COVID-19: Are Africa's diagnostic challenges blunting response effectiveness?

Diagnostics for detection and surveillance of priority epidemic-prone diseases in Africa: an assessment of testing capacity and laboratory strengthening needs

In 2023, Africa experienced 180 public health emergencies, of which 90% were infectious diseases and 75% were related to zoonotic diseases. Testing capacity for epidemic-prone diseases is essential to enable rapid and accurate identification of causative agents, and for action to prevent disease spread. Moreover, testing is pivotal in monitoring disease transmission, evaluating public health interventions and informing targeted resource allocation during outbreaks. An online, self-assessment survey was conducted in African Union Member States to identify major challenges in testing for epidemic-prone diseases. The survey assessed current capacity for diagnosing priority epidemic-prone diseases at different laboratory levels. It explored challenges in establishing and maintaining testing capacity to improve outbreak response and mitigate public health impact. Survey data analysed diagnostic capacity for priority infectious diseases, diagnostic technologies in use, existing surveillance programmes and challenges limiting diagnostic capacity, by country. The survey result from 15 Member States who responded to the survey, showed high variability in testing capacity and technologies across countries and diverse factors limiting testing capacity for certain priority diseases like dengue and Crimean-Congo haemorrhagic fever. At the same time diagnostic capacity is better for coronavirus disease 2019 (COVID-19), polio, and measles due to previous investments. Unfortunately, many countries are not utilizing multiplex testing, despite its potential to improve diagnostic access. The challenges of limited laboratory capacity for testing future outbreaks are indeed significant. Recent disease outbreaks in Africa have underscored the urgent need to strengthen diagnostic capacity and introduce cost-effective technologies. Small sample sizes and differing disease prioritisation within each country limited the analysis. These findings suggest the benefits of evaluating laboratory testing capacity for epidemic-prone diseases and highlight the importance of effectively addressing challenges to detect diseases and prevent future pandemics.

Transmission of SARS-CoV-2 among underserved pastoralist communities in Kajiado County, Kenya: 2020-2022

Initial transmission of severe acute respiratory syndrome virus-2 (SARS-CoV-2) was highest in densely populated regions of Kenya. Transmission gradually trickled down to the less densely populated, remote and underserved regions such as the pastoral regions of Kajiado County which are characterized by poor healthcare systems. Molecular assays that were pivotal for COVID-19 diagnosis were not available in these regions. Serology is an alternative method for retrospectively tracking the transmission of SARS-CoV-2 in such populations. Dry blood spots (DBS) were prepared from consenting patients attending six health facilities in Kajiado County from March 2020 to March 2022. Upon elution, we conducted an enzyme-linked immunosorbent assay (ELISA) for the detection of SARS-Cov-2 IgG antibodies. Of the 908 DBSs we analyzed, 706 (78%) were from female participants. The overall seropositivity to SARS-Cov-2 antibodies was 7.3% (95% CI 5.7-9.1). The elderly (over 60 years) and male participants had a high likelihood of testing positive for SAR-CoV-2 infections. Mashuru (15.6%, 14/90) and Meto (15%, 19/127) health facilities registered the highest proportion of seropositive participants. Evidence of SARS-CoV-2 transmission among pastoralists in the remote and underserved regions of Kajiado County was established by DBS sampling and serologic testing.

Efficient transplacental transfer of SARS-CoV-2 antibodies between naturally exposed mothers and infants in Accra, Ghana

We aimed to determine SARS-CoV-2 antibody seropositivity among pregnant women and the transplacental transfer efficiency of SARS-CoV-2-specific antibodies relative to malaria antibodies among SARS-CoV-2 seropositive mother-cord pairs. This cross-sectional study was conducted in Accra, Ghana, from March to May 2022. Antigen- specific IgG antibodies against SARS-CoV-2 (nucleoprotein and spike-receptor binding domain) and malarial antigens (circumsporozoite protein and merozoite surface protein 3) in maternal and cord plasma were measured by ELISA. Plasma from both vaccinated and unvaccinated pregnant women were tested for neutralizing antibodies using commercial kit. Of the unvaccinated pregnant women tested, 58.12% at antenatal clinics and 55.56% at the delivery wards were seropositive for both SARS-CoV-2 nucleoprotein and RBD antibodies. Anti-SARS-CoV-2 antibodies in cord samples correlated with maternal antibody levels (N antigen rs = 0.7155, p < 0.001; RBD rs = 0.8693, p < 0.001). Transplacental transfer of SARS-CoV-2 nucleoprotein antibodies was comparable to circumsporozoite protein antibodies (p = 0.9999) but both were higher than transfer rates of merozoite surface protein 3 antibodies (p < 0.001). SARS-CoV-2 IgG seropositivity among pregnant women in Accra is high with a boost of SARS-CoV-2 RBD-specific IgG in vaccinated women. Transplacental transfer of anti-SARS-CoV-2 and malarial antibodies was efficient, supporting vaccination of mothers as a strategy to protect infants against SARS-CoV-2.

Lessons from the pandemic: new best practices in selecting molecular diagnostics for point-of-care testing of infectious diseases in sub-Saharan Africa

INTRODUCTION

Point-of-care molecular diagnostics offer solutions to the limited diagnostic availability and accessibility in resource-limited settings. During the COVID-19 pandemic, molecular diagnostics became essential tools for accurate detection and monitoring of SARS-CoV-2. The unprecedented demand for molecular diagnostics presented challenges and catalyzed innovations which may provide lessons for the future selection of point-of-care molecular diagnostics.

AREAS COVERED

We searched PubMed from January 2020 to August 2023 to identify lessons learned from the COVID-19 pandemic which may impact the selection of point-of-care molecular diagnostics for future use in sub-Saharan Africa. We evaluated this in the context of REASSURED criteria (Real-time connectivity; Ease of specimen collection; Affordable; Sensitive; Specific; User-friendly; Rapid and robust; Equipment free; and Deliverable to users at the point of need) for point-of-care diagnostics for resource-limited settings.

EXPERT OPINION

The diagnostic challenges and successes during the COVID-19 pandemic affirmed the importance of the REASSURED criteria but demonstrated that these are not sufficient to ensure new diagnostics will be appropriate for public health emergencies. Capacity for rapid scale-up of diagnostic testing and transferability of assays, data, and technology are also important, resulting in updated REST-ASSURED criteria. Few diagnostics will meet all criteria, and trade-offs between criteria will need to be context-specific.

Prevalence and determinants of post-acute sequelae of COVID-19 in Liberia

BACKGROUND

Evidence from resource-rich settings indicates that many people continue to have persistent symptoms following acute SARS-CoV-2 infection, called post-acute sequelae of COVID-19 (PASC). Only a few studies have described PASC in sub-Saharan Africa (SSA). We aimed to describe PASC in Liberia.

METHODS

We randomly sampled all people who were reported from the most populous county to the Liberian Ministry of Health (MOH) as having a laboratory-confirmed SARS-CoV-2 infection from June to August 2021. We interviewed individuals by phone 3 to 6 months later. Those with persistence of at least one symptom were considered to have PASC.

RESULTS

From among 2848 people reported to the MOH from Montserrado County during the period of interest, we randomly selected 650; of these, 548 (84.3%) were reached and 505 (92.2%) of those who were contacted were interviewed. The median age was 38 years (interquartile range (IQR), 30-49), and 43.6% were female. During acute infection, 40.2% were asymptomatic, 53.9% had mild/moderate disease and 6.9% had severe/critical disease. Among the 59.8% (n = 302) who were initially symptomatic, 50.2% (n = 152) reported at least one persistent symptom; the most common persistent symptoms were fatigue (21.2%), headache (16.2%) and cough (12.6%); 40.1% reported that PASC significantly affected their daily activities. Being hospitalized with moderate disease [adjusted prevalence ratio (aPR), 2.00 (95% CI, 1.59 to 2.80] or severe/critical disease [aPR, 2.11 (95% CI, 1.59 to 2.80)] was associated with PASC, compared with those not hospitalized. Females were more likely than males to report persistent fatigue [aPR, 1.67 (95% CI, 1.08 to 2.57)].

CONCLUSIONS

Our findings suggest that persistent symptoms may have affected a large proportion of people with initially symptomatic COVID-19 in west Africa and highlight the need to create awareness among infected people and health care professionals.

