scholarly journals Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings

2021 ◽  
Author(s):  
Meredith S. Muller ◽  
Srijana Bhattarai Chhetri ◽  
Christopher Basham ◽  
Tyler Rapp ◽  
Feng-Chang Lin ◽  
...  
Keyword(s):  
Cold Chain ◽  
Nasopharyngeal Swab ◽  
Resource Constrained ◽  
Viral Loads ◽  
Acute Infections ◽  
Viral Transport ◽  
Self Testing ◽  
Nasal Swabs ◽  
3D Printed ◽  
Rna Stabilization

ABSTRACTBackgrounStandard nasopharyngeal swab testing for SARS-CoV-2 detection by PCR is not always feasible due to limitations in trained personnel, personal protective equipment, swabs, PCR reagents, and access to cold chain and biosafety hoods.MethodWe piloted the collection of nasal mid-turbinate swabs amenable to self-testing, including both standard polyester flocked swabs as well as 3D printed plastic lattice swabs, placed into either viral transport media or an RNA stabilization agent. Quantitative SARS-CoV-2 viral detection by RT-qPCR was compared to that obtained by nasopharyngeal sampling as the reference standard. Pooling specimens in the lab versus pooling swabs at the point of collection was also evaluated.ResultsAmong 275 participants, flocked nasal swabs identified 104/121 individuals who were PCR-positive for SARS-CoV-2 by nasopharyngeal sampling (sensitivity 87%, 95% CI 79-92%), mostly missing those with low viral load (<10^3 viral copies/uL). 3D-printed nasal swabs showed similar sensitivity. When nasal swabs were placed directly into an RNA stabilizer, the mean 1.4 log decrease in viral copies/uL compared to nasopharyngeal samples was reduced to <1 log, even when samples were left at room temperature for up to 7 days. Pooling sample specimens or swabs both successfully detected samples >102viral copies/uL.ConclusionsNasal swabs are likely adequate for clinical diagnosis of acute infections to help expand testing capacity in resource-constrained settings. When collected into an RNA preservative that also inactivates infectious virus, nasal swabs yielded quantitative viral loads approximating those obtained by nasopharyngeal sampling.

Effective optimization of SARS-CoV-2 laboratory testing variables in an era of supply chain constraints

2020 ◽  
Vol 15 (15) ◽  
pp. 1483-1487
Author(s):  
Nikhil S Sahajpal ◽  
Ashis K Mondal ◽  
Allan Njau ◽  
Sudha Ananth ◽  
Kimya Jones ◽  
...  
Keyword(s):  
Supply Chain ◽  
Rna Extraction ◽  
Nasopharyngeal Swab ◽  
Sample Collection ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Short Supply ◽  
Viral Transport ◽  
3D Printed ◽  
Bridging Studies

RT-PCR-based assays for the detection of SARS-CoV-2 have played an essential role in the current COVID-19 pandemic. However, the sample collection and test reagents are in short supply, primarily due to supply chain issues. Thus, to eliminate testing constraints, we have optimized three key process variables: RNA extraction and RT-PCR reactions, different sample types and media to facilitate SARS-CoV-2 testing. By performing various validation and bridging studies, we have shown that various sample types such as nasopharyngeal swab, bronchioalveolar lavage and saliva, collected using conventional nasopharyngeal swabs, ESwab or 3D-printed swabs and, preserved in viral transport media, universal transport media, 0.9% sodium chloride or Amies media are compatible with RT-PCR assay for COVID-19. Besides, the reduction of PCR reagents by up to fourfold also produces reliable results.

scholarly journals Innovative design of 3D-printed nasopharyngeal pediatric swab for COVID-19 detection

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Ameerah Alazemi ◽  
Ghadeer AbdulHussain ◽  
Abdullah Alawwam ◽  
Ali Al-Shatti ◽  
Mohammad Alghounaim ◽  
...  
Keyword(s):  
3D Printing ◽  
Nasopharyngeal Swab ◽  
High Demand ◽  
Innovative Design ◽  
Clinical Specimens ◽  
3 Dimensional ◽  
3D Printing Technology ◽  
Nasal Swabs ◽  
3D Printed ◽  
Upper Respiratory

Abstract3-dimensional (3D) printing technology provides a solution to meet the high demand for producing adult nasal swabs. A smaller, more flexible nasopharyngeal swab needs to be developed for children and infants suspected of having coronavirus. The information shared here presents a novel 3D-printed pediatric swab for the purpose of collecting upper respiratory clinical specimens.

scholarly journals Innovative Design of 3D-Printed Nasopharyngeal Pediatric Swab for COVID-19 Detection

