High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale

OBJECTIVES

To compare the prevalence of SARS-CoV-2 and other respiratory viruses in saliva and bioaerosols between two winters and to model the probability of virus detection in classroom air for different viruses.

METHODS

We analysed saliva, air, and air cleaner filter samples from studies conducted in two Swiss secondary schools (students aged 14-17 years) over 7 weeks during the winters of 2021/22 and 2022/23. Two bioaerosol sampling devices and high efficiency particulate air (HEPA) filters from air cleaners were used to collect airborne virus particles in four classrooms. Daily bioaerosol samples were pooled for each sampling device before PCR analysis of a panel of 19 respiratory viruses and viral subtypes. The probability of detection of airborne viruses was modelled using an adjusted Bayesian logistic regression model.

RESULTS

Three classes (58 students) participated in 2021/22, and two classes (38 students) in 2022/23. During winter 2021/22, SARS-CoV-2 dominated in saliva (19 of 21 positive samples) and bioaerosols (9 of 10). One year later, there were 50 positive saliva samples, mostly influenza B, rhinovirus, and adenovirus, and two positive bioaerosol samples, one rhinovirus and one adenovirus. The weekly probability of airborne detection was 34% (95% credible interval [CrI] 22-47%) for SARS-CoV-2 and 10% (95% CrI 5-16%) for other respiratory viruses.

DISCUSSION

There was a distinct shift in the distribution of respiratory viruses from SARS-CoV-2 during the omicron wave to other respiratory viruses one year later. SARS-CoV-2 is more likely to be detected in the air than other endemic respiratory viruses, possibly reflecting differences in viral characteristics and the composition of virus-carrying particles that facilitate airborne long-range transmission.

Kinetics of SARS-CoV-2 infection biomarkers in a household transmission study

SARS-CoV-2 is the causative agent of COVID-19. Timely and accurate diagnostic testing is vital to contain the spread of infection, reduce delays in treatment and care, and inform patient management. Optimal specimen type (e.g. nasal swabs or saliva), timing of sampling, viral marker assayed (RNA or antigen), and correlation with viral infectivity and COVID-19 symptoms severity remain incompletely defined. We conducted a field study to evaluate SARS-CoV-2 viral marker kinetics starting from very early times after infection. We measured RNA and antigen levels in nasal swabs and saliva, virus outgrowth in cell culture from nasal swabs, and antibody levels in blood in a cohort of 30 households. Nine household contacts (HHC) became infected with SARS-CoV-2 during the study. Viral RNA was detected in saliva specimens approximately 1-2 days before nasal swabs in six HHC. Detection of RNA was more sensitive than of antigen, but antigen detection was better correlated with culture positivity, a proxy for contagiousness. Anti-nucleocapsid antibodies peaked one to three weeks post-infection. Viral RNA and antigen levels were higher in specimens yielding replication competent virus in cell culture. This study provides important data that can inform how to optimally interpret SARS-CoV-2 diagnostic test results.

Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic

AIMS OF THE STUDY

Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting.

METHODS

This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests.

RESULTS

Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures.

CONCLUSIONS

Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.

Air Cleaners and Respiratory Infections in Schools: A Modeling Study Based on Epidemiologic, Environmental, and Molecular Data

Background

Using a multiple-measurement approach, we examined the real-world effectiveness of portable HEPA air filtration devices (air cleaners) in a school setting.

Methods

We collected data over 7 weeks during winter 2022/2023 in 2 Swiss secondary school classes: environmental (CO2, particle concentrations), epidemiologic (absences related to respiratory infections), audio (coughing), and molecular (bioaerosol and saliva samples). Using a crossover design, we compared particle concentrations, coughing, and risk of infection with and without air cleaners.

Results

All 38 students participated (age, 13-15 years). With air cleaners, mean particle concentration decreased by 77% (95% credible interval, 63%-86%). There were no differences in CO2 levels. Absences related to respiratory infections were 22 without air cleaners vs 13 with them. Bayesian modeling suggested a reduced risk of infection, with a posterior probability of 91% and a relative risk of 0.73 (95% credible interval, 0.44-1.18). Coughing also tended to be less frequent (posterior probability, 93%), indicating that fewer symptomatic students were in class. Molecular analysis detected mainly non-SARS-CoV-2 viruses in saliva (50/448 positive) but not in bioaerosols (2/105) or on the HEPA filters of the air cleaners (4/160). The molecular detection rate in saliva was similar with and without air cleaners. Spatiotemporal analysis of positive saliva samples identified several likely transmissions.

Conclusions

Air cleaners improved air quality and showed potential benefits in reducing respiratory infections. Airborne detection of non-SARS-CoV-2 viruses was rare, suggesting that these viruses may be more difficult to detect in the air. Future studies should examine the importance of close contact and long-range transmission and the cost-effectiveness of using air cleaners.

Cross-protective HCoV immunity reduces symptom development during SARS-CoV-2 infection