Hyperglycemia and elevated C-reactive protein are independent predictors of hospital mortality in hospitalized COVID-19 patients in South-Kivu, eastern Democratic Republic of the Congo: A cross-sectional study

Background and Aim

The coronavirus disease 2019 (COVID-19) pandemic was a priority public health problem because of its high mortality rate. This study mainly aimed to determine factors associated with a poor outcome in COVID-19 hospitalized patients in South-Kivu, an eastern province of the Democratic Republic of the Congo (DRC).

Methods

This observational study retrospectively evaluated medical records of patients consecutively admitted for probable or confirmed COVID-19 between May 01 and July 31, 2020 at the Hôpital Provincial Général de Référence de Bukavu (HPGRB), a tertiary hospital located in South-Kivu. A binary logistic regression model was performed to determine the predictors of mortality.

Results

A total of 157 hospitalized COVID-19 patients aged 57.7 (13.2) years were included in this study. Male gender (69.4%), older age (52.9%), medical history of diabetes (38.2%), and arterial hypertension (35.1%) were the most frequent risk factors. Most patients presented with fever (73.3%), cough (72.6%), and dyspnea (66.2%). Overall, 45.1% of patients died. Intrahospital mortality was significantly associated with advanced age [odds ratio, OR (95% confidence interval, CI) = 2.34 (1.06-5.38)], hypoxemia [OR (95% CI) = 4.67 (2.02-10.77)], hyperglycemia [OR (95% CI) = 2.14 (1.06-4.31)], kidney failure [OR (95% CI) = 2.82 (1.4-5.68)], hyperleukocytosis [OR (95% CI) = 3.33 (1.67-6.66)], and higher C-reactive protein (CRP) levels [OR (95% CI) = 3.93 (1.93-8.01)]. After adjustment for various covariates, only higher CRP levels [OR (95% CI) = 3.23 (1.23-8.5)] and hyperglycemia [OR (95% CI) = 2.5 (1.02-6.11)] at admission were independently associated with mortality.

Conclusion

Hyperglycemia and marked inflammatory syndrome were the major predictors of poor outcomes in patients hospitalized for COVID-19 in South-Kivu. These two factors should be quantified at hospital admission to establish the patient's prognosis.

Estimating the number of probable new SARS-CoV-2 infections among tested subjects from the number of confirmed cases

OBJECTIVES

In most African countries, confirmed COVID-19 case counts underestimate the number of new SARS-CoV-2 infection cases. We propose a multiplying factor to approximate the number of biologically probable new infections from the number of confirmed cases.

METHODS

Each of the first thousand suspect (or alert) cases recorded in South Kivu (DRC) between 29 March and 29 November 2020 underwent a RT-PCR test and an IgM and IgG serology. A latent class model and a Bayesian inference method were used to estimate (i) the incidence proportion of SARS-CoV-2 infection using RT-PCR and IgM test results, (ii) the prevalence using RT-PCR, IgM and IgG test results; and, (iii) the multiplying factor (ratio of the incidence proportion on the proportion of confirmed -RT-PCR+- cases).

RESULTS

Among 933 alert cases with complete data, 218 (23%) were RT-PCR+; 434 (47%) IgM+; 464 (~ 50%) RT-PCR+, IgM+, or both; and 647 (69%) either IgG + or IgM+. The incidence proportion of SARS-CoV-2 infection was estimated at 58% (95% credibility interval: 51.8-64), its prevalence at 72.83% (65.68-77.89), and the multiplying factor at 2.42 (1.95-3.01).

CONCLUSIONS

In monitoring the pandemic dynamics, the number of biologically probable cases is also useful. The multiplying factor helps approximating it.

Improving testing capacity for COVID-19: experiences and lessons from Senegal, Uganda, Nigeria, and the Democratic Republic of Congo

Background

African countries leveraged testing capacities to enhance public health action in response to the COVID-19 pandemic. This paper describes experiences and lessons learned during the improvement of testing capacity throughout the COVID-19 response in Senegal, Uganda, Nigeria, and the Democratic Republic of the Congo (DRC).

Methods

The four countries' testing strategies were studied using a mixed-methods approach. Desk research on COVID-19 testing strategies was conducted and complemented by interviewing key informants. The findings were synthesized to demonstrate learning outcomes across the four countries.

Results

The four countries demonstrated severely limited testing capacities at the onset of the pandemic. These countries decentralized COVID-19 testing services by leveraging preexisting laboratory systems such as PCR and GeneXpert used for the diagnosis of tuberculosis (TB) to address this gap and the related inequities, engaging the private sector, establishing new laboratories, and using rapid diagnostic tests (RDTs) to expand testing capacity and reduce the turnaround time (TAT). The use of digital platforms improved the TAT. Testing supplies were sourced through partners, although access to global markets was challenging. Case detection remains suboptimal due to high costs, restrictive testing strategies, testing access challenges, and misinformation, which hinder the demand for testing. The TAT for PCR remained a challenge, while RDT use was underreported, although Senegal manufactured RDTs locally. Key findings indicate that regionally coordinated procurement and manufacturing mechanisms are required, that testing modalities must be simplified for improved access, and that the risk-based testing strategy limits comprehensive understanding of the disease burden.

Conclusion

Although testing capacities improved significantly during the pandemic, case detection and access to testing remained suboptimal. The four countries could benefit from further simplification of testing modalities and cost reduction. Local manufacturing and pooled procurement mechanisms for diagnostics are needed for optimal pandemic preparedness and response.

Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study

The mortality impact of COVID-19 in Africa remains controversial because most countries lack vital registration. We analysed excess mortality in Kilifi Health and Demographic Surveillance System, Kenya, using 9 years of baseline data. SARS-CoV-2 seroprevalence studies suggest most adults here were infected before May 2022. During 5 waves of COVID-19 (April 2020-May 2022) an overall excess mortality of 4.8% (95% PI 1.2%, 9.4%) concealed a significant excess (11.6%, 95% PI 5.9%, 18.9%) among older adults ( ≥ 65 years) and a deficit among children aged 1-14 years (-7.7%, 95% PI -20.9%, 6.9%). The excess mortality rate for January 2020-December 2021, age-standardised to the Kenyan population, was 27.4/100,000 person-years (95% CI 23.2-31.6). In Coastal Kenya, excess mortality during the pandemic was substantially lower than in most high-income countries but the significant excess mortality in older adults emphasizes the value of achieving high vaccine coverage in this risk group.

Results of German external quality assessment schemes for SARS-CoV-2 antigen detection

The COVID-19 pandemic illustrated the important role of diagnostic tests, including lateral flow tests (LFTs), in identifying patients and their contacts to slow the spread of infections. INSTAND performed external quality assessments (EQA) for SARS-CoV-2 antigen detection with lyophilized and chemically inactivated cell culture supernatant of SARS-CoV-2 infected Vero cells. A pre-study demonstrated the suitability of the material. Participants reported qualitative and/or quantitative antigen results using either LFTs or automated immunoassays for five EQA samples per survey. 711 data sets were reported for LFT detection in three surveys in 2021. This evaluation focused on the analytical sensitivity of different LFTs and automated immunoassays. The inter-laboratory results showed at least 94% correct results for non-variant of concern (VOC) SARS-CoV-2 antigen detection for viral loads of ≥ 4.75 × 106 copies/mL and SARS-CoV-2 negative samples. Up to 85% had success for a non-VOC viral load of ~ 1.60 × 106 copies/mL. A viral load of ~ 1.42 × 107 copies/mL of the Delta VOC was reported positive in > 96% of results. A high specificity was found with almost 100% negative SARS-CoV-2 antigen results for HCoV 229E and HCoV NL63 positive samples. Quantitative results correlated with increasing SARS-CoV-2 viral load but showed a broad scatter. This study shows promising SARS-CoV-2 antigen test performance of the participating laboratories, but further investigations with the now predominant Omicron VOC are needed.

Application of Hybridization Chain Reaction/CRISPR-Cas12a for the Detection of SARS-CoV-2 Infection

Globally, the emergence of the coronavirus disease (COVID-19) has had a significant impact on life. The need for ongoing SARS-CoV-2 screening employing inexpensive and quick diagnostic approaches is undeniable, given the ongoing pandemic and variations in vaccine administration in resource-constrained regions. This study presents results as proof of concept to use hybridization chain reaction (HCR) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a complex for detecting SARS-CoV-2. HCR hairpin probes were designed using the NUPACK web-based program and further used to amplify the SARS-CoV-2 N gene in archived nasopharyngeal samples. The results were visualized using agarose gels and CRISPR Cas12a-based lateral flow strips. The assay was evaluated using the gold standard, real-time polymerase chain reaction (RT-PCR), as recommended by the World Health Organization (WHO). The results show the comparative efficiency of HCR to RT-PCR. This study shows that HCR and CRISPR are viable alternatives for diagnosing SARS-CoV-2 in samples.