2021 ◽  
Author(s):  
Ameerah Alazemi ◽  
Ghadeer AbdulHussain ◽  
Abdullah Alawwam ◽  
Ali Al-Shatti ◽  
Mohammad alghounaim ◽  
...  
Keyword(s):  
3D Printing ◽  
Nasopharyngeal Swab ◽  
High Demand ◽  
Innovative Design ◽  
Clinical Specimens ◽  
3 Dimensional ◽  
3D Printing Technology ◽  
Nasal Swabs ◽  
3D Printed ◽  
Upper Respiratory

Abstract 3-dimensional (3D) printing technology provides a solution to meet the high demand for producing adult nasal swabs. A smaller, more flexible nasopharyngeal swab needs to be developed for children and infants suspected of having coronavirus. The information shared here presents a novel 3D-printed pediatric swab for the purpose of collecting upper respiratory clinical specimens.

scholarly journals Pooled Saliva Specimens for SARS-CoV-2 Testing

2020 ◽  
Author(s):  
Bidisha Barat ◽  
Sanchita Das ◽  
Valeria De Giorgi ◽  
David K. Henderson ◽  
Stacy Kopka ◽  
...  
Keyword(s):  
Viral Load ◽  
Screening Program ◽  
High Viral Load ◽  
Load Cycle ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Viral Loads ◽  
Viral Transport ◽  
Average Loss ◽  
Positive Agreement

We evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The percent positive agreement increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion®, and Roche COBAS® 6800. The average loss of signal upon pooling was 2-3 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 94%, 90%, and 94% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

scholarly journals Pooled Saliva Specimens for SARS-CoV-2 Testing

2020 ◽  
Author(s):  
Bidisha Barat ◽  
Sanchita Das ◽  
Valeria De Giorgi ◽  
David K. Henderson ◽  
Stacy Kopka ◽  
...  
Keyword(s):  
Viral Load ◽  
Screening Program ◽  
High Viral Load ◽  
Load Cycle ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Lower Viral Load ◽  
Viral Loads ◽  
Viral Transport ◽  
Positive Specimen

AbstractWe evaluated saliva (SAL) specimens for SARS-CoV-2 RT-PCR testing by comparison of 459 prospectively paired nasopharyngeal (NP) or mid-turbinate (MT) swabs from 449 individuals with the aim of using saliva for asymptomatic screening. Samples were collected in a drive-through car line for symptomatic individuals (N=380) and in the emergency department (ED) (N=69). The percent positive and negative agreement of saliva compared to nasopharyngeal swab were 81.1% (95% CI: 65.8% – 90.5%) and 99.8% (95% CI: 98.7% – 100%), respectively. The sensitivity increased to 90.0% (95% CI: 74.4% – 96.5%) when considering only samples with moderate to high viral load (Cycle threshold (Ct) for the NP <=34). Pools of five saliva specimens were also evaluated on three platforms: bioMérieux NucliSENS easyMAG with ABI 7500Fast (CDC assay), Hologic Panther Fusion, and Roche COBAS 6800. The median loss of signal upon pooling was 2-4 Ct values across the platforms. The sensitivity of detecting a positive specimen in a pool compared with testing individually was 100%, 93%, and 95% for CDC 2019-nCoV Real-Time RT-PCR, Panther Fusion® SARS-CoV-2 assay, and cobas® SARS-CoV-2 test respectively, with decreased sample detection trending with lower viral load. We conclude that although pooled saliva testing, as collected in this study, is not quite as sensitive as NP/MT testing, saliva testing is adequate to detect individuals with higher viral loads in an asymptomatic screening program, does not require swabs or viral transport media for collection, and may help to improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

scholarly journals Polyester Nasal Swabs Collected in a Dry Tube are a Robust and Inexpensive, Minimal Self-Collection Kit for SARS-CoV-2 Testing

2020 ◽  
Author(s):  
Leah R. Padgett ◽  
Lauren A. Kennington ◽  
Charlotte L. Ahls ◽  
Delini K. Samarasinghe ◽  
Yuan-Po Tu ◽  
...  
Keyword(s):  
Elevated Temperatures ◽  
Quantitative Polymerase Chain Reaction ◽  
High Capacity ◽  
Cold Chain ◽  
Load Testing ◽  
Clinical Specimens ◽  
Viral Loads ◽  
Nasal Swabs ◽  
Polymerase Chain ◽  
Phosphate Buffered Saline