Numerous clinical parameters link to severe coronavirus disease 2019, but factors that prevent symptomatic disease remain unknown. We investigated the impact of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and endemic human coronavirus (HCoV) antibody responses on symptoms in a longitudinal children cohort (n = 2,917) and a cross-sectional cohort including children and adults (n = 882), all first exposed to SARS-CoV-2 (March 2020 to March 2021) in Switzerland. Saliva (n = 4,993) and plasma (n = 7,486) antibody reactivity to the four HCoVs (subunit S1 [S1]) and SARS-CoV-2 (S1, receptor binding domain, subunit S2 [S2], nucleocapsid protein) was determined along with neutralizing activity against SARS-CoV-2 Wuhan, Alpha, Delta, and Omicron (BA.2) in a subset of individuals. Inferred recent SARS-CoV-2 infection was associated with a strong correlation between mucosal and systemic SARS-CoV-2 anti-spike responses. Individuals with pre-existing HCoV-S1 reactivity exhibited significantly higher antibody responses to SARS-CoV-2 in both plasma (IgG regression coefficients = 0.20, 95% CI = [0.09, 0.32], P < 0.001) and saliva (IgG regression coefficient = 0.60, 95% CI = [0.088, 1.11], P = 0.025). Saliva neutralization activity was modest but surprisingly broad, retaining activity against Wuhan (median NT50 = 32.0, 1Q-3Q = [16.4, 50.2]), Alpha (median NT50 = 34.9, 1Q-3Q = [26.0, 46.6]), and Delta (median NT50 = 28.0, 1Q-3Q = [19.9, 41.7]). In line with a rapid mucosal defense triggered by cross-reactive HCoV immunity, asymptomatic individuals presented with higher pre-existing HCoV-S1 activity in plasma (IgG HKU1, odds ratio [OR] = 0.53, 95% CI = [0.29,0.97], P = 0.038) and saliva (total HCoV, OR = 0.55, 95% CI = [0.33, 0.91], P = 0.019) and higher SARS-CoV-2 reactivity in saliva (IgG S2 fold change = 1.26, 95% CI = [1.03, 1.54], P = 0.030). By investigating the systemic and mucosal immune responses to SARS-CoV-2 and HCoVs in a population without prior exposure to SARS-CoV-2 or vaccination, we identified specific antibody reactivities associated with lack of symptom development.IMPORTANCEKnowledge of the interplay between human coronavirus (HCoV) immunity and severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection is critical to understanding the coexistence of current endemic coronaviruses and to building knowledge potential future zoonotic coronavirus transmissions. This study, which retrospectively analyzed a large cohort of individuals first exposed to SARS-CoV-2 in Switzerland in 2020-2021, revealed several key findings. Pre-existing HCoV immunity, particularly mucosal antibody responses, played a significant role in improving SARS-CoV-2 immune response upon infection and reducing symptoms development. Mucosal neutralizing activity against SARS-CoV-2, although low in magnitude, retained activity against SARS-CoV-2 variants underlining the importance of maintaining local mucosal immunity to SARS-CoV-2. While the cross-protective effect of HCoV immunity was not sufficient to block infection by SARS-CoV-2, the present study revealed a remarkable impact on limiting symptomatic disease. These findings support the feasibility of generating pan-protective coronavirus vaccines by inducing potent mucosal immune responses.

Air cleaners and respiratory infections in schools: A modeling study using epidemiological, environmental, and molecular data

Background

Using a multiple-measurement approach, we examined the real-world effectiveness of portable HEPA-air filtration devices (air cleaners) in a school setting.

Methods

We collected environmental (CO2, particle concentrations), epidemiological (absences related to respiratory infections), audio (coughing), and molecular data (bioaerosol and saliva samples) over seven weeks during winter 2022/2023 in two Swiss secondary school classes. Using a cross-over study design, we compared particle concentrations, coughing, and the risk of infection with vs without air cleaners.

Results

All 38 students (age 13-15 years) participated. With air cleaners, mean particle concentration decreased by 77% (95% credible interval 63%-86%). There were no differences in CO2 levels. Absences related to respiratory infections were 22 without vs 13 with air cleaners. Bayesian modeling suggested a reduced risk of infection, with a posterior probability of 91% and a relative risk of 0.73 (95% credible interval 0.44-1.18). Coughing also tended to be less frequent (posterior probability 93%). Molecular analysis detected mainly non-SARS-CoV-2 viruses in saliva (50/448 positive), but not in bioaerosols (2/105 positive) or HEPA-filters (4/160). The detection rate was similar with vs without air cleaners. Spatiotemporal analysis of positive saliva samples identified several likely transmissions.

Conclusions

Air cleaners improved air quality, showed a potential benefit in reducing respiratory infections, and were associated with less coughing. Airborne detection of non-SARS-CoV-2 viruses was rare, suggesting that these viruses may be more difficult to detect in the air. Future studies should examine the importance of close contact and long-range transmission, and the cost-effectiveness of using air cleaners.

COVID-19 on Oral Health: A New Bilateral Connection for the Pandemic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission are generally known to be produced by respiratory droplets and aerosols from the oral cavity (O.C.) of infected subjects, as stated by the World Health Organization. Saliva also retains the viral particles and aids in the spread of COVID-19. Angiotensin-converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) are two of the numerous factors that promote SARS-CoV-2 infection, expressed by O.C. structures, various mucosa types, and the epithelia of salivary glands. A systemic SARS-CoV-2 infection might result from viral replication in O.C. cells. On the other hand, cellular damage of different subtypes in the O.C. might be associated with various clinical signs and symptoms. Factors interfering with SARS-CoV-2 infection potential might represent fertile ground for possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the O.C., finally representing a way to reduce COVID-19 incidence and severity.

Twice weekly polymerase chain reaction (PCR) surveillance swabs are not as effective as daily antigen testing for containment of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) outbreaks: A modeling study based on real world data from a child and adolescent psychiatry clinic

OBJECTIVE

In the coronavirus disease 2019 (COVID-19) pandemic, child and adolescent psychiatry wards face the risk of severe acute respiratory coronavirus 2 (SARS-CoV-2) introduction and spread within the facility. In this setting, mask and vaccine mandates are hard to enforce, especially for younger children. Surveillance testing may detect infection early and enable mitigation measures to prevent viral spread. We conducted a modeling study to determine the optimal method and frequency of surveillance testing and to analyze the effect of weekly team meetings on transmission dynamics.

DESIGN AND SETTING

Simulation with an agent-based model reflecting ward structure, work processes, and contact networks from a real-world child and adolescent psychiatry clinic with 4 wards, 40 patients, and 72 healthcare workers.

METHODS

We simulated the spread of 2 SARS-CoV-2 variants over 60 days under surveillance testing with polymerase chain reaction (PCR) tests and rapid antigen tests in different scenarios. We measured the size, peak, and the duration of an outbreak. We compared medians and percentage of spillover events to other wards from 1,000 simulations for each setting.

RESULTS

The outbreak size, peak, and duration were dependent on test frequency, test type, SARS-CoV-2 variant, and ward connectivity. Under surveillance conditions, joint staff meetings and therapists shared between wards did not significantly change median outbreak size under surveillance conditions. With daily antigen testing, outbreaks were mostly confined to 1 ward and median outbreak sizes were lower than with twice-weekly PCR testing (1 vs 22; P < .001).

CONCLUSION

Modeling can help to understand transmission patterns and guide local infection control measures.

The Diagnostic Performance of Various Clinical Specimens for the Detection of COVID-19: A Meta-Analysis of RT-PCR Studies

BACKGROUND

The diagnostic performance of numerous clinical specimens to diagnose COVID-19 through RT-PCR techniques is very important, and the test result outcome is still unclear. This review aimed to analyze the diagnostic performance of clinical samples for COVID-19 detection by RT-PCR through a systematic literature review process.