Global prevalence of coronavirus disease 2019 reinfection: a systematic review and meta-analysis

BACKGROUND

In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged with a high transmissibility rate and resulted in numerous negative impacts on global life. Preventive measures such as face masks, social distancing, and vaccination helped control the pandemic. Nonetheless, the emergence of SARS-CoV-2 variants, such as Omega and Delta, as well as coronavirus disease 2019 (COVID-19) reinfection, raise additional concerns. Therefore, this study aimed to determine the overall prevalence of reinfection on global and regional scales.

METHODS

A systematic search was conducted across three databases, PubMed, Scopus, and ProQuest Central, including all articles pertaining to COVID-19 reinfection without language restriction. After critical appraisal and qualitative synthesis of the identified relevant articles, a meta-analysis considering random effects was used to pool the studies.

RESULTS

We included 52 studies conducted between 2019 and 2022, with a total sample size of 3,623,655 patients. The overall prevalence of COVID-19 reinfection was 4.2% (95% confidence interval [CI]: 3.7-4.8%; n = 52), with high heterogeneity between studies. Africa had the highest prevalence of 4.7% (95% CI: 1.9-7.5%; n = 3), whereas Oceania and America had lower estimates of 0.3% (95% CI: 0.2-0.4%; n = 1) and 1% (95% CI: 0.8-1.3%; n = 7), respectively. The prevalence of reinfection in Europe and Asia was 1.2% (95% CI: 0.8-1.5%; n = 8) and 3.8% (95% CI: 3.4-4.3%; n = 43), respectively. Studies that used a combined type of specimen had the highest prevalence of 7.6% (95% CI: 5.8-9.5%; n = 15) compared with those that used oropharyngeal or nasopharyngeal swabs only that had lower estimates of 6.7% (95% CI: 4.8-8.5%; n = 8), and 3.4% (95% CI: 2.8-4.0%; n = 12) respectively.

CONCLUSION

COVID-19 reinfection occurs with varying prevalence worldwide, with the highest occurring in Africa. Therefore, preventive measures, including vaccination, should be emphasized to ensure control of the pandemic.

The effect of vaccine on COVID-19 spread by function-on-scalar regression model: a case study of Africa

Aim

This paper aimed to study the effect of the vaccine on the reproduction rate of coronavirus in Africa from January 2021 to November 2021.

Subject and methods

Functional data analysis (FDA), a relatively new area in statistics, can describe, analyze, and predict data collected over time, space, or other continuum measures in many countries every day and is increasingly common across scientific domains. For our data, the first step of functional data is smoothing. We used the B-spline method to smooth our data. Then, we apply the function-on-scalar and Bayes function-on-scalar models to fit our data.

Results

Our results indicate a statistically significant relationship between the vaccine and the rate of virus reproduction and spread. When the vaccination rate falls, the reproduction rate also decreases. Furthermore, we found that the effect of latitude and the region on the reproduction rate depends on the region. We discovered that in Middle Africa, from the beginning of the year until the end of the summer, the impact is negative, implying that the virus spread due to a decrease in the vaccination rates.

Conclusion

The study found that vaccination rates significantly impact the virus's reproduction rate.

Pediatric coronavirus disease 2019 in Africa

PURPOSE OF REVIEW

Three years into the coronavirus disease 2019 (COVID-19) pandemic, data on pediatric COVID-19 from African settings is limited. Understanding the impact of the pandemic in this setting with a high burden of communicable and noncommunicable diseases is critical to implementing effective interventions in public health programs.

RECENT FINDINGS

More severe COVID-19 has been reported in African settings, with especially infants and children with underlying comorbidities at highest risk for more severe disease. Data on the role of tuberculosis and HIV remain sparse. Compared to better resourced settings more children with multisystem inflammatory disease (MISC) are younger than 5 years and there is higher morbidity in all settings and increased mortality in some settings. Several reports suggest decreasing prevalence and severity of MIS-C disease with subsequent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variant waves. Whether this decrease continues remains to be determined. Thus far, data on long-COVID in African settings is lacking and urgently needed considering the severity of the disease seen in the African population.

SUMMARY

Considering the differences seen in the severity of disease and short-term outcomes, there is an urgent need to establish long-term outcomes in children with COVID-19 and MIS-C in African children, including lung health assessment.

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

Access to COVID-19 vaccines and testing in Africa: the importance of COVAX - Nigeria as a case study

Since pandemic declaration, the vulnerability of countries with serious economic challenges and limited health resources became evident. This vulnerability has been put to the test once again with the appearance of Omicron as another variant of concern. Although great efforts have been made to develop effective and safe vaccines, they need to be made available globally at an affordable price to all governments and distributed equitably to maximize immediate and long-term efforts to contain the virus and advance global public health. Potential sources of unfair allocation of COVID-19 vaccines are not hard to find. The COVID-19 Vaccine Global Access Facility (COVAX) has so far shipped over 406 million COVID-19 vaccines to 144 eligible participants. From that batches, about 115 million doses (28%) were allocated to 49 African countries. If proactive measures are not undertaken, Nigeria, pointed here as a case study, and Sub-Saharan Africa countries may not be self-reliant for COVID-19 vaccines. This report raises a discussion on the difficulties in accessing vaccines and diagnostics in sub-Saharan Africa, compared to high- and middle-income countries. Now more than ever, it is crucial to note that there is no overcoming a pandemic without coordinated action for actions that go beyond borders. The coordinated effort to raise vaccination rates in the African continent is not a humanitarian action aimed exclusively at Africa, but more than that, it is an effort for the benefit of global public health.

The Role of Remote Sensing and Geospatial Analysis for Understanding COVID-19 Population Severity: A Systematic Review

Remote sensing (RS), satellite imaging (SI), and geospatial analysis have established themselves as extremely useful and very diverse domains for research associated with space, spatio-temporal components, and geography. We evaluated in this review the existing evidence on the application of those geospatial techniques, tools, and methods in the coronavirus pandemic. We reviewed and retrieved nine research studies that directly used geospatial techniques, remote sensing, or satellite imaging as part of their research analysis. Articles included studies from Europe, Somalia, the USA, Indonesia, Iran, Ecuador, China, and India. Two papers used only satellite imaging data, three papers used remote sensing, three papers used a combination of both satellite imaging and remote sensing. One paper mentioned the use of spatiotemporal data. Many studies used reports from healthcare facilities and geospatial agencies to collect the type of data. The aim of this review was to show the use of remote sensing, satellite imaging, and geospatial data in defining features and relationships that are related to the spread and mortality rate of COVID-19 around the world. This review should ensure that these innovations and technologies are instantly available to assist decision-making and robust scientific research that will improve the population health diseases outcomes around the globe.

Multilevel Governance and Control of the COVID-19 Pandemic in the Democratic Republic of Congo: Learning from the Four First Waves

The COVID-19 pandemic continues to impose a heavy burden on people around the world. The Democratic Republic of the Congo (DRC) has also been affected. The objective of this study was to explore national policy responses to the COVID-19 pandemic in the DRC and drivers of the response, and to generate lessons for strengthening health systems' resilience and public health capacity to respond to health security threats. This was a case study with data collected through a literature review and in-depth interviews with key informants. Data analysis was carried out manually using thematic content analysis translated into a logical and descriptive summary of the results. The management of the response to the COVID-19 pandemic reflected multilevel governance. It implied a centralized command and a decentralized implementation. The centralized command at the national level mostly involved state actors organized into ad hoc structures. The decentralized implementation involved state actors at the provincial and peripheral level including two other ad hoc structures. Non-state actors were involved at both levels. These ad hoc structures had problems coordinating the transmission of information to the public as they were operating outside the normative framework of the health system. Conclusions: Lessons that can be learned from this study include the strategic organisation of the response inspired by previous experiences with epidemics; the need to decentralize decision-making power to anticipate or respond quickly and adequately to a threat such as the COVID-19 pandemic; and measures decided, taken, or adapted according to the epidemiological evolution (cases and deaths) of the epidemic and its effects on the socio-economic situation of the population. Other countries can benefit from the DRC experience by adapting it to their own context.

