scholarly journals Pooling of Samples for SARS-CoV-2 Detection Using a Rapid Antigen Test

2021 ◽  
Vol 2 ◽  
Author(s):  
Nol Salcedo ◽  
Alexander Harmon ◽  
Bobby Brooke Herrera
Keyword(s):  
Positive Sample ◽  
Diagnostic Efficiency ◽  
Rt Pcr ◽  
Middle Income ◽  
Pooled Testing ◽  
Middle Income Countries ◽  
Pooling Strategy ◽  
Polymerase Chain ◽  
Antigen Tests ◽  
Antigen Testing

While molecular assays, such as reverse-transcription polymerase chain reaction (RT-PCR), have been widely used throughout the coronavirus disease 2019 (COVID-19) pandemic, the technique is costly and resource intensive. As a means to reduce costs and increase diagnostic efficiency, pooled testing using RT-PCR has been implemented. However, pooling samples for antigen testing has not been evaluated. Here, we propose a proof-of-concept pooling strategy for antigen testing that would significantly expand SARS-CoV-2 surveillance, especially for low-to-middle income countries, schools, and workplaces. Our laboratory-based testing demonstrates that combining of up to 20 nasal swab specimens per pool can expand surveillance with antigen tests, even if a pool contains only one positive sample.

scholarly journals Pooling of samples for SARS-CoV-2 detection using rapid antigen tests

2021 ◽  
Author(s):  
Nol Salcedo ◽  
Alexander Harmon ◽  
Bobby Brooke Herrera
Keyword(s):  
Positive Sample ◽  
Diagnostic Efficiency ◽  
Rt Pcr ◽  
Middle Income ◽  
Pooled Testing ◽  
Middle Income Countries ◽  
Pooling Strategy ◽  
Polymerase Chain ◽  
Antigen Tests ◽  
Antigen Testing

AbstractWhile molecular assays, such as reverse-transcription polymerase chain reaction (RT- PCR), have been widely used throughout the coronavirus disease 2019 (COVID-19) pandemic, the technique is resource intensive and costly. As a means to reduce costs and expand diagnostic efficiency, pooled testing using RT-PCR has been implemented. However, pooled testing using rapid antigen tests has not been evaluated. Here, we propose a pooling strategy for rapid antigen testing that would significantly expand COVID-19 surveillance, especially for low-to-middle income countries, and schools and workplaces. Our data demonstrate that combining of up to 20 samples per pool can expand surveillance with rapid antigen tests, even if a pool contains only one positive sample.

scholarly journals Combining Rapid Antigen Testing and Syndromic Surveillance Improves Community-Based COVID-19 Detection in Low-to-Middle-Income Countries

2022 ◽  
Author(s):  
Fergus Chadwick ◽  
Jessica Clark ◽  
Shayan Chowdhury ◽  
Tasnuva Chowdhury ◽  
David Pascall ◽  
...  
Keyword(s):  
Low Income ◽  
Syndromic Surveillance ◽  
Classification Performance ◽  
Test Results ◽  
Rapid Diagnostics ◽  
Antigen Test ◽  
Middle Income ◽  
Middle Income Countries ◽  
Antigen Tests ◽  
Antigen Testing

Abstract Diagnostics for COVID-19 detection are limited in many settings. Syndromic surveillance is often the only means to identify cases, but lacks specificity. Rapid antigen testing is inexpensive and easy-to-deploy but concerns remain about sensitivity. We examine how combining these approaches can improve surveillance for guiding interventions in low-income communities in Dhaka, Bangladesh. Rapid-antigen-tests and PCR validation was performed on 1172 symptomatically-identified individuals at home. Statistical models were fit to predict PCR status using rapid-antigen-test results, syndromic data, and their combination. Model predictive and classification performance was examined under contrasting epidemiological scenarios to evaluate their potential for improving diagnoses. Models combining rapid-antigen-test and syndromic data yielded equal-to-better performance to rapid-antigen-test-only models across all scenarios. These results show that drawing on complementary strengths across two rapid diagnostics, improves COVID-19 detection, and reduces false-positive and -negative diagnoses to match local requirements; improvements achievable without additional expense, or changes for patients or practitioners.

scholarly journals Screening, Diagnostic and Prognostic Tests for COVID-19: A Comprehensive Review

