scholarly journals Prospective Comparison of Saliva and Nasopharyngeal Swab Sampling for Mass Screening for COVID-19

2021 ◽  
Vol 8 ◽  
Author(s):  
Mathieu Nacher ◽  
Mayka Mergeay-Fabre ◽  
Denis Blanchet ◽  
Orelie Benoit ◽  
Tristan Pozl ◽  
...  
Keyword(s):  
Mass Screening ◽  
Saliva Sample ◽  
Field Testing ◽  
Contact Tracing ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Prospective Comparison ◽  
Asymptomatic Patients ◽  
Patient Groups

Current testing for COVID-19 relies on reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. One hundred sixty two had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples vs. nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values <25 for three genes. For symptomatic patients for whom the interval between symptoms onset and sampling was <10 days sensitivity was 77% but when excluding persons with isolated N gene positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts <30, sensitivity was 83 or 88.9% when considering two genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.

scholarly journals Prospective comparison of saliva and nasopharyngeal swab sampling for mass screening for COVID-19

2020 ◽  
Author(s):  
◽  
mathieu nacher ◽  
magalie demar
Keyword(s):  
Mass Screening ◽  
Saliva Sample ◽  
Field Testing ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Prospective Comparison ◽  
Asymptomatic Patients ◽  
Patient Groups ◽  
Trained Staff

Current testing for COVID-19 relies on quantitative reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. 162 had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples versus nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values<25. For symptomatic patients for whom the interval between symptoms onset and sampling was <10 days sensitivity was 77% but when excluding persons with isolated Ngen positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts <30, sensitivity was 83% or 88.9% when considering 2 genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.

scholarly journals Performance of Unobserved Self-Collected Nasal Swabs for Detection of SARS-CoV-2 by RT-PCR Utilizing a Remote Specimen Collection Strategy

2021 ◽  
Author(s):  
Ron M Kagan ◽  
Amy A Rogers ◽  
Gwynngelle A Borillo ◽  
Nigel J Clarke ◽  
Elizabeth M Marlowe
Keyword(s):  
Return To Work ◽  
Screening Program ◽  
False Negative ◽  
N Gene ◽  
Rt Pcr ◽  
Pooled Testing ◽  
Specimen Collection ◽  
Asymptomatic Patients ◽  
Nasal Swabs ◽  
The Impact

Abstract Background The use of a remote specimen collection strategy employing a kit designed for unobserved self-collection for SARS-CoV-2 RT-PCR can decrease the use of PPE and exposure risk. To assess the impact of unobserved specimen self-collection on test performance, we examined results from a SARS-CoV-2 qualitative RT-PCR test for self-collected specimens from participants in a return-to-work screening program and assessed the impact of a pooled testing strategy in this cohort. Methods Self-collected anterior nasal swabs from employee return to work programs were tested using the Quest Diagnostics SARS-CoV-2 RT-PCR EUA. The Ct values for the N1 and N3 N-gene targets and a human RNase P (RP) gene control target were tabulated. For comparison, we utilized Ct values from a cohort of HCP-collected specimens from patients with and without COVID-19 symptoms. Results Among 47,923 participants, 1.8% were positive. RP failed to amplify for 13/115,435 (0.011%) specimens. The median (IQR) Cts were 32.7 (25.0-35.7) for N1 and 31.3 (23.8-34.2) for N3. Median Ct values in the self-collected cohort were significantly higher than those of symptomatic, but not asymptomatic patients. Based on Ct values, pooled testing with 4 specimens would have yielded inconclusive results in 67/1,268 (5.2%) specimens but only a single false-negative result. Conclusions Unobserved self-collection of nasal swabs provides adequate sampling for SARS-CoV-2 RT-PCR testing. These findings alleviate concerns of increased false negatives in this context. Specimen pooling could be used for this population as the likelihood of false negative results is very low due when using a sensitive, dual-target methodology.

scholarly journals SARS-CoV-2 in peritoneal swabs from asymptomatic patients undergoing emergency abdominal surgery