Using drones to transport suspected COVID-19 samples; experiences from the second largest testing centre in Ghana, West Africa

BACKGROUND

The declaration of COVID-19 as a pandemic on March 11 2020, by the World Health Organisation prompted the need for a sustained and a rapid international response. In a swift response, the Government of Ghana, in partnership with Zipline company, launched the use of Unmanned Automated Vehicles (UAV) to transport suspected samples from selected districts to two foremost testing centres in the country. Here, we present the experiences of employing this technology and its impact on the transport time to the second largest testing centre, the Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR) in Kumasi, Ghana.

METHODS

Swab samples collected from suspected COVID-19 patients were transported to the Zipline office by health workers. Information on the samples were sent to laboratory personnel located at KCCR through a WhatsApp platform to get them ready to receive the suspected COVID-19 samples while Zipline repackaged samples and transported them via drone. Time of take-off was reported as well as time of drop-off.

RESULTS

A total of 2537 COVID-19 suspected samples were received via drone transport from 10 districts between April 2020 to June 2021 in 440 deliveries. Ejura-Sekyedumase District Health Directorate delivered the highest number of samples (765; 30%). The farthest district to use the drone was Pru East, located 270 km away from KCCR in Kumasi and 173 km to the Zipline office in Mampong. Here, significantly, it took on the average 39 minutes for drones to deliver samples compared to 117 minutes spent in transporting samples by road (p<0.001).

CONCLUSION

The use of drones for sample transport during the COVID-19 pandemic significantly reduced the travel time taken for samples to be transported by road to the testing site. This has enhanced innovative measures to fight the pandemic using technology.

HIV viral load suppression before and after COVID-19 in Kinshasa and Haut Katanga, Democratic Republic of the Congo

Background

The coronavirus disease 2019 (COVID-19) pandemic resulted in unique programmatic opportunities to test hypotheses related to the initiation of antiretroviral treatment (ART) and viral load (VL) suppression during a global health crisis, which would not otherwise have been possible.

Objectives

To generate practice-relevant evidence on the impact of initiating ART pre-COVID-19 versus during the COVID-19 pandemic on HIV VL.

Method

Logistic regression was performed on data covering 6596 persons with HIV whose VL data were available, out of 36 585 persons who were initiated on ART between 01 April 2019 and 30 March 2021.

Results

After controlling for covariates such as age, gender, duration on ART, tuberculosis status at the time of the last visit, and rural vs urban status, the odds of having a VL < 1000 copies/mL were significantly higher for clients who started ART during the COVID-19 pandemic than the year before COVID-19 (adjusted odds ratio [AOR]: 2.50; confidence interval [CI]: 1.55–4.01; P < 0.001). Odds of having a VL < 1000 copies/mL were also significantly higher among female participants than male (AOR: 1.23; CI: 1.02–1.48), among patients attending rural clinics compared to those attending urban clinics (AOR: 1.83; CI: 1.47–2.28), and in clients who were 15 years or older at the time of their last visit (AOR: 1.50; CI: 1.07–2.11).

Conclusion

Viral loads did not deteriorate despite pandemic-induced changes in HIV services such as the expansion of multi-month dispensing (MMD), which may have played a protective role regardless of the general negative impacts of response to the COVID-19 crises on communities and individuals.

What this study adds

This research capitalises on the natural experiment of COVID-19-related changes in HIV services and provides new practice-relevant research evidence.

Positive SARS-CoV-2 RT-qPCR of a nasal swab spot after 30 days of conservation on filter paper at room temperature

We tested the use of nasal swabs spotted onto filter paper (Whatman 3M) for the molecular diagnosis of SARS-CoV-2 infection. Spots of a positive nasal swab in conservation medium (B.1.177 strain, 21Ct) were still positive (duo E-gene/IP4) after 10, 20, and 30 days of conservation at room temperature, with Ct values of 28, 27, and 26, respectively. Direct spotting of the swab at bedside (omicron strain) still gave a positive result after 10 days in two RT-qPCR systems: 33.7 Ct using duo E-gene/IP4, and 34.8 using a specific Omicron system. Spotting of a dilution range of media spiked with the Delta (strain 2021/FR/0610, lineage B 1.617.2) and Omicron strains (strain UVE/SARS-CoV-2/2021/FR/1514) showed a threshold of 0.04 TCID₅₀ after 10 days of conservation. We show, for the first time, that this simple and low-cost conservation method can be used to store samples for RT-qPCR against SARS-CoV-2 for up to at least 1 month.

Informing healthcare operations with integrated pathology, clinical, and epidemiology data: Lessons from a single institution in Kenya during COVID-19 waves

Pathology, clinical care teams, and public health experts often operate in silos. We hypothesized that large data sets from laboratories when integrated with other healthcare data can provide evidence that can be used to optimize planning for healthcare needs, often driven by health-seeking or delivery behavior. From the hospital information system, we extracted raw data from tests performed from 2019 to 2021, prescription drug usage, and admission patterns from pharmacy and nursing departments during the COVID-19 pandemic in Kenya (March 2020 to December 2021). Proportions and rates were calculated. Regression models were created, and a t-test for differences between means was applied for monthly or yearly clustered data compared to pre-COVID-19 data. Tests for malaria parasite, Mycobacterium tuberculosis, rifampicin resistance, blood group, blood count, and histology showed a statistically significant decrease in 2020, followed by a partial recovery in 2021. This pattern was attributed to restrictions implemented to control the spread of COVID-19. On the contrary, D-dimer, fibrinogen, CRP, and HbA1c showed a statistically significant increase (p-value <0.001). This pattern was attributed to increased utilization related to the clinical management of COVID-19. Prescription drug utilization revealed a non-linear relationship to the COVID-19 positivity rate. The results from this study reveal the expected scenario in the event of similar outbreaks. They also reveal the need for increased efforts at diabetes and cancer screening, follow-up of HIV, and tuberculosis patients. To realize a broader healthcare impact, pathology departments in Africa should invest in integrated data analytics, for non-communicable diseases as well.

Preadmission testing for COVID-19 as a screening strategy: a retrospective chart review from a tertiary hospital in Kenya

Background

Since COVID-19 was declared a pandemic in March 2020, hospitals and patient care facilities have faced challenges in protecting healthcare workers and patients from being exposed to the infection. The main challenge has been how exposure to COVID-19 can be controlled when asymptomatic patientscan transmit the infection. This study aims to evaluate pre-admission testing of COVID-19 in patients at the Aga Khan University Hospital, Nairobi as a screening strategy for understanding, preventing and controlling exposure to COVID-19.

Methods

This was a descriptive retrospective chart review study that analysed the incidence of COVID-19, incidental detection of laboratory-confirmed COVID-19 and effects on plan of care in patients prior to admission at the Aga Khan University Hospital from April to December 31, 2020. Demographic data, clinical characteristics, COVID-19 test report and plan of care were retrieved from patients medical records review.

Results

A total of 8837 pre-admission tests were done between April 2020 and December 2020, with a COVID-19 prevalence rate of 10.9% (961/8837). Among the positive pre-admission tests, 14.3% were incidental positive results (138/961). Among the 138 incidental positive tests 21% (30) had their plan of care affected, 14.5% [20] had their care interventions delayed, 4.3% [6] had their hospital stay shortened, 1.4% [2] their hospital stay prolonged and 0.7% [1] had their care diagnostics delayed.

Conclusion

While community spread of COVID-19 fluctuated during this period; depending on the level of compliance to infection control measures, pre-admission prevalence rates were increasing as the year progressed. Mandatory testing of COVID-19 in hospital facilities remains an important admission requirement in controlling asymptomatic transmission of the virus. COVID-19 health burden justifies resource allocation for universal screening of all patients before hospital admission.

Investigation of possible preventable causes of COVID-19 deaths in the Kampala Metropolitan Area, Uganda, 2020-2021

BACKGROUND

Identifying preventable causes of COVID-19 deaths is key to reducing mortality. We investigated possible preventable causes of COVID-19 deaths over a six-month period in Uganda.

METHODS

A case-patient was a person testing reverse transcription polymerase chain reaction-positive for SARS-CoV-2 who died in Kampala Metropolitan Area hospitals from August 2020 to February 2021. We reviewed records and interviewed health workers and case-patient caretakers.

RESULTS

We investigated 126 (65%) of 195 reported COVID-19 deaths during the investigation period; 89 (71%) were male, and the median age was 61 years. A total of 98 (78%) had underlying medical conditions. Most (118, 94%) had advanced disease at admission to the hospital where they died. A total of 44 (35%) did not receive a COVID-19 test at their first presentation to a health facility despite having consistent symptoms. A total of 95 (75%) needed intensive care unit admission, of whom 45 (47%) received it; 74 (59%) needed mechanical ventilation, of whom 47 (64%) received it.

