Performance of at-home self-collected saliva and nasal-oropharyngeal swabs in the surveillance of COVID-19

Evaluating User Experience and DNA Yield from Self-Collection Devices

BACKGROUND

The COVID-19 pandemic emphasized an urgent need for devices used in the self-collection of biospecimens in an evolving patient care system. The mailing of biospecimen self-collection kits to patients, with samples returned via mail, provides a more convenient testing regimen, but could also impart patient sampling variabilities. User compliance with device directions is central to downstream testing of collected biospecimens and clear instructions are central to this goal.

METHODS

Here, we performed an evaluation of 10 oral DNA collection devices involving either swab or saliva self-collection and analyzed ease of use and comfort level with a device, as well as DNA recovery quantity/quality and sample stability.

RESULTS

We show that while these DNA quality/quantity metrics are comparable between devices, users prefer direct saliva collection over swab-based devices.

CONCLUSIONS

This information is useful in guiding future experiments including their use in human RNA, microbial, or viral sample collection/recovery and their use in clinical testing.

Salivette® Cortisol versus oropharyngeal swabbing for the detection of SARS-CoV-2 infection

BACKGROUND

Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by naso/oropharyngeal swabbing may expose health-care workers to the virus and is technically challenging. The Salivette® is an alternative saliva-collection device with an oral cotton swab containing citric acid to stimulate saliva production, which may have an unpleasant taste. We present a pilot study comparing the Salivette® Cortisol (SC), which uses a synthetic swab without citric acid, against oropharyngeal swabbing for the detection of SARS-CoV-2 by reverse transcription quantitative polymerase chain reaction (RT-qPCR).

RESEARCH DESIGN AND METHODS

Symptomatic SARS-CoV-2-positive patients were sampled at various timepoints. The number of patients positive/negative for SARS-CoV-2 in oropharyngeal swab and SC samples and the percentage of patients testing true positive/true negative for SARS-CoV-2 from SC samples were determined. Positivity was defined by RT-qPCR amplification of 2/3 target SARS-CoV-2 N, ORF1, and S gene sequences.

RESULTS

SC demonstrated 100% specificity, 52.2% sensitivity, and positive correlation with oropharyngeal swabbing for the detection of the SARS-CoV-2 S gene. In later-stage disease, lower viral load was observed in SC samples compared with oropharyngeal swabs.

CONCLUSIONS

The SC may be an alternative for SARS-CoV-2 detection where naso/oropharyngeal swabbing is not feasible/available. This technique also confirms observations that the detection of SARS-CoV-2 in the upper airway may vary due to viral load over the disease course.

TRIAL REGISTRATION

NCT04599959.

The Cabarrus County COVID-19 Prevalence and Immunity (C3PI) Study: design, methods, and baseline characteristics

OBJECTIVES

Coronavirus Disease 2019 (COVID-19) is a viral illness with public health importance. The Cabarrus County COVID-19 Prevalence and Immunity (C3PI) Study is a prospective, longitudinal cohort study designed to contribute valuable information on community prevalence of active COVID-19 infection and SARS-CoV-2 antibodies as the pandemic and responses to it have and continue to evolve. We present the rationale, study design, and baseline characteristics of the C3PI Study.

METHODS

We recruited 1,426 participants between June 2020 and August 2020 from the Measurement to Understand the Reclassification of Disease of Cabarrus/Kannapolis (MURDOCK) Study Community Registry and Biorepository, a previously established, community-based, longitudinal cohort. Participants completed a baseline survey and follow-up surveys every two weeks. A nested weighted, random sub-cohort (n=300) was recruited to measure the incidence and prevalence of active COVID-19 infection and SARS-CoV-2 IgG antibodies.

RESULTS

The sub-cohort was younger (56 vs 61 years), had more men (39.0% vs 30.9%), and a higher proportion of Hispanic (11.0% vs 5.1%) and Black participants (17.0% vs 8.2%) compared with the overall cohort. They had similar anthropometrics and medical histories, but a greater proportion of the sub-cohort had a higher educational degree (36.1% vs 31.3%) and reported a pre-pandemic annual household income of >$90,000 (57.1% vs 47.9%).

