SVS system amongst healthcare workers (HCWs) who are involved with managing stock levels of medicines in primary health care facilities in the Eastern Cape Province. This will help identify potential barriers and facilitators to implementation of the system and contribute to the development of strategies to improve its efficiency and effectiveness. A qualitative research design was employed, including semi-structured interviews with 64 HCWs working in primary health care facilities in the OR Tambo district, Eastern Cape Province in South Africa. Data was transcribed verbatim and analyzed using thematic analysis. Most HCWs understood the SVS as a system for reporting stock levels to managers and conveyed commitment to ensuring the system works. However, they highlighted a number of factors that demotivated efficient usage of the system: inadequate training, staff shortages and high staff turnover, lack of responses from the managers, the extra workload that comes with the system, amongst others. HCWs made various suggestions for how the system might be improved, most pertinently the need for more pharmacists and pharmacy assistants and for these cadres to be primarily in-charge of stock management and the use of the SVS. While HCWs are committed to addressing vaccine stock-outs, they face various barriers to an effective and efficient implementation of the SVS system. We make various recommendations for how these barriers might be addressed.

Cochrane corner: personal protective equipment for preventing highly infectious diseases such as COVID-19 in healthcare staff.

As coronavirus disease (COVID-19) cases continue to increase in Africa, healthcare workers (HCWs) have a high risk of being infected and the risks may be higher among those who work closely with patients. The risks of HCW infections can be mitigated with adequate precautions within healthcare facilities, especially with the use of personal protective equipment (PPE). We highlight and contextualise the findings of a Cochrane review on the type of PPE that protects best, the best way to put PPE on (donning) or to remove PPE (doffing) and how to train HCWs to use PPE. The review found low-certainty of evidence that full body PPE offer more protection, but HCWs may be faced with difficulty during donning and doffing. Following standard guidelines may be helpful in reducing infection and increasing compliance among HCWs. Video training and simulations may be better methods for training on the correct use of PPE than traditional methods of teaching. Countries must, therefore, ensure that HCWs undergo compulsory training on the correct use of PPE; regardless of their professional category. Of the 24 studies included in this review, none was conducted on the African continent. There is thus an urgent need for well conducted studies on the experiences of HCWs using full-body covering PPE within the African context. Such studies could lead to tailored interventions that will improve the proper use of PPE among HCWs.

Data on prevalence and distribution of antimicrobial resistance determinants of Salmonella enterica isolates from the formal and informal meat sector.

Foodborne pathogen such Salmonella enterica is a leading cause of human gastroenteritis worldwide. The potential to cause more severe and prolonged infection increases when the bacteria harbour resistant gene. In this dataset, S. enterica PCR confirmed isolates recovered from the formal (n = 33) and informal (n = 15) meat sector were further tested against 15 antimicrobials and 20 resistance determinants using the disc-diffusion method on Muller-Hinton agar and the genotypic antimicrobial resistance determinants by PCR. In addition, multiple antimicrobial resistance phenotype and the multiple antimicrobial resistance indexes were shown. The data suggest that meat from the formal sector harbour resistance capacity than meat from the informal sector.

A scoping review of interventions for vaccine stock management in primary health-care facilities.

One of the challenges facing the success of immunization programs is shortages of vaccines at health facilities, which could result from inadequate vaccine stock management. Several approaches have been designed by countries to improve vaccine stock management. This review summarizes currently available information on interventions for vaccine stock management.We considered both randomized trials and non-randomized studies eligible for inclusion in this review. The following databases were searched: PubMed, Embase, Cochrane Central Register of Controlled Trials, World Health Organization Library Information System, Web of Science, and PDQ-Evidence. We searched the websites of the World Health Organization, Global Alliance for Vaccine and Immunization, PATH's Vaccine Resources Library, and United Nations Children's Fund. The reference lists of all the included studies were also searched. Two authors independently screened search outputs, reviewed full texts of potentially eligible articles, evaluated risk of bias, and extracted data; resolving disagreements through consensus.Four studies met our inclusion criteria (three before-after studies and one randomized trial). Three studies were conducted in low- and middle-income countries while one was conducted in Canada (a high-income country). All the studies had various limitations and were classified as having a high risk of bias. Study findings suggest that the use of digital information systems to improve information and stock visibility, coupled with other interventions (such as training of health-care workers on the use of innovative tools and redesign of the supply chain to tackle certain bottlenecks), has the potential to increase vaccine availability, reduce response times, and improve the quality of vaccine records.