CONCLUSION

Among hospitalized patients with COVID-19 who died in this investigation, early opportunities for diagnosis were frequently missed, and there was inadequate intensive care unit capacity. Emphasis is needed on COVID-19 as a differential diagnosis, early testing, and care-seeking at specialized facilities before the illness reaches a critical stage. Increased capacity for intensive care is needed.

Perceptions of COVID-19 transmission risk and testing readiness in rural Southwest Nigeria

Although community screening and testing have been recommended by the World Health Organization, the extent of readiness and the associated factors among rural populations remain unknown. We investigated the factors associated with perception of the COVID-19 transmission risk and readiness for testing in rural areas of Southwest Nigeria.

Using a multistage cluster sampling technique, cross-sectional data was collected from 922 adults aged 18 years and above who were resident in rural communities selected across three States in the Southwest region between June and August 2020. Descriptive statistics and binary logit models with robust standard errors were utilized for analysis.

Mean age of respondents was 37.0 (SD = 15.8) years; 58.6% female; 46.5% had secondary education; and most were traders (33.2%) and artisans (29.9%). Only 149 respondents (16.2%) had a accurate perception of COVID-19 transmission risk. Adjusted logit models showed that independent factors associated with accurate perception of COVID-19 transmission risk include: age 18&19 years (OR = 0.50, CI: 0.34–0.73); exposure to electronic media (OR = 1.84, CI: 1.07–3.18); and being an in-migrant (OR = 3.38, CI: 2.44–4.68). Less than one-third (28.8%) were willing to test for COVID-19. Severe fear of COVID-19 (OR = 3.99, CI: 1.36–11.74) was associated with willingness to undergo COVID-19 testing. Socio-demographic predictors of testing readiness included: male sex (OR = 1.51, CI: 1.36–1.68); traditional religion (OR = 2.81, CI: 1.05–7.53); and exposure to electronic media (OR = 1.31, CI: 1.06–1.62). Awareness campaigns need to be scaled up to improve perception and preparedness to test for COVID-19.

Evaluation of SARS-CoV-2 diagnostics and risk factors associated with SARS-CoV-2 infection in Zambia

OBJECTIVES

To conduct a diagnostic validation study of SARS-CoV-2 diagnostic kits.

METHODS

We compared SARS-CoV-2 diagnostic test results from 3 RT-PCR assays used by the Zambian government between November 2020 and February 2021 (Panther Fusion assay, Da An Gene's 2019-nCoV RNA kit and Maccura's PCR Kit) with the Altona RealStar RT-PCR kit which served as the gold standard. We also evaluated results from rapid antigen testing and whether comorbidities were linked with increased odds of infection.

RESULTS

We recruited 244 participants, 61% (149/244) were positive by at least 1 PCR assay. Da An Gene, Maccura, and Panther Fusion assays had sensitivities of 0.0% (95% confidence interval [CI] 0%-41%), 27.1% (95% CI 15%-42%), and 76% (95% CI 65%-85%), respectively, but specificity was low (<85% for all 3 assays). HIV and TB were not associated with SARS-CoV-2, whereas female sex (OR 0.5 [0.3-0.9], p = 0.026) and chronic pulmonary disease (0.1 [0.0-0.8], p = 0.031) were associated with lower odds of SARS-CoV-2 infection. Of 44 samples, 84% sequenced were Beta variant.

CONCLUSIONS

The RT-PCR assays evaluated did not meet WHO recommended minimum sensitivity of 80%. Local diagnostic validation studies should be embedded within preparedness plans for future outbreaks to improve the public health response.

The Value of Lung Ultrasound to Detect the Early Pleural and Pulmonary Pathologies in Nonhospitalized COVID-19-Suspected Cases in a Population With a Low Prevalence of COVID-19 Infection: A Prospective Study in 297 Subjects

OBJECTIVES

This prospective study aimed to evaluate the value of B-mode lung ultrasound (LUS) for the early diagnosis of coronavirus disease 2019 (COVID-19) infection in nonhospitalized COVID-19 suspected cases in a population with a low prevalence of disease.

METHODS

From April 2020 to June 2020, in an ambulatory testing center for COVID-19-suspected cases, 297 subjects were examined by LUS before a nasopharyngeal swab was taken for a reverse transcription polymerase chain reaction (RT-PCR) test. The following LUS findings were defined as pathological ultrasound findings and were analyzed: the presence of 1) pleural effusion, 2) B-lines, 3) fragmented visceral pleura, 4) consolidation, and 5) air bronchogram in the consolidation. The LUS findings were compared with the RT-PCR test results.

RESULTS

The result of the RT-PCR test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was positive in 11 and negative in 286 subjects, and the prevalence of COVID-19 infection in the study participants was 3.7%. On LUS, a pathological finding could be detected in 56/297 (18.9%) study participants. The LUS revealed a sensitivity of 27.3%, a specificity of 81.5%, a positive predictive value of 5.4%, a negative predictive value of 96.7%, and a diagnostic accuracy of 79.9% for the identification of COVID-19 infection.

CONCLUSIONS

For the identification of COVID-19 infection, LUS is highly sensitive to the patient spectrum and to the prevalence of the disease. Due to the low diagnostic performance in nonhospitalized COVID-19 cases in low-prevalence areas, LUS cannot be considered to be an adequate method for making a diagnosis in this group.

Performance of COVID-19 case-based surveillance system in FCT, Nigeria, March 2020 –January 2021

Introduction

The emergence of novel SARS-CoV-2 has caused a pandemic of Coronavirus Disease 19 (COVID-19) which has spread exponentially worldwide. A robust surveillance system is essential for correct estimation of the disease burden and containment of the pandemic. We evaluated the performance of COVID-19 case-based surveillance system in FCT, Nigeria and assessed its key attributes.

Methods

We used a cross-sectional study design, comprising a survey, key informant interview, record review and secondary data analysis. A self-administered, semi-structured questionnaire was administered to key stakeholders to assess the attributes and process of operation of the surveillance system using CDC’s Updated Guidelines for Evaluation of Public Health Surveillance System 2001. Data collected alongside surveillance data from March 2020 to January 2021 were analyzed and summarized using descriptive statistics.

Results

Out of 69,338 suspected cases, 12,595 tested positive with RT-PCR with a positive predictive value (PPV) of 18%. Healthcare workers were identified as high-risk group with a prevalence of 23.5%. About 82% respondents perceived the system to be simple, 85.5% posited that the system was flexible and easily accommodates changes, 71.4% reported that the system was acceptable and expressed willingness to continue participation. Representativeness of the system was 93%, stability 40%, data quality 56.2% and timeliness 45.5%, estimated result turnaround time (TAT) was suboptimal.

Conclusion

The system was found to be useful, simple, flexible, sensitive, acceptable, with good representativeness but the stability, data quality and timeliness was poor. The system meets initial surveillance objectives but rapid expansion of sample collection and testing sites, improvement of TAT, sustainable funding, improvement of electronic database, continuous provision of logistics, supplies and additional trainings are needed to address identified weaknesses, optimize the system performance and meet increasing need of case detection in the wake of rapidly spreading pandemic. More risk-group persons should be tested to improve surveillance effectiveness.

Seroprevalence of anti-SARS-CoV-2 antibodies in a population living in Bomassa village, Republic of Congo

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No presence of anti-SARS-CoV-2 antibodies in individuals before the pandemic

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28% seroprevalence of anti-SARS-CoV-2 antibodies in asymptomatic adults

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4% active SARS-CoV-2 infection in villagers

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57% of IgG-positive individuals also had neutralizing antibodies

Objectives

With limited data available from Central Africa, the aim of our study was to evaluate the anti-SARS-CoV-2 Ab prevalence in indigenous residents of Bomassa, a village located in the Sangha region in the Republic of Congo.

Methods

Plasma and oropharyngeal swab samples were collected from 304 healthy adult individuals, randomly recruited in May 2021 before vaccine introduction in the area. In addition, 82 plasma samples from the same area in 2019 were included as controls for the investigation of cross-reactivity against other coronaviruses. The SARS-CoV-2 virus was detected by qRT-PCR and sequenced using next-generation sequencing. ELISA was used for detecting IgG, IgM, and neutralizing Ab against SARS-CoV-2 antigens.

Results

Around 4.9% (15/304) of the participants were SARS-CoV-2 positive, with B.1.631 being the only variant identified. Of 109 individuals harboring anti-SARS-CoV-2 IgG and/or IgM Ab, 45.9% (50/109) had anti-SARS-CoV-2 neutralizing Ab. Of the control samples collected before the pandemic, 3.7% (3/82) were positive for IgG, but negative for neutralizing Ab.