CONCLUSION

This study is part of a multisite consortium that will provide critical data on the epidemiology of COVID-19 and community perspectives about the pandemic, behaviors and mitigation strategies, and individual and community burden in North Carolina.

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.

ESCMID COVID-19 guidelines: diagnostic testing for SARS-CoV-2

SCOPE

The objective of these guidelines is to identify the most appropriate diagnostic test and/or diagnostic approach for SARS-CoV-2. The recommendations are intended to provide guidance to clinicians, clinical microbiologists, other health care personnel, and decision makers.

METHODS

An ESCMID COVID-19 guidelines task force was established by the ESCMID Executive Committee. A small group was established, half appointed by the chair and the remaining selected with an open call. Each panel met virtually once a week. For all decisions, a simple majority vote was used. A list of clinical questions using the PICO (population, intervention, comparison, outcome) format was developed at the beginning of the process. For each PICO, two panel members performed a literature search focusing on systematic reviews, with a third panellist involved in case of inconsistent results. Quality of evidence assessment was based on the GRADE-ADOLOPMENT (Grading of Recommendations Assessment, Development and Evaluation - adoption, adaptation, and de novo development of recommendations) approach.

RECOMMENDATIONS

A total of 43 PICO questions were selected that involve the following types of populations: (a) patients with signs and symptoms of COVID-19; (b) travellers, healthcare workers, and other individuals at risk for exposure to SARS-CoV-2; (c) asymptomatic individuals, and (d) close contacts of patients infected with SARS-CoV-2. The type of diagnostic test (commercial rapid nucleic acid amplification tests and rapid antigen detection), biomaterial, time since onset of symptoms/contact with an infectious case, age, disease severity, and risk of developing severe disease are also taken into consideration.

Use of Saliva and RT-PCR Screening for SARS-CoV-2 Variants of Concern: Surveillance and Monitoring

Genomic surveillance has been applied since the beginning of the COVID-19 pandemic to track the spread of virus, leading to characterization of multiple SARS-CoV-2 variants, including Variants of Concern (VOC). Although sequencing is the standard method, rapid molecular test for screening and surveillance of VOC is considered for detection. Furthermore, using alternative saliva as specimen collection, facilitates the implementation of a less invasive, self-collected sample. In this study, we applied a combinatory strategy of saliva collection and RT-PCR for SARS-CoV-2 VOC detection. Saliva samples from patients attending at a tertiary hospital with suspected COVID-19 were collected and SARS-CoV-2 RNA was detected using SARS-CoV-2 RT-qPCR reagent kit (PerkinElmer). Positive saliva samples were screened for SARS-CoV-2 VOC with previously described RT-PCR for Alpha, Beta and Gamma variants. Saliva samples were positive in 171 (53%) of 324 tested. A total of 108 (74%) from positive samples were also positive for VOC by RT-PCR screening. Those samples were found between January and August 2021. This approach allowed us to successfully use an alternative and complementary tool to genomic surveillance to monitoring the circulation of SARS-CoV-2 VOC in the studied population. This article is protected by copyright. All rights reserved.

Saliva as a diagnostic specimen for SARS-CoV-2 detection: a scoping review

Objectives

This scoping review aims to summarize the diagnostic value of saliva assessed from current studies that (1) compare its performance in reverse transcriptase‐polymerase chain reaction testing to nasopharyngeal swabs, (2) evaluate its performance in rapid and point‐of‐care COVID‐19 diagnostic tests, and (3) explore its use as a specimen for detecting anti‐SARS‐CoV‐2 antibodies.

Materials and Methods

A systematic search was performed on the following databases: Medline and Embase (Ovid), World Health Organization, Centers for Disease Control and Prevention, and Global Health (Ovid) from January 2019 to September 2021. Of the 657 publications identified from the searches, n = 146 articles were included in the final scoping review.

Results

Our findings showcase that salivary samples exceed nasopharyngeal swabs in detecting SARS‐CoV‐2 using reverse transcriptase‐polymerase chain reaction testing in several studies. A select number of rapid antigen and point‐of‐care tests from the literature were also identified capable of high detection rates using saliva. Moreover, anti‐SARS‐CoV‐2 antibodies have been shown to be detectable in saliva through biochemical assays.