METHODOLOGY

A compressive literature search was performed in PubMed/Medline, Scopus, Embase, and Cochrane Library from inception to November 2022. A snowball search on Google, Google Scholar, Research Gate, and MedRxiv, as well as bibliographic research, was performed to identify any other relevant articles. Observational studies that assessed the clinical usefulness of the RT-PCR technique in different human samples for the detection or screening of COVID-19 among patients or patient samples were considered for this review. The primary outcomes considered were sensitivity and specificity, while parameters such as positive predictive value (PPV), negative predictive value (NPV), and kappa coefficient were considered secondary outcomes.

RESULTS

A total of 85 studies out of 10,213 non-duplicate records were included for the systematic review, of which 69 articles were considered for the meta-analysis. The meta-analysis indicated better pooled sensitivity with the nasopharyngeal swab (NPS) than saliva (91.06% vs. 76.70%) and was comparable with the combined NPS/oropharyngeal swab (OPS; 92%). Nevertheless, specificity was observed to be better with saliva (98.27%) than the combined NPS/OPS (98.08%) and NPS (95.57%). The other parameters were comparable among different samples. The respiratory samples and throat samples showed a promising result relative to other specimens. The sensitivity and specificity of samples such as nasopharyngeal swabs, saliva, combined nasopharyngeal/oropharyngeal, respiratory, sputum, broncho aspirate, throat swab, gargle, serum, and the mixed sample were found to be 91.06%, 76.70%, 92.00%, 99.44%, 86%, 96%, 94.4%, 95.3%, 73.63%, and above 98; and 95.57%, 98.27%, 98.08%, 100%, 37%, 100%, 100%, 97.6%, and above 97, respectively.

CONCLUSIONS

NPS was observed to have relatively better sensitivity, but not specificity when compared with other clinical specimens. Head-to-head comparisons between the different samples and the time of sample collection are warranted to strengthen this evidence.

Comparison between Nasopharyngeal and Saliva Samples for the Detection of Respiratory Viruses in Children with Acute Lower Respiratory Tract Infections: A Pilot Study

PURPOSE

During the COVID-19 pandemic, the use of salivary swabs (SS) to detect the SARS-CoV-2 virus has been implemented and widely studied in adults and children. However, the role of SS in detecting other common respiratory viruses in children is poorly investigated.

METHODS

Children younger than 18 years of age admitted with respiratory signs and symptoms underwent both nasopharyngeal and SS procedures. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of SS were calculated, considering the nasopharyngeal swab result as the gold standard.

RESULTS

A total of 83 patients (44 females, 53%) underwent both nasopharyngeal and SS procedures. Overall, the sensitivity of SS was 49.4%. Sensitivity according to different respiratory viruses ranged from 0% to 71.43%, while the specificity ranged from 96% to 100%. Negative predictive value ranged from 68.06% to 98.8%, while positive predictive value ranged from 0 to 100%. SS sensitivity in patients younger than 12 months of age was 39.47%, while in patients older than or equal to 12 months of age it was 57.78%. Patients with negative SS had a significantly lower median age (8.5 months (15.25) vs. 23 months (34), p = 0.001) and a significantly lower quantity of median saliva collected for salivary analysis (0 μL (213) vs. 300 μL (100), p < 0.001).

CONCLUSIONS

SS has a relatively low sensitivity in detecting common respiratory viruses in children with LRTI, with a lower probability in younger children (and in particular those younger than 6 months of age) or those from whom we have collected lesser amounts of saliva. New strategies to improve saliva collection are needed for testing on a larger study population.

Parallel dynamics in the yield of universal SARS-CoV-2 admission screening and population incidence

The majority of SARS-CoV-2 transmissions originates from either asymptomatic or presymptomatic individuals. To prevent unnoticed introduction of SARS-CoV-2, many hospitals have implemented universal admission screening during the COVID-19 pandemic. The present study aimed to investigate associations between results of an universal SARS-CoV-2 admission screening and public SARS-CoV-2 incidence. Over a study period of 44 weeks, all patients admitted to a large tertiary care hospital were tested for SARS-CoV-2 by polymerase chain reaction. SARS-CoV-2 positive patients were retrospectively categorized as symptomatic or asymptomatic at admission. Cantonal data were used to calculate weekly incidence rates per 100,000 inhabitants. We used regression models for count data to assess the association of the weekly cantonal incidence rate and the proportion of positive SARS-CoV-2 tests in the canton with (a) the proportion of SARS-CoV-2 positive individuals and (b) the proportion of asymptomatic SARS-CoV-2 infected individuals identified in universal admission screening, respectively. In a 44-week period, a total of 21,508 admission screenings were performed. SARS-CoV-2 PCR was positive in 643 (3.0%) individuals. In 97 (15.0%) individuals, the positive PCR reflected residual viral replication after recent COVID-19, 469 (72.9%) individuals had COVID-19 symptoms and 77 (12.0%) SARS-CoV-2 positive individuals were asymptomatic. Cantonal incidence correlated with the proportion of SARS-CoV-2 positive individuals [rate ratio (RR): 2.03 per 100 point increase of weekly incidence rate, 95%CI 1.92-2.14] and the proportion of asymptomatic SARS-CoV-2 positive individuals (RR: 2.40 per 100 point increase of weekly incidence rate, 95%CI 2.03-2.82). The highest correlation between dynamics in cantonal incidence and results of admission screening was observed at a lag time of one week. Similarly, the proportion of positive SARS-CoV-2 tests in the canton of Zurich correlated with the proportion of SARS-CoV-2 positive individuals (RR: 2.86 per log increase in the proportion of positive SARS-CoV-2 tests in the canton, 95%CI 2.56-3.19) and the proportion of asymptomatic SARS-CoV-2 positive individuals (RR: 6.50 per log increase in the proportion of positive SARS-CoV-2 tests in the canton, 95%CI 3.93-10.75) in admission screening. Around 0.36% of admission screenings were positive in asymptomatic patients. Admission screening results paralleled changes in population incidence with a brief lag.

Sensitivity of nasopharyngeal swab and saliva specimens in the detection of SARS-CoV-2 virus among boarding school girls

Objectives

With the reopening of schools, the detection of coronavirus disease 2019 (COVID-19) in children is very important in order to prevent outbreaks in schools and to reduce the risk of more severe post-COVID-19 complications. Various specimens can be used to detect the SARS-CoV-2 virus, and saliva has been considered as an alternative specimen in adults. However, data in children are lacking, especially among the female population. This study compared the efficacy of saliva specimens with nasopharyngeal swab specimens for the detection of severe acute respiratory syndrome coronavirus-2 using reverse transcriptase polymerase chain reaction.

