Diagnostic Salivary Tests for SARS-CoV-2

On the feasibility of Vis-NIR spectroscopy and machine learning for real time SARS-CoV-2 detection

The pandemic caused by Covid-19 is still present around the world. Despite advances in combating the disease, such as vaccine development, identifying infected individuals is still essential to optimize the control of human-to-human transmission of the virus. The main technique for detecting the virus is the RT-PCR method, which, despite its high relative cost, has a high accuracy in detecting the coronavirus. Given this, a method capable of performing the identification quickly, accurately, and inexpensively is necessary. Thus, this work aimed to analyze the feasibility of a new technique for identifying SARS-CoV-2 through the use of optical spectroscopy in the visible and near-infrared range (Vis-NIR) combined with machine learning algorithms. Spectral signals were obtained from nasopharyngeal swab samples previously analyzed using the RT-PCR method. The specimens were provided by the Molecular Diagnosis Laboratory of Covid-19 at Univasf. A total of 314 samples were analyzed, comprising 42 testing positive and 272 testing negative for Covid-19. Digital signal processing techniques, such as Savitzky-Golay filters and statistical methods were used to eliminate spurious elements from the original data and extract relevant features. Supervised machine learning algorithms such as SVM, Random Forest, and Naive Bayes classifiers were used to perform automatic sample identification. To evaluate the performance of the models, a 5-fold cross-validation technique was applied. With the proposed methodology, it was possible to achieve an accuracy of 75%, a sensitivity of 80%, and a specificity of 70%, in addition to an area under the ROC curve of 0.81, in the identification of nasopharyngeal swab samples from previously diagnosed individuals. From these results, it was possible to conclude that Vis-NIR spectroscopy is a promising, fast and relatively low cost technique to identify the SARS-CoV-2.

Self-Diagnosis of SARS-CoV-2 from Saliva Samples at Home: Isothermal Amplification Enabled by Do-It-Yourself Portable Incubators and Laminated Poly-ethyl Sulfonate Membranes

COVID-19 made explicit the need for rethinking the way in which we conduct testing for epidemic emergencies. During the COVID-19 pandemic, the dependence on centralized lab facilities and resource-intensive methodologies (e.g., RT-qPCR methods) greatly limited the deployment of widespread testing efforts in many developed and underdeveloped countries. Here, we illustrate the development of a simple and portable diagnostic kit that enables self-diagnosis of COVID-19 at home from saliva samples. We describe the development of a do-it-yourself (DIY) incubator for Eppendorf tubes that can be used to conduct SARS-CoV-2 detection with competitive sensitivity and selectivity from saliva at home. In a proof-of-concept experiment, we assembled Eppendorf-tube incubators at our home shop, prepared a single-tube mix of reagents and LAMP primers in our lab, and deployed these COVID-19 detection kits using urban delivery systems (i.e., Rappifavor or Uber) to more than 15 different locations in Monterrey, México. This straightforward strategy enabled rapid and cost-effective at-home molecular diagnostics of SARS-CoV-2 from real saliva samples with a high sensitivity (100%) and high selectivity (87%).

Detection of anti-SARS-CoV-2 salivary antibodies in vaccinated adults

Since the introduction of efficient anti-SARS-CoV-2 vaccines, the detection of antibodies becomes useful for immunological monitoring and COVID-19 control. Therefore, this longitudinal study aimed to evaluate the detection of SARS-CoV-2 antibodies in the serum and saliva of COVID-19-vaccinated adults. The study included 13 not vaccinated and 35 vaccinated participants with two doses of CoronaVac (Sinovac/Butantan) vaccine who subsequently received BNT162b2 (Pfizer-BioNTech) vaccine as a booster dose. Vaccinated participants donated saliva and serum in three different time points. Enzyme-linked immunosorbent assay was used for antibody detection. In our results, the serum neutralizing antibodies (NAb) were detected in 34/35 samples after second dose and in 35/35 samples one and five months after the booster dose. In saliva, NAb were detected in 30/35 samples after second dose and in 35/35 of samples one and five months after the booster dose. IgA was detected in 19/34 saliva samples after second dose, in 18/35 one month after the booster and in 30/35 five months after. IgG in saliva was detected in 1/34 samples after second dose, 33/35 samples one month after the booster dose and in 20/35 five months after. A strong correlation was found between IgG and neutralizing activity in saliva, and salivary IgA would be a sign of recent exposure to the virus. In conclusion, saliva can be suitable for monitoring antibodies anti-SARS-CoV-2 after vaccination. Heterologous vaccination contributed to increase anti-SARS-CoV-2 antibodies in the Brazilian health context. Complementary studies with large groups are mandatory to conclude the interest in following mucosal immunity.

Development of practical techniques for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants

Countless individuals have fallen victim to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have generated antibodies, reducing the risk of secondary infection in the short term. However, with the emergence of mutated strains, the probability of subsequent infections remains high. Consequently, the demand for simple and accessible methods for distinguishing between different variants is soaring. Although monitoring viral gene sequencing is an effective approach for differentiating between various types of SARS-CoV-2 variants, it may not be easily accessible to the general public. In this article, we provide an overview of the reported techniques that use combined approaches and adaptable testing methods that use editable recognition receptors for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. These techniques employ straightforward detection strategies, including tests capable of simultaneously identifying and differentiating between different variants. Furthermore, we recommend advancing the development of uncomplicated protocols for distinguishing between current and emerging variants. Additionally, we propose further development of facile protocols for the differentiation of existing and emerging variants.

Oral manifestations of COVID-19 in unvaccinated patients: a cross-sectional study

BACKGROUND

Early studies have highlighted the possible development of dysgeusia and anosmia in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, and these manifestations should be considered a potential indication of coronavirus disease 19 (COVID-19). As potential contributors to these symptoms, dentists should perform careful oral and oropharyngeal examinations and document suspicious oral lesions in patients with COVID-19, especially in those who complain of loss of taste and smell. The study's objective was to assess the prevalence of oral manifestations among ambulatory unvaccinated symptomatic patients with suspected COVID-19 during the acute phase of the disease.

METHODS

This cross-sectional study evaluated oral manifestations in adults (aged ≥ 18 years) with suspected and confirmed SARS-CoV-2 infection. Chi-square and Fisher's exact tests were used to compare data between the groups (rRT-PCR-positive and rRT-PCR-negative patients).

RESULTS

One hundred thirty-six participants were included. Most were female (n = 79; 58.1%), with a mean age of 39.53 (± 14.17) years. Of these, 54 (39.7%) had a positive rRT-PCR test, and 82 (60.3%) had negative rRT-PCR results. Oral manifestations were observed in 40 participants (74.1%) in the rRT-PCR-positive group and 67 participants (81.7%) in the rRT-PCR-negative group. The most common oral manifestations were xerostomia (n = 85; 62.5%) and dysgeusia/ageusia (n = 57; 41.9%). Different rates of gingivitis (n = 12; 22.2% vs. n = 5; 6.1%; p = 0.005) and halitosis (n = 7; 13.0% vs. n = 1; 1.2%; p = 0.007) were observed between the rRT-PCR-positive and -negative groups, respectively. Mouth ulcers, glossitis, tongue coating, and petechiae were reported in both groups without significant differences.