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Jasim AlAradi ◽  
Rawan A Rahman AlHarmi ◽  
Mariam AlKooheji ◽  
Sayed Ali Almahari ◽  
Mohamed Abdulla Isa ◽  
...  
Keyword(s):  
Peritoneal Fluid ◽  
Case Series ◽  
Rapid Test ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Protective Measures ◽  
The Public ◽  
Asymptomatic Patients ◽  
Number Of Patients ◽  
Viral Transfer

Abstract This is a case series of five patients with acute abdomen requiring surgery who tested positive for coronavirus disease 2019 (COVID-19) and were asymptomatic, with the purpose of detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in peritoneal fluid. Nasopharyngeal swab was done as a prerequisite for admission or prior to admission as part of random testing. Two methods of viral testing were employed: Xpert® Xpress SARS-CoV-2 (rapid test) and real-time reverse transcription polymerase chain reaction (RT-PCR). Either or both tests were done, with the former performed for patients requiring surgery immediately. Surgery was performed within 24–36 h from admission. Peritoneal fluid swabs were obtained for the detection of SARS-CoV-2 using RT-PCR test. Swabs were immediately placed in viral transfer media and delivered to the public health laboratory in an ice bag. SARS-CoV-2 was not detected in peritoneal swabs. Due to the limited number of patients, further studies are required; yet, protective measures should still be taken by surgeons when dealing with COVID-19 cases.

scholarly journals Transmission dynamics of the delta variant of SARS-CoV-2 infections in Daejeon, South Korea

2021 ◽  
Author(s):  
Hari Hwang ◽  
Jun-Sik Lim ◽  
Sun-Ah Song ◽  
Chiara Achangwa ◽  
Woobeom Sim ◽  
...  
Keyword(s):  
South Korea ◽  
Symptom Onset ◽  
Credible Interval ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Strict Adherence ◽  
Virus Shedding ◽  
Viral Shedding ◽  
Asymptomatic Patients

Abstract Background The delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear. Methods We analyzed all case patients in local clusters and temporal patterns of viral shedding using contact tracing data from 405 cases associated with the delta variant of SARS-CoV-2 between 22 June and 31 July 2021 in Daejeon, South Korea. Results Overall, half of the cases were aged under 19 years, and 20% were asymptomatic at the time of epidemiological investigation. We estimated the mean serial interval as 3.26 days (95% credible interval 2.92, 3.60), and 12% of the transmission occurred before symptom onset of the infector. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63% (52/82). We estimated that 15% (95% confidence interval, 13–18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from asymptomatic patients, and the highest viral load was observed two days after symptom onset. The temporal pattern of viral shedding did not differ between children and adults (P = 0.48). Conclusions Our findings suggest that the delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, and strict adherence to public health measures are needed to mitigate the community transmission of the delta variant.

scholarly journals SARS-CoV-2 show no infectivity at later stages in a prolonged COVID-19 patient despite positivity in RNA testing

2021 ◽  
Author(s):  
Xiu-Feng Wan ◽  
Cynthia Y Tang ◽  
Detlef Ritter ◽  
Yang Wang ◽  
Tao Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Onset ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Virus Growth ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Asymptomatic Patients ◽  
Hospitalization Period ◽  
Polymerase Chain

Inpatient COVID-19 cases present enormous costs to patients and health systems. Many hospitalized patients may still test COVID-19 positive, even after resolution of symptoms. Thus, a pressing concern for clinicians is the safety of discharging these asymptomatic patients if they have any remaining infectivity. This case report explores the viral viability in a patient with persistent COVID-19 over the course of a two-month hospitalization. Positive nasopharyngeal swab samples, analyzed by quantitative reverse transcription polymerase chain reactions (qRT-PCR), were collected and isolated in the laboratory, and infectious doses were analyzed throughout the hospitalization period. The patient experienced waning symptoms by hospital day 40 and had no viable virus growth in the laboratory by hospital day 41, suggesting no risk of infectivity, despite positive RT-PCR results, which prolonged his hospital stay. Notably, this case showed infectivity for at least 24 days from disease onset, which is longer than the discontinuation of transmission-based precautions recommendation by CDC. Thus, our findings suggest that the timeline for discontinuing transmission-based precautions may need to be extended for patients with prolonged illness. Additional large-scale studies are needed to draw definitive conclusions on the appropriate clinical management for these patients.