Methods

This study evaluated the diagnostic performance of saliva among boarding school girls at three time points: diagnosis, and days 7 and 14 since first confirmation using a nasopharyngeal swab specimen. Eighty-four paired samples from 36 individuals were compared. Nasopharyngeal samplings were carried out by trained health officers, while saliva samplings were performed independently by children.

Results

The overall percentage agreement (OPA) between saliva and nasopharyngeal swabs was 50.2%. The OPA was 52.8% at diagnosis, and this increased slightly to 54.2% at day 7, and subsequently decreased to 45.8% at day 14. Saliva specimens had sensitivity of 44.6%, specificity of 80.0%, positive predictive value of 94.2% and negative predictive value of 16.3% compared with nasopharyngeal swab specimens for the diagnosis of COVID-19.

Conclusions

The use of saliva as an alternative specimen for the diagnosis of COVID-19 in children should be considered carefully. Thorough sampling instructions should be given in order to minimize bias in the findings.

Use of saliva as an alternative diagnostic method for diagnosis of COVID-19

Background

Mass population testing has been recommended to contain the spread of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, the use of nasopharyngeal swab specimens has caused many logistic challenges. This study investigated the sensitivity and specificity of saliva as a non-invasively-obtained specimen for molecular detection of SARS-CoV-2 RNA.

Methods

In total, 153 patients with confirmed coronavirus disease 2019 (COVID-19) who had been admitted to the regional referral hospital or who self-isolated at home were included in this study. Nasopharyngeal swab specimens and saliva samples were collected on the same day, and were tested for SARS-CoV-2 infection using reverse transcriptase polymerase chain reaction.

Results

The sensitivity and specificity of saliva samples were 81.5% and 76.4%, respectively, in cases that had been confirmed as COVID-19 using nasopharyngeal swab samples. Positive predictive values and negative predictive values were 92.3% and 54.1%, respectively. The highest detection rates were found among samples collected 4-7 days since symptom onset.

Conclusion

Saliva samples showed comparable performance to nasopharyngeal swab specimens for the diagnosis of COVID-19 in adults. The performance of saliva as a diagnostic specimen for COVID-19 testing is particularly significant during the first week of symptoms.

SARS-CoV-2 transmission with and without mask wearing or air cleaners in schools in Switzerland: A modeling study of epidemiological, environmental, and molecular data

BACKGROUND

Growing evidence suggests an important contribution of airborne transmission to the overall spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in particular via smaller particles called aerosols. However, the contribution of school children to SARS-CoV-2 transmission remains uncertain. The aim of this study was to assess transmission of airborne respiratory infections and the association with infection control measures in schools using a multiple-measurement approach.

METHODS AND FINDINGS

We collected epidemiological (cases of Coronavirus Disease 2019 (COVID-19)), environmental (CO2, aerosol and particle concentrations), and molecular data (bioaerosol and saliva samples) over 7 weeks from January to March 2022 (Omicron wave) in 2 secondary schools (n = 90, average 18 students/classroom) in Switzerland. We analyzed changes in environmental and molecular characteristics between different study conditions (no intervention, mask wearing, air cleaners). Analyses of environmental changes were adjusted for different ventilation, the number of students in class, school and weekday effects. We modeled disease transmission using a semi-mechanistic Bayesian hierarchical model, adjusting for absent students and community transmission. Molecular analysis of saliva (21/262 positive) and airborne samples (10/130) detected SARS-CoV-2 throughout the study (weekly average viral concentration 0.6 copies/L) and occasionally other respiratory viruses. Overall daily average CO2 levels were 1,064 ± 232 ppm (± standard deviation). Daily average aerosol number concentrations without interventions were 177 ± 109 1/cm3 and decreased by 69% (95% CrI 42% to 86%) with mask mandates and 39% (95% CrI 4% to 69%) with air cleaners. Compared to no intervention, the transmission risk was lower with mask mandates (adjusted odds ratio 0.19, 95% CrI 0.09 to 0.38) and comparable with air cleaners (1.00, 95% CrI 0.15 to 6.51). Study limitations include possible confounding by period as the number of susceptible students declined over time. Furthermore, airborne detection of pathogens document exposure but not necessarily transmission.

CONCLUSIONS

Molecular detection of airborne and human SARS-CoV-2 indicated sustained transmission in schools. Mask mandates were associated with greater reductions in aerosol concentrations than air cleaners and with lower transmission. Our multiple-measurement approach could be used to continuously monitor transmission risk of respiratory infections and the effectiveness of infection control measures in schools and other congregate settings.

Extreme differences in SARS-CoV-2 viral loads among respiratory specimen types during presumed pre-infectious and infectious periods

SARS-CoV-2 viral-load measurements from a single-specimen type are used to establish diagnostic strategies, interpret clinical-trial results for vaccines and therapeutics, model viral transmission, and understand virus-host interactions. However, measurements from a single-specimen type are implicitly assumed to be representative of other specimen types. We quantified viral-load timecourses from individuals who began daily self-sampling of saliva, anterior-nares (nasal), and oropharyngeal (throat) swabs before or at the incidence of infection with the Omicron variant. Viral loads in different specimen types from the same person at the same timepoint exhibited extreme differences, up to 10⁹ copies/mL. These differences were not due to variation in sample self-collection, which was consistent. For most individuals, longitudinal viral-load timecourses in different specimen types did not correlate. Throat-swab and saliva viral loads began to rise as many as 7 days earlier than nasal-swab viral loads in most individuals, leading to very low clinical sensitivity of nasal swabs during the first days of infection. Individuals frequently exhibited presumably infectious viral loads in one specimen type while viral loads were low or undetectable in other specimen types. Therefore, defining an individual as infectious based on assessment of a single-specimen type underestimates the infectious period, and overestimates the ability of that specimen type to detect infectious individuals. For diagnostic COVID-19 testing, these three single-specimen types have low clinical sensitivity, whereas a combined throat-nasal swab, and assays with high analytical sensitivity, was inferred to have significantly better clinical sensitivity to detect presumed pre-infectious and infectious individuals.

Comparative evaluation of saliva and nasopharyngeal swab for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia

BACKGROUND

Nasopharyngeal swab (NPS) remains the recommended sample type for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) diagnosis. However, the collection procedure causes discomfort and irritation to the patients, lowering the quality of the sample and exposing healthcare workers to risk. Furthermore, there is also a shortage of flocked swabs and personnel protective equipment in low-income settings. Therefore, this necessitates an alternative diagnostic specimen. The purpose of this study was to evaluate the performance of saliva against NPS for SARS-CoV-2 detection using RT-qPCR among COVID-19 suspected patients at Jigjiga, Eastern Ethiopia.

