Rapid, Cheap, and Effective COVID-19 Diagnostics for Africa

Comparative evaluation of RT-PCR and antigen-based rapid diagnostic tests (Ag-RDTs) for SARS-CoV-2 detection: performance, variant specificity, and clinical implications

The COVID-19 pandemic has highlighted the critical need for accurate and efficient diagnostic tools for detecting severe acute respiratory coronavirus 2 (SARS-CoV-2) infections. This study presents a comparison of two diagnostic tests: RT-PCR and antigen detection rapid diagnostic tests (Ag-RDTs). This study focused on their performance, variant specificity, and their clinical implications. A simultaneous testing of 268 samples was carried out for SARS-CoV-2 using RT-PCR and Ag-RDTs [flourescence immunoassay (FIA) and lateral flow immunoassay (LFIA)]. Viral load was quantified, and variant identification was performed using a PCR-based assay. The prevalence was found to be 30.2% using reverse transcription PCR (RT-PCR), 26.5% using FIA, and 25% using LFIA. When comparing the FIA and LFIA, the overall diagnostic performance was found to be 80.25% vs 76.54%, 96.79% vs 97.33%, 91.55% vs 90.51%, and 91.88% vs 92.56% for sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), respectively. Both Ag-RDTs showed a strong agreement with RT-PCR (κ = 0.78-0.80). The overall accuracies of the FIA and LFIA were 92.41% and 92.13%, respectively. The FIA showed higher sensitivity (73.68%) and PPV (92.08%) than the LFIA (65.79% and 90.56%, respectively) in asymptomatic patients. At low Ct values (<25), both Ag-RDTs had 100% sensitivity, but the sensitivity reduced to 31.82% for FIA and 27.27% for LFIA at Ct values > 30. The diagnostic sensitivity of FIA compared to LFIA for detecting the Alpha variant was 78.85% vs. 69.23% and 72.22% vs. 83.33% for the Delta variant. Both Ag-RDTs had 100% sensitivity for detecting Omicron. Both Ag-RDTs performed well in patients with high viral loads and Omicron variant infections compared to those infected with Alpha and Delta variants. This study confirms the comparable performance of RT-PCR and Ag-RDTs, specifically FIA and LFIA, for SARS-CoV-2 detection. The FIA showed higher sensitivity and PPV in asymptomatic cases, while both Ag-RDTs exhibited strong agreement with RT-PCR results. Notably, Ag-RDTs, particularly FIA, proved effective in detecting the Omicron variant and cases with high viral loads, highlighting their potential clinical utility in managing the COVID-19 pandemic.IMPORTANCEThis study is of utmost importance in providing effective responses to manage the COVID-19 pandemic. It rigorously compares the diagnostic accuracy, variant specificity, and practical considerations of reverse transcription PCR (RT-PCR) and antigen detection rapid diagnostic tests (Ag-RDTs) for severe acute respiratory coronavirus 2 (SARS-CoV-2), answering critical questions. The results of this study will help healthcare professionals choose the appropriate testing methods, allocate resources effectively, and enhance public health strategies. Given the evolution of the virus, understanding the performance of these diagnostic tools is crucial to adapting to emerging variants. Additionally, the study provides insights into logistical challenges and accessibility issues, which will contribute to refining testing workflows, particularly in resource-limited settings. Ultimately, the study's impact extends to global healthcare, providing valuable information for policymakers, clinicians, and public health officials as they work together for mitigating the impact of the pandemic.

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.

Advances in nanobiosensors during the COVID-19 pandemic and future perspectives for the post-COVID era

The unprecedented threat of the highly contagious virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes exponentially increased infections of coronavirus disease 2019 (COVID-19), highlights the weak spots of the current diagnostic toolbox. In the midst of catastrophe, nanobiosensors offer a new opportunity as an alternative tool to fill a gap among molecular tests, rapid antigen tests, and serological tests. Nanobiosensors surpass the potential of antigen tests because of their enhanced sensitivity, thus enabling us to see antigens as stable and easy-to-access targets. During the first three years of the COVID-19 pandemic, a substantial number of studies have reported nanobiosensors for the detection of SARS-CoV-2 antigens. The number of articles on nanobiosensors and SARS-CoV-2 exceeds the amount of nanobiosensor research on detecting previous infectious diseases, from influenza to SARS-CoV and MERS-CoV. This unprecedented publishing pace also implies the significance of SARS-CoV-2 and the present pandemic. In this review, 158 studies reporting nanobiosensors for detecting SARS-CoV-2 antigens are collected to discuss the current challenges of nanobiosensors using the criteria of point-of-care (POC) diagnostics along with COVID-specific issues. These advances and lessons during the pandemic pave the way for preparing for the post-COVID era and potential upcoming infectious diseases.