CONCLUSIONS

A high prevalence of oral manifestations was observed in symptomatic patients with suspected or confirmed COVID-19.

CLINICAL RELEVANCE

This study highlights the importance of routine oral examinations by dentists as part of the multidisciplinary care of COVID-19 patients.

Identification of SARS-CoV-2 biomarkers in saliva by transcriptomic and proteomics analysis

The detection of SARS-CoV-2 biomarkers by real time PCR (rRT-PCR) has shown that the sensitivity of the test is negatively affected by low viral loads and the severity of the disease. This limitation can be overcome by the use of more sensitive approaches such as mass spectrometry (MS), which has not been explored for the detection of SARS-CoV-2 proteins in saliva. Thus, this study aimed at assessing the translational applicability of mass spectrometry-based proteomics approaches to identify viral proteins in saliva from people diagnosed with COVID-19 within fourteen days after the initial diagnosis, and to compare its performance with rRT-PCR. After ethics approval, saliva samples were self-collected by 42 COVID-19 positive and 16 healthy individuals. Samples from people positive for COVID-19 were collected on average on the sixth day (± 4 days) after initial diagnosis. Viable viral particles in saliva were heat-inactivated followed by the extraction of total proteins and viral RNA. Proteins were digested and then subjected to tandem MS analysis (LC-QTOF-MS/MS) using a data-dependent MS/MS acquisition qualitative shotgun proteomics approach. The acquired spectra were queried against a combined SARS-CoV-2 and human database. The qualitative detection of SARS-CoV-2 specific RNA was done by rRT-PCR. SARS-CoV-2 proteins were identified in all COVID-19 samples (100%), while viral RNA was detected in only 24 out of 42 COVID-19 samples (57.1%). Seven out of 18 SARS-CoV-2 proteins were identified in saliva from COVID-19 positive individuals, from which the most frequent were replicase polyproteins 1ab (100%) and 1a (91.3%), and nucleocapsid (45.2%). Neither viral proteins nor RNA were detected in healthy individuals. Our mass spectrometry approach appears to be more sensitive than rRT-PCR for the detection of SARS-CoV-2 biomarkers in saliva collected from COVID-19 positive individuals up to 14 days after the initial diagnostic test. Based on the novel data presented here, our MS technology can be used as an effective diagnostic test of COVID-19 for initial diagnosis or follow-up of symptomatic cases, especially in patients with reduced viral load.

Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle

Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.

Acceptability and Feasibility of Saliva-delivered PCR Coronavirus 2019 Tests for Young Children

OBJECTIVES

Access to readily available, reliable, and easy-to-use coronavirus disease 2019 (COVID-19) tests remains critical, despite great vaccination progress. Universal back-to-school testing offered at early care and education ([ECE]; ie, preschool) sites to screen for positive cases may help preschoolers safely return to, and stay in, ECE. We examined the acceptability and feasibility of using a quantitative polymerase chain reaction COVID-19 saliva test for young children (n = 227, 54.0% girls: mean age = 52.3 ± 8.1 months) and their caregivers (n = 70 teachers: mean = 36.6 ± 14.7 years; n = 227 parents: mean = 35.5 ± 9.1 years) to mitigate the spread of COVID-19 and reduce days of school and work missed for households with children who test positive.

METHODS

Participants were recruited at ECE sites serving low-income communities as part of the Rapid Acceleration of Diagnostic Testing-Underserved Populations Back to Early Care and Education Safely with Sustainability via Active Garden Education project (NCT05178290).

RESULTS

Surveys in English or Spanish administered at testing events to children and caregivers at ECE sites showed child and adult acceptability and feasibility ratings were generally high. More favorable child and parent ratings were positively associated with child age and whether the child was able to produce a saliva sample. Language preference was not associated with any outcomes.

CONCLUSIONS

Saliva sampling for COVID-19 at ECE sites is an acceptable strategy as an additional layer of protection for 4- and 5-year-olds; however, alternate testing strategies may be needed for younger children.

Reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay as a rapid molecular diagnostic tool for COVID-19 in healthcare workers

In December 2019, the Chinese Center for Disease Control (CDC of China) reported an outbreak of pneumonia in the city of Wuhan (Hubei province, China) that haunted the world, resulting in a global pandemic. This outbreak was caused by a betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Several of these cases have been observed in healthcare professionals working in hospitals and providing care on the pandemic's frontline. In the present study, nasopharyngeal swab samples of healthcare workers were used to assess the performance of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay and subsequently compared with the real-time reverse-transcription quantitative PCR (RT-qPCR) method. Thus, in this study, we validated a method for detecting SARS-CoV-2 based on RT-LAMP that can be used to diagnose these workers. The methodology used was based on analyzing the sensitivity, specificity, evaluation of the detection limit, and cross-reaction with other respiratory viruses. The agreement was estimated using a dispersion diagram designed using the Bland-Altman method. A total of 100 clinical specimens of nasopharyngeal swabs were collected from symptomatic and asymptomatic healthcare workers in Pelotas, Brazil, during the SARS-CoV-2 outbreak. RT-LAMP assay, it was possible to detect SARS-CoV-2 in 96.7% of the healthcare professionals tested using the E gene and N gene primers approximately and 100% for the gene of human β-actin. The observed agreement was considered excellent for the primer set of the E and N genes (k = 0.957 and k = 0.896), respectively. The sensitivity of the RT-LAMP assay was positive for the primer set of the E gene, detected to approximately 2 copies per reaction. For the primer set of the N gene, the assay was possible to verify an LoD of approximately 253 copies per reaction. After executing the RT-LAMP assay, no positive reactions were observed for any of the virus respiratory tested. Therefore, we conclude that RT-LAMP is effective for rapid molecular diagnosis during the COVID-19 outbreak period in healthcare professionals.

Smartphone-based corona virus detection using saliva: A mini-review

During the ongoing worldwide epidemic, SARS-CoV-2 has infected millions of individuals and taken the lives of numerous victims. It is clear that early detection of infected individuals, especially asymptomatic carriers, is possible with the development of innovative analytical tools for rapid identification of COVID-19 present in nasopharyngeal swabs, serum, and saliva. The saliva, as a diagnostic sample, can be easily collected by the patient with almost no discomfort and needs specialized healthcare personnel to manage, which reduces the risks for the operator. Moreover, smartphone-based sensing systems are one of the most attractive techniques that can speed up the detection time of COVID-19 agents without the need for professional staff and clinical centers. In this review, recent advances in precise salivary-based SARS-CoV-2 diagnosis using smartphones via viral RNA detection, antibody identification, and viral antigen identification were summarized. Finally, the conclusion and future perspective of this field are described in brief.

