Adverse effects of nasopharyngeal swabs: Three-dimensional printed versus commercial swabs

Scanning Electron Microscopy and EDX Spectroscopy of Commercial Swabs Used for COVID-19 Lateral Flow Testing

The chemical composition of COVID test swabs has not been examined beyond the manufacturer's datasheets. The unprecedented demand for swabs to conduct rapid lateral flow tests and nucleic acid amplification tests led to mass production, including 3D printing platforms. Manufacturing impurities could be present in the swabs and, if so, could pose a risk to human health. We used scanning electron microscopy and energy dispersive X-ray (EDX) spectroscopy to examine the ultrastructure of seven assorted brands of COVID test swabs and to identify and quantify their chemical elements. We detected eight unexpected elements, including transition metals, such as titanium and zirconium, the metalloid silicon, as well as post-transition metals aluminium and gallium, and the non-metal elements sulphur and fluorine. Some of the elements were detected as trace amounts, but for others, the amount was close to reported toxicological thresholds for inhalation routes. Experimental studies have shown that the detrimental effects of unexpected chemical elements include moderate to severe inflammatory states in the exposed epithelium as well as proliferative changes. Given the massive testing still being used in the context of the COVID pandemic, we urge caution in continuing to recommend repeated and frequent testing, particularly of healthy, non-symptomatic, individuals.

Providing Evidence for Dogma: Risk of Epistaxis After COVID-19 Nasal-Screening Swab

OBJECTIVE

There is anecdotal evidence SARS-CoV-2 (COVID) RT-PCR screening nasal swabs confer an elevated epistaxis risk. We aimed to assess the association between epistaxis and exposure to a COVID nasal swab.

STUDY DESIGN

A matched pairs design was used.

SETTING

The study was performed in a single, integrated healthcare system.

METHODS

All patients who received a single COVID nasal swab at our institution between April 2020 and March 2021 were included. McNemar's test was used to compare rates of epistaxis between the 7 days following the index COVID swab (hazard period), and the 7 days preceding the index COVID swab (control period). Conditional logistic regression was used to evaluate sociodemographic and clinical risk factors for epistaxis.

RESULTS

A total of 827,987 participants were included, with 1047 epistaxis encounters. The prevalence of epistaxis during the hazard and control periods were 0.08% and 0.04%, respectively. Swab exposure was associated with 1.92-fold odds of epistaxis during the hazard period (95% confidence interval [1.73, 2.12]). Older age, Asian/Pacific Islander (PI) (compared to white), male sex, hypertension, prior facial trauma, and warfarin or direct-acting oral anticoagulant use were also associated with significantly increased odds of epistaxis (p ≦ 0.01).

CONCLUSION

COVID nasal swabs are associated with increased odds of epistaxis. Physicians should counsel patients, particularly those at the highest risk, including a history of prior facial trauma, anticoagulants/antiplatelets, or hypertension.

High—throughput and automated screening for COVID-19

The COVID-19 pandemic has become a global challenge for the healthcare systems of many countries with 6 million people having lost their lives and 530 million more having tested positive for the virus. Robust testing and a comprehensive track and trace process for positive patients are essential for effective pandemic control, leading to high demand for diagnostic testing. In order to comply with demand and increase testing capacity worldwide, automated workflows have come into prominence as they enable high-throughput screening, faster processing, exclusion of human error, repeatability, reproducibility and diagnostic precision. The gold standard for COVID-19 testing so far has been RT-qPCR, however, different SARS-CoV-2 testing methods have been developed to be combined with high throughput testing to improve diagnosis. Case studies in China, Spain and the United Kingdom have been reviewed and automation has been proven to be promising for mass testing. Free and Open Source scientific and medical Hardware (FOSH) plays a vital role in this matter but there are some challenges to be overcome before automation can be fully implemented. This review discusses the importance of automated high-throughput testing, the different equipment available, the bottlenecks of its implementation and key selected case studies that due to their high effectiveness are already in use in hospitals and research centres.