Conclusion

We highlight the potential of saliva as an all‐rounded specimen in detecting SARS‐CoV‐2. However, future large‐scale clinical studies will be needed to support its widespread use as a non‐invasive clinical specimen for COVID‐19 testing.

Towards the direct detection of viral materials at the surface of protective face masks via infrared spectroscopy

The ongoing COVID-19 pandemic represents a considerable risk for the general public and especially for health care workers. To avoid an overloading of the health care system and to control transmission chains, the development of rapid and cost-effective techniques allowing for the reliable diagnosis of individuals with acute respiratory infections are crucial. Uniquely, the present study focuses on the development of a direct face mask sampling approach, as worn (i.e., used) disposable face masks contain exogenous environmental constituents, as well as endogenously exhaled breath aerosols. Optical techniques—and specifically infrared (IR) molecular spectroscopic techniques—are promising tools for direct virus detection at the surface of such masks. In the present study, a rapid and non-destructive approach for monitoring exposure scenarios via medical face masks using attenuated total reflection infrared spectroscopy is presented. Complementarily, IR external reflection spectroscopy was evaluated in comparison for rapid mask analysis. The utility of a face mask-based sampling approach was demonstrated by differentiating water, proteins, and virus-like particles sampled onto the mask. Data analysis using multivariate statistical algorithms enabled unambiguously classifying spectral signatures of individual components and biospecies. This approach has the potential to be extended towards the rapid detection of SARS-CoV-2—as shown herein for the example of virus-like particles which are morphologically equivalent to authentic virus—without any additional sample preparation or elaborate testing equipment at laboratory facilities. Therefore, this strategy may be implemented as a routine large-scale monitoring routine, e.g., at health care institutions, nursing homes, etc. ensuring the health and safety of medical personnel.

Provider Perspectives on the Current Use of Lithium Medications and Lithium Monitoring Practices for Psychiatric Conditions

PURPOSE

Despite lithium being a gold standard treatment for bipolar disorder, the percentage of patients with bipolar disorder who are prescribed lithium medication has declined in many parts of the world over the past two decades. The use of lithium is limited by its narrow therapeutic window and adverse side effects, which necessitates frequent serum lithium monitoring; hence, there is a critical need for improved ways to monitor lithium levels in psychiatric patients. We have recently shown that saliva lithium levels are highly correlated with those in blood, thereby presenting an alternative to venipuncture. Saliva sampling could open the door for at-home collections - potential that has been exemplified throughout the COVID-19 pandemic - thereby allowing samples to be collected remotely and delivered to a specific site for testing. In addition, prototype point-of-care devices have been developed by others for serum lithium monitoring, suggesting potential for a saliva lithium monitoring device. Our objective was to query the perspectives of American psychiatrists on lithium treatment practices and obstacles, the potential for at-home saliva collection and point-of-care devices, for lithium monitoring, as an alternative to pathology-based blood testing.

METHODS

Data was collected through an online, anonymous survey, distributed to American psychiatric societies.

RESULTS

Sixty-five respondents from 21 American states completed the survey. The majority of respondents were female, over 65 years of age, and/or had practiced for 30 years or more. The most frequent obstacles encountered with regard to lithium monitoring were adverse drug effects, and the need for monitoring. Overall, respondents believed saliva lithium monitoring and point-of-care devices would be useful, however raised concerns regarding validity and time-delay.

CONCLUSION

Point-of-care devices and saliva lithium monitoring are promising alternatives to blood testing that would be welcomed by psychiatric societies, however, require extensive development and validation before implementation into a clinical setting.

Acceptability of Community Saliva Testing in Controlling the COVID-19 Pandemic: Lessons Learned from Two Case Studies in Nursing Homes and Schools

Current public health debate centers on COVID-19 testing methods and strategies. In some communities, high transmission risk may justify routine testing, and this requires test methods that are safe and efficient for both patients and the administrative or health-care workers administering them. Saliva testing appears to satisfy those criteria. There is, however, little documentation on the acceptability of this method among beneficiaries. This article presents the lessons learned from a pilot study on the use of saliva testing for routine screening of nursing home and secondary school personnel in Wallonia (the French-speaking part of Belgium), conducted in December 2020 to April 2021, respectively. Administrators at the facilities in question seemed to think highly of saliva testing and wished to continue it after the pilot study was over. This result reinforces the criteria (the noninvasive aspect, in particular) supporting a key role for saliva testing in monitoring community spread of the virus. Nevertheless, wider-scale deployment of this particular method will only be possible if the testing strategy as a whole takes a health promotion approach.

Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage

Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful alternative. However, there are limited data directly comparing several different types of self-collected materials to determine which material is preferable. A total of 102 predominantly symptomatic adults with a confirmed SARS-CoV-2 infection self-collected native saliva, a tongue swab, a mid-turbinate nasal swab, saliva obtained by chewing a cotton pad and gargle lavage, within 48 h of initial diagnosis. Sample collection was unsupervised. Both native saliva and gargling with tap water had high diagnostic sensitivity of 92.8% and 89.1%, respectively. Nasal swabs had a sensitivity of 85.1%, which was not significantly inferior to saliva (p = 0.092), but 16.6% of participants reported they had difficult in self-collection of this sample. A tongue swab and saliva obtained by chewing a cotton pad had a significantly lower sensitivity of 74.2% and 70.2%, respectively. Diagnostic sensitivity was not related to the presence of clinical symptoms or to age. When comparing self-collected specimens from different material, saliva, gargle lavage or mid-turbinate nasal swabs may be considered for most symptomatic patients. However, complementary experiments are required to verify that differences in performance observed among the five sampling modes were not attributed to collection impairment.

Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic

Without modern medical management and vaccines, the severity of the Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) might approach the magnitude of 1894-plague (12 million deaths) and 1918-A(H1N1) influenza (50 million deaths) pandemics. The COVID-19 pandemic was heralded by the 2003 SARS epidemic which led to the discovery of human and civet SARS-CoV-1, bat SARS-related-CoVs, Middle East respiratory syndrome (MERS)-related bat CoV HKU4 and HKU5, and other novel animal coronaviruses. The suspected animal-to-human jumping of 4 betacoronaviruses including the human coronaviruses OC43(1890), SARS-CoV-1(2003), MERS-CoV(2012), and SARS-CoV-2(2019) indicates their significant pandemic potential. The presence of a large reservoir of coronaviruses in bats and other wild mammals, culture of mixing and selling them in urban markets with suboptimal hygiene, habit of eating exotic mammals in highly populated areas, and the rapid and frequent air travels from these areas are perfect ingredients for brewing rapidly exploding epidemics. The possibility of emergence of a hypothetical SARS-CoV-3 or other novel viruses from animals or laboratories, and therefore needs for global preparedness should not be ignored. We reviewed representative publications on the epidemiology, virology, clinical manifestations, pathology, laboratory diagnostics, treatment, vaccination, and infection control of COVID-19 as of 20 January 2021, which is 1 year after person-to-person transmission of SARS-CoV-2 was announced. The difficulties of mass testing, labour-intensive contact tracing, importance of compliance to universal masking, low efficacy of antiviral treatment for severe disease, possibilities of vaccine or antiviral-resistant virus variants and SARS-CoV-2 becoming another common cold coronavirus are discussed.

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.

Feasibility of Rapid Diagnostic Technology for SARS-CoV-2 Virus Using a Trace Amount of Saliva

Containment of SARS-CoV-2 has become an urgent global issue. To overcome the problems of conventional quantitative polymerase chain reaction (qPCR) tests, we verified the usefulness of a mobile qPCR device that utilizes mouthwash to obtain a saliva sample with the aim of developing a rapid diagnostic method for SARS-CoV-2. First, we examined whether anyone could easily operate this device. Then, we examined whether RNA in the mouthwash could be detected in a short time. In addition, we investigated whether it was possible to diagnose SARS-CoV-2 infection using mouthwash obtained from COVID-19 patients undergoing hospitalization. The results revealed that all subjects were able to complete the operation properly without error. In addition, RNase P was detected in the mouthwash without pretreatment. The average detection time was 18 min, which is significantly shorter than conventional qPCR devices. Furthermore, this device detected SARS-CoV-2 in the mouthwash of a COVID-19 patient undergoing hospitalization. The above findings verified the efficacy of this diagnostic method, which had a low risk of infection, was technically simple, and provided stable results. Therefore, this method is useful for the rapid detection of SARS-CoV-2.