Protocol for a systematic review of the effects of interventions for vaccine stock management.

BACKGROUND: Inadequate vaccine stock management in health facilities leads to vaccine stock-outs. The latter threatens the success of immunisation programmes. Countries have used various approaches to reduce stock-outs and improve vaccine availability, but we are not aware of a systematic review of these interventions. This protocol describes the methods we will use to assess the effects of existing approaches for improving vaccine stock management. METHODS: We include randomised and non-randomised studies identified through a compehensive search of peer-reviewed and grey literature databases. We will search PubMed, Cochrane Central Register of Controlled Trials, Embase, Web of Science, PDQ-Evidence and Scopus. We will also search websites of the World Health Organisation (WHO), Global Alliance for Vaccine and Immunisation, PATH Vaccine Resources Library and United Nations Children's Fund. In addition, we will search the WHO International Clinical Trials Registry Platform and reference lists of included studies and relevant reviews. Finally, we plan to do a citation search for included studies. We will use Cochrane recommended methods to screen search outputs, assess study eligibility and risk of bias, extract and analyse study results. We will use the Grading of Recommendations Assessment, Development and Evaluation (GRADE) tool to assess the certainty of the evidence on the effects of the interventions. DISCUSSION: We believe that the findings of this review will serve as valuable information for policy makers on ways to improve vaccine stock management and vaccine availability. When vaccine availability is improved, those who need them, especially children, will be adequately protected from vaccine-preventable diseases. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42018092215.

Pandemic influenza preparedness in the WHO African region: are we ready yet?

BACKGROUND: Prior to the 2009 pandemic H1N1, and the unprecedented outbreak of Highly Pathogenic Avian Influenza (HPAI) caused by the H5N1 virus, the World Health Organization (WHO) called upon its Member States to develop preparedness plans in response to a new pandemic in humans. The WHO Member States responded to this call by developing national pandemic plans in accordance with the International Health Regulations (IHR) to strengthen the capabilities of Member States to respond to different pandemic scenarios. In this study, we aim to evaluate the quality of the preparedness plans in the WHO African region since their inception in 2005. METHODS: A standard checklist with 61 binary indicators ("yes" or "no") was used to assess the quality of the preparedness plans. The checklist was categorised across seven thematic areas of preparedness: preparation (16 indicators); coordination and partnership (5 indicators); risk communication (8 indicators); surveillance and monitoring (7 indicators); prevention and containment (10 indicators); case investigation and treatment (10 indicators) and ethical consideration (5 indicators). Four assessors independently scored the plans against the checklist. RESULTS: Of the 47 countries in the WHO African region, a total of 35 national pandemic plans were evaluated. The composite score for the completeness of the pandemic plans across the 35 countries was 36%. Country-specific scores on each of the thematic indicators for pandemic plan completeness varied, ranging from 5% in Côte d'Ivoire to 79% in South Africa. On average, preparation and risk communication scored 48%, respectively, while coordination and partnership scored the highest with an aggregate score of 49%. Surveillance and monitoring scored 34%, while prevention and containment scored 35%. Case investigation and treatment scored 25%, and ethical consideration scored the lowest of 14% across 35 countries. Overall, our assessment shows that pandemic preparedness plans across the WHO African region are inadequate. CONCLUSIONS: Moving forward, these plans must address the gaps identified in this study and demonstrate clarity in their goals that are achievable through drills, simulations and tabletop exercises.

Multidrug-Resistant Salmonella Isolates from Swine in the Eastern Cape Province, South Africa.