scholarly journals Salivary detection of COVID-19. Clinical performance of oral sponge sampling for SARS-CoV-2 testing

2021 ◽  
Author(s):  
Charles Hugo Marquette ◽  
Jacques Boutros ◽  
Jonathan Benzaquen ◽  
Marius Ilié ◽  
Mickelina Labaky ◽  
...  
Keyword(s):  
Mass Screening ◽  
Clinical Performance ◽  
Close Contact ◽  
Low Cost ◽  
Sampling Technique ◽  
Contact Tracing ◽  
Rt Pcr ◽  
Community Based ◽  
Attending Physician ◽  
Close Contacts

ABSTRACTBackgroundThe current diagnostic standard for coronavirus 2019 disease (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with naso-pharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for SARS-CoV-2 testing.MethodsOver a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening center. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n=147) or by the contact tracing staff of the French public health insurance since they were considered as close contacts of a laboratory-confirmed COVID-19 case (n=262).ResultsIn symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95%CI: 89.6-94.8) concordance with NP testing, and, a 93.3% [95%CI: 89.1-97.3] sensitivity. In close contacts the NP-OS concordance (93.8% [95%CI: 90.9-96.7]) and OS sensitivity (71.9% [95%CI: 66.5-77.3]) were slightly lower.ConclusionThese results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.Summary of the “take home” messageOS sampling for SARS-CoV2 RT-PCR is an easy to perform, straightforward self-administered sampling technique, which has a sensitivity of up to 93.3% in symptomatic patients and 71% in close contact subjects.

scholarly journals An integrated lab-on-a-chip device for RNA extraction, amplification and CRISPR-Cas12a-assisted detection for COVID-19 screening in resource-limited settings

2022 ◽  
Author(s):  
Bongkot Ngamsom ◽  
Alexander Iles ◽  
Moses Kamita ◽  
Racheal Kimani ◽  
Pablo Rodriguez-Mateos ◽  
...  
Keyword(s):  
Saliva Sample ◽  
Rna Extraction ◽  
Lab On A Chip ◽  
Cross Reactivity ◽  
Contact Tracing ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Sample Collection ◽  
Middle Income ◽  
Specificity And Sensitivity

In response to the ongoing COVID-19 pandemic and disparities of vaccination coverage in low-and middle-income countries, it is vital to adopt a widespread testing and screening programme, combined with contact tracing, to monitor and effectively control the infection dispersion in areas where medical resources are limited. This work presents a lab-on-a-chip platform, namely IFAST-CRISPR, as an affordable, rapid and high-precision molecular diagnostic means for SARS-CoV-2 detection. The herein proposed sample-to-answer platform integrates RNA extraction, amplification and CRISPR-Cas-based detection with lateral flow readout in one device. The microscale dimensions of the device containing immiscible liquids, coupled with the use of silica paramagnetic beads and GuHCl, streamline sample preparation, including RNA concentration, extraction and purification, in 15 min with minimal hands-on steps. By combining RT-LAMP with CRISPR-Cas12 assays targeting the nucleoprotein (N) gene, visual identification of ≥ 470 copies mL-1 genomic SARS-CoV-2 samples was achieved in 45 min, with no cross-reactivity towards HCoV-OC43 nor H1N1. On-chip assays showed the ability to isolate and detect SARS-CoV-2 from 1,000 genome copies mL-1 of replication-deficient viral particles in 1 h. This simple, affordable and integrated platform demonstrated a visual, faster, and yet specificity and sensitivity-comparable alternative to the costly gold-standard RT-PCR assay, requiring only a simple heating source. Further investigations on multiplexing and direct interfacing of the accessible Swan-brand cigarette filter for saliva sample collection could provide a complete work flow for COVID-19 diagnostics from saliva samples suitable for low-resource settings.

scholarly journals Clinical Performance of the Luminex NxTAG CoV Extended Panel for SARS-CoV-2 Detection in Nasopharyngeal Specimens from COVID-19 Patients in Hong Kong