Nanomaterials-based sensors for the detection of COVID-19: A review

With the threat of increasing SARS-CoV-2 cases looming in front of us and no effective and safest vaccine available to curb this pandemic disease due to its sprouting variants, many countries have undergone a lockdown 2.0 or planning a lockdown 3.0. This has upstretched an unprecedented demand to develop rapid, sensitive, and highly selective diagnostic devices that can quickly detect coronavirus (COVID-19). Traditional techniques like polymerase chain reaction have proven to be time-inefficient, expensive, labor intensive, and impracticable in remote settings. This shifts the attention to alternative biosensing devices that can be successfully used to sense the COVID-19 infection and curb the spread of coronavirus cases. Among these, nanomaterial-based biosensors hold immense potential for rapid coronavirus detection because of their noninvasive and susceptible, as well as selective properties that have the potential to give real-time results at an economical cost. These diagnostic devices can be used for mass COVID-19 detection to understand the rapid progression of the infection and give better-suited therapies. This review provides an overview of existing and potential nanomaterial-based biosensors that can be used for rapid SARS-CoV-2 diagnostics. Novel biosensors employing different detection mechanisms are also highlighted in different sections of this review. Practical tools and techniques required to develop such biosensors to make them reliable and portable have also been discussed in the article. Finally, the review is concluded by presenting the current challenges and future perspectives of nanomaterial-based biosensors in SARS-CoV-2 diagnostics.

Saliva as an alternative specimen to nasopharyngeal swabs for COVID-19 diagnosis: Review

Almost 2 years ago, the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered to be the causative agent of the disease COVID-19. Subsequently, SARS-CoV-2 has spread across the world infecting millions of people, resulting in the ongoing COVID-19 pandemic. The current 'gold standard' for COVID-19 diagnosis involves obtaining a nasopharyngeal swab (NPS) from the patient and testing for the presence of SARS-CoV-2 RNA in the specimen using real-time reverse transcription PCR (RT-qPCR). However, obtaining a NPS specimen is an uncomfortable and invasive procedure for the patient and is limited in its applicability to mass testing. Interest in saliva as an alternative diagnostic specimen is of increasing global research interest due to its malleability to mass testing, greater patient acceptability and overall ease of specimen collection. However, the current literature surrounding the sensitivity of saliva compared to NPS is conflicting. The aim of this review was to analyse the recent literature to assess the viability of saliva in COVID-19 diagnosis. We hypothesize that the discrepancies in the current literature are likely due to the variations in the saliva collection and processing protocols used between studies. The universal adaptation of an optimised protocol could alleviate these discrepancies and see saliva specimens be as sensitive, if not more, than NPS for COVID-19 diagnosis. Whilst saliva specimens are more complimentary to mass-testing, with the possibility of samples being collected from home, the RT-qPCR diagnostic process remains to be the rate-limiting step and therefore interest in salivary rapid antigen tests, which negate the wait-times of RT-qPCR with results available within 15-30 min, may be an answer to this.

CFD based analysis of 3D printed nasopharyngeal swabs for COVID-19 diagnostics

BACKGROUND AND OBJECTIVE

Additive manufacturing of nasopharyngeal (NP) swabs using 3D printing technology presents a viable alternative to address the immediate shortage problem of standard flock-headed swabs for rapid COVID-19 testing. Recently, several geometrical designs have been proposed for 3D printed NP swabs and their clinical trials are already underway. During clinical testing of the NP swabs, one of the key criteria to compare the efficacy of 3D printed swabs with traditional swabs is the collection efficiency. In this study, we report a numerical framework to investigate the collection efficiency of swabs utilizing the computational fluid dynamics (CFD) approach.

METHODS

Three-dimensional computational domain comprising of NP swab dipped in the liquid has been considered in this study to mimic the dip test procedure. The volume of fluid (VOF) method has been employed to track the liquid-air interface as the NP swab is pulled out of the liquid. The governing equations of the multiphase model have been solved utilizing finite-volume-based ANSYS Fluent software by imposing appropriate boundary conditions. Taguchi's based design of experiment analysis has also been conducted to evaluate the influence of geometric design parameters on the collection efficiency of NP swabs. The developed model has been validated by comparing the numerically predicted collection efficiency of different 3D printed NP swabs with the experimental findings.

RESULTS

Numerical predictions of the CFD model are in good agreement with the experimental results. It has been found that there prevails huge variability in the collection efficiency of the 3D printed designs of NP swabs available in the literature, ranging from 2 µl to 120 µl. Furthermore, even the smallest alteration in the geometric design parameter of the 3D printed NP swab results in significant changes in the amount of fluid captured.

CONCLUSIONS

The proposed framework would assist in quantifying the collection efficiency of the 3D printed designs of NP swabs, rapidly and at a low cost. Moreover, we demonstrate that the developed framework can be extended to optimize the designs of 3D printed swabs to drastically improve the performances of the existing designs and achieve comparable efficacy to that of conventionally manufactured swabs.