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 561
Author(s):  
Mariana Ulinici ◽  
Serghei Covantev ◽  
James Wingfield-Digby ◽  
Apostolos Beloukas ◽  
Alexander G. Mathioudakis ◽  
...  
Keyword(s):  
Point Of Care ◽  
Standard Test ◽  
Current Evidence ◽  
Molecular Testing ◽  
Rt Pcr ◽  
Diagnostic Screening ◽  
Comprehensive Review ◽  
Prognostic Tests ◽  
Polymerase Chain ◽  
Antigen Testing

While molecular testing with real-time polymerase chain reaction (RT-PCR) remains the gold-standard test for COVID-19 diagnosis and screening, more rapid or affordable molecular and antigen testing options have been developed. More affordable, point-of-care antigen testing, despite being less sensitive compared to molecular assays, might be preferable for wider screening initiatives. Simple laboratory, imaging and clinical parameters could facilitate prognostication and triage. This comprehensive review summarises current evidence on the diagnostic, screening and prognostic tests for COVID-19.

scholarly journals Pooled Testing for Expanding COVID-19 Mass Surveillance

2020 ◽  
Vol 14 (3) ◽  
pp. e42-e43 ◽  
Author(s):  
Angela Felicia Sunjaya ◽  
Anthony Paulo Sunjaya
Keyword(s):  
Diagnostic Testing ◽  
Pcr Amplification ◽  
The United States ◽  
Positive Sample ◽  
Pooled Testing ◽  
Blood Banks ◽  
Massive Scale ◽  
Polymerase Chain ◽  
Pool Test ◽  
Mass Surveillance

ABSTRACTDiagnostic testing to identify patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role to control the coronavirus disease (COVID-19) pandemic. While several countries have implemented the use of diagnostic testing in a massive scale as a cornerstone for infection control and surveillance, other countries affected by the pandemic are hampered by its limited testing capacity. Pooled testing was first introduced in the 1940s and is now used for screening in blood banks. Testing is done by pooling multiple individual samples together. Only in the case of a positive pool test would individual samples of the pool be tested, thus substantially reducing the number of tests needed. Several studies regarding their use for SARS CoV-2 have been done in the United States, Israel, and Germany. Studies have shown that an individual positive sample can still be detected in pools of up to 32 samples, and possibly even 64 samples, provided that additional polymerase chain reaction (PCR) amplification cycles are conducted with a sensitivity of 96%. Simulation studies to determine optimal pool size and pooling techniques have also been conducted. Based on these studies, pooled testing is shown to be able to detect positive samples with sufficient accuracy and can easily be used with existing equipment and personnel for population-wide screening.

scholarly journals Sensitivity of rapid antigen testing and RT-PCR performed on nasopharyngeal swabs versus saliva samples in COVID-19 hospitalized patients: results of a prospective comparative trial (RESTART)

2021 ◽  
Author(s):  
Antonios Kritikos ◽  
Giorgia Caruana ◽  
René Brouillet ◽  
John-Paul Miroz ◽  
Abed-Maillard Samia ◽  
...  
Keyword(s):  
Comparative Trial ◽  
Hospitalized Patients ◽  
Rt Pcr ◽  
Duration Of Symptoms ◽  
Non Invasive ◽  
Viral Transport Medium ◽  
One Step ◽  
Antigen Tests ◽  
Low Sensitivity ◽  
Antigen Testing

AbstractObjectivesSaliva sampling could serve as an alternative non-invasive sample for SARS-CoV-2 diagnosis while rapid antigen testing (RAT) might help to mitigate the shortage of reagents sporadically encountered with RT-PCR. Thus, in the RESTART study we compared antigen and RT-PCR testing methods on nasopharyngeal (NP) swabs and salivary samples.MethodsWe conducted a prospective observational study among COVID-19 hospitalized patients between 10th December 2020 and 1st February 2021. Paired saliva and NP samples were investigated by RT-PCR (Cobas 6800, Roche-Switzerland) and by two rapid antigen tests: One Step Immunoassay Exdia® COVID-19 Ag (Precision Biosensor, Korea) and Standard Q® COVID-19 Rapid Antigen Test (Roche-Switzerland).ResultsA total of 58 paired NP-saliva specimens were collected. Thirty-two of 58 (55%) patients were hospitalized in the intensive care unit and the median duration of symptoms was 11 days (IQR 5-19). NP and salivary RT-PCR exhibited sensitivity of 98% and 69% respectively whereas the specificity of these RT-PCRs assays were of 100%. NP RAT exhibited much lower diagnostic performances with sensitivities of 35% and 41% for the Standard Q® and Exdia® assays respectively, when a wet-swab approach was used (i.e. when the swab was diluted in the viral transport medium (VTM) before testing). The sensitivity of the dry-swab approach was slightly better (47%). These antigen tests exhibited very low sensitivity (4 and 8%) when applied to salivary swabs.ConclusionsNasopharyngeal RT-PCR is the most accurate test for COVID-19 diagnosis in hospitalized patients. RT-PCR on salivary samples may be used when nasopharyngeal swabs are contraindicated. RAT are not appropriate for hospitalized patients.