Saliva-based microfluidic point-of-care diagnostic

There has been a long-standing interest in point-of-care (POC) diagnostics as a tool to improve patient care because it can provide rapid, actionable results near the patient. Some of the successful examples of POC testing include lateral flow assays, urine dipsticks, and glucometers. Unfortunately, POC analysis is somewhat limited by the ability to manufacture simple devices to selectively measure disease specific biomarkers and the need for invasive biological sampling. Next generation POCs are being developed that make use of microfluidic devices to detect biomarkers in biological fluids in a non-invasive manner, addressing the above-mentioned limitations. Microfluidic devices are desirable because they can provide the ability to perform additional sample processing steps not available in existing commercial diagnostics. As a result, they can provide more sensitive and selective analysis. While most POC methods make use of blood or urine as a sample matrix, there has been a growing push to use saliva as a diagnostic medium. Saliva represents an ideal non-invasive biofluid for detecting biomarkers because it is readily available in large quantities and analyte levels reflect those in blood. However, using saliva in microfluidic devices for POC diagnostics is a relatively new and an emerging field. The overarching aim of this review is to provide an update on recent literature focused on the use of saliva as a biological sample matrix in microfluidic devices. We will first cover the characteristics of saliva as a sample medium and then review microfluidic devices that are developed for the analysis of salivary biomarkers.

Advances in RT-LAMP for COVID-19 testing and diagnosis

INTRODUCTION

The SARS-CoV-2 pandemic, and the subsequent limitations on standard diagnostics, has vastly expanded the user base of Reverse Transcription Loop-mediated isothermal Amplification (RT-LAMP) in fundamental research and development. RT-LAMP has also penetrated commercial markets, with emergency use authorizations for clinical diagnosis.

AREAS COVERED

This review discusses the role of RT-LAMP within the context of other technologies like RT-qPCR and rapid antigen tests, progress in sample preparation strategies to enable simplified workflow for RT-LAMP directly from clinical specimens, new challenges with primer and assay design for the evolving pandemic, prominent detection modalities including colorimetric and CRISPR-mediated methods, and translational research and commercial development of RT-LAMP for clinical applications.

EXPERT OPINION

RT-LAMP occupies a middle ground between RT-qPCR and rapid antigen tests. The simplicity approaches that of rapid antigen tests, making it suitable for point-of-care use, but the sensitivity nears that of RT-qPCR. RT-LAMP still lags RT-qPCR in fundamental understanding of the mechanism, and the interplay between sample preparation and assay performance. Industry is now beginning to address issues around scalability and usability, which could finally enable LAMP and RT-LAMP to find future widespread application as a diagnostic for other conditions, including other pathogens with pandemic potential.

Cross-Sectional Study on Lateral Skull Radiographs to Design a New Nasopharyngeal Swab for Simplified COVID-19 and Respiratory Infections Diagnostic Testing in Children

Nasopharyngeal swab sample collection is the first-line testing method for diagnosing COVID-19 infection and other respiratory infections. Current information on how to properly perform nasopharyngeal swabbing in children is largely defective. This study aimed at collecting nostril to nasopharynx distance measurements on lateral skull radiographs of children and adolescents to design a nasopharyngeal swab meant to standardize and facilitate the sample collection procedure. A total of 323 cephalograms of 152 male and 171 female children aged 4-14 years taken for orthodontic reasons were selected. On each cephalogram, the shortest distance between the most anterosuperior point of the nostril contour and the nasopharynx outline was measured in mm parallel to the palatal plane. Descriptive statistics of the measurements were calculated for each age group. The lower limit of the 95% confidence intervals of the measurements was taken as a reference to design a swab shaft with marks that, at each age, delimitate a safety boundary for swab progression up to the posterior nasopharyngeal wall. The simplification of the procedure enabled by the newly designed nasopharyngeal swab is valuable to help healthcare providers perform specimen collection on children in a safe and effective way, perhaps under the less-than-ideal conditions possibly occurring in 'point-of-need' contexts.

Microscopic observations of SARS-CoV-2 like particles in different oral samples

The emerging coronavirus pneumonia epidemic caused by the SARS-CoV-2 infection has spread rapidly around the world. The main routes of transmission of SARS-CoV-2 are currently recognised as aerosol/droplet inhalation. However, the involvement of the oral cavity in coronavirus disease 2019 (COVID-19) is poorly known. The current data indicates the presence of viral RNA in oral samples, suggesting the implication of saliva in SARS-CoV-2 transmission, however, no direct observation of SARS-CoV-2 particles in different oral samples has been reported. In this study, we investigated whether particles of SARS-CoV-2 were present in oral samples collected from three symptomatic COVID-19 patients. Using scanning electron microscopy (SEM), the correlative strategy of light microscopy and electron microscopy and immunofluorescence staining, we showed the presence of SARS-like particles in RT-qPCR SARS-CoV-2-positive saliva, dental plaque and gingival crevicular fluid (GCF) samples. In the saliva samples, we demonstrated the presence of epithelial oral cells with morphogenetic features of SARS-CoV-2 infected cells. Inside those cells, vacuoles filled with nascent particles were observed, suggesting the potential infection and replication of SARS-CoV-2 in oral tissues. Our results corroborate previous studies and confirm that the oral cavity may be a potential niche for SARS-CoV-2 infection and a potential source of transmission.

Transmission of SARS-CoV-2 during indoor clubbing events: A clustered randomized, controlled, multicentre trial protocol

Introduction

The SARS-CoV-2 pandemic led to the implementation of several non-pharmaceutical interventions (NPIs), from closings of bars and restaurants to curfews and lockdowns. Vaccination campaigns started hoping it could efficiently alleviate NPI. The primary objective of the "Indoor Transmission of COVID-19" (ITOC) study is to determine among a fully vaccinated population the relative risk of SARS-CoV-2 transmission during one indoor clubbing event. Secondary objectives are to assess the transmission of other respiratory viruses, risk exposure, and attitudes toward COVID-19 vaccination, health pass, and psychological impact of indoor club closing.

Methods and analysis

Four thousand four hundred healthy volunteers aged 18-49 years and fully vaccinated will be included in Paris region. The intervention is an 8-hour indoor clubbing event with no masks, no social distance, maximum room capacity, and ventilation. A reservation group of up to 10 people will recruit participants, who will be randomized 1:1 to either the experimental group (2,200 volunteers in two venues with capacities of 1,000 people each) or the control group (2,200 volunteers asked not to go to the club). All participants will provide a salivary sample on the day of the experiment and 7 days later. They also will answer several questionnaires. Virological analyses include polymerase chain reaction (PCR) of salivary samples and air of the venue, investigating SARS-CoV-2 and 18 respiratory viruses.

Ethics and dissemination

Ethical clearance was first obtained in France from the institutional review board (Comité de Protection des Personnes Ile de France VII - CPP), and the trial received clearance from the French National Agency for Medicines and Health Products (Agence National de Sécurité du Médicament - ANSM). The trial is supported and approved by The Agence Nationale Recherche sur le SIDA, les hépatites et maladies émergences (ANRS-MIE). Positive, negative, and inconclusive results will be published in peer-reviewed scientific journals.

Trial registration number

IDR-CB 2021-A01473-38. Clinicaltrial.gov, identifier: NCT05311865.

Infection of the oral cavity with SARS-CoV-2 variants: Scope of salivary diagnostics

Coronaviruses, including SARS-CoV-2, have caused pandemics in the past two decades. The most prevalent SARS-CoV-2 variants of concern can re-infect individuals who have been previously infected with other variants or had protection from vaccines targeting the original SARS-CoV-2 variant. Given the high risk of transmission of coronavirus via aerosols produced during dental procedures, it is important to understand the future risk of coronavirus infection for oral health professionals and to diagnose quickly early stages of outbreaks. Testing of saliva for coronavirus may be the least invasive and most convenient method for following the outbreak at the individual and community level. This review will describe strategies for diagnosis of coronavirus in saliva.

