Dataset Information

Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2.

ABSTRACT: In the setting of supply chain shortages of nasopharyngeal (NP) swabs, we sought to compare the ability of nasopharyngeal, midturbinate nasal, and oropharyngeal swabs (NPS, MTS, and OPS) to detect SARS-CoV-2. Community and hospitalized participants post-COVID-19 diagnosis were swabbed and tested for SARS-CoV-2 by PCR. Thirty-six participants had all 3 swabs collected. Using detection at any site as the standard, the percent positive agreements were 90% (95% CI 74.4-96.5), 80% (70.3-94.7) and 87% (62.7-90.5) for NPS, MTS, and OPS, respectively. Subsequently, 43 participants had OPS and NPS collected. Thirty-nine were positive with a percent positive agreement of 82.1% (95% CI 67.3-91.0) for OPS and 87.2% (73.3-94.4) for NPS. Combining all 79 patients tested, 67 were positive at either site with a positive agreement was 86.5% (76.4-92.7) for OPS and 91.1% (81.8-95.8) for NPS. OPS are an acceptable alternative to NPS for the detection of SARS-CoV-2 infections.

SUBMITTER: Berenger BM

PROVIDER: S-EPMC8675123 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2.

Berenger Byron M BM Fonseca Kevin K Schneider Angela R AR Hu Jia J Zelyas Nathan N

Diagnostic microbiology and infectious disease 20211216 4

In the setting of supply chain shortages of nasopharyngeal (NP) swabs, we sought to compare the ability of nasopharyngeal, midturbinate nasal, and oropharyngeal swabs (NPS, MTS, and OPS) to detect SARS-CoV-2. Community and hospitalized participants post-COVID-19 diagnosis were swabbed and tested for SARS-CoV-2 by PCR. Thirty-six participants had all 3 swabs collected. Using detection at any site as the standard, the percent positive agreements were 90% (95% CI 74.4-96.5), 80% (70.3-94.7) and 87% ...[more]

PMID: 35007959

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Project description:Large-scale population testing is a key tool to mitigate the spread of respiratory pathogens, such as the current COVID-19 pandemic, where swabs are used to collect samples in the upper airways (e.g., nasopharyngeal and midturbinate nasal cavities) for diagnostics. However, the high volume of supplies required to achieve large-scale population testing has posed unprecedented challenges for swab manufacturing and distribution, resulting in a global shortage that has heavily impacted testing capacity worldwide and prompted the development of new swabs suitable for large-scale production. Newly designed swabs require rigorous preclinical and clinical validation studies that are costly and time-consuming (i.e., months to years long); reducing the risks associated with swab validation is therefore paramount for their rapid deployment. To address these shortages, we developed a 3D-printed tissue model that mimics the nasopharyngeal and midturbinate nasal cavities, and we validated its use as a new tool to rapidly test swab performance. In addition to the nasal architecture, the tissue model mimics the soft nasal tissue with a silk-based sponge lining, and the physiological nasal fluid with asymptomatic and symptomatic viscosities of synthetic mucus. We performed several assays comparing standard flocked and injection-molded swabs. We quantified the swab pickup and release and determined the effect of viral load and mucus viscosity on swab efficacy by spiking the synthetic mucus with heat-inactivated SARS-CoV-2 virus. By molecular assay, we found that injected molded swabs performed similarly or superiorly in comparison to standard flocked swabs, and we underscored a viscosity-dependent difference in cycle threshold values between the asymptomatic and symptomatic mucuses for both swabs. To conclude, we developed an in vitro nasal tissue model that corroborated previous swab performance data from clinical studies; this model will provide to researchers a clinically relevant, reproducible, safe, and cost-effective validation tool for the rapid development of newly designed swabs.

Project description:Saliva is an attractive sample for detecting SARS-CoV-2. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs. We followed close contacts of COVID-19 cases for up to 14 days from the last exposure and collected self-reported symptoms, midturbinate swabs (MTS), and saliva every 2 or 3 days. Ct values, viral load, and frequency of viral detection by MTS and saliva were compared. Fifty-eight contacts provided 200 saliva-MTS pairs, and 14 contacts (13 with symptoms) had one or more positive samples. Saliva and MTS had similar rates of viral detection (P = 0.78) and substantial agreement (κ = 0.83). However, sensitivity varied significantly with time since symptom onset. Early on (days -3 to 2), saliva had 12 times (95% CI: 1.2, 130) greater likelihood of viral detection and 3.2 times (95% CI: 2.8, 3.8) higher RNA copy numbers compared to MTS. After day 2 of symptoms, there was a nonsignificant trend toward greater sensitivity using MTS. Saliva and MTS demonstrated high agreement making saliva a suitable alternative to MTS for SARS-CoV-2 detection. Saliva was more sensitive early in the infection when the transmission was most likely to occur, suggesting that it may be a superior and cost-effective screening tool for COVID-19. IMPORTANCE The findings of this manuscript are increasingly important with new variants that appear to have shorter incubation periods emerging, which may be more prone to detection in saliva before detection in nasal swabs. Therefore, there is an urgent need to provide the science to support the use of a detection method that is highly sensitive and widely acceptable to the public to improve screening rates and early detection. The manuscript presents the first evidence that saliva-based RT-PCR is more sensitive than MTS-based RT-PCR in detecting SARS-CoV-2 during the presymptomatic period - the critical period for unwitting onward transmission. Considering other advantages of saliva samples, including the lower cost, greater acceptability within the general population, and less risk to health care workers, our findings further supported the use of saliva to identify presymptomatic infection and prevent transmission of the virus.

Dataset Information

Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2.

Publications

Clinical evaluation of nasopharyngeal, midturbinate nasal and oropharyngeal swabs for the detection of SARS-CoV-2.

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