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

Diagnostics ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2105
Author(s):  
Lukman Yusuf ◽  
Mark Appeaning ◽  
Taiwo Gboluwaga Amole ◽  
Baba Maiyaki Musa ◽  
Hadiza Shehu Galadanci ◽  
...  
Keyword(s):  
Low Income ◽  
Nucleic Acid Amplification ◽  
High Rate ◽  
Low Income Countries ◽  
Rt Pcr ◽  
Antibody Testing ◽  
Middle Income ◽  
Diagnostic Assays ◽  
Middle Income Countries ◽  
To Come

Background: Although comprehensive public health measures such as mass quarantine have been taken internationally, this has generally been ineffective, leading to a high infection and mortality rate. Despite the fact that the COVID-19 pandemic has been downgraded to epidemic status in many countries, the real number of infections is unknown, particularly in low-income countries. However, precision shielding is used in COVID-19 management, and requires estimates of mass infection in key groups. As a result, rapid tests for the virus could be a useful screening tool for asymptomatic virus shedders who are about to come into contact with sensitive groups. In Africa and other low- and middle-income countries there is high rate of COVID-19 under-diagnosis, due to the high cost of molecular assays. Exploring alternate assays to the reverse transcriptase polymerase chain reaction (RT-PCR) for COVID-19 diagnosis is highly warranted. Aim: This review explored the feasibility of using alternate molecular, rapid antigen, and serological diagnostic assays to accurately and precisely diagnose COVID-19 in African populations, and to mitigate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR diagnostic challenges in Africa. Method: We reviewed publications from internet sources and searched for appropriate documents available in English. This included Medline, Google Scholar, and Ajol. We included primary literature and some review articles that presented knowledge on the current trends on SARS-CoV-2 diagnostics in Africa and globally. Results: Based on our analysis, we highlight the utility of four different alternatives to RT-PCR. These include two isothermal nucleic acid amplification assays (loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA)), rapid antigen testing, and antibody testing for tackling difficulties posed by SARS-CoV-2 RT-PCR testing in Africa. Conclusion: The economic burden associated COVID-19 mass testing by RT-PCR will be difficult for low-income nations to meet. We provide evidence for the utility and deployment of these alternate testing methods in Africa and other LMICs.

scholarly journals Systematic Review and Meta-analysis of Real-time Polymerase Chain Reaction assay for the detection of COVID-19 from clinical samples in low-and middle-income countries: Protocol

2021 ◽  
Author(s):  
Emmanuel Oladipo Babafemi
Keyword(s):  
Systematic Review ◽  
Polymerase Chain Reaction ◽  
Real Time ◽  
Meta Analysis ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Middle Income ◽  
Polymerase Chain

Abstract Background: COVID-19 has spread globally since its discovery in Hubei province, China in December 2019 and became pandemic in 2020. COVID-19 is a new betacoronavirus and a variant of severe acute respiratory syndrome coronavirus 2 (SARA- CoV-2). Rapid, accurate and reliable diagnosis of COVID-19 will prevent the spread and allow for appropriate management. The main objective of this systematic review is to identify, appraise and summarise the published evidence on the diagnostic performance and effectiveness of SARS-CoV-2 virus in the diagnosis of current or previous COVID-19 using real-time polymerase chain reaction (RT-PCR) assay in low-and middle-income countries (LMICs). Methods: We will search MEDLINE/PubMed, EMBASE, BIOSIS, LILACS, Cochrane Infectious Diseases Group Specialised Register (CIDG SR), Global Health, and CINAHL for published studies for the diagnosis of COVID-19 using real-time polymerase chain reaction assay in LMICs There will be no restriction regarding the language, date of publication, and publication status. We will include retrospective, cross-sectional and cohort observational studies will be included in the review. Selection of studies, data extraction and management, assessment of risk of bias, and quality of evidence will be performed by two independent reviewers (EB and BC). A third researcher (GM) will be consulted in case of discrepancies. Depending on the availability and quality of the data, a meta-analysis will be performed. Otherwise, findings will be qualitatively reported. Discussion: To our knowledge, this is the first systematic review and meta-analysis to assess the uptake of RT-PCR assay for SARS-CoV-2 detection from clinical samples in human in LMICs. This review will make available evidence on the uptake, accuracy, approach, and interpretation of results of this assay in the context of COVID-19 diagnosis which will meet an urgent need, considering the diagnostic challenges of RT-PCR assay for COVID-19 diagnosis in humans. Systematic review registration: PROSPERO CRD42021271894