Performance study of the anterior nasal AMP SARS-CoV-2 rapid antigen test in comparison with nasopharyngeal rRT-PCR

Introduction.

The gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is real-time reverse transcription PCR (rRT-PCR), which is expensive, has a long turnaround time and requires special equipment and trained personnel. Nasopharyngeal swabs are uncomfortable, not suitable for certain patient groups and do not allow self-testing. Convenient, well-tolerated rapid antigen tests (RATs) for SARS-CoV-2 detection are called for.

Gap statement.

More real-life performance data on anterior nasal RATs are required.

Aim.

We set out to evaluate the anterior nasal AMP RAT in comparison with rRT-PCR in a hospital cohort.

Methodology.

The study included 175 patients, either hospitalized in a coronavirus disease 2019 (COVID-19) ward or screened in a preadmittance outpatient clinic. Two swabs were collected per patient: an anterior nasal one for the RAT and a combined naso-/oropharyngeal one for the rRT-PCR. Sixty-five patients (37%) were rRT-PCR-positive [cycle threshold (C_t) <40].

Results.

The anterior nasal AMP RAT showed an overall sensitivity and specificity of 29.2 % (18.6–41.8, 95 % CI) and 100.0 % (96.7–100.0, 95 % CI) respectively. In patients with a C_t value <25, <30 and <33, higher sensitivities were observed. Time since symptom onset was significantly higher in patients with a false-negative RAT (P=0.02).

Conclusion.

The anterior nasal AMP RAT showed low sensitivities in this cohort, especially in patients with a longer time since symptom onset. Further knowledge concerning the viral load and antigen expression over time and in different swabbing locations is needed to outline the usage time frame for SARS-CoV-2 RAT.

Complications Associated With Nasopharyngeal COVID-19 Testing: An Analysis of the MAUDE Database and Literature Review

BACKGROUND

Nasopharyngeal swab testing, which has greatly increased in utilization due to the COVID-19 pandemic, is generally safe and well-tolerated, although it may be rarely associated with adverse events.

METHODS

Publicly reported adverse events associated with nasopharyngeal COVID-19 testing within the Manufacturer and User Facility Device Experience (MAUDE) database and the published literature were queried.

RESULTS

A total of 129 adverse events were reported, including 66 from the MAUDE database and 63 from literature review. The most common complications were swab fracture resulting in retained foreign body (47%), followed by epistaxis (17%), and headache (11%). Seven (12%) of the reported retained foreign body cases required removal under general anesthesia, while 1 (5%) of the epistaxis cases required surgical intervention. The most serious adverse event was meningitis following cerebrospinal fluid leak.

CONCLUSIONS

Patients and healthcare providers should be aware of the potential risks associated with testing, with attention to ensuring proper technique, and be prepared to recognize and manage adverse events.

Role of the otolaryngologist in nasopharyngeal swab training: A case report and review of the literature

Nasopharyngeal swabs are commonly done in the medical field for a multitude of reasons, and they recently have been an essential component of widespread testing to control the spread of COVID-19. Although rare, improper technique when performing nasopharyngeal swabs has the potential to lead to injury or misleading test results. We present a case of uncontrolled epistaxis requiring hospitalization following a routine nasopharyngeal swab in a healthy patient. Both the complexity and variability of the anatomy of the nasopharynx can contribute to poor swabbing technique. Otolaryngologists should be encouraged to educate and support other healthcare workers to improve the yield and reduce the risk of harm due to nasopharyngeal swabs. Increased comfort levels with performing nasopharyngeal swabs will also improve the sensitivity of screening tests for common respiratory viruses such as influenza, Epstein-Barr virus (EBV), or bacteria such as Staphylococcus aureus.

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing. Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRp and N1 gene targets in NPS and saliva, respectively. Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833-0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample ( p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens. Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.