The exposure of farm animals to antimicrobials for treatment, prophylaxis, or growth promotion can select for resistant bacteria that can be transmitted to humans, and Salmonella as an important zoonotic pathogen can act as a potential reservoir of antimicrobial resistance determinants. We assessed the antibiogram profiles of Salmonella species isolated from pig herds in two commercial farms in South Africa. Two hundred fifty-eight presumptive Salmonella isolates were recovered from the fecal samples of 500 adult pigs. Specific primers targeting Salmonella serogroups A, B, C1, C2, and D were used to determine the prevalence of different serogroups. Only serogroup A (n = 48) was detected, while others were not. Antimicrobial susceptibility of the confirmed Salmonella serogroup A isolates was performed by using the disk diffusion method against a panel of 18 antibiotics. All the 48 isolates were resistant to tetracycline and oxytetracycline, while 75% were resistant to ampicillin, sulphamethoxazole-trimethoprim, nalidixic acid, and streptomycin. All the isolates exhibited multidrug resistance, with the predominant phenotype being against 11 antibiotics, and multiple antibiotic resistance index ranged between 0.3 and 0.6. The incidence of genes encoding resistance against ampicillin (ampC), tetracycline (tetA), and streptomycin (strA) were 54, 61, and 44%, respectively. We conclude that healthy pigs are potential reservoirs of multidrug-resistant Salmonella that could be transmitted to humans through the food chain and, hence, a significant public health threat.

Occurrence of non-O157 Shiga toxin-producing Escherichia coli in two commercial swine farms in the Eastern Cape Province, South Africa.

Shiga toxin-producing Escherichia coli (STEC) is one of the most significant causes of food-borne infections capable of causing serious health complications in humans. Even though ruminants are known to be the major reservoirs of STEC, other non-ruminant food producing animals may also harbour pathogenic E. coli strains. In this study, we investigated the prevalence of E. coli serogroups O26, O111, O121, O145, and O157 and their associated virulence genes (stx1, stx2, eae, and ehxA) in swine faecal samples obtained from the two major commercial farms located in the Nkonkobe Municipality, Eastern Cape, South Africa. The proportions of serogroups detected were O26; 35 (7%), O145; 14 (2.8%), and O157:H7; 43 (8.6%) of the total animals sampled. Out of the 500 animals sampled, 22 isolates of E. coli (1.4%) tested positive for the stx2 gene, and 7 of these isolates belonged to E. coli O26 serogroup, while the remaining 15 most likely belonged to serogroups untargeted in this study. Other virulence genes (stx1, eae, and ehxA) that we screened for were not detected. These findings reveal that pigs within the Eastern Cape Province of South Africa can harbour Shiga toxin-producing E. coli.

Multiple antibiotic resistances among Shiga toxin producing Escherichia coli O157 in feces of dairy cattle farms in Eastern Cape of South Africa.

BACKGROUND: Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a well-recognized cause of bloody diarrhea and hemolytic-uremic syndrome (HUS). The ability of STEC strains to cause human disease is due to the production of Shiga toxins. The objectives of this study were to determinate the prevalence, serotypes, antibiotic susceptibility patterns and the genetic capability for Shiga toxin production in Escherichia coli (STEC) strains isolated from dairy cattle farms in two rural communities in the Eastern Cape Province of South Africa. METHODS: Fecal samples were collected between March and May 2014, from individual cattle (n=400) in two commercial dairy farms having 800 and 120 cattle each. Three hundred presumptive isolates obtained were subjected to polymerase chain reactions (PCR) for identification of O157 serogroup and Shiga toxin producing genes (stx1, stx2) on genomic DNA extracted by boiling method. Susceptibility of the isolates to 17 antibiotics was carried out in vitro by the standardized agar disc-diffusion method. RESULTS: Based on direct PCR detection, 95 (31.7%) isolates were identified as O157 serogroup. The genetic repertoire for Shiga toxin production was present in 84 (88.42%) isolates distributed as stx1 (37), stx2 (38) and stx1/2 (9) respectively while 11 of the isolates did not harbor Shiga toxin producing genes. Multiple antibiotic resistances were observed among the isolates and genetic profiling of resistance genes identified bla ampC 90%, blaCMY 70%, blaCTX-M 65%, blaTEM 27% and tetA 70% and strA 80% genes among the antimicrobial resistance determinants examined. CONCLUSION: We conclude that dairy cattle farms in the Eastern Cape Province are potential reservoirs of antibiotic resistance determinants in the province.