Conclusions

Seroprevalence against SARS-CoV-2 occurred in 25% of the indigenous population sample, with almost 50% of these seropositive participants possessing neutralizing antibodies. These findings suggest that the spread of SARS-CoV-2 has been underestimated in the Republic of Congo.

Assessment of performance and implementation characteristics of rapid point of care SARS-CoV-2 antigen testing

Background: The COVID-19 pandemic has resulted in a need for rapid identification of infectious cases. Testing barriers have prohibited adequate screening for SARS-CoV-2, resulting in significant delays in commencement of treatment and outbreak control measures. This study aimed to generate evidence on the performance and implementation characteristics of the BD Veritor™ Plus System rapid antigen test as compared to reverse transcription polymerase chain reaction (RT-PCR) for diagnosis of SARS-CoV-2 in Kenya. Methods: This was a field test performance evaluation in adults undergoing testing for SARS-CoV-2. Recruited participants were classified as SARS-CoV-2-positive based on RT-PCR carried out on nasopharyngeal swabs. Antigen tests were performed with simultaneous RT-PCR on 272 participants, allowing estimation of sensitivity, specificity, positive and negative predictive values for the rapid antigen test. Implementation characteristics were assessed. Results: We enrolled 97 PCR negative symptomatic and 128 PCR negative asymptomatic, and 28 PCR positive symptomatic and 19 PCR positive asymptomatic participants. Compared to RT-PCR, the sensitivity of the rapid antigen test was 94% (95% confidence interval [CI] 86.6 to 100.0) while the specificity was 98% (95% CI 96 to 100). There was no association between sensitivity and symptom status, or between the cycle threshold value and sensitivity of the BD Veritor. The rapid test had a quick turnaround time, required minimal resources, and laboratory personnel conducting testing found it easier to use than RT-PCR. The relatively high sensitivity of BD Veritor may be partially attributed to shortages of RT-PCR testing materials, resulting in specimen analysis delays and potential degradation of viral genetic material. Therefore, in resource-constrained settings, rapid antigen tests may perform better than the reference RT-PCR, resulting in prompt institution of isolation and treatment measures.  Conclusion: The BD Veritor rapid antigen test’s high sensitivity should be interpreted with consideration to the challenges occasioned by RT-PCR testing in resource-constrained settings.

Performance of a rapid antigen test for SARS-CoV-2 in Kenya

Testing for SARS-CoV-2 in resource-poor settings remains a considerable challenge. Gold standard nucleic acid tests are expensive and depend on availability of expensive equipment and highly trained laboratory staff. More affordable and easier rapid antigen tests are an attractive alternative. This study assessed field performance of such a test in western Kenya. We conducted a prospective multi-facility field evaluation study of NowCheck COVID-19 Ag-RDT compared to gold standard PCR. Two pairs of oropharyngeal and nasopharyngeal swabs were collected for comparative analysis. With 997 enrolled participants the Ag-RDT had a sensitivity 71.5% (63.2-78.6) and specificity of 97.5% (96.2-98.5) at cycle threshold value <40. Highest sensitivity of 87.7% (77.2-94.5) was observed in samples with cycle threshold values ≤30. NowCheck COVID-19 Ag-RDT performed well at multiple healthcare facilities in an African field setting. Operational specificity and sensitivity were close to WHO-recommended thresholds.

Coronavirus Disease 2019 Diagnostics: Key to Africa's Recovery

With the coronavirus disease of 2019 (COVID-19) becoming a full-blown outbreak in Africa, coupled with many other challenges faced on the African continent, it is apparent that Africa continues to need diagnostics to enable case identification and recovery to this and future challenges. With the slow vaccination rates across the continent, reliable diagnostic tests will be in demand, likely for years to come. Thus, access to reliable diagnostic tools to detect the severe acute respiratory syndrome of the coronavirus-2 (SARS-CoV-2), the virus responsible for COVID-19, remain a critical pillar to monitor and contain new waves of COVID-19. Increasing the local capacity to manufacture and roll-out vaccines and decentralized COVID-19 testing are paramount for fighting the pandemic in Africa.

Possible Reasons Why Sub-Saharan Africa Experienced a Less Severe COVID-19 Pandemic in 2020

Both scientific authorities and governments of nations worldwide were found lacking in their COVID-19 response and management, resulting in significant distrust by the general public in 2020. Scientific and medical bodies often failed to give the right counsel on the appropriate course of action on COVID-19, because proven steps were not known, while many governments around the world took ineffective, late or inappropriate COVID-19 control and containment strategies. If the 2020 COVID-19 incidence rates are to be believed, much of sub-Saharan Africa had a lower disease prevalence than expected. We put forward six factors peculiar to much of sub-Saharan Africa that may have accounted for the pandemic landscape there in 2020. We also discuss why the situation has become more serious in 2021.

The COVID-19 pandemic and healthcare systems in Africa: a scoping review of preparedness, impact and response

BACKGROUND

The COVID-19 pandemic has overwhelmed health systems in both developed and developing nations alike. Africa has one of the weakest health systems globally, but there is limited evidence on how the region is prepared for, impacted by and responded to the pandemic.

METHODS

We conducted a scoping review of PubMed, Scopus, CINAHL to search peer-reviewed articles and Google, Google Scholar and preprint sites for grey literature. The scoping review captured studies on either preparedness or impacts or responses associated with COVID-19 or covering one or more of the three topics and guided by Arksey and O'Malley's methodological framework. The extracted information was documented following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension checklist for scoping reviews. Finally, the resulting data were thematically analysed.

RESULTS

Twenty-two eligible studies, of which 6 reported on health system preparedness, 19 described the impacts of COVID-19 on access to general and essential health services and 7 focused on responses taken by the healthcare systems were included. The main setbacks in health system preparation included lack of available health services needed for the pandemic, inadequate resources and equipment, and limited testing ability and surge capacity for COVID-19. Reduced flow of patients and missing scheduled appointments were among the most common impacts of the COVID-19 pandemic. Health system responses identified in this review included the availability of telephone consultations, re-purposing of available services and establishment of isolation centres, and provisions of COVID-19 guidelines in some settings.

CONCLUSIONS

The health systems in Africa were inadequately prepared for the pandemic, and its impact was substantial. Responses were slow and did not match the magnitude of the problem. Interventions that will improve and strengthen health system resilience and financing through local, national and global engagement should be prioritised.

Prevalence and characteristics of malaria among COVID-19 individuals: A systematic review, meta-analysis, and analysis of case reports

BACKGROUND

The world population is currently at a very high risk of Coronavirus disease-2019 (COVID-19), caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). People who live in malaria-endemic areas and get infected by SARS-CoV-2 may be at increased risk of severe COVID-19 or unfavorable disease outcomes if they ignore their malaria status. Therefore, the present study aimed to synthesize, qualitatively and quantitatively, information on the prevalence and characteristics of malaria infection among COVID-19-infected individuals. The findings will help us better understand this particular comorbidity during the COVID-19 pandemic.

METHODS

The systematic review protocol was registered at the International Prospective Register of Systematic Reviews (PROSPERO) with the identification number: CRD42021247521. We searched for studies reporting on the coinfection of COVID-19 and malaria in PubMed, Web of Science, and Scopus from inception to March 27, 2021 using Medical Subject Headings (MeSH) terms. The study's methodological quality in the search output was assessed using the Joanna Briggs Institute (JBI) Critical Appraisal Tools for cross-sectional study. The pooled prevalence of Plasmodium spp. infection among patients infected with COVID-19 was estimated using the random effect model and then graphically presented as forest plots. The heterogeneity among the included studies was assessed using Cochrane Q and I2 statistics. The characteristics of patients co-infected with COVID-19 and malaria were derived from case reports and series and were formally analyzed using simple statistics.

RESULTS

Twelve of 1,207 studies reporting the coinfection of COVID-19 and malaria were selected for further analysis. Results of quantitative synthesis show that the pooled prevalence of Plasmodium spp. infection (364 cases) among COVID-19 individuals (1,126 cases) is 11%, with a high degree of heterogeneity (95% CI: 4%-18%, I2: 97.07%, 5 studies). Most of the coinfections were reported in Nigeria (336 cases), India (27 cases), and the Democratic Republic of Congo (1 case). Results of qualitative synthesis indicate that patients with coinfection are typically symptomatic at presentation with mild or moderate parasitemia. An analysis of case reports and series indicates that co-infected individuals often display thrombocytopenia, lymphopenia, and elevated bilirubin levels. Among four patients (30%) who required treatment with intravenous artesunate, one experienced worsened clinical status after administering the drug. One serious outcome of coinfection involved a pregnant woman who experienced fetal abortion due to the initial misdiagnosis of malaria.