Robust Saliva-Based RNA Extraction-Free One-Step Nucleic Acid Amplification Test for Mass SARS-CoV-2 Monitoring

Early diagnosis with rapid detection of the virus plays a key role in preventing the spread of infection and in treating patients effectively. In order to address the need for a straightforward detection of SARS-CoV-2 infection and assessment of viral spread, we developed rapid, sensitive, extraction-free one-step reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and reverse transcription loop-mediated isothermal amplification (RT-LAMP) tests for detecting SARS-CoV-2 in saliva. We analyzed over 700 matched pairs of saliva and nasopharyngeal swab (NSB) specimens from asymptomatic and symptomatic individuals. Saliva, as either an oral cavity swab or passive drool, was collected in an RNA stabilization buffer. The stabilized saliva specimens were heat-treated and directly analyzed without RNA extraction. The diagnostic sensitivity of saliva-based RT-qPCR was at least 95% in individuals with subclinical infection and outperformed RT-LAMP, which had at least 70% sensitivity when compared to NSBs analyzed with a clinical RT-qPCR test. The diagnostic sensitivity for passive drool saliva was higher than that of oral cavity swab specimens (95% and 87%, respectively). A rapid, sensitive one-step extraction-free RT-qPCR test for detecting SARS-CoV-2 in passive drool saliva is operationally simple and can be easily implemented using existing testing sites, thus allowing high-throughput, rapid, and repeated testing of large populations. Furthermore, saliva testing is adequate to detect individuals in an asymptomatic screening program and can help improve voluntary screening compliance for those individuals averse to various forms of nasal collections.

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.

Potential Roles of the Free Salivary Microbiome Dysbiosis in Periodontal Diseases

Saliva is a vital mediator in the oral cavity. The dysbiosis of free bacteria in saliva might be related to the onset, development, prognosis, and recurrence of periodontal diseases, but this potential relationship is still unclear. The objective of this study was to investigate the potential roles of the free salivary microbiome in different periodontal statuses, their reaction to nonsurgical periodontal therapy, and differences between diseased individuals after treatment and healthy persons. We recruited 15 healthy individuals, 15 individuals with gingivitis, and 15 individuals with stage I/II generalized periodontitis. A total of 90 unstimulated whole saliva samples were collected and sequenced using full-length bacterial 16S rRNA gene sequencing. We found that as the severity of disease increased, from healthy to gingivitis and periodontitis, the degree of dysbiosis also increased. A higher abundance of Prevotella intermedia and Catonella morbi and a lower abundance of Porphyromonas pasteri, Prevotella nanceiensis, and Haemophilus parainfluenzae might be biomarkers of periodontitis, with an area under curve (AUC) reaching 0.9733. When patients received supragingival scaling, there were more pathogens related to recolonization in the saliva of periodontitis patients than in healthy persons. Even after effective nonsurgical periodontal therapy, individuals with periodontitis displayed a more dysbiotic and pathogenic microbial community in their saliva than healthy individuals. Therefore, the gradual transition in the entire salivary microbial community from healthy to diseased includes a gradual shift to dysbiosis. Free salivary pathogens might play an important role in the recolonization of bacteria as well as the prognosis and recurrence of periodontal diseases.

Feasibility and Diagnostic Accuracy of Saliva-Based SARS-CoV-2 Screening in Educational Settings and Children Aged <12 Years