Saliva testing among teachers during the COVID-19 pandemic: Effects on health concerns, well-being, and precautionary behavior

RATIONALE

At the start of 2021, several SARS-CoV-2 cluster outbreaks in schools threatened in-person education and created a fairly chaotic and frightening environment for school personnel. To keep the schools open while preventing COVID-19 outbreaks, intensive diagnostic testing in teachers and school personnel was strongly recommended but missing at the time.

OBJECTIVES

A project was launched in Belgian schools to weekly analyze the morning saliva of school personnel using PCR-testing to detect and prevent COVID-19 positive cases. In this quasi-experimental study, we aimed to examine whether the implementation of this saliva testing project impacted school personnel's pandemic-related health concerns, well-being, and adherence to the health-protective measures, contrasting experimental with control schools.

METHODS

The data were collected during the third wave (Alpha-wave, February-March 2021) of the pandemic. The sample consisted of 435 participants from 34 different schools across Flanders (Belgium) (78.8% female; M age = 43.87 years, range = 21-67) of which 82% participated in the weekly saliva tests (i.e., experimental group) and 18% took part in the control group.

RESULTS

Results from a series of linear mixed regression models showed that saliva testing buffered against an increase in health concerns among tested school personnel but did not affect participants' general well-being. Slight declines in adherence to the health-protective behaviors were observed, yet this was only the case for participants who felt less supported by their school principal. High degrees of principals' support also fostered the sharpest decreases in school staff's pandemic-related health concerns.

CONCLUSIONS

When keeping the schools open in unstable pandemic times, weekly saliva testing is a promising strategy to prevent cluster outbreaks while simultaneously safeguarding health concerns among school personnel. School principals appear to play a critical role in the implementation of saliva testing to secure positive effects.

Saliva sample for detection of SARS-CoV-2: A possible alternative for mass testing

Molecular diagnostic testing has played a critical role in the global response to the novel Coronavirus disease (COVID-19) pandemic, since its first outbreak in late 2019. At the inception of the COVID-19 pandemic, nasopharyngeal swab sample analysis for COVID-19 diagnosis using the real-time polymerase chain reaction (RT-PCR) technique was the most widely used. However, due to the high cost and difficulty of sample collection, the number of available sample types for COVID-19 diagnosis is rapidly increasing, as is the COVID-19 diagnostic literature. The use of nasal swabs, saliva, and oral fluids as viable sample options for the effective detection of SARS-CoV-2 has been implemented successfully in different settings since 2020. These alternative sample type provides a plethora of advantages including decreasing the high exposure risk to frontline workers, enhancing the chances of home self-sampling, reducing the cost, and significantly increasing testing capacity. This study sought to ascertain the effectiveness of Saliva samples as an alternative for COVID-19 diagnosis in Nigeria. Demographic data, paired samples of Nasopharyngeal Swab and Drooling Saliva were obtained from 309 consenting individuals aged 8–83 years presenting for COVID-19 testing. All samples were simultaneously assayed for the detection of SARS-CoV-2 RdRp, N, and E genes using the GeneFinder^™ COVID-19 Plus RT-PCR test kit. Out of 309 participants, only 299 with valid RT-PCR results comprising 159 (53.2%) males and 140 (46.8%) females were analyzed in this study using the R Statistical package. Among the 299 samples analyzed, 39 (13.0%) had SARS-CoV-2 detected in at least one specimen type. Both swabs and saliva were positive in 20 (51.3%) participants. Ten participants (25.6%) had swab positive/saliva-negative results and 9 participants (23.1%) had saliva positive/swab-negative results. The percentage of positive and negative agreement of the saliva samples with the nasopharyngeal swab were 67% and 97% respectively with positive and negative predictive values as 69% and 96% respectively. The findings indicate that drooling saliva samples have good and comparable diagnostic accuracy to the nasopharyngeal swabs with moderate sensitivities and high specificities.

Visual Detection of COVID-19 from Materials Aspect

ABSTRACT

In the recent COVID-19 pandemic, World Health Organization emphasized that early detection is an effective strategy to reduce the spread of SARS-CoV-2 viruses. Several diagnostic methods, such as reverse transcription-polymerase chain reaction (RT-PCR) and lateral flow immunoassay (LFIA), have been applied based on the mechanism of specific recognition and binding of the probes to viruses or viral antigens. Although the remarkable progress, these methods still suffer from inadequate cellular materials or errors in the detection and sampling procedure of nasopharyngeal/oropharyngeal swab collection. Therefore, developing accurate, ultrafast, and visualized detection calls for more advanced materials and technology urgently to fight against the epidemic. In this review, we first summarize the current methodologies for SARS-CoV-2 diagnosis. Then, recent representative examples are introduced based on various output signals (e.g., colorimetric, fluorometric, electronic, acoustic). Finally, we discuss the limitations of the methods and provide our perspectives on priorities for future test development.

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.

Diagnostic accuracy of CRISPR technology for detecting SARS-CoV-2: a systematic review and meta-analysis

OBJECTIVE

To evaluate the diagnostic accuracy of CRISPR-Cas technology for SARS-CoV-2.

METHODS

In our study, RT-qPCR is defined as the reference standard. Data was collected independently and assessed by Quality Assessment of Diagnostic Accuracy Studies (QUADAS)-2 tool. A bivariate model for pooling was employed to estimates of sensitivity and specificity and subgroups analysis was used to explore heterogeneity.

RESULTS

2264 samples and 6 countries from 28 articles were extracted for evaluating the accuracy of CRISPR technology for diagnosing SARS-CoV-2. The overall pooled sensitivity and specificity of CRISPR technology were 0.98 (95% CI: 0.95-0.99) and 1.0 (95% CI: 0.98-1.00), respectively. As for literature quality assessment, high risks in patient selection bias and unclear risk of index test bias may affect accuracy. Subgroup analysis draws significant conclusions. CRISPR-Cas12 is more applicable for molecular diagnostics for its active editing characteristics. RT-LAMP and RT-RPA are usually used for pre-amplification and combined with fluorescence detection to output results quantitatively. Nasopharyngeal swabs and dual-genes perform greatly in our study.

CONCLUSION

The results concluded from all studies showed that CRISPR technology is a promising and accurate molecular method for detecting SARS-CoV-2. Standard methods including comparable sample material, patient selection, operating procedure and operators should be established.

