scholarly journals The Use of Saliva as a Diagnostic Specimen for SARS CoV-2 Molecular Diagnostic Testing for Pediatric Patients

Author(s):  
Meghan Delaney ◽  
Joelle Simpson ◽  
Bobbe Thomas ◽  
Christal Ralph ◽  
Michael Evangalista ◽  
...  

ABSTRACTBackgroundChildren are an important population to test for COVID-19 infection, particularly because they may shed the virus without displaying symptoms. Testing children for COVID-19 via sensitive molecular methods is important, although collecting nasopharyngeal (NP) specimens can be challenging. A less invasive mode of specimen collection that yields test results comparable to those from NP specimens would be beneficial to simplify sample collection.MethodsTo demonstrate that saliva is a suitable specimen for collection from children, the clinical usability/acceptability and the analytic performance of saliva were compared to NP specimens suspended in viral transport medium. Four different FDA EUA-approved real-time RT-PCR assays and one EUA approved saliva collection device were investigated.ResultsThe study population included 526 patients between the ages of 3 and 61 years, 461 (88%) were <18 years, 425 were asymptomatic (81.1%), 92 were symptomatic (17.6%). Saliva mixed with saliva stabilizing buffer was found to yield comparable sensitivity to NP specimens when tested on the AllPlex SARS-CoV-2 molecular test (Seegene Inc). The analytic sensitivity of the AllPlex assay during testing of spiked saliva mixed with SpectrumDNA saliva stabilizer was found to be 250 genomic copies/mL.ConclusionsOf the four FDA EUA-approved SARS-CoV-2 PCR assays studied, we found the AllPlex assay to be best suited for testing saliva specimens collected from children 5 years of age or older. The sensitivity of viral detection was equivalent to NP specimens when saliva specimens were mixed with the saliva stabilizer.

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1019
Author(s):  
Kyungjin Hong ◽  
Gabriella Iacovetti ◽  
Ali Rahimian ◽  
Sean Hong ◽  
Jon Epperson ◽  
...  

Blood sample collection and rapid separation—critical preanalytical steps in clinical chemistry—can be challenging in decentralized collection settings. To address this gap, the Torq™ zero delay centrifuge system includes a lightweight, hand-portable centrifuge (ZDrive™) and a disc-shaped blood collection device (ZDisc™) enabling immediate sample centrifugation at the point of collection. Here, we report results from clinical validation studies comparing performance of the Torq System with a conventional plasma separation tube (PST). Blood specimens from 134 subjects were collected and processed across three independent sites to compare ZDisc and PST performance in the assessment of 14 analytes (K, Na, Cl, Ca, BUN, creatinine, AST, ALT, ALP, total bilirubin, albumin, total protein, cholesterol, and triglycerides). A 31-subject precision study was performed to evaluate reproducibility of plasma test results from ZDiscs, and plasma quality was assessed by measuring hemolysis and blood cells from 10 subject specimens. The ZDisc successfully collected and processed samples from 134 subjects. ZDisc results agreed with reference PSTs for all 14 analytes with mean % biases well below clinically significant levels. Results were reproducible across different operators and ZDisc production lots, and plasma blood cell counts and hemolysis levels fell well below clinical acceptance thresholds. ZDiscs produce plasma samples equivalent to reference PSTs. Results support the suitability of the Torq System for remotely collecting and processing blood samples in decentralized settings.


2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S139-S139
Author(s):  
J C Lownik ◽  
J S Farrar ◽  
G Way ◽  
R K Martin

Abstract Introduction/Objective Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler. Methods/Case Report We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler. Results (if a Case Study enter NA) This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes. Conclusion We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.


Author(s):  
Alyssa M. Pandolfo ◽  
Robert Horne ◽  
Yogini Jani ◽  
Tom W. Reader ◽  
Natalie Bidad ◽  
...  

Abstract Background Rapid molecular diagnostic tests to investigate the microbial aetiology of pneumonias may improve treatment and antimicrobial stewardship in intensive care units (ICUs). Clinicians’ endorsement and uptake of these tests is crucial to maximise engagement; however, adoption may be impeded if users harbour unaddressed concerns or if device usage is incompatible with local practice. Accordingly, we strove to identify ICU clinicians’ beliefs about molecular diagnostic tests for pneumonias before implementation at the point-of-care. Methods We conducted semi-structured interviews with 35 critical care doctors working in four ICUs in the United Kingdom. A clinical vignette depicting a fictitious patient with signs of pneumonia was used to explore clinicians’ beliefs about the importance of molecular diagnostics and their concerns. Data were analysed thematically. Results Clinicians’ beliefs about molecular tests could be grouped into two categories: perceived potential of molecular diagnostics to improve antibiotic prescribing (Molecular Diagnostic Necessity) and concerns about how the test results could be implemented into practice (Molecular Diagnostic Concerns). Molecular Diagnostic Necessity stemmed from beliefs that positive results would facilitate targeted antimicrobial therapy; that negative results would signal the absence of a pathogen, and consequently that having the molecular diagnostic results would bolster clinicians’ prescribing confidence. Molecular Diagnostic Concerns included unfamiliarity with the device’s capabilities, worry that it would detect non-pathogenic bacteria, uncertainty whether it would fail to detect pathogens, and discomfort with withholding antibiotics until receiving molecular test results. Conclusions Clinicians believed rapid molecular diagnostics for pneumonias were potentially important and were open to using them; however, they harboured concerns about the tests’ capabilities and integration into clinical practice. Implementation strategies should bolster users’ necessity beliefs while reducing their concerns; this can be accomplished by publicising the tests’ purpose and benefits, identifying and addressing clinicians’ misconceptions, establishing a trial period for first-hand familiarisation, and emphasising that, with a swift (e.g., 60–90 min) test, antibiotics can be started and refined after molecular diagnostic results become available.