AbstractBackgroundPolyester nasal swabs stored in saline or in a dry tube were evaluated as an alternative to foam nasal swabs for SARS-CoV-2 testing by reverse transcription quantitative polymerase chain reaction (RT-qPCR) since they may be inexpensively manufactured at high capacity.MethodsSurrogate clinical specimens were prepared by inoculating foam and polyester nasal swabs with residual SARS-CoV-2 positive clinical specimens diluted in porcine or human matrix. Dry swab elution with phosphate buffered saline (PBS) was evaluated by vortex, swab swirling, and passive methodologies. Surrogate and clinical nasal specimen stability were evaluated at refrigerated (4°C) and elevated temperatures (40°C for 12 hours, 32°C hold) through 72 hours.ResultsPolyester swabs demonstrated equivalent performance to foam swabs for detection of low and high SARS-CoV-2 viral loads. Dry swab elution performed with PBS and mechanical disruption by vortex resulted in nearly complete quantitative recovery of virus. Dry polyester and foam surrogate specimens were stable through 72 hours both when refrigerated and after high temperature excursion, which simulated specimen transport without cold chain. Similarly, clinical specimens collected with polyester swabs and stored dry were stable through 72 hours in the presence and absence of cold chain. Polyester surrogate specimens stored in saline were stable through 72 hours refrigerated but only through 48 hours at elevated temperatures.ConclusionsPolyester nasal swabs stored in dry collection tubes comprise a robust and inexpensive self-collection method for SARS-CoV-2 viral load testing, which is stable under conditions required for home collection and shipment to the laboratory.

scholarly journals SARS COV-2 PANDEMIC: EXPERIENCE AT REFERENCE VIROLOGY LABORATORY SHORT RUNNING TITLE: SARS COV-2 PANDEMIC EXPERIENCE

2021 ◽  
Vol 71 (4) ◽  
pp. 1175-78
Author(s):  
Misbah Noor ◽  
Eijaz Ghani ◽  
Saifullah Khan Niazi ◽  
Muhammad Ali Rathore ◽  
Faud Ahmad Siddiqi ◽  
...  
Keyword(s):  
Large Scale ◽  
Armed Forces ◽  
Cold Chain ◽  
P Value ◽  
Nasopharyngeal Swab ◽  
Age Group ◽  
Viral Transport ◽  
Viral Transport Medium ◽  
Two Peaks ◽  
Patient Department

Objective: To share our large scale SARS CoV-2 PCR test experience in Northern Pakistan. Study Design: Prospective observational study. Place and Duration of Study: Virology Department, Armed Forces Institute of Pathology, Rawalpindi, from Feb to Dec 2020. Methodology: All the patients reporting to COVID-19 desk both indoor and outdoor were included in study. Nasopharyngeal swab specimen was taken from the patients arriving at reception. For hospitalized patient’s samples were received at reception placed in viral transport medium maintaining cold chain. Results: Among 193656 samples tested for SARS CoV-2 RNA by RT-PCR, 24338 (12.6%) were found positive and 169318 (87.4%) were negative. Mean age of patients was 38.25 ± 16.73 (1-110 years). 138781 (71.7%) were males and 54875 (28.3%) were females. 109765 (56.7%) samples were received from in patient department and 83891 (43.3%) samples were received from outpatient department. Highest number of cases (n=6224) seen during month of June followed by 5813 cases during May and 4786 cases during November (p-value <0.001). Most of the positive cases were in age group 21-40 years; 11122 (6%), followed by age group 41-60 years; 8133 (4.2%). More positive samples 14890 (7.7%) were received from in patient department and males 17928 (9.3%) were affected more than females. Conclusion: The two peaks of COVID-19 pandemic in Pakistan were observed during the months of May to July and again during October to December. Most positive patients in our setup were males in age group 21-40 years as this age group is more exposed to external environment.

scholarly journals Abnormal upregulation of cardiovascular disease biomarker PLA2G7 induced by proinflammatory macrophages in COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yang Li ◽  
Yongzhong Jiang ◽  
Yi Zhang ◽  
Naizhe Li ◽  
Qiangling Yin ◽  
...  
Keyword(s):  
Cardiovascular Disease ◽  
Normal Limit ◽  
Genomic Analysis ◽  
High Rate ◽  
Hub Gene ◽  
Viral Loads ◽  
Protein Levels ◽  
Nasal Swabs ◽  
Positive Rate ◽  
Validation Stage