Development of an alternative saliva test for diagnosis of SARS-CoV-2 using TRIzol: Adapting to countries with lower incomes looking for a large-scale detection program

The use of saliva for the diagnosis of SARS-CoV-2 has shown to be a good alternative to nasopharyngeal swabs (NPS), since it permits self-collection, avoids the exposure of healthy persons to infected patients, reduces waiting times, eliminates the need of personal protective equipment and is non-invasive. Yet current saliva testing is still expensive due to the need of specialized tubes containing buffers to stabilize the RNA of SARS-CoV-2 and inactivate the virus. These tubes are expensive and not always accessible in sufficient quantities. We now developed an alternative saliva testing method, using TRIzol for extraction, viral inactivation, and storage of SARS-CoV-2 RNA, combined with RT-qPCR, which was comparable in its performance to NPS. Paired saliva samples and NPS were taken from 15 asymptomatic healthcare workers and one patient with SARS-CoV-2. Further 13 patients with SARS-CoV-2 were only saliva-tested. All the tests were performed according to CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel. Saliva (4 mL) was taken in sterile 50 mL tubes, 1.5 mL TRIzol were added and mixed. Our results show that 5 μL of saliva RNA extracted with TRIzol allow for an adequate detection of the virus in patients positive for SARS-CoV-2 and was equally sensitive to NPS in TRIzol. We conclude that saliva testing using TRIzol is a recommendable method for diagnosis of SARS-CoV-2 since it has several advantages over currently used saliva tests: it can be done with normal sterile tubes, does not need cold-chain handling, is stable at room temperature, is non-invasive and less costly, making it more accessible for low-income countries. Cheaper saliva testing using TRIzol is especially relevant for low-income countries to optimize diagnosis and help define quarantine durations for families, healthcare workers, schools, and other public workplaces, thus decreasing infections and mortality caused by SARS-CoV-2.

Complications of nasal SARS-CoV-2 testing: a review

Transnasal swab testing for the detection of SARS-CoV-2 is well established. The Centers for Disease Control and Prevention advocates swabbing either of the anterior nares, middle turbinate, or nasopharynx for specimen collection depending on available local resources. The purpose of this review is to investigate complications related to transnasal SARS-CoV-2 testing with specific attention to specimen collection site and swab approach. The literature demonstrates that while nasopharyngeal swabbing is associated with an increased risk of complications, it should remain the gold-standard test due to greater diagnostic accuracy relative to anterior nasal and middle turbinate swabs.

Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing

Introduction: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited. The aim of our study was to to assess SalivaDirect as an alternative method for COVID-19 testing. Methods: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings, respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using RdRP and N1 gene targets in NPS and saliva, respectively. Results: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833-0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample ( p=0.860). A highly significant correlation (r = 0.475, p<0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens. Conclusions: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Accurate and less invasive saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.

How to forget a "traumatic" experience: a case report of transient global amnesia after nasopharyngeal swab for Coronavirus disease 19

Background

Transient global amnesia (TGA) is a clinical syndrome characterized by a temporary short-term memory loss with inability to retain new memories, usually lasting 2 to 8 h. TGA may be related to several medical procedures, including angiography, general anesthesia, gastroscopy.

Case presentation

We report a 58-year-old woman who experiencing TGA one hour after the execution of her first-time nasopharyngeal swab for COVID-19. Brain MRI showed a typical punctate Diffusion Weight Image (DWI) hippocampal lesion.

Conclusions

This is the first report of TGA after the execution of nasopharyngeal swab for COVID-19. This association lengthen the list of medical procedures associated with TGA, and we discuss the possible plausible mechanisms by which a nasopharyngeal swab could trigger TGA.

Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

Preseptal cellulitis and infraorbital abscess as a complication of a routine COVID-19 swab

This case report describes a significant complication of a routine COVID-19 swab in a previously fit and well young patient who developed preseptal cellulitis and an infraorbital abscess as a consequence of the mentioned nasal swabbing. Other authors have previously reported various complications in connection with the use of nasal swabs, including retained swab fragments, epistaxis and cerebrospinal fluid leakage. To our knowledge, to date, this is the first reported case of an abscess as a consequence of COVID-19 swabbing. There has been a clear growth in the use of nasal swabbing worldwide over the last 9 months and many healthcare workers involved in COVID-19 prevention may not be aware of the potential risks of nasopharyngeal swabbing. The presented case highlights the need for better awareness of the complications of these routine tests and we hope that it will also lead to their safer implementation.

Nasopharyngeal Swab for COVID-19 Test Necessitating Mechanical Ventilation and Tracheostomy

We present the first-ever reported case of massive epistaxis following nasopharyngeal (NP) swabbing requiring intubation and tracheostomy. A 67-year-old male with a mechanical aortic valve on warfarin presented from a nursing home to the emergency department with hypoxia. NP swab for coronavirus disease 2019 (COVID-19) was obtained, immediately followed by significant epistaxis. Patient desaturated to low 80s requiring intubation for airway protection and hypoxemic respiratory failure. Anterior nasal packing was performed. The COVID-19 test resulted negative. Extubation was unsuccessful on days four and nine. The patient subsequently underwent tracheostomy and percutaneous endoscopic gastrostomy (PEG) tube placement. The patient was transferred to sub-acute rehabilitation with a tracheostomy tube on minimal ventilator support.