2020 ◽  
Author(s):  
Daniel G. Federman ◽  
Shaili Gupta ◽  
Gary Stack ◽  
Sheldon M. Campbell ◽  
David R. Peaper ◽  
...  

AbstractBackgroundThe global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown.MethodsWe compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay.ResultsOf the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%).ConclusionWe found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.


Author(s):  
Carolyn Piggott ◽  
Cerin John ◽  
Helen Bruce ◽  
Sally C Benton

Background Quantitative faecal immunochemical tests (FIT) for haemoglobin are being used for colorectal cancer (CRC) screening for asymptomatic populations and are being indicated as a suitable test to rule out CRC in symptomatic populations. Faecal samples are typically collected by patients using a probe attached to the cap of a device which is inserted into a collection device into the preservative buffer, passing through a collar to remove excess sample: this process has potential for pre-analytical error. This study investigates whether faecal haemoglobin concentration (f-Hb) results are affected by the mass and method of sample collection. Methods Faecal samples with detectable f-Hb were loaded into collection devices from four manufacturers using increasing masses of sample. The f-Hb in the device buffer was measured using the relevant analyser. The results from the minimum recommended load were compared with results of ‘sample overloading’. Results The variation in the faecal mass added to the probe (overall CVs: EXTEL HEMO AUTO-MC Collection Picker 300%, OC-Auto Sampling Bottle 3 237%, SENTiFIT pierceTube 264%, Specimen Collection Container A 250%), was more than the variation in f-Hb (respective overall CVs: 62%, 35%, 47%, 39%). The mass of faeces added to the probes increased significantly ( P < 0.0001 for all four devices), but the f-Hb did not increase significantly (EXTEL HEMO AUTO-MC Collection Picker P = 0.6820, OC-Auto Sampling Bottle 3 P = 0.9368, SENTiFIT pierceTube P = 0.7551, Specimen Collection Container A P = 0.6864). Conclusion The mass of sample loaded onto the probe did not impact the f-Hb significantly using all four tested devices.


Author(s):  
Rose A. Lee ◽  
Joshua C. Herigon ◽  
Andrea Benedetti ◽  
Nira R. Pollock ◽  
Claudia M. Denkinger

ABSTRACTBackgroundNasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs.MethodsWe systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias.ResultsFrom 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (0.82, 95% CI: 0.73-0.90), OP (0.84, 95% CI: 0.57-1.0), saliva (0.88, 95% CI: 0.81 – 0.93)] than NP swabs, while combined OP/NS matched NP performance (0.97, 95% CI: 0.90-1.0). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield.ConclusionsNP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.


2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S48-S49
Author(s):  
Marybeth Marshall ◽  
Melphine Harriott ◽  
Leonard B Johnson

Abstract Background The use of rapid molecular diagnostic testing to identify microorganisms and resistance markers has great potential to optimize medical care and assist with antimicrobial stewardship. We implemented the Verigene bloodstream infection testing panel along with a pharmacy notification system to clinicians and assessed efficacy of the system. Methods In November 2019, we implemented the Verigene gram positive and negative panels for patients with positive blood cultures. Our antimicrobial stewardship committee developed a recommended treatment algorithm for pharmacists to use when notified of Verigene results. The first positive bottle per patient and per admission was tested. Subsequent positive bottles were not tested on the Verigene unless a different morphology was noted on the gram stain. A gram stain was performed on all positive cultures and this result was called to the patient’s nurse (if inpatient) and the covering physician was notified of the result. After the Verigene result was available, an assigned pharmacist was notified of these results (organism identification and resistance markers if identified). Pharmacists notified covering physicians of the test results and the recommended antibiotic management. Pharmacists documented the frequency that the test result changed the antibiotic management, including escalation, de-escalation or no change in therapy. The data from the first six months was summarized. Results From 11/19/19-5/18/20, a total of 575 test results were called into the pharmacist (average 3.2/day). Among these, 165 (28.7%) were considered likely contaminants, 106 had no change in therapy and 59 had antibiotic de-escalation. Among the remaining 410 patients, 156 had de-escalation, 53 had escalation, 30 were not on any antibiotics and appropriate antibiotics were started. Overall, antibiotic management changed in 298/575 (51.8%) of isolates run by Verigene in our institution including 215 (37.4%) de-escalations. The most frequent antibiotics that were stopped included vancomycin (142) and cefepime (53). Conclusion Our pharmacist-based algorithm for notification and treatment recommendation based on Verigene results was highly successful in optimizing antibiotic management and improving antimicrobial stewardship in our institution. Disclosures All Authors: No reported disclosures