METHODS

Comparative cross-sectional study was conducted from June 28 to July 30, 2022. A total of 227 paired saliva and NPS samples were collected from 227 COVID-19 suspected patients. Saliva and NPS samples were collected and transported to the Somali Regional Molecular Laboratory. Extraction was conducted using DaAn kit (DaAn Gene Co., Ltd China). Veri-Q RT-qPCR was used for amplification and detection (Mico BioMed Co, Ltd, Republic of Korea). The data were entered into Epi-data version 4.6 and analyzed using SPSS 25. McNemar's test was used to compare the detection rate. Agreement between NPS and saliva was performed using Cohen's Kappa. The mean and median of cycle threshold values were compared using paired t-tests and the correlation between cycle threshold values was measured using Pearson correlation coefficient. P value < 0.05 was considered statistically significant.

RESULTS

The overall positivity rate of SARS-CoV-2 RNA was 22.5% (95% CI 17-28%). Saliva showed higher sensitivity (83.8%, 95% CI, 73-94.5%) than NPS (68.9%, 95% CI 60.8-76.8%). The specificity of saliva was 92.6% (95% CI, 80.6% - 100%) compared to NPS (96.7%, 95% CI, 87% - 100%). The positive, negative, and overall percent agreement between NPS and saliva was 83.8%, 92.6%, and 91.2% respectively (κ = 0.703, 95% CI 0.58-0.825, P = 0.00). The concordance rate between the two samples was 60.8%. NPS showed a higher viral load than saliva. There was low positive correlation between the cycle threshold values of the two samples (r = 0.41, 95% CI -1.69 to -0.98, P >0.05).

CONCLUSION

Saliva showed a higher detection rate for SARS-CoV-2 molecular diagnosis than NPS and there was significant agreement between the two specimens. Therefore, saliva could be suitable and easily obtainable alternative diagnostic specimen for SARS-CoV-2 molecular diagnosis.

Validation of RT-qPCR test for SARS-CoV-2 in saliva specimens

Background

Saliva samples may be an easier, faster, safer, and cost-saving alternative to NPS samples, and can be self-collected by the patient. Whether SARS-CoV-2 RT-qPCR in saliva is more accurate than in nasopharyngeal swaps (NPS) is uncertain. We evaluated the accuracy of the RT-qPCR in both types of samples, assuming both approaches were imperfect.

Methods

We assessed the limit of detection (LoD) of RT-qPCR in each type of sample. We collected paired NPS and saliva samples and tested them using the Berlin Protocol to detect SARS-CoV-2 envelope protein (E). We used a Bayesian latent class analysis (BLCA) to estimate the sensitivity and specificity of each test, while accounting for their conditional dependence.

Results

The LoD were 10 copies/mL in saliva and 100 copies/mL in NPS. Paired samples of saliva and NPS were collected in 412 participants. Out of 68 infected cases, 14 were positive only in saliva. RT-qPCR sensitivity ranged from 82.7% (95% CrI: 54.8, 94.8) in NPS to 84.5% (50.9, 96.5) in saliva. Corresponding specificities were 99.1 (95% CrI: 95.3, 99.8) and 98.4 (95% CrI: 92.8, 99.7).

Conclusions

SARS-CoV-2 RT-qPCR test in saliva specimens has a similar or better accuracy than RT-qPCR test in NPS. Saliva specimens may be ideal for surveillance in general population, particularly in children, and in healthcare or other personnel in need of serial testing.

Diagnostic performance of patient self-collected oral swab (tongue and cheek) in comparison with healthcare worker-collected nasopharyngeal swab for severe acute respiratory syndrome coronavirus-2 detection

The present study was conducted to compare the performance of patient self-collected oral swab (OS) with healthcare worker (HCW)-collected nasopharyngeal swab (NPS) for SARS-CoV-2 detection by reverse transcription polymerase chain reaction (RT-PCR) in real-world setting. Paired OS and NPS were collected from 485 consecutive individuals presenting with symptoms of coronavirus disease-19 (COVID-19) or asymptomatic contacts of COVID-19 cases. Both specimens were processed for RT-PCR and cycle threshold (Ct) value for each test was obtained. Positive percent agreement (PPA), negative percent agreement (NPA), overall percent agreement (OPA) and kappa were calculated for OS RT-PCR compared with NPS RT-PCR as reference. A total of 116/485 (23.9%) participants were positive by NPS RT-PCR. OS had PPA of 71.6%, NPA of 98.8%, OPA of 92.4% and kappa of 0.771. Almost all participants (483/485, 99.6%) reported OS as a convenient and comfortable sample for SARS-CoV-2 testing over NPS. All participants with Ct values <25 and majority (90.8%) with Ct values <30 were detected by OS. To conclude, OS self-sampling was preferred in comparison with NPS due the ease and comfort during collection. The performance of OS RT-PCR for SARS-CoV-2 detection, however, was sub-optimal in comparison with NPS RT-PCR.

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.

A fast, ultrasensitive SERS immunoassay to detect SARS-CoV-2 in saliva

The COVID-19 pandemic has emphasized the need for accurate, rapid, point-of-care diagnostics to control disease transmission. We have developed a simple, ultrasensitive single-particle surface-enhanced Raman spectroscopy (SERS) immunoassay to detect the SARS-CoV-2 spike protein in saliva. This assay relies on the use of single chain Fv (scFv) recombinant antibody expressed in E. coli to bind the SARS-CoV-2 spike protein. Recombinant scFv labeled with a SERS-active dye in solution is mixed with unlabeled scFv conjugated to gold-coated magnetic nanoparticles and a sample to be tested. In the presence of the SARS-CoV-2 spike protein, immunocomplexes form and concentrate the labeled scFv close to the gold surface of the nanoparticles, causing an increased SERS signal. The assay detects inactivated SARS-CoV-2 virus and spike protein in saliva at concentrations of 1.94 × 103 genomes mL-1 and 4.7 fg mL-1, respectively, making this direct detection antigen test only 2-3 times less sensitive than some qRT-PCR tests. All tested SARS-CoV-2 spike proteins, including those from alpha, beta, gamma, delta, and omicron variants, were detected without recognition of the closely related SARS and MERS spike proteins. This 30 min, no-wash assay requires only mixing, a magnetic separation step, and signal measurements using a hand-held, battery-powered Raman spectrometer, making this assay ideal for ultrasensitive detection of the SARS-CoV-2 virus at the point-of-care.