2020 ◽  
Vol 58 (8) ◽  
Author(s):  
Jonathan Hon-Kwan Chen ◽  
Cyril Chik-Yan Yip ◽  
Jasper Fuk-Woo Chan ◽  
Rosana Wing-Shan Poon ◽  
Kelvin Kai-Wang To ◽  
...  
Keyword(s):  
Hong Kong ◽  
High Throughput ◽  
Clinical Performance ◽  
Diagnostic System ◽  
Molecular Diagnostic ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Gene Target ◽  
E Gene

ABSTRACT In December 2019, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first reported in the Hubei province of China and later spread all over the world. There was an urgent need of a high-throughput molecular test for screening the COVID-19 patients in the community. The Luminex NxTAG CoV extended panel is a high-throughput FDA emergency use-authorized molecular diagnostic assay for SARS-CoV-2 detection. This system targets three genes (ORF1ab, N, and E genes) of SARS-CoV-2, the ORF1ab region of SARS-CoV, and the ORF5 region of MERS-CoV. In this study, we evaluated the diagnostic performance of this system with nasopharyngeal swab specimens of 214 suspected COVID-19 patients in Hong Kong. The results were compared with our routine COVID-19 reverse transcription-PCR (RT-PCR) protocol with a LightMix SarbecoV E-gene kit and an in-house RdRp/Hel RT-PCR assay. The NxTAG CoV extended panel demonstrated 97.8% sensitivity and 100% specificity to SARS-CoV-2 in nasopharyngeal specimens. On low-viral load specimens, the sensitivity of the NxTAG panel could still maintain at 85.71%. Strong agreement was observed between the NxTAG panel and the routine COVID-19 RT-PCR protocol (kappa value = 0.98). Overall, the E gene target of the NxTAG panel demonstrated the highest sensitivity among the three SARS-CoV-2 targets, while the N gene targets demonstrated the least. In conclusion, the NxTAG CoV extended panel is simple to use, and it has high diagnostic sensitivity and specificity to SARS-CoV-2 in nasopharyngeal specimens. We recommend this diagnostic system for high-throughput COVID-19 screening in the community.

scholarly journals Sensitivity of Nasopharyngeal Swabs and Saliva for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2

2020 ◽  
Author(s):  
Alainna J Jamal ◽  
Mohammad Mozafarihashjin ◽  
Eric Coomes ◽  
Jeff Powis ◽  
Angel X Li ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Real Time ◽  
Saliva Sample ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Sample Pair

Abstract We enrolled 91 consecutive inpatients with COVID-19 at 6 hospitals in Toronto, Canada, and tested 1 nasopharyngeal swab/saliva sample pair from each patient using real-time RT-PCR for severe acute respiratory syndrome coronavirus 2. Sensitivity was 89% for nasopharyngeal swabs and 72% for saliva (P = .02). Difference in sensitivity was greatest for sample pairs collected later in illness.

scholarly journals Pooling of Nasopharyngeal Swab Specimens for SARS-CoV-2 detection by RT-PCR

2020 ◽  
Author(s):  
Ignacio Torres ◽  
Eliseo Albert ◽  
David Navarro
Keyword(s):  
Large Population ◽  
Rdrp Gene ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Case Identification ◽  
E Gene ◽  
Sample Pooling ◽  
Community Transmission ◽  
Pcr Targeting

ABSTRACTSystematic testing of large population groups by RT-PCR is mandatory to Covid-19 case identification and contact tracing in order to minimize the likelyhood of resurgence in contagion. Sample pooling for RT-PCR has been effectively used to detect community transmission of SARS CoV-2. Nevertheless, this procedure may decrease the sensitivity of RT-PCR assays due to specimen dilution. We evaluated the efficacy of this strategy for diagnosis of Covid-19 using a sensitive commercially-available RT-PCR targeting SARS CoV-2 E and RdRp genes in a single reaction. A total of 20 mini-pools containing either 5 (n=10) or 10 (n=10) nasopharyngeal exudates collected in universal transport medium were made, each of which including a unique positive NP specimen. Positive specimens yielding CT <32 for the E gene (6 out of 10) or <35.2 for the RdRP gene (7 out of 10) were detected in mini-pools of both sizes. In contrast, most NP samples displaying CTs > 35.8 for the E gene or 35.7 for the RdRP gene remained undetected in mini-pools of 5 specimens (3/4 and 2/3, respectively) or in mini-pools of 10 samples (4/4 and 3/3, respectively.

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