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.

Development of an optimized RT-LAMP test for the detection of SARS-CoV-2

SARS-COV-2 is the causative agent of an acute respiratory syndrome called Coronavirus disease 2019 (COVID-19) with a varying mortality rate from 2019 to 2022. There are several measures for control and prevention of Covid-19 including using mask, vaccine injections, as well as screening the potential cases. We aimed to design and develop a molecular method (RT-LAMP) for detecting coronavirus in biological samples that is cheaper, faster and easier than conventional molecular methods. In this study, various reaction components were explored to make the optimal combination of an RT-LAMP master mix composition. The results revealed the ability of this RT-LAMP test in specifically identifying 100 copies of mixture of N and E genes in just 30-45 min. This study demonstrated the reliable performance of the RT-LAMP method for the detection of SARS-COV-2 in biological samples. Given the significant advantages of this method compared to the gold standard qRT-PCR, it can be employed as a promising tool for the diagnosis of coronavirus as well as other pathogenic viruses.

Diagnostic performance of standardized typical CT findings for COVID-19: a systematic review and meta-analysis

OBJECTIVE

To meta-analyze diagnostic performance measures of standardized typical CT findings for COVID-19 and examine these measures by region and national income.

METHODS

MEDLINE and Embase were searched from January 2020 to April 2022 for diagnostic studies using the Radiological Society of North America (RSNA) classification or the COVID-19 Reporting and Data System (CO-RADS) for COVID-19. Patient and study characteristics were extracted. We pooled the diagnostic performance of typical CT findings in the RSNA and CO-RADS systems and interobserver agreement. Meta-regression was performed to examine the effect of potential explanatory factors on the diagnostic performance of the typical CT findings.

RESULTS

We included 42 diagnostic performance studies with 6777 PCR-positive and 9955 PCR-negative patients from 18 developing and 24 developed countries covering the Americas, Europe, Asia, and Africa. The pooled sensitivity was 70% (95% confidence interval [CI]: 65%, 74%; I² = 92%), and the pooled specificity was 90% (95% CI 86%, 93%; I² = 94%) for the typical CT findings of COVID-19. The sensitivity and specificity of the typical CT findings did not differ significantly by national income and the region of the study (p > 0.1, respectively). The pooled interobserver agreement from 19 studies was 0.72 (95% CI 0.63, 0.81; I² = 99%) for the typical CT findings and 0.67 (95% CI 0.61, 0.74; I² = 99%) for the overall CT classifications.

CONCLUSION

The standardized typical CT findings for COVID-19 provided moderate sensitivity and high specificity globally, regardless of region and national income, and were highly reproducible between radiologists.

CRITICAL RELEVANCE STATEMENT

Standardized typical CT findings for COVID-19 provided a reproducible high diagnostic accuracy globally.

KEY POINTS

Standardized typical CT findings for COVID-19 provide high sensitivity and specificity. Typical CT findings show high diagnosability regardless of region or income. The interobserver agreement for typical findings of COVID-19 is substantial.

Implementing SARS-CoV-2 antigen testing scale-up in Rwanda: retrospective analysis of national programme data and qualitative findings

OBJECTIVES

Reverse transcriptase PCR is the most sensitive test for SARS-CoV-2 diagnosis. However, the scale-up of these tests in low-income and middle-income countries (LMICs) has been limited due to infrastructure and cost. Antigen rapid diagnostic tests are an alternative option for diagnosing active infection that may allow for faster, easier, less expensive and more widespread testing. We compared the implementation of antigen and PCR testing programmes in Rwanda.

DESIGN

We retrospectively reviewed routinely collected PCR and antigen testing data for all reported tests conducted nationally. We administered semiquantitative surveys to healthcare workers (HCWs) involved in COVID-19 testing and care and clients receiving antigen testing.

SETTING

Rwanda, November 2020-July 2021.