CONCLUSIONS

All individuals in malaria-endemic regions who are febrile or display symptoms of COVID-19 should be evaluated for malaria to avoid serious complications. Further prospective studies are required to investigate the burden and outcomes of COVID-19 in malaria-endemic regions. Prompt management is required to prevent serious outcomes in individuals co-infected with COVID-19 and malaria.

Correlating WHO COVID-19 interim guideline 2020.5 and testing capacity, accuracy, and logistical challenges in Africa

Coronavirus disease 2019 (COVID-19), a severe acute respiratory syndrome caused by SARS-CoV-2 was declared a global pandemic by the World Health Organization (WHO) in March 2020. As of 21^st April 2021, the disease had affected more than 143 million people with more than 3 million deaths worldwide. Urgent effective strategies are required to control the scourge of the pandemic. Rapid sample collection and effective testing of appropriate specimens from patients meeting the suspect case definition for COVID-19 is a priority for clinical management and outbreak control. The WHO recommends that suspected cases be screened for SARS-CoV-2 virus with nucleic acid amplification tests such as real-time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR). Other COVID-19 screening techniques such as serological and antigen tests have been developed and are currently being used for testing at ports of entry and for general surveillance of population exposure in some countries. However, there are limited testing options, equipment, and trained personnel in many African countries. Previously, positive patients have been screened more than twice to determine viral clearance prior to discharge after treatment. In a new policy directive, the WHO now recommends direct discharge after treatment of all positive cases without repeated testing. In this review, we discuss COVID-19 testing capacity, various diagnostic methods, test accuracy, as well as logistical challenges in Africa with respect to the WHO early discharge policy.

Modeling a deep transfer learning framework for the classification of COVID-19 radiology dataset

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Coronavirus-2 or SARS-CoV-2), which came into existence in 2019, is a viral pandemic that caused coronavirus disease 2019 (COVID-19) illnesses and death. Research showed that relentless efforts had been made to improve key performance indicators for detection, isolation, and early treatment. This paper used Deep Transfer Learning Model (DTL) for the classification of a real-life COVID-19 dataset of chest X-ray images in both binary (COVID-19 or Normal) and three-class (COVID-19, Viral-Pneumonia or Normal) classification scenarios. Four experiments were performed where fine-tuned VGG-16 and VGG-19 Convolutional Neural Networks (CNNs) with DTL were trained on both binary and three-class datasets that contain X-ray images. The system was trained with an X-ray image dataset for the detection of COVID-19. The fine-tuned VGG-16 and VGG-19 DTL were modelled by employing a batch size of 10 in 40 epochs, Adam optimizer for weight updates, and categorical cross-entropy loss function. The results showed that the fine-tuned VGG-16 and VGG-19 models produced an accuracy of 99.23% and 98.00%, respectively, in the binary task. In contrast, in the multiclass (three-class) task, the fine-tuned VGG-16 and VGG-19 DTL models produced an accuracy of 93.85% and 92.92%, respectively. Moreover, the fine-tuned VGG-16 and VGG-19 models have MCC of 0.98 and 0.96 respectively in the binary classification, and 0.91 and 0.89 for multiclass classification. These results showed strong positive correlations between the models' predictions and the true labels. In the two classification tasks (binary and three-class), it was observed that the fine-tuned VGG-16 DTL model had stronger positive correlations in the MCC metric than the fine-tuned VGG-19 DTL model. The VGG-16 DTL model has a Kappa value of 0.98 as against 0.96 for the VGG-19 DTL model in the binary classification task, while in the three-class classification problem, the VGG-16 DTL model has a Kappa value of 0.91 as against 0.89 for the VGG-19 DTL model. This result is in agreement with the trend observed in the MCC metric. Hence, it was discovered that the VGG-16 based DTL model classified COVID-19 better than the VGG-19 based DTL model. Using the best performing fine-tuned VGG-16 DTL model, tests were carried out on 470 unlabeled image dataset, which was not used in the model training and validation processes. The test accuracy obtained for the model was 98%. The proposed models provided accurate diagnostics for both the binary and multiclass classifications, outperforming other existing models in the literature in terms of accuracy, as shown in this work.

The toll of COVID-19 on African children: A descriptive analysis on COVID-19-related morbidity and mortality among the pediatric population in Sub-Saharan Africa

Introduction

Few data on the COVID-19 epidemiological characteristics among the pediatric population in Africa exists. This paper examines the age and sex distribution of the morbidity and mortality rate in children with COVID-19 and compares it to the adult population in 15 Sub-Saharan African countries.

Methods

A merge line listing dataset shared by countries within the Regional Office for Africa was analyzed. Patients diagnosed within 1 March and 1 September 2020 with a confirmed positive RT-PCR test for SARS-CoV-2 were analyzed. Children's data were stratified into three age groups: 0-4 years, 5-11 years, and 12-17 years, while adults were combined. The cumulative incidence of cases, its medians, and 95% confidence intervals were calculated.

Results

9% of the total confirmed cases and 2.4% of the reported deaths were pediatric cases. The 12-17 age group in all 15 countries showed the highest cumulative incidence proportion in children. Adults had a higher case incidence per 100,000 people than children.

Conclusion

The cases and deaths within the children's population were smaller than the adult population. These differences may reflect biases in COVID-19 testing protocols and reporting implemented by countries, highlighting the need for more extensive investigation and focus on the effects of COVID-19 in children.

Prediction of individual COVID-19 diagnosis using baseline demographics and lab data

The global surge in COVID-19 cases underscores the need for fast, scalable, and reliable testing. Current COVID-19 diagnostic tests are limited by turnaround time, limited availability, or occasional false findings. Here, we developed a machine learning-based framework for predicting individual COVID-19 positive diagnosis relying only on readily-available baseline data, including patient demographics, comorbidities, and common lab values. Leveraging a cohort of 31,739 adults within an academic health system, we trained and tested multiple types of machine learning models, achieving an area under the curve of 0.75. Feature importance analyses highlighted serum calcium levels, temperature, age, lymphocyte count, smoking, hemoglobin levels, aspartate aminotransferase levels, and oxygen saturation as key predictors. Additionally, we developed a single decision tree model that provided an operable method for stratifying sub-populations. Overall, this study provides a proof-of-concept that COVID-19 diagnosis prediction models can be developed using only baseline data. The resulting prediction can complement existing tests to enhance screening and pandemic containment workflows.

Impacts of COVID-19 Pandemic on Psychological Well-Being of Older Chronic Kidney Disease Patients

COVID-19 pandemic has been a major global issue, its eventual influences on the population welfare, global markets, public security, and everyday activities remain uncertain. Indeed, the pandemic has arisen a significant global threat. Its psychological impact is predicted to be severe and enduring, but the absolute magnitude is still largely unclear. Chronic kidney disease (CKD) is a complication markedly contributes to the mortality of COVID-19 cases, meanwhile several studies have demonstrated the high frequency and seriousness of the COVID-19 in CKD patients receiving dialysis. Importantly, the influence of COVID-19 among CKD patients without dialysis is still largely unexplored. Thus, we systemically summarized how mental health affects the spreading of COVID-19 to virtually worldwide, covering perspectives from several countries across a wide range of fields and clinical contexts. This review aims to provide the latest details and reveal potential concerns on the public health including psychological well-being of the older patients with CKD.

Transmission of SARS-CoV-2 in northern Ghana: insights from whole-genome sequencing

Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.

Health, Psychosocial, and Social Issues Emanating From the COVID-19 Pandemic Based on Social Media Comments: Text Mining and Thematic Analysis Approach

Background

The COVID-19 pandemic has caused a global health crisis that affects many aspects of human lives. In the absence of vaccines and antivirals, several behavioral change and policy initiatives such as physical distancing have been implemented to control the spread of COVID-19. Social media data can reveal public perceptions toward how governments and health agencies worldwide are handling the pandemic, and the impact of the disease on people regardless of their geographic locations in line with various factors that hinder or facilitate the efforts to control the spread of the pandemic globally.

Objective

This paper aims to investigate the impact of the COVID-19 pandemic on people worldwide using social media data.