Severe acute respiratory syndrome coronavirus 2 detection by real time polymerase chain reaction using pooling strategy of nasal samples

COVID-19 is a life-threatening multisistemic infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection control relies on timely identification and isolation of infected people who can alberg the virus for up to 14 days, providing important opportunities for undetected transmission. This note describes the application of rRT-PCR test for simpler, faster and less invasive monitoring of SARS-CoV-2 infection using pooling strategy of samples. Seventeen positive patients were provided with sterile dry swabs and asked to self-collected 2 nasal specimens (#NS1 and #NS2). The #NS1 was individually placed in a single tube and the #NS2 was placed in another tube together with 19 NSs collected from 19 negative patients. Both tubes were then tested with conventional molecular rRT-PCR and the strength of pooling nasal testing was compared with the molecular test performed on the single NS of each positive patient. The pooling strategy detected SARS-CoV-2 RNA to a similar extent to the single test, even when Ct value is on average high (Ct 37–38), confirming that test sensibility is not substantially affected even if the pool contains only one low viral load positive sample. Furthermore, the pooling strategy have benefits for SARS-CoV-2 routinary monitoring of groups in regions with a low SARS-CoV-2 prevalence.

On-Site Viral Inactivation and RNA Preservation of Gargle and Saliva Samples Combined with Direct Analysis of SARS-CoV-2 RNA on Magnetic Beads

Samples of nasopharyngeal swabs (NPS) are commonly used for the detection of SARS-CoV-2 and diagnosis of COVID-19. As an alternative, self-collection of saliva and gargle samples minimizes transmission to healthcare workers and relieves the pressure of resources and healthcare personnel during the pandemic. This study aimed to develop an enhanced method enabling simultaneous viral inactivation and RNA preservation during on-site self-collection of saliva and gargle samples. Our method involves the addition of saliva or gargle samples to a newly formulated viral inactivation and RNA preservation (VIP) buffer, concentration of the viral RNA on magnetic beads, and detection of SARS-CoV-2 using reverse transcription quantitative polymerase chain reaction directly from the magnetic beads. This method has a limit of detection of 25 RNA copies per 200 μL of gargle or saliva sample and 9-111 times higher sensitivity than the viral RNA preparation kit recommended by the United States Centers for Disease Control and Prevention. The integrated method was successfully used to analyze more than 200 gargle and saliva samples, including the detection of SARS-CoV-2 in 123 gargle and saliva samples collected daily from two NPS-confirmed positive SARS-CoV-2 patients throughout the course of their infection and recovery. The VIP buffer is stable at room temperature for at least 6 months. SARS-CoV-2 RNA (65 copies/200 μL sample) is stable in the VIP buffer at room temperature for at least 3 weeks. The on-site inactivation of SARS-CoV-2 and preservation of the viral RNA enables self-collection of samples, reduces risks associated with SARS-CoV-2 transmission, and maintains the stability of the target analyte.

Effect of RNA quality to SARS-CoV-2 RT-qPCR detection from saliva

Saliva is an alternative sample material to nasopharyngeal swab in SARS-CoV-2 diagnostics. We investigated possible aspects to improve the reliability of SARS-CoV-2 detection from saliva. Saliva was collected from asymptomatic healthy subjects (n=133) and COVID-19 patients (n=9). SARS-CoV-2 detection was performed with quantitative reverse-transcriptase PCR (RT-qPCR) with two viral and one host target serving as an internal control. The use of internal control revealed that in the first RT-qPCR run 25-30 % of assays failed. The failure is associated with poor RNA quality. When the amount of RNA was cut down to half from the original amount, the performance of RT-qPCR was greatly enhanced (95 % of the assays succeeded). The quality of RNA was not affected by the use of different nucleic acid stabilizing buffers. Our study showed that saliva is suitable material for RT-qPCR based SARS-CoV-2 diagnostics, but the use of internal control is essential to distinguish the true negative samples from failed assays.

SARS-CoV-2 infection among Brazilian dentists: a seroprevalence study

This cross-sectional study aimed to determine the seroprevalence of SARS-CoV-2 infection among Brazilian dentists and its associated factors. Stratified random sampling of dentists from 33 administrative regions of the Federal District (Brazil) was performed. The presence of antibodies was verified by the OnSite COVID-19 IgG/IgM Rapid Test. Participants answered a survey about sociodemographic characteristics, exposure to COVID-19, and professional practice. A chi-square test was performed between serostatus and exposure variables. Mann-Whitney tests were carried out for quantitative variables. Odds ratio (OR) and 95% confidence intervals (95%CI) were calculated. A series of binomial logistic regression models was performed. The seroprevalence of SARS-CoV-2 infection among 324 selected dentists was 19.1%. There was a statistically significant association between seropositivity and previous confirmed diagnosis of COVID-19, loss of taste or smell, diagnosis of COVID-19 in a household member, and treatment of a patient with fever. Dentists with a previous confirmed diagnosis of COVID-19 had 29.5 [12.7-68.4] higher odds to exhibit positive serology test results. Dentists with confirmed diagnosis of COVID-19 in a household member had 2.5 [1.1-5.3] times higher odds to exhibit positive serology test results. Professionals with loss of taste or smell in the last 15 days had 5.24 [1.1-24.1] times higher odds to exhibit positive serology test results, and, for those who had treated patients with fever, there were 2.99 [1.03-8.7] times higher odds to exhibit negative serology test results. There was a similar prevalence rate of infection among dentists and in the general population. Nevertheless, this finding applies to the epidemiological situation in 2020, before the development of vaccines and the emergence of SARS-CoV-2 Delta variant.

Novel impacts of saliva with regard to oral health

The maintenance of balanced oral homeostasis depends on saliva. A readily available and molecularly rich source of biological fluid, saliva fulfills many functions in the oral cavity, including lubrication, pH buffering, and tooth mineralization. Saliva composition and flow can be modulated by different factors, including circadian rhythm, diet, age, drugs, and disease. Recent events have revealed that saliva plays a central role in the dissemination and detection of the SARS-CoV-2 coronavirus. A working knowledge of saliva function and physiology is essential for dental health professionals.

Diagnostic techniques for COVID-19: A mini-review

COVID-19, a new respiratory infectious disease, was first reported at the end of 2019, in Wuhan, China. Now, COVID-19 is still causing major loss of human life and economic productivity in almost all countries around the world. Early detection, early isolation, and early diagnosis of COVID-19 patients and asymptomatic carriers are essential to blocking the spread of the pandemic. This paper briefly reviewed COVID-19 diagnostic assays for clinical application, including nucleic acid tests, immunological methods, and Computed Tomography (CT) imaging. Nucleic acid tests (NAT) target the virus genome and indicates the existence of the SARS-CoV-2 virus. Currently, real-time quantitative PCR (qPCR) is the most widely used NAT and, basically, is the most used diagnostic assay for COVID-19. Besides qPCR, many novel rapid and sensitive NAT assays were also developed. Serological testing (detection of serum antibodies specific to SARS-CoV-2), which belongs to the immunological methods, is also used in the diagnosis of COVID-19. The positive results of serological testing indicate the presence of antibodies specific to SARS-CoV-2 resulting from being infected with the virus. Viral antigen detection assays are also important immunological methods used mainly for rapid virus detection. However, only a few of these assays had been reported. CT imaging is still an important auxiliary diagnosis tool for COVID-19 patients, especially for symptomatic patients in the early stage, whose viral load is low and different to be identified by NAT. These diagnostic techniques are all good in some way and applying a combination of them will greatly improve the accuracy of COVID-19 diagnostics.