PARTICIPANTS

National SARS-CoV-2 testing data; 49 HCWs involved in COVID-19 testing and care; 145 clients receiving antigen testing.

INTERVENTIONS

None (retrospective analysis of programme data).

PRIMARY AND SECONDARY OUTCOME MEASURES

Test volumes, turnaround times, feasibility and acceptability of antigen testing.

RESULTS

Data from 906 204 antigen tests and 445 235 PCR tests were included. Antigen testing increased test availability and case identification compared with PCR and had a median results return time of 0 days (IQR: 0-0). In contrast, PCR testing time ranged from 1 to 18 days depending on the sample collection site/district. Both HCWs and clients indicated that antigen testing was feasible and acceptable. Some HCWs identified stockouts and limited healthcare staff as challenges.

CONCLUSIONS

Antigen testing facilitated rapid expansion and decentralisation of SARS-CoV-2 testing across lower tier facilities in Rwanda, contributed to increased case identification, reduced test processing times, and was determined to be feasible and acceptable to clients and providers. Antigen testing will be an essential component of SARS-CoV-2 test and treat programmes in LMICs.

The COVID-19 wave was already here: High seroprevalence of SARS-CoV-2 antibodies among staff and students in a Cameroon University

Background

Seroprevalence studies, to estimate the proportion of people that has been infected by SARS-CoV-2 are importance in African countries, where incidence is among the lowest in the world.

Objective

This study aimed at evaluating the exposure to SARS-CoV-2 within a university setting of Cameroon.

Methods

A cross-sectional study performed in December 2020 - December 2021, among students and staffs of the Evangelical University of Cameroon. COVID-19 antigen rapid detection test (RDT) was performed using Standard Q Biosensor, and one year after SARS-CoV-2 antibody-test was performed within the same population using RDT and chemiluminescence immunoassay (CLIA).

Results

106 participants were enrolled (80% students), female sex was the most represented. Positivity to SARS-CoV-2 was 0.0% based on antigen RDTs. The seroprevalence of SARSCoV- 2 antibodies was estimated at 73.6% (95% CI. 64.5-81.0) for IgG and 1.9% (95% CI. 0.2-6.8) for IgM/IgG with RDTs, and 91.9% (95% CI. 84.7-96.4) for anti-nucleocapsid with CLIA. 95.3% (101) reported having developed at least one of the known COVID-19 symptoms (cough and headache being the most common). 90.3% (28) of people who experienced at least one of these symptoms developed IgG antibodies. 40.6% (43) of participants took natural herbs, whereas 55.7% (59) took conventional drugs. The most used herb was Zingiber officinale, while the most used drugs were antibiotics.

Conclusion

In this Cameroonian University community, SARS-CoV-2 seroprevalence is high, with a greater detection using advanced serological assays. This indicates a wide viral exposure, and the need to adequate control measures especially for those experiencing any related COVID-19 symptoms.

Dupilumab therapy in Atopic Dermatitis is safe during COVID-19 infection era: A systematic review and meta-analysis of 1611 patients

The aim of this meta‐analysis is to evaluate the safety of dupilumab use in the management of atopic dermatitis (AD) during the current pandemic regarding the risk and the hazards of COVID‐19 infection. Seven databases (Google Scholar, Web of Science, Scopus, Virtual Health Library, PubMed, System for Information on Gray Literature in Europe, and The New York Academy of Medicine) were searched for eligible studies from inception until November 24, 2021. The quality of evidence was rated using the National Institute of Health and the Joanna Briggs Institute Critical Appraisal tool. Meta‐analysis was performed when the outcome is presented ≥2 studies. A total of 12 papers including 1611 AD patients were included in the study. The prevalence of COVID‐19 in AD treated with dupilumab was 3.2% (95% confidence interval [CI]: 1.7–5.8). COVID‐19 symptoms were reported by five patients who were presented with one or more of the following symptoms (fatigue, loss of taste and smell, runny nose, conjunctivitis, gastrointestinal symptoms, fever, cough, and dyspnea). Only three cases of COVID‐19 were hospitalized with a prevalence of 4.5%, while no patients with COVID‐19 died. Dupilumab is safe regarding the risk and the hazards of COVID‐19 in AD patients. Thus, based on these results continuation of dupilumab in AD patients is recommended, since dupilumab seems to be safe and crucial for a better disease outcome.