Methods

We applied natural language processing (NLP) and thematic analysis to understand public opinions, experiences, and issues with respect to the COVID-19 pandemic using social media data. First, we collected over 47 million COVID-19–related comments from Twitter, Facebook, YouTube, and three online discussion forums. Second, we performed data preprocessing, which involved applying NLP techniques to clean and prepare the data for automated key phrase extraction. Third, we applied the NLP approach to extract meaningful key phrases from over 1 million randomly selected comments and computed sentiment score for each key phrase and assigned sentiment polarity (ie, positive, negative, or neutral) based on the score using a lexicon-based technique. Fourth, we grouped related negative and positive key phrases into categories or broad themes.

Results

A total of 34 negative themes emerged, out of which 15 were health-related issues, psychosocial issues, and social issues related to the COVID-19 pandemic from the public perspective. Some of the health-related issues were increased mortality, health concerns, struggling health systems, and fitness issues; while some of the psychosocial issues were frustrations due to life disruptions, panic shopping, and expression of fear. Social issues were harassment, domestic violence, and wrong societal attitude. In addition, 20 positive themes emerged from our results. Some of the positive themes were public awareness, encouragement, gratitude, cleaner environment, online learning, charity, spiritual support, and innovative research.

Conclusions

We uncovered various negative and positive themes representing public perceptions toward the COVID-19 pandemic and recommended interventions that can help address the health, psychosocial, and social issues based on the positive themes and other research evidence. These interventions will help governments, health professionals and agencies, institutions, and individuals in their efforts to curb the spread of COVID-19 and minimize its impact, and in reacting to any future pandemics.

The first and second waves of the COVID-19 pandemic in Africa: a cross-sectional study

BACKGROUND

Although the first wave of the COVID-19 pandemic progressed more slowly in Africa than the rest of the world, by December, 2020, the second wave appeared to be much more aggressive with many more cases. To date, the pandemic situation in all 55 African Union (AU) Member States has not been comprehensively reviewed. We aimed to evaluate reported COVID-19 epidemiology data to better understand the pandemic's progression in Africa.

METHODS

We did a cross-sectional analysis between Feb 14 and Dec 31, 2020, using COVID-19 epidemiological, testing, and mitigation strategy data reported by AU Member States to assess trends and identify the response and mitigation efforts at the country, regional, and continent levels. We did descriptive analyses on the variables of interest including cumulative and weekly incidence rates, case fatality ratios (CFRs), tests per case ratios, growth rates, and public health and social measures in place.

FINDINGS

As of Dec 31, 2020, African countries had reported 2 763 421 COVID-19 cases and 65 602 deaths, accounting for 3·4% of the 82 312 150 cases and 3·6% of the 1 798 994 deaths reported globally. Nine of the 55 countries accounted for more than 82·6% (2 283 613) of reported cases. 18 countries reported CFRs greater than the global CFR (2·2%). 17 countries reported test per case ratios less than the recommended ten to 30 tests per case ratio range. At the peak of the first wave in Africa in July, 2020, the mean daily number of new cases was 18 273. As of Dec 31, 2020, 40 (73%) countries had experienced or were experiencing their second wave of cases with the continent reporting a mean of 23 790 daily new cases for epidemiological week 53. 48 (96%) of 50 Member States had five or more stringent public health and social measures in place by April 15, 2020, but this number had decreased to 36 (72%) as of Dec 31, 2020, despite an increase in cases in the preceding month.

INTERPRETATION

Our analysis showed that the African continent had a more severe second wave of the COVID-19 pandemic than the first, and highlights the importance of examining multiple epidemiological variables down to the regional and country levels over time. These country-specific and regional results informed the implementation of continent-wide initiatives and supported equitable distribution of supplies and technical assistance. Monitoring and analysis of these data over time are essential for continued situational awareness, especially as Member States attempt to balance controlling COVID-19 transmission with ensuring stable economies and livelihoods.

FUNDING

None.

Setting up a molecular diagnostic laboratory for SARS-CoV-2 testing: Experience of a single centre in a resource-constrained setting

Background

Molecular detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is at the forefront of the global response to the coronavirus disease 2019 (COVID-19) pandemic. However, molecular diagnostic capabilities are poorly developed in many African countries. Efforts by the Nigeria Centre for Disease Control and other public health agencies to scale up facilities for molecular testing across the continent are well documented, but there are few accounts from the laboratories at the frontline.

Intervention

As part of an institutional response to the COVID-19 pandemic, the University of Benin Teaching Hospital, Benin City, Nigeria, signed a memorandum of understanding with a World Bank-supported institution to obtain a non-proprietary testing platform, renovated an existing molecular virology laboratory and validated the test process to make SARS-CoV-2 testing readily available for decision-making by frontline health workers. These efforts resulted in the University of Benin Teaching Hospital’s inclusion in the Nigeria Centre for Disease Control COVID-19 molecular laboratory network. The laboratory achieved a turnover of 12 123 tests within 7 months of operation. Challenges faced and dealt with include incompatible equipment, limited skilled manpower, unstable (unreliable) electric power supply, disrupted procurement and supply chain, and significant overhead costs.

Lessons learnt

Molecular diagnostic capability is essential in laboratory preparedness for pandemic response and can be achieved by establishing collaborative networks in low-resource settings.

Recommendations

Molecular diagnostic capabilities attained during the COVID-19 pandemic should be maintained by governmental support of the local biotechnology sector, collaboration with partners and stakeholders and the expansion of diagnostics to include other diseases of public health importance.

Quantifying the potential value of antigen-detection rapid diagnostic tests for COVID-19: a modelling analysis

BACKGROUND

Testing plays a critical role in treatment and prevention responses to the COVID-19 pandemic. Compared to nucleic acid tests (NATs), antigen-detection rapid diagnostic tests (Ag-RDTs) can be more accessible, but typically have lower sensitivity and specificity. By quantifying these trade-offs, we aimed to inform decisions about when an Ag-RDT would offer greater public health value than reliance on NAT.

METHODS

Following an expert consultation, we selected two use cases for analysis: rapid identification of people with COVID-19 amongst patients admitted with respiratory symptoms in a 'hospital' setting and early identification and isolation of people with mildly symptomatic COVID-19 in a 'community' setting. Using decision analysis, we evaluated the health system cost and health impact (deaths averted and infectious days isolated) of an Ag-RDT-led strategy, compared to a strategy based on NAT and clinical judgement. We adopted a broad range of values for 'contextual' parameters relevant to a range of settings, including the availability of NAT and the performance of clinical judgement. We performed a multivariate sensitivity analysis to all of these parameters.

RESULTS

In a hospital setting, an Ag-RDT-led strategy would avert more deaths than a NAT-based strategy, and at lower cost per death averted, when the sensitivity of clinical judgement is less than 90%, and when NAT results are available in time to inform clinical decision-making for less than 85% of patients. The use of an Ag-RDT is robustly supported in community settings, where it would avert more transmission at lower cost than relying on NAT alone, under a wide range of assumptions.

CONCLUSIONS

Despite their imperfect sensitivity and specificity, Ag-RDTs have the potential to be simultaneously more impactful, and have a lower cost per death and infectious person-days averted, than current approaches to COVID-19 diagnostic testing.

Lyrics and artistic improvisations in health promotion for the COVID-19 pandemic control in East Africa

News about the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan City, Hubei Province, China in December 2019 diffused gradually to East Africa through mainstream media and social media. The general public construed the pandemic threat as being 'far away' and associated it with foreign practices and behaviours. Social media discourse was initially replete with indifference about the perceived risk. Conflicting views about the possibility of the pandemic spreading to Africa and the complexity of explaining its causes delayed the desired understanding of the reality of the global public health concern. The popular public response to the COVID-19 control discourse is therefore characterised by ambivalence about embracing the pandemic control protocols. Drawing on content and discourse analysis of musical and poetic compositions on COVID-19 by artists in East Africa and shared among WhatsApp users in Kenya, this article describes local perspectives on COVID-19 risk and their health promotion implications. It explores local construction of the meaning of the COVID-19 pandemic and its consequences for effective health promotion. The article considers the spontaneous musical and poetic performances by experienced and amateur artists as local attempts to enhance compliance with the global COVID-19 control protocols and popular participation in local health promotion. The basic premise is that artists' creation and sharing of digital COVID-19 lyrics denote their attempt to go beyond the medical logic of health promotion by including broad aspects of a cultural logic of care. This approach would establish an integrated and sustainable health promotion framework to prevent the spread of COVID-19 and its impact on local societal wellbeing.