Evaluation of SARS-CoV-2 rapid antigen diagnostic tests for saliva samples

Using saliva samples would facilitate sample collection, diagnostic feasibility, and mass screening of SARS-CoV-2. We tested two rapid antigen (RAD) immunochromatographic tests designed for detection of SARS-CoV-2 in saliva: Rapid Response™ COVID-19 Antigen Rapid Test Cassette for oral fluids and DIAGNOS™ COVID-19 Antigen Saliva Test. Evaluation of detection limit was performed with purified SARS-CoV-2 nucleocapsid protein and live SARS-CoV-2 virus. Sensitivity and specificity were further evaluated with reverse transcription quantitative PCR (RT-qPCR) positive and negative saliva samples from hospitalized individuals with COVID-19 (n = 39) and healthcare workers (n = 20). DIAGNOS showed higher sensitivity than Rapid Response for both nucleocapsid protein and live virus. The limit of detection of the saliva test from DIAGNOS was further comparable with the Abbott Panbio™ COVID-19 Ag Rapid Test designed for nasopharyngeal samples. DIAGNOS and Rapid Response detected nine (50.0%) and seven (38.9%), respectively, of the 18 RT-qPCR positive saliva samples. All RT-qPCR negative saliva (n = 41) were negative with both tests. Only one of the RT-qPCR positive saliva samples contained infectious virus as determined by cell culture and was also positive using the saliva RADs. The results show that the DIAGNOS may be an important and easy-to-use saliva RAD complement to detect SARS-CoV-2 positive individuals, but validation with a larger sample set is warranted.

Looking at COVID-19 from a Systems Biology Perspective

The sudden outbreak and worldwide spread of the SARS-CoV-2 pandemic pushed the scientific community to find fast solutions to cope with the health emergency. COVID-19 complexity, in terms of clinical outcomes, severity, and response to therapy suggested the use of multifactorial strategies, characteristic of the network medicine, to approach the study of the pathobiology. Proteomics and interactomics especially allow to generate datasets that, reduced and represented in the forms of networks, can be analyzed with the tools of systems biology to unveil specific pathways central to virus-human host interaction. Moreover, artificial intelligence tools can be implemented for the identification of druggable targets and drug repurposing. In this review article, we provide an overview of the results obtained so far, from a systems biology perspective, in the understanding of COVID-19 pathobiology and virus-host interactions, and in the development of disease classifiers and tools for drug repurposing.

Validation of a Methodology for the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva by Real-Time Reverse Transcriptase-PCR

In January 2021, the Chilean city of Concepción experienced a second wave of coronavirus 2019 (COVID-19) while in early April 2021, the entire country faced the same situation. This outbreak generated the need to modify and validate a method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva, thereby expanding the capacity and versatility of testing for COVID-19. This study was conducted in February 2021 in the Chilean city of Concepción during which time, the town was under total quarantine. The study participants were mostly symptomatic (87.4%), not hospitalized, and attended care centers because of their health status rather than being asked by the researchers. People coming to the health center in Concepción to be tested for COVID-19 (via reverse transcriptase polymerase chain reaction [RT-PCR]) from a specimen of nasopharyngeal swab (NPS) were then invited to participate in this study. A total of 131 participants agreed to sign an informed consent and to provide saliva and NPS specimens to validate a method in terms of sensitivity, specificity, and statistical analysis of the cycle threshold (Ct) values from the RT-PCR. Calculations pertaining to the 127 participants who were ultimately included in the analysis showed sensitivity and specificity at 94.34% (95% CI: 84.34–98.82%) and 98.65% (95% CI: 92.70–99.97%), respectively. The saliva specimen showed a performance comparable to NPS as demonstrated by the diagnostic parameters. This RT-PCR method from the saliva specimen is a highly sensitive and specific alternative compared to the reference methodology, which uses the NPS specimen. This modified and validated method is intended for use in the in vitro diagnosis of SARS-CoV-2, which provides health authorities in Chile and local laboratories with a real testing alternative to RT-PCR from NPS.

A Comparison of Less Invasive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Diagnostic Specimens in Nursing Home Residents-Arkansas, June-August 2020

Background

SARS-CoV-2 testing remains essential for early identification and clinical management of cases. We compared the diagnostic performance of three specimen types for characterizing SARS-CoV-2 in infected nursing home residents.

Methods

A convenience sample of 17 residents were enrolled within 15 days of first positive SARS-CoV-2 result by real-time reverse transcription polymerase chain reaction (RT-PCR) and prospectively followed for 42 days. Anterior nasal swabs (AN), oropharyngeal swabs (OP), and saliva specimens (SA) were collected on the day of enrollment, every 3 days for the first 21 days, then weekly for 21 days. Specimens were tested for presence of SARS-CoV-2 RNA using RT-PCR and replication-competent virus by viral culture.

Results

Comparing the three specimen types collected from each participant at each time point, the concordance of paired RT-PCR results ranged from 80–88%. After the first positive result, SA and OP were RT-PCR–positive for ≤48 days; AN were RT-PCR–positive for ≤33 days. AN had the highest percentage of RT-PCR–positive results (81%; 21/26) when collected ≤10 days of participants’ first positive result. Eleven specimens were positive by viral culture: nine AN collected ≤19 days following first positive result and two OP collected ≤5 days following first positive result.

Conclusions

AN, OP, and SA were effective methods for repeated testing in this population. More AN than OP were positive by viral culture. SA and OP remained RT-PCR–positive longer than AN, which could lead to unnecessary interventions if RT-PCR detection occurred after viral shedding has likely ceased.

Role of Laboratory Medicine in SARS-CoV-2 Diagnostics. Lessons Learned from a Pandemic

Since the 2019 novel coronavirus outbreak began in Wuhan, China, diagnostic methods in the field of molecular biology have been developing faster than ever under the vigilant eye of world's research community. Unfortunately, the medical community was not prepared for testing such large volumes or ranges of biological materials, whether blood samples for antibody immunological testing, or salivary/swab samples for real-time PCR. For this reason, many medical diagnostic laboratories have made the switch to working in the field of molecular biology, and research undertaken to speed up the flow of samples through laboratory. The aim of this narrative review is to evaluate the current literature on laboratory techniques for the diagnosis of SARS-CoV-2 infection available on pubmed.gov, Google Scholar, and according to the writers' knowledge and experience of the laboratory medicine. It assesses the available information in the field of molecular biology by comparing real-time PCR, LAMP technique, RNA sequencing, and immunological diagnostics, and examines the newest techniques along with their limitations for use in SARS-CoV-2 diagnostics.

Developing a Paper-Based Antigen Assay to Differentiate between Coronaviruses and SARS-CoV-2 Spike Variants

COVID-19 first appeared in December of 2019 in Wuhan, China. Since then, it has become a global pandemic. A robust and scalable diagnostics strategy is crucial for containing and monitoring the pandemic. RT-PCR is a known, reliable method for COVID-19 diagnostics, which can differentiate between SARS-CoV-2 and other viruses. However, PCR is location-dependent, time-consuming, and relatively expensive. Thus, there is a need for a more flexible method, which may be produced in an off-the-shelf format and distributed more widely. Paper-based immunoassays can fulfill this function. Here, we present the first steps toward a paper-based test, which can differentiate between different spike proteins of various coronaviruses, SARS-CoV-1, SARS-CoV-2, and CoV-HKU1, with negligible cross-reactivity for HCoV-OC43 and HCoV-229E in a single assay, which takes less than 30 min. Furthermore, our test can distinguish between fractions of the same spike protein. This is done by an altered assay design with four test line locations where each antigen builds a unique, identifiable binding pattern. The effect of several factors, such as running media, immunoprobe concentration, and antigen interference, is considered. We find that running media has a significant effect on the final binding pattern where human saliva provides results while human serum leads to the lowest signal quality.