Children have been disproportionately affected during the COVID-19 pandemic. We aimed to assess a saliva-based algorithm for SARS-CoV-2 testing to be used in schools and childcare institutions under pandemic conditions. A weekly SARS-CoV-2 sentinel study in primary schools, kindergartens, and childcare facilities was conducted over a 12-week-period. In a sub-study covering 7 weeks, 1895 paired oropharyngeal and saliva samples were processed for SARS-CoV-2 rRT-PCR testing in both asymptomatic children (n = 1243) and staff (n = 652). Forty-nine additional concurrent swab and saliva samples were collected from SARS-CoV-2 infected patients (patient cohort). The Salivette^® system was used for saliva collection and assessed for feasibility and diagnostic performance. For children, a mean of 1.18 mL saliva could be obtained. Based on results from both cohorts, the Salivette^® testing algorithm demonstrated the specificity of 100% (95% CI 99.7–100) and sensitivity of 94.9% (95% CI 81.4–99.1) with oropharyngeal swabs as reference. Agreement between sampling systems was 100% for moderate to high viral load situations (defined as Ct-values <33 from oropharyngeal swabs). Comparative analysis of Ct-values derived from saliva vs. oropharyngeal swabs demonstrated a significant difference (mean 4.23; 95% CI 2.48–6.00). In conclusion, the Salivette^® system proved to be an easy-to-use, safe and feasible saliva collection method and a more pleasant alternative to oropharyngeal swabs for SARS-CoV-2 testing in children aged 3 years and above.

Science's Response to CoVID-19

CoVID-19 is a multi-symptomatic disease which has made a global impact due to its ability to spread rapidly, and its relatively high mortality rate. Beyond the heroic efforts to develop vaccines, which we do not discuss herein, the response of scientists and clinicians to this complex problem has reflected the need to detect CoVID-19 rapidly, to diagnose patients likely to show adverse symptoms, and to treat severe and critical CoVID-19. Here we aim to encapsulate these varied and sometimes conflicting approaches and the resulting data in terms of chemistry and biology. In the process we highlight emerging concepts, and potential future applications that may arise out of this immense effort.

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.

Evaluation of RNA Extraction-Free Method for Detection of SARS-CoV-2 in Salivary Samples for Mass Screening for COVID-19

In this COVID-19 pandemic, there is a dire need for cost-effective and less time-consuming alternatives for SARS-CoV-2 testing. The RNA extraction-free method for detecting SARS-CoV-2 in saliva is a promising option. This study found that it has high sensitivity (85.34%), specificity (95.04%), and was comparable to the gold standard nasopharyngeal swab (NPS) sample tests. The method showed good agreement between salivary and NPS samples, with a kappa coefficient of 0.797. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fisher Applied Biosystems showed high sensitivity, positive predictive value (PPV), and negative predictive value (NPV) but also showed a higher percentage of invalid reports. On the other hand, the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples, and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction-free method for salivary sample serves as an effective alternative screening method for COVID-19.

Screening for SARS-CoV-2 by RT-PCR: Saliva or nasopharyngeal swab? Rapid review and meta-analysis

BACKGROUND

Diagnosis of COVID-19 in symptomatic patients and screening of populations for SARS-CoV-2 infection require access to straightforward, low-cost and high-throughput testing. The recommended nasopharyngeal swab tests are limited by the need of trained professionals and specific consumables and this procedure is poorly accepted as a screening method In contrast, saliva sampling can be self-administered.

METHODS

In order to compare saliva and nasopharyngeal/oropharyngeal samples for the detection of SARS-CoV-2, we designed a meta-analysis searching in PubMed up to December 29th, 2020 with the key words "(SARS-CoV-2 OR COVID-19 OR COVID19) AND (salivary OR saliva OR oral fluid)) NOT (review[Publication Type]) NOT (PrePrint[Publication Type])" applying the following criteria: records published in peer reviewed scientific journals, in English, with at least 15 nasopharyngeal/orapharyngeal swabs and saliva paired samples tested by RT-PCR, studies with available raw data including numbers of positive and negative tests with the two sampling methods. For all studies, concordance and sensitivity were calculated and then pooled in a random-effects model.

FINDINGS

A total of 377 studies were retrieved, of which 50 were eligible, reporting on 16,473 pairs of nasopharyngeal/oropharyngeal and saliva samples. Meta-analysis showed high concordance, 92.5% (95%CI: 89.5-94.7), across studies and pooled sensitivities of 86.5% (95%CI: 83.4-89.1) and 92.0% (95%CI: 89.1-94.2) from saliva and nasopharyngeal/oropharyngeal swabs respectively. Heterogeneity across studies was 72.0% for saliva and 85.0% for nasopharyngeal/oropharyngeal swabs.

INTERPRETATION

Our meta-analysis strongly suggests that saliva could be used for frequent testing of COVID-19 patients and "en masse" screening of populations.