Multiplexed reverse-transcriptase quantitative polymerase chain reaction using plasmonic nanoparticles for point-of-care COVID-19 diagnosis

Quantitative polymerase chain reaction (qPCR) offers the capabilities of real-time monitoring of amplified products, fast detection, and quantitation of infectious units, but poses technical hurdles for point-of-care miniaturization compared with end-point polymerase chain reaction. Here we demonstrate plasmonic thermocycling, in which rapid heating of the solution is achieved via infrared excitation of nanoparticles, successfully performing reverse-transcriptase qPCR (RT-qPCR) in a reaction vessel containing polymerase chain reaction chemistry, fluorescent probes and plasmonic nanoparticles. The method could rapidly detect SARS-CoV-2 RNA from human saliva and nasal specimens with 100% sensitivity and 100% specificity, as well as two distinct SARS-CoV-2 variants. The use of small optical components for both thermocycling and multiplexed fluorescence monitoring renders the instrument amenable to point-of-care use. Overall, this study demonstrates that plasmonic nanoparticles with compact optics can be used to achieve real-time and multiplexed RT-qPCR on clinical specimens, towards the goal of rapid and accurate molecular clinical diagnostics in decentralized settings.

Performance of saliva compared with nasopharyngeal swab for diagnosis of COVID-19 by NAAT in cross-sectional studies: Systematic review and meta-analysis

Nucleic acid amplification testing (NAAT) is the preferred method to diagnose coronavirus disease 2019 (COVID-19). Saliva has been suggested as an alternative to nasopharyngeal swabs (NPS), but previous systematic reviews were limited by the number and types of studies available. The objective of this systematic review and meta-analysis was to assess the diagnostic performance of saliva compared with NPS for COVID-19. We searched Ovid MEDLINE, Embase, Cochrane, and Scopus databases up to 24 April 2021 for studies that directly compared paired NPS and saliva specimens taken at the time of diagnosis. Meta-analysis was performed using an exact binomial rendition of the bivariate mixed-effects regression model. Risk of bias was assessed using the QUADAS-2 tool. Of 2683 records, we included 23 studies with 25 cohorts, comprising 11,582 paired specimens. A wide variety of NAAT assays and collection methods were used. Meta-analysis gave a pooled sensitivity of 87 % (95 % CI = 83-90 %) and specificity of 99 % (95 % CI = 98-99 %). Subgroup analyses showed the highest sensitivity when the suspected individual is tested in an outpatient setting and is symptomatic. Our results support the use of saliva NAAT as an alternative to NPS NAAT for the diagnosis of COVID-19.

Saliva as a sample type for SARS-CoV-2 detection: implementation successes and opportunities around the globe

INTRODUCTION

Symptomatic testing and asymptomatic screening for SARS-CoV-2 continue to be essential tools for mitigating virus transmission. Though COVID-19 diagnostics initially defaulted to oropharyngeal or nasopharyngeal sampling, the worldwide urgency to expand testing efforts spurred innovative approaches and increased diversity of detection methods. Strengthening innovation and facilitating widespread testing remains critical for global health, especially as additional variants emerge and other mitigation strategies are recalibrated.

AREAS COVERED

A growing body of evidence reflects the need to expand testing efforts and further investigate the efficiency, sensitivity, and acceptability of saliva samples for SARS-CoV-2 detection. Countries have made pandemic response decisions based on resources, costs, procedures, and regional acceptability - the adoption and integration of saliva-based testing among them. Saliva has demonstrated high sensitivity and specificity while being less invasive relative to nasopharyngeal swabs, securing saliva's position as a more acceptable sample type.

EXPERT OPINION

Despite the accessibility and utility of saliva sampling, global implementation remains low compared to swab-based approaches. In some cases, countries have validated saliva-based methods but face challenges with testing implementation or expansion. Here, we review the localities that have demonstrated success with saliva-based SARS-CoV-2 testing approaches and can serve as models for transforming concepts into globally-implemented best practices.

Antibodies from convalescent plasma promote SARS-CoV-2 clearance in individuals with and without endogenous antibody response

BACKGROUNDNeutralizing antibodies are considered a key correlate of protection by current SARS-CoV-2 vaccines. The manner in which human infections respond to therapeutic SARS-CoV-2 antibodies, including convalescent plasma therapy, remains to be fully elucidated.METHODSWe conducted a proof-of-principle study of convalescent plasma therapy based on a phase I trial in 30 hospitalized COVID-19 patients with a median interval between onset of symptoms and first transfusion of 9 days (IQR, 7-11.8 days). Comprehensive longitudinal monitoring of the virological, serological, and disease status of recipients allowed deciphering of parameters on which plasma therapy efficacy depends.RESULTSIn this trial, convalescent plasma therapy was safe as evidenced by the absence of transfusion-related adverse events and low mortality (3.3%). Treatment with highly neutralizing plasma was significantly associated with faster virus clearance, as demonstrated by Kaplan-Meier analysis (P = 0.034) and confirmed in a parametric survival model including viral load and comorbidity (adjusted hazard ratio, 3.0; 95% CI, 1.1-8.1; P = 0.026). The onset of endogenous neutralization affected viral clearance, but even after adjustment for their pretransfusion endogenous neutralization status, recipients benefitted from plasma therapy with high neutralizing antibodies (hazard ratio, 3.5; 95% CI, 1.1-11; P = 0.034).CONCLUSIONOur data demonstrate a clear impact of exogenous antibody therapy on the rapid clearance of viremia before and after onset of the endogenous neutralizing response, and point beyond antibody-based interventions to critical laboratory parameters for improved evaluation of current and future SARS-CoV-2 therapies.TRIAL REGISTRATIONClinicalTrials.gov NCT04869072.FUNDINGThis study was funded via an Innovation Pool project by the University Hospital Zurich; the Swiss Red Cross Glückskette Corona Funding; Pandemiefonds of the UZH Foundation; and the Clinical Research Priority Program "Comprehensive Genomic Pathogen Detection" of the University of Zurich.

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.