AbstractHigh rate of cardiovascular disease (CVD) has been reported among patients with coronavirus disease 2019 (COVID-19). Importantly, CVD, as one of the comorbidities, could also increase the risks of the severity of COVID-19. Here we identified phospholipase A2 group VII (PLA2G7), a well-studied CVD biomarker, as a hub gene in COVID-19 though an integrated hypothesis-free genomic analysis on nasal swabs (n = 486) from patients with COVID-19. PLA2G7 was further found to be predominantly expressed by proinflammatory macrophages in lungs emerging with progression of COVID-19. In the validation stage, RNA level of PLA2G7 was identified in nasal swabs from both COVID-19 and pneumonia patients, other than health individuals. The positive rate of PLA2G7 were correlated with not only viral loads but also severity of pneumonia in non-COVID-19 patients. Serum protein levels of PLA2G7 were found to be elevated and beyond the normal limit in COVID-19 patients, especially among those re-positive patients. We identified and validated PLA2G7, a biomarker for CVD, was abnormally enhanced in COVID-19 at both nucleotide and protein aspects. These findings provided indications into the prevalence of cardiovascular involvements seen in patients with COVID-19. PLA2G7 could be a potential prognostic and therapeutic target in COVID-19.

scholarly journals Direct diagnostic testing of SARS-CoV-2 without the need for prior RNA extraction

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shan Wei ◽  
Esther Kohl ◽  
Alexandre Djandji ◽  
Stephanie Morgan ◽  
Susan Whittier ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Cost Effective ◽  
Clinical Samples ◽  
Nasopharyngeal Swab ◽  
Percentage Agreement ◽  
Testing Method ◽  
Viral Transport

AbstractThe COVID-19 pandemic has resulted in an urgent need for a rapid, point of care diagnostic testing that could be rapidly scaled on a worldwide level. We developed and tested a highly sensitive and robust assay based on reverse transcription loop mediated isothermal amplification (RT-LAMP) that uses readily available reagents and a simple heat block using contrived spike-in and actual clinical samples. RT-LAMP testing on RNA-spiked samples showed a limit of detection (LoD) of 2.5 copies/μl of viral transport media. RT-LAMP testing directly on clinical nasopharyngeal swab samples in viral transport media had an 85% positive percentage agreement (PPA) (17/20), and 100% negative percentage agreement (NPV) and delivered results in 30 min. Our optimized RT-LAMP based testing method is a scalable system that is sufficiently sensitive and robust to test for SARS-CoV-2 directly on clinical nasopharyngeal swab samples in viral transport media in 30 min at the point of care without the need for specialized or proprietary equipment or reagents. This cost-effective and efficient one-step testing method can be readily available for COVID-19 testing world-wide, especially in resource poor settings.

scholarly journals Comparison of Quidel Sofia SARS FIA Test to Hologic Aptima SARS-CoV-2 TMA Test for Diagnosis of COVID-19 in Symptomatic Outpatients

2020 ◽  
Author(s):  
Eric T. Beck ◽  
Wendy Paar ◽  
Lara Fojut ◽  
Jordan Serwe ◽  
Renee R. Jahnke
Keyword(s):  
Symptom Onset ◽  
Care Center ◽  
Urgent Care ◽  
Molecular Diagnostic ◽  
Nasopharyngeal Swab ◽  
Urgent Care Center ◽  
Ct Value ◽  
High Prevalence ◽  
Nasal Swabs ◽  
Molecular Diagnostic Test

The Quidel Sofia SARS FIA test (SOFIA) is a rapid antigen immunoassay for detection of SARS-CoV-2 viral proteins from nasal or nasopharyngeal swab specimens. The purpose of this study was to compare the results of the SOFIA test to the Hologic Aptima SARS-CoV-2 TMA test (APTIMA TMA), a high-throughput molecular diagnostic test that uses transcription mediated amplification for detection of SARS-CoV-2 nucleic acid from upper respiratory specimens. Three hundred and 40-seven symptomatic patients, from an urgent care center in an area with a high prevalence of SARS-CoV-2 infections, were tested in parallel using nasal swabs on the SOFIA test and nasopharyngeal swabs on the APTIMA TMA test. The SOFIA test demonstrated an 82.0% positive percent agreement (PPA) compared to the APTIMA TMA test for symptomatic patients tested ≤ 5 days from symptom onset and a 54.5% PPA for symptomatic patients > 5 days from symptom onset. The Cepheid Xpert Xpress SARS-CoV-2 RT-PCR test was used to determine the cycle threshold (Ct) value from any specimens that were discrepant between the SOFIA and APTIMA TMA tests. Using a Ct value of ≤ 35 as a surrogate for SARS-CoV-2 culture positivity, we estimate that the SOFIA test detected 87.2% of symptomatic patients tested ≤ 5 days from symptom onset that were likely to be culture positive.

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