The World Health Organization (WHO) has recommended obtaining an NP swab in COVID-19 suspects to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcriptase polymerase chain reaction (PCR).A study found that NP swabbing was associated with epistaxis in approximately 5-10% of the cases. Nursing home populations are at higher risk for COVID-19 and also reported to have increased use of oral anticoagulation for chronic atrial fibrillation with other co-morbidities (high CHADVASc score) which may increase bleeding risk with NP swabbing. Less invasive methods such as salivary and mid-turbinate sampling, nasal swab or saliva can be a better alternative sample for detecting SARS-CoV-2 as recommended by the Centers for Disease Control and Prevention (CDC) and suggested by FDA. Positive PCR testing beyond nine days of illness is likely due to persistent dead virus particles and thus repeat testing is not suggested. Obtaining a history of bleeding diathesis, use of oral anticoagulants and consideration of NP anatomy is advised before swabbing.

This case report raises the concern against inadvertent NP swabbing in cases with a low pretest probability of COVID-19 infection with higher bleeding risk.

Prospective clinical validation of 3D printed nasopharyngeal swabs for diagnosis of COVID-19

COVID-19 greatly disrupted the global supply chain of nasopharyngeal swabs, and thus new products have come to market with little data to support their use. In this prospective study, 2 new 3D printed nasopharyngeal swab designs were evaluated against the standard, flocked nasopharyngeal swab for the diagnosis of COVID-19. Seventy adult patients (37 COVID-positive and 33 COVID-negative) underwent consecutive diagnostic reverse transcription polymerase chain reaction testing, with a flocked swab followed by one or two 3D printed swabs. The "Lattice Swab" (manufacturer Resolution Medical) demonstrated 93.3% sensitivity (95% CI, 77.9%-99.2%) and 96.8% specificity (83.3%-99.9%), yielding κ = 0.90 (0.85-0.96). The "Origin KXG" (manufacturer Origin Laboratories) demonstrated 83.9% sensitivity (66.3%-94.6%) and 100% specificity (88.8%-100.0%), yielding κ = 0.84 (0.77-0.91). Both 3D printed nasopharyngeal swab results have high concordance with the control swab results. The decision to use 3D printed nasopharyngeal swabs during the COVID-19 pandemic should be strongly considered by clinical and research laboratories.

Sensitive detection and quantification of SARS-CoV-2 in saliva

Saliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

The Yield and Consistency of the Detection of SARS-CoV-2 in Multiple Respiratory Specimens

Background

Few studies have compared the yield of reverse transcription polymerase chain reaction (RT-PCR) assays in nasopharyngeal swabs, oropharyngeal swabs, and sputum for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection.

Methods

We conducted an observational study in Beijing Ditan Hospital, China. Specimens including nasopharyngeal swabs, oropharyngeal swabs, and sputum from confirmed coronavirus 2019 patients were collected for RT-PCR testing. Disease duration was calculated from the date of symptom onset to the date of specimen collection and divided into 3 groups: ≤14 days, 14–21 days, and >21 days. We compared positive rates across the 3 specimens collected. The kappa coefficient was used to evaluate the consistency of RT-PCR results between different specimens.

Results

A total of 291 specimens were collected and tested from 43 confirmed patients. Among specimens collected with a disease duration of ≤14 days, the positive rate was highest in sputum (79.2%); this rate was significantly higher than that in nasopharyngeal swabs (37.5%; P = .003) and oropharyngeal swabs (20.8%; P < .001). Similar findings were observed with the disease durations of 14–21 days and >21 days. The consistency of testing results between nasopharyngeal swabs and oropharyngeal swabs was low with the disease durations of ≤14 days and >21 days. The consistency between the sputum and oropharyngeal swabs and between the sputum and nasopharyngeal swabs was very low across all 3 disease durations, with statistical significance.

Conclusions

Compared with nasopharyngeal swabs and oropharyngeal swabs, sputum had the highest yield of SARS-CoV-2 detection. Nasopharyngeal swabs and oropharyngeal swabs had a similar yield. If sputum is not feasible, a nasopharyngeal swab can be recommended for the detection of SARS-CoV-2, and early testing is needed.