Diagnosis of SARS-Cov-2 Infection by RT-PCR Using Specimens Other Than Naso- and Oropharyngeal Swabs: A Systematic Review and Meta-Analysis

The rapid and accurate testing of SARS-CoV-2 infection is still crucial to mitigate, and eventually halt, the spread of this disease. Currently, nasopharyngeal swab (NPS) and oropharyngeal swab (OPS) are the recommended standard sampling techniques, yet, these have some limitations such as the complexity of collection. Hence, several other types of specimens that are easier to obtain are being tested as alternatives to nasal/throat swabs in nucleic acid assays for SARS-CoV-2 detection. This study aims to critically appraise and compare the clinical performance of RT-PCR tests using oral saliva, deep-throat saliva/posterior oropharyngeal saliva (DTS/POS), sputum, urine, feces, and tears/conjunctival swab (CS) against standard specimens (NPS, OPS, or a combination of both). In this systematic review and meta-analysis, five databases (PubMed, Scopus, Web of Science, ClinicalTrial.gov and NIPH Clinical Trial) were searched up to the 30th of December, 2020. Case-control and cohort studies on the detection of SARS-CoV-2 were included. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2). We identified 1560 entries, 33 of which (1.1%) met all required criteria and were included for the quantitative data analysis. Saliva presented the higher accuracy, 92.1% (95% CI: 70.0-98.3), with an estimated sensitivity of 83.9% (95% CI: 77.4-88.8) and specificity of 96.4% (95% CI: 89.5-98.8). DTS/POS samples had an overall accuracy of 79.7% (95% CI: 43.3-95.3), with an estimated sensitivity of 90.1% (95% CI: 83.3-96.9) and specificity of 63.1% (95% CI: 36.8-89.3). The remaining index specimens could not be adequately assessed given the lack of studies available. Our meta-analysis shows that saliva samples from the oral region provide a high sensitivity and specificity; therefore, these appear to be the best candidates for alternative specimens to NPS/OPS in SARS-CoV-2 detection, with suitable protocols for swab-free sample collection to be determined and validated in the future. The distinction between oral and extra-oral salivary samples will be crucial, since DTS/POS samples may induce a higher rate of false positives. Urine, feces, tears/CS and sputum seem unreliable for diagnosis. Saliva testing may increase testing capacity, ultimately promoting the implementation of truly deployable COVID-19 tests, which could either work at the point-of-care (e.g. hospitals, clinics) or at outbreak control spots (e.g., schools, airports, and nursing homes).

Self-Collected Oral Fluid Saliva Is Insensitive Compared With Nasal-Oropharyngeal Swabs in the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Outpatients

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic control will require widespread access to accurate diagnostics. Salivary sampling circumvents swab supply chain bottlenecks, is amenable to self-collection, and is less likely to create an aerosol during collection compared with the nasopharyngeal swab.

METHODS

We compared real-time reverse-transcription polymerase chain reaction Abbott m2000 results from matched salivary oral fluid (gingival crevicular fluid collected in an Oracol device) and nasal-oropharyngeal (OP) self-collected specimens in viral transport media from a nonhospitalized, ambulatory cohort of coronavirus disease 2019 (COVID-19) patients at multiple time points. These 2 sentences should be at the beginning of the results.

RESULTS

There were 171 matched specimen pairs. Compared with nasal-OP swabs, 41.6% of the oral fluid samples were positive. Adding spit to the oral fluid percent collection device increased the percent positive agreement from 37.2% (16 of 43) to 44.6% (29 of 65). The positive percent agreement was highest in the first 5 days after symptoms and decreased thereafter. All of the infectious nasal-OP samples (culture positive on VeroE6 TMPRSS2 cells) had a matched SARS-CoV-2 positive oral fluid sample.

CONCLUSIONS

In this study of nonhospitalized SARS-CoV-2-infected persons, we demonstrate lower diagnostic sensitivity of self-collected oral fluid compared with nasal-OP specimens, a difference that was especially prominent more than 5 days from symptom onset. These data do not justify the routine use of oral fluid collection for diagnosis of SARS-CoV-2 despite the greater ease of collection. It also underscores the importance of considering the method of saliva specimen collection and the time from symptom onset especially in outpatient populations.