Author(s):  
Rose A. Lee ◽  
Joshua C. Herigon ◽  
Andrea Benedetti ◽  
Nira R. Pollock ◽  
Claudia M. Denkinger

Background: Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. Methods: We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval October 1st, 2020) for comparative studies of alternative specimen types [saliva, oropharyngeal (OP), and nasal (NS) swabs] versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in sub-groups. The QUADAS 2 tool was used to assess bias. Results: From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives [NS (82%, 95% CI: 73-90%), OP (84%, 95% CI: 57-100%), saliva (88%, 95% CI: 81 – 93%)] than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90-100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield. Conclusions: NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric vs. adult, late vs. early in disease course) and head-to head studies of sampling strategies are urgently needed.


2020 ◽  
Author(s):  
Monique Melo Costa ◽  
Nicolas Benoit ◽  
Jerome Dormoi ◽  
Remy Amalvict ◽  
Nicolas Gomez ◽  
...  

AbstractBackgroundCurrently, COVID-19 diagnosis relies on quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) from nasopharyngeal swab (NPS) specimens, but NPSs present several limitations. The simplicity, low invasive and possibility of self-collection of saliva imposed this specimen as a relevant alternative for SARS-CoV-2 detection. However, the discrepancy of saliva test results compared to NPSs made of its use controversial. Here, we proposed to assess Salivettes®, as a standardized saliva collection device, and to compare SARS-CoV-2 positivity on paired NPS and saliva specimens.MethodsA total of 303 individuals randomly selected among those investigated for SARS-CoV-2 were enrolled, including 30 (9.9%) patients previously positively tested using NPS (follow-up group), 90 (29.7%) mildly symptomatic and 183 (60.4%) asymptomatic.ResultsThe RT-qPCR revealed a positive rate of 11.6% (n=35) and 17.2% (n=52) for NPSs and saliva samples, respectively. The sensitivity and specificity of saliva samples were 82.9% and 91.4%, respectively, using NPS as reference. The highest proportion of discordant results concerned the follow-up group (33.3%). Although in the symptomatic and asymptomatic groups the agreement exceeded 90.0%, 17 individuals were detected positive only in saliva samples, with consistent medical arguments.ConclusionSaliva collected with Salivette® demonstrated more sensitive for detecting symptomatic and pre-symptomatic infections.


2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S296-S297
Author(s):  
Trini A Mathew ◽  
Jonathan Hopkins ◽  
Diane Kamerer ◽  
Shagufta N Ali ◽  
Daniel Ortiz ◽  
...  

Abstract Background The novel Coronavirus SARS CoV-2 (COVID-19) outbreak was complicated by the lack of diagnostic testing kits. In early March 2020, leadership at Beaumont Hospital, Royal Oak Michigan (Beaumont) identified the need to develop high capacity testing modalities with appropriate sensitivity and specificity and rapid turnaround time. We describe the molecular diagnostic testing experience since initial rollout on March 16, 2020 at Beaumont, and results of repeat testing during the peak of the COVID-19 pandemic in MI. Methods Beaumont is an 1100 bed hospital in Southeast MI. In March, testing was initially performed with the EUA Luminex NxTAG CoV Extended Panel until March 28, 2020 when testing was converted to the EUA Cepheid Xpert Xpress SARS-CoV-2 for quicker turnaround times. Each assay was validated with a combination of patient samples and contrived specimens. Results During the initial week of testing there was &gt; 20 % specimen positivity. As the prevalence grew the positivity rate reached 68% by the end of March (Figure 1). Many state and hospital initiatives were implemented during the outbreak, including social distancing and screening of asymptomatic patients to increase case-finding and prevent transmission. We also adopted a process for clinical review of symptomatic patients who initially tested negative for SARS-CoV-2 by a group of infectious disease physicians (Figure 2). This process was expanded to include other trained clinicians who were redeployed from other departments in the hospital. Repeat testing was performed to allow consideration of discontinuation of isolation precautions. During the surge of community cases from March 16 to April 30, 2020, we identified patients with negative PCR tests who subsequently had repeat testing based on clinical evaluation, with 7.1% (39/551) returning positive for SARS- CoV2. Of the patients who expired due to COVID-19 during this period, 4.3% (9/206) initially tested negative before ultimately testing positive. Figure 1 BH RO testing Epicurve Figure 2: Screening tool for repeat COVID19 testing and precautions Conclusion Many state and hospital initiatives helped us flatten the curve for COVID-19. Our hospital testing experience indicate that repeat testing may be warranted for those patients with clinical features suggestive of COVID-19. We will further analyze these cases and clinical features that prompted repeat testing. Disclosures All Authors: No reported disclosures


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