A Multiplex One-Step RT-qPCR Protocol to Detect SARS-CoV-2 in NP/OP Swabs and Saliva

Since December 2019, SARS‐CoV‐2 has spread extensively throughout the world, with more than 117 million reported cases and 2.6 million deaths (Johns Hopkins coronavirus resource center, https://coronavirus.jhu.edu/map.html). Detecting the virus is the first step in diagnosing the infection, followed by quarantine to prevent transmission. Nasopharyngeal/oropharyngeal swabs (NP/OP) and saliva are two specimen types that are most often analyzed to detect SARS‐CoV‐2 by molecular tests that detect viral RNA or by antigen/antibody tests that detect viral proteins and/or the host immune response against the virus. Compared to antigen/antibody tests, molecular tests are highly sensitive and specific for detecting the virus. A significant drawback is that specimen collection requirements are specific to each test and cannot be interchanged with another test. Some tests are qualified to be used on NP swabs or saliva, but not both specimen types. Even with NP swabs, a test may be qualified to detect the virus only with swabs collected in viral transport medium (VTM) but not in other media. These restrictive pre‐analytic steps are disadvantageous in that a lab would have to develop and validate different tests for SARS‐CoV‐2 depending on the specimen type and collection media, with added setup cost, infrastructure, and training requirements. To overcome these problems, we developed and validated a cost‐effective multiplex reverse‐transcription real‐time PCR assay that can be used to detect SARS‐CoV‐2 in different specimen types. The assay is highly sensitive and specific, can be used to detect the virus in saliva as well as NP swabs collected in different media such as VTM, saline, and commercial preservative fluid, and serves as one test for all applications. The protocol also describes an optimal laboratory setup and unidirectional workflow for detecting SARS‐CoV‐2 by RT‐qPCR. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Manual viral nucleic acid extraction from NP/OP swabs collected in different media, and from saliva

Alternate Protocol 1: Low‐throughput automated extraction on the Qiagen EZ1 Advanced XL machine (1‐14 samples)

Alternate Protocol 2: High‐throughput automated extraction on the Kingfisher Flex machine (1‐96 samples)

Basic Protocol 2: Multiplex RT‐qPCR protocol to detect SARS‐CoV‐2

Alternate Protocol 3: Multiplex one‐step RT‐qPCR protocol to detect SARS‐CoV‐2 with S and E gene probes labeled with the same fluorochrome

Presence of SARS-CoV-2 and Its Entry Factors in Oral Tissues and Cells: A Systematic Review

Background and Objectives: The aim of this systematic review is to summarize the current data about the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its entry factors in oral tissues and cells. Materials and Methods: This systematic review was carried out based on the Preferred Reporting Items for a Systematic Review and Meta-Analysis (PRISMA). Three databases were analyzed (Pubmed, Web of science and Scopus) by three independent researchers. From the 18 identified studies, 10 of them met the inclusion criteria. The presence of SARS-CoV-2 or its entry factors (angiotensin-converting enzyme II (ACE2), transmembrane serine proteases (TMPRSS), and furin) was analyzed in these 10 studies during the pandemic. Results: ACE2 expression was analyzed in 9 of the 10 studies. ACE2 is expressed mainly in the tongue, oral mucosa, salivary glands and epithelial cells. The expression of the TMPRSS2 gene or protein was analyzed in 6 studies. These studies reported that the expression of TMPRSS2 was mainly in the salivary glands, tongue, sulcular epithelium and oral mucosa; as well as in cells of the salivary glands (ductal, acinar and myoepithelial cells) and the tongue (the spinous-based cell layer, horny layer and the epithelial surface). Other TMPRSS were also reported. The expression of TMPRSS3, TMPRSS4, TMPRSS5, TMPRSS7 and TMPRSS11D was reported mainly in salivary glands and in epithelial-type cells. Furan expression was analyzed in three studies. The expression of furin was detected mainly in epithelial cells of the tongue. A variety of methods were used to carry out the detection of SARS-CoV-2 or its input molecules. Conclusions: These results show that SARS-CoV-2 can infect a wide variety of oral tissues and cells, and that together with the theories dedicated to explaining the oral symptoms present in SARS-CoV-2 positive patients, it provides us with a good scientific basis for understanding the virus infection in the oral cavity and its consequences.

Proposal for Tier-Based Resumption of Dental Practice Determined by COVID-19 Rate, Testing and COVID-19 Vaccination: A Narrative Perspective

Since the emergence of the new coronavirus disease (COVID-19), profound alterations in general and specialist dental practice have been imposed to provide safe dental care. The guidelines introduced in response to the COVID-19 pandemic to mitigate healthcare disruption are inconsistent regarding the dental practice re-installation, particularly during a transitional time. Despite the successful mass vaccination campaigns rolled out in 2021, the presence of more than 80 genotypes of COVID-19, rapid neutralisation of antibodies within a short period of seropositivity, and the likelihood of recurrent infection raise some doubts on whether vaccination alone will provide long-term immunity against COVID-19 and its variants. Here, from this perspective, we aim to provide an initial proposal for dental services reinstallation, easily applicable in various care settings. We discuss the potential options for the transition of dental services, as well as challenges and opportunities to adapt to new circumstances after mass COVID-19 vaccination. The proposal of the universal three-tier system of dental services resumption, determined by regional COVID-19 rates, testing accessibility, and vaccination rollout has been presented. Following herd COVID-19 immunity enhancement, it would be prudent to confer various preventative measures until virus spread naturally diminishes or becomes less virulent. Based on modelling data, dental practices may not return to normal, routine operation even after global vaccination as there would still be a significant risk of outbreaks of infection. Variable, multi-level measures will still be required, depending on the local COVID-19 cases rate, to secure safe dental care provision, despite predicted success of vaccination agendas. This approach can be implemented by achievable, practical means as a part of risk assessment, altered work pattern, and re-arrange of dental surgery facilities. The adequate standard operating procedure, with the support of rapid point-of-care testing at workplace, would vastly intensify the uninterrupted recovery of the dental care sector.

Feasibility of large-scale population testing for SARS-CoV-2 detection by self-testing at home

The simplicity and low cost of rapid point-of-care tests greatly facilitate large-scale population testing, which can contribute to controlling the spread of the COVID-19 virus. We evaluated the applicability of a self-testing strategy for SARS-CoV2 in a population-based, cross-sectional study in Cantabria, Spain, between April and May 2020. For the self-testing strategy, participants received the necessary material for the self-collection of blood and performance of a rapid antibody test using lateral flow immunoassay at home without the supervision of healthcare personnel. A total of 1,022 participants were enrolled. Most participants correctly performed the COVID-19 self-test the first time (91.3% [95% CI 89.4–92.9]). Only a minority of the participants (0.7%) needed the help of healthcare personnel, while 6.9% required a second kit delivery, for a total valid test result in 96.9% of the participants. Incorrect use of the self-test was not associated with the educational level, age over 65, or housing area. Prevalence of IgG antibodies against SARS-CoV2 for subjects with a valid rapid test result was 3.1% (95% CI 2.2–4.4), similar to the seroprevalence result obtained using a conventional approach carried out by healthcare professionals. In conclusion, COVID-19 self-testing should be considered as a screening tool.