Bean Extract-Based Gargle for Efficient Diagnosis of Active COVID-19 Infection Using Rapid Antigen Tests

The antigen-based rapid diagnostic test (Ag-RDT) using saliva specimens is fast, noninvasive, and suitable for SARS-CoV-2 self-testing, unlike nasopharyngeal swab (NPS) testing. We evaluated a novel Beanguard gargle (BG)-based virus collection method that can be applied to Ag-RDT as an alternative to the current RT-PCR with an NPS for early diagnosis of COVID-19. This clinical trial comprised 102 COVID-19-positive patients hospitalized after a governmental screening process and 100 healthy individuals. Paired NPS and BG-based saliva specimens from COVID-19 patients and healthy individuals were analyzed using NPS-RT-PCR, BG-RT-PCR, and BG-Ag-RDTs, whose diagnostic performance for detecting SARS-CoV-2 was compared. BG-Ag-RDTs showed high sensitivity (97.8%) and specificity (100%) in 45 patients within 6 days of illness and detected all cases of SARS-CoV-2 Alpha and Delta variants. In 11 asymptomatic active COVID-19 cases, both BG-Ag-RDTs and BG-RT-PCR showed sensitivities and specificities of 100%. Sensitivities of BG-Ag-RDT and BG-RT-PCR toward salivary viral detection were highly concordant, with no discrimination between symptomatic (97.0%), asymptomatic (100%), or SARS-CoV-2 variant (100%) cases. The intermolecular interactions between SARS-CoV-2 spike proteins and truncated canavalin, an active ingredient from the bean extract (BE), were observed in terms of physicochemical properties. The detachment of the SARS-CoV-2 receptor-binding domain from hACE2 increased as the BE concentration increased, allowing the release of the virus from hACE2 for early diagnosis. Using BG-based saliva specimens remarkably enhances the Ag-RDT diagnostic performance as an alternative to NPS and enables noninvasive, rapid, and accurate COVID-19 self-testing and mass screening, supporting efficient COVID-19 management.

IMPORTANCE An Ag-RDT is less likely to be accepted as an initial test method for early diagnosis owing to its low sensitivity. However, our self-collection method, Ag-RDT using BG-based saliva specimens, showed significantly enhanced detection sensitivity and specificity toward SARS-CoV-2 including the Alpha and Delta variants in all patients tested within 6 days of illness. The method represents an attractive alternative to nasopharyngeal swabs for the early diagnosis of symptomatic and asymptomatic COVID-19 cases. The evidence suggests that the method could have a potential for mass screening and monitoring of COVID-19 cases.

Oral Pathology in COVID-19 and SARS-CoV-2 Infection-Molecular Aspects

This review article was designed to evaluate the existing evidence related to the molecular processes of SARS-CoV-2 infection in the oral cavity. The World Health Organization stated that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and transmission is produced by respiratory droplets and aerosols from the oral cavity of infected patients. The oral cavity structures, keratinized and non-keratinized mucosa, and salivary glands' epithelia express SARS-CoV-2 entry and transmission factors, especially angiotensin converting enzyme Type 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). Replication of the virus in cells leads to local and systemic infection spread, and cellular damage is associated with clinical signs and symptoms of the disease in the oral cavity. Saliva, both the cellular and acellular fractions, holds the virus particles and contributes to COVID-19 transmission. The review also presents information about the factors modifying SARS-CoV-2 infection potential and possible local pharmacotherapeutic interventions, which may confine SARS-CoV-2 virus entry and transmission in the oral cavity. The PubMed and Scopus databases were used to search for suitable keywords such as: SARS-CoV-2, COVID-19, oral virus infection, saliva, crevicular fluid, salivary gland, tongue, oral mucosa, periodontium, gingiva, dental pulp, ACE2, TMPRSS2, Furin, diagnosis, topical treatment, vaccine and related words in relevant publications up to 28 December 2021. Data extraction and quality evaluation of the articles were performed by two reviewers, and 63 articles were included in the final review.

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.

Salivary Interleukin-6 and C-Reactive Protein/Mean Platelet Volume Ratio in the Diagnosis of Late-Onset Neonatal Pneumonia

Neonatal pneumonia is a serious respiratory infectious disease with a high rate of case fatality in developing countries. Salivary cytokines could serve as interesting noninvasive markers in the diagnosis of neonatal pneumonia. The aim was to assess the diagnostic role of salivary and serum interleukin-6 (IL-6), C-reactive protein/mean platelet volume (CRP/MPV) ratio, and the combination of these markers in the diagnosis of late-onset neonatal pneumonia in full-term neonates. Seventy full-term neonates, 35 with late-onset neonatal pneumonia and 35 controls, were enrolled in this prospective case-control study. Complete blood count (CBC), salivary and serum IL-6, and CRP concentrations were measured for all the study subjects. The sensitivity, specificity, positive predictive value, and negative predictive value of salivary IL-6, serum IL-6, and CRP/MPV ratio for the diagnosis of late-onset neonatal pneumonia were determined. At the cutoff point of >34 pg/ml, salivary IL-6 showed 82.86% sensitivity and 91.43% specificity. CRP/MPV ratio showed a sensitivity of 97.14% and specificity of 85.71% at a cutoff value > 0.88. The combination of salivary IL-6 and CRP/MPV ratio improved the sensitivity and specificity to 100%. The current study shows for the first time that both salivary IL-6 and CRP/MPV ratio are suitable markers for the diagnosis of late-onset neonatal pneumonia in full-term neonates.

Diagnostic Accuracy of SARS-CoV-2 Rapid Antigen Detection Testing in Symptomatic and Asymptomatic Children in the Clinical Setting

Antigen-based rapid diagnostic tests (RDTs) are used in children despite the lack of data. We evaluated the diagnostic performance of the Panbio-COVID-19 Ag Rapid Test Device (P-RDT) in children. Symptomatic and asymptomatic participants 0 to 16 years old had two nasopharyngeal swabs (NPS) for both reverse transcription-PCR (RT-PCR) and P-RDT. A total of 822 participants completed the study, of which 533 (64.9%) were symptomatic. Among the 119 (14.5%) RT-PCR-positive patients, the P-RDT sensitivity was 0.66 (95% confidence interval [CI] 0.57 to 0.74). Mean viral load (VL) was higher among P-RDT-positive patients than negative ones (P < 0.001). Sensitivity was 0.91 in specimens with VL of >1.0E6 IU/ml (95% CI 0.83 to 0.99) and decreased to 0.75 (95% CI 0.66 to 0.83) for specimens >1.0E3 IU/ml. Among symptomatic participants, the P-RDT displayed a sensitivity of 0.73 (95% CI 0.64 to 0.82), which peaked at 1.00 at 2 days post-onset of symptoms (DPOS) (95% CI 1.00 to 1.00), then decreased to 0.56 (95% CI 0.23 to 0.88) at 5 DPOS. There was a trend toward lower P-RDT sensitivity in symptomatic children <12 years (0.62 [95% CI 0.45 to 0.78]) versus ≥12 years (0.80 [95% CI 0.69 to 0.91]; P = 0.09). In asymptomatic participants, the P-RDT displayed a sensitivity of 0.43 (95% CI 0.26 to 0.61). Specificity was 1.00 in symptomatic and asymptomatic children (95% CI 0.99 to 1.00). The overall 73% and 43% sensitivities of P-RDT in symptomatic and asymptomatic children, respectively, was below the 80% cutoff recommended by the World Health Organization. We observed a correlation between VL and P-RDT sensitivity, as well as variation of sensitivity according to DPOS, a major determinant of VL. These data highlight the limitations of RDTs in children, with the potential exception in early symptomatic children ≥12yrs.