scholarly journals Norovirus Infections and Disease in Lower‐Middleand Low‐Income Countries, 1997–2018

Viruses ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 341 ◽  
Author(s):  
Mans
Keyword(s):  
Low Income ◽  
Low Income Countries ◽  
Viral Gastroenteritis ◽  
Healthy Controls ◽  
Limited Data ◽  
Middle Income ◽  
Predominant Genotype ◽  
Middle Income Countries ◽  
High Prevalence ◽  
Polymerase Chain

Noroviruses are a major cause of viral gastroenteritis. The burden of the norovirus in lowresourcesettings is not well‐established due to limited data. This study reviews the norovirusprevalence, epidemiology, and genotype diversity in lower‐middle‐income countries (LMIC) andin low‐income countries (LIC). PubMed was searched up to 14 January 2019 for norovirus studiesfrom all LIC and LMIC (World Bank Classification). Studies that tested gastroenteritis cases and/orasymptomatic controls for norovirus by reverse transcription‐polymerase chain reaction (RT‐PCR)were included. Sixty‐four studies, the majority on children <5 years of age, were identified, and 14%(95% confidence interval; CI 14–15, 5158/36,288) of the gastroenteritis patients and 8% (95% CI 7–9,423/5310) of healthy controls tested positive for norovirus. In LMIC, norovirus was detected in 15%(95% CI 15–16) of cases and 8% (95% CI 8–10) of healthy controls. In LIC, 11% (95% CI 10–12) ofsymptomatic cases and 9% (95% CI 8–10) of asymptomatic controls were norovirus positive.Norovirus genogroup II predominated overall. GII.4 was the predominant genotype in all settings,followed by GII.3 and GII.6. The most prevalent GI strain was GI.3. Norovirus causes a significantamount of gastroenteritis in low‐resource countries, albeit with high levels of asymptomaticinfection in LIC and a high prevalence of coinfections

scholarly journals Screening for Human Papillomavirus in a Low- and Middle-Income Country

2019 ◽  
pp. JGO.18.00233 ◽  
Author(s):  
Aaron E. Atkinson ◽  
Carlos Alberto Matute Mandujano ◽  
Suyapa Bejarano ◽  
Linda S. Kennedy ◽  
Gregory J. Tsongalis
Keyword(s):  
Cervical Cancer ◽  
Polymerase Chain Reaction ◽  
Human Papillomavirus ◽  
Chain Reaction ◽  
Middle Income ◽  
Middle Income Countries ◽  
Hpv Genotypes ◽  
Polymerase Chain ◽  
High Risk Hpv ◽  
Low And Middle Income

PURPOSE Low- and middle-income countries have high incidences of cervical cancer linked to human papillomavirus (HPV), and without resources for cancer screenings these countries bear 85% of all cervical cancer cases. To address some of these needs, brigade-style screening combined with sensitive polymerase chain reaction–based HPV testing to detect common high-risk HPV genotypes may be necessary. METHODS We deployed an inexpensive DNA extraction technique and a real-time polymerase chain reaction–based HPV genotyping assay, as well as Papanicolaou testing, in a factory in San Pedro Sula, Honduras, where 1,732 women were screened for cervical cancer. RESULTS We found that 28% of participants were positive for high-risk HPV, with 26% of HPV-positive participants having more than one HPV infection. Moreover, the most common HPV genotypes detected were different than those routinely found in the United States. CONCLUSION This work demonstrates a deployable protocol for HPV screening in low- and middle-income countries with limited resources to perform cytopathology assessment of Pap smears.

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