Splatters and Aerosols Contamination in Dental Aerosol Generating Procedures

Dental aerosol-generating procedures produce a large amount of splatters and aerosols that create a major concern for airborne disease transmission, such as COVID-19. This study established a method to visualise splatter and aerosol contamination by common dental instrumentation, namely ultrasonic scaling, air-water spray, high-speed and low-speed handpieces. Mock dental procedures were performed on a mannequin model, containing teeth in a typodont and a phantom head, using irrigation water containing fluorescein dye as a tracer. Filter papers were placed in 10 different locations to collect splatters and aerosols, at distances ranging from 20 to 120 cm from the source. All four types of dental equipment produced contamination from splatters and aerosols. At 120 cm away from the source, the high-speed handpiece generated the greatest amount and size (656 ± 551 μm) of splatter particles, while the triplex syringe generated the largest amount of aerosols (particle size: 1.73 ± 2.23 μm). Of note, the low-speed handpiece produced the least amount and size (260 ± 142 μm) of splatter particles and the least amount of aerosols (particle size: 4.47 ± 5.92 μm) at 120 cm. All four dental AGPs produce contamination from droplets and aerosols, with different patterns of distribution. This simple model provides a method to test various preventive strategies to reduce risks from splatter and aerosols.

COVID-19 and Dentistry in 72 Questions: An Overview of the Literature

The outbreak of Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has significantly affected the dental care sector. Dental professionals are at high risk of being infected, and therefore transmitting SARS-CoV-2, due to the nature of their profession, with close proximity to the patient's oropharyngeal and nasal regions and the use of aerosol-generating procedures. The aim of this article is to provide an update on different issues regarding SARS-CoV-2 and COVID-19 that may be relevant for dentists. Members of the French National College of Oral Biology Lecturers ("Collège National des EnseignantS en Biologie Orale"; CNESBO-COVID19 Task Force) answered seventy-two questions related to various topics, including epidemiology, virology, immunology, diagnosis and testing, SARS-CoV-2 transmission and oral cavity, COVID-19 clinical presentation, current treatment options, vaccine strategies, as well as infection prevention and control in dental practice. The questions were selected based on their relevance for dental practitioners. Authors independently extracted and gathered scientific data related to COVID-19, SARS-CoV-2 and the specific topics using scientific databases. With this review, the dental practitioners will have a general overview of the COVID-19 pandemic and its impact on their practice.

Antigen tests for COVID-19

PCR diagnosis has been considered as the gold standard for coronavirus disease 2019 (COVID-19) and other many diseases. However, there are many problems in using PCR, such as non-specific (i.e., false-positive) and false-negative amplifications, the limits of a target sample volume, deactivation of the enzymes used, complicated techniques, difficulty in designing probe sequences, and the expense. We, thus, need an alternative to PCR, for example an ultrasensitive antigen test. In the present review, we summarize the following three topics. (1) The problems of PCR are outlined. (2) The antigen tests are surveyed in the literature that was published in 2020, and their pros and cons are discussed for commercially available antigen tests. (3) Our own antigen test on the basis of an ultrasensitive enzyme-linked immunosorbent assay (ELISA) is introduced. Finally, we discuss the possibility that our antigen test by an ultrasensitive ELISA technique will become the gold standard for diagnosis of COVID-19 and other diseases.

COVID-19 Management in Clinical Dental Care. Part I: Epidemiology, Public Health Implications, and Risk Assessment

Coronavirus disease 2019 (COVID-19), a viral disease declared a pandemic by the World Health Organization (WHO) in March 2020, has posed great changes to many sectors of society across the globe. Its virulence and rapid dissemination have forced the adoption of strict public health measures in most countries, which, collaterally, resulted in economic hardship.

This article is the first in a series of 3 that aims to contextualise the clinical impact of COVID-19 for the dental profession. It presents the epidemiological conditions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), namely, its modes of transmission, incubation, and transmissibility period, signs and symptoms, immunity, immunological tests, and risk management in dental care.

Individuals in dental care settings are exposed to 3 potential sources of contamination with COVID-19: close interpersonal contacts (<1 m), contact with saliva, and aerosol-generating dental procedures. Thus, a risk management model is propsoed for the provision of dental care depending on the epidemiological setting, the patient's characteristics, and the type of procedures performed in the office environment.

Although herd immunity seems difficult to achieve, a significant number of people has been infected throughout the first 9 months of the pandemic and vaccination has been implemented, which means that there will be a growing number of presumable “immune” individuals that might not require many precautions that differ from those before COVID-19.

In conclusion, dental care professionals may manage their risk by following the proposed model, which considers the recommendations by local and international health authorities, thus providing a safe environment for both professionals and patients.

Sensitivity of the Molecular Test in Saliva for Detection of COVID-19 in Pediatric Patients With Concurrent Conditions

Background: The reference standard for the molecular diagnostic testing for COVID-19 is the use of nasopharyngeal or combined nasopharyngeal and oropharyngeal (NP/OP) swabs. Saliva has been proposed as a minimally invasive specimen whose collection reduces the risks for health care personnel. Objective: To assess the suitability of saliva for COVID-19 diagnosis as a replacement of the reference standard NP/OP swab in the setting of a tertiary care pediatric unit. Study design: A paired study based in the prospective cohort design in patients suspected of having COVID-19. Methods: RT-PCR was used to detect SARS-CoV-2 in paired samples of saliva and NP/OP swab collected from May through August 2020 from 156 pediatric participants, of whom 128 has at least one comorbidity and 91 showed clinical symptoms related to SARS-CoV-2 infection. Additionally, we studied a group of 326 members of the hospital staff, of whom 271 had symptoms related to SARS-CoV-2 infection. Results: In the group of pediatric participants the sensitivity of the diagnostic test in saliva was 82.3% (95% CI 56.6-96.2) and the specificity 95.6% (95% CI 90.8-98.4). The prevalence of COVID-19 was 10.9% (17/156). In 6 of the 23 participants who tested positive for SARS-CoV-2 in at least one specimen type, the virus was detected in saliva but not in NP/OP swab, while in 3 participants the NP/OP swab was positive and saliva negative. In the group of adults, the sensitivity of the test in saliva was 77.8% (95% CI 67.2-86.3) and prevalence 24.8% (81/326). Discordant results between the two types of specimens showed a significant association with low viral load in the pharynx of adults but not of pediatric participants. Interpretation: In the context of a pediatric tertiary care hospital, the sensibility of the test in saliva is not high enough to replace the use of NP/OP swab for COVID-19 diagnosis. Neither NP/OP swab nor saliva could detect all the participants infected with SARS-CoV-2.