Reduced Relative Sensitivity of the Elecsys SARS-CoV-2 Antigen Assay in Saliva Compared to Nasopharyngeal Swabs

Early identification and isolation of SARS-CoV-2-infected individuals is central to contain the COVID-19 pandemic. Nasopharyngeal swabs (NPS) serve as a specimen for detection by RT-PCR and rapid antigen screening tests. Saliva has been confirmed as a reliable alternative specimen for RT-PCR and has been shown to be valuable for diagnosing children and in repetitive mass testing due to its non-invasive collection. Combining the advantages of saliva with those of antigen tests would be highly attractive to further increase test capacities. Here, we evaluated the performance of the Elecsys SARS-CoV-2 Antigen assay (Roche) in RT-PCR-positive paired NPS and saliva samples (N = 87) and unpaired NPS (N = 100) with confirmed SARS-CoV-2 infection (Roche cobas SARS-CoV-2 IVD test). We observed a high positive percent agreement (PPA) of the antigen assay with RT-PCR in NPS, reaching 87.2% across the entire cohort, whereas the overall PPA for saliva was insufficient (40.2%). At Ct values ≤ 28, PPA were 100% and 91.2% for NPS and saliva, respectively. At lower viral loads, the sensitivity loss of the antigen assay in saliva was striking. At Ct values ≤ 35, the PPA for NPS remained satisfactory (91.5%), whereas the PPA for saliva dropped to 46.6%. In conclusion, saliva cannot be recommended as a reliable alternative to NPS for testing with the Elecsys Anti-SARS-CoV-2 Antigen assay. As saliva is successfully used broadly in combination with RT-PCR testing, it is critical to create awareness that suitability for RT-PCR cannot be translated to implementation in antigen assays without thorough evaluation of each individual test system.

Saliva Testing is a Robust Non-Invasive Method for SARS-CoV-2 RNA Detection

Purpose

The precise diagnostic testing is of high importance in fighting the coronavirus pandemic. While nasopharyngeal (NP) swab testing is currently the gold standard, the SARS-CoV-2 virus could be also detected in some other body fluids. In this study, we aimed to compare the SARS-CoV-2 RNA detection results, obtained using saliva samples and NP swab samples, collected from infected patients and healthy volunteers.

Patients and Methods

A total of 111 individuals were enrolled in this study: 53 healthy volunteers, participating in routine testing and 58 COVID-19 patients. Diagnosis for both groups was confirmed using a set of diagnostic CE-IVD labeled RT-qPCR kits. Most of the saliva samples were collected within 48 hours after the NP swabs were taken. RNA was purified from saliva samples and analyzed using a laboratory-developed kit (Diagnolita). Detection results for both sample types were compared and analyzed in terms of result agreement, Ct variation, and quantity of internal control, as well as population analysis.

Results

We found a good concordance between the NP swab and saliva samples. The positive percent agreement was 98.28% (CI 90.76–99.96%) and negative percent agreement was 98.11% (CI 89.93–99.95%). Additionally, we observed a statistically significant (p<0.05) and moderately strong (R = 0.53) correlation between Ct values in saliva and NP swab samples. The saliva collection method is more robust since the Ct variation of internal control ribonuclease P mRNA detection is lower in saliva samples.

Conclusion

Saliva sample testing is a robust and reliable non-invasive alternative to the NP swab method for SARS-CoV-2 RNA detection, as well as a promising tool for COVID-19 screening.

Adding saliva testing to oropharyngeal and deep nasal swab testing increases PCR detection of SARS-CoV-2 in primary care and children

Objective

To compare the concordance and acceptability of saliva testing with standard‐of‐care oropharyngeal and bilateral deep nasal swab testing for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) in children and in general practice.

Design

Prospective multicentre diagnostic validation study.

Setting

Royal Children’s Hospital, and two general practices (cohealth, West Melbourne; Cirqit Health, Altona North) in Melbourne, July–October 2020.

Participants

1050 people who provided paired saliva and oropharyngeal‐nasal swabs for SARS‐CoV‐2 testing.

Main outcome measures

Numbers of cases in which SARS‐CoV‐2 was detected in either specimen type by real‐time polymerase chain reaction; concordance of results for paired specimens; positive percent agreement (PPA) for virus detection, by specimen type.

Results

SARS‐CoV‐2 was detected in 54 of 1050 people with assessable specimens (5%), including 19 cases (35%) in which both specimens were positive. The overall PPA was 72% (95% CI, 58–84%) for saliva and 63% (95% CI, 49–76%) for oropharyngeal‐nasal swabs. For the 35 positive specimens from people aged 10 years or more, PPA was 86% (95% CI, 70–95%) for saliva and 63% (95% CI, 45–79%) for oropharyngeal‐nasal swabs. Adding saliva testing to standard‐of‐care oropharyngeal‐nasal swab testing increased overall case detection by 59% (95% CI, 29–95%). Providing saliva was preferred to an oropharyngeal‐nasal swab by most participants (75%), including 141 of 153 children under 10 years of age (92%).

Conclusion

In children over 10 years of age and adults, saliva testing alone may be suitable for SARS‐CoV‐2 detection, while for children under 10, saliva testing may be suitable as an adjunct to oropharyngeal‐nasal swab testing for increasing case detection.

Sample-Pooling Strategy for SARS-CoV-2 Detection among Students and Staff of the University of Sannio

Since the beginning of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, it has been clear that testing large groups of the population was the key to stem infection and prevent the effects of the coronavirus disease of 2019, mostly among sensitive patients. On the other hand, time and cost-sustainability of virus detection by molecular analysis such as reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) may be a major issue if testing is extended to large communities, mainly asymptomatic large communities. In this context, sample-pooling and test grouping could offer an effective solution. Here we report the screening on 1195 oral-nasopharyngeal swabs collected from students and staff of the Università degli Studi del Sannio (University of Sannio, Benevento, Campania, Italy) and analyzed by an in-house developed multiplex RT-qPCR for SARS-CoV-2 detection through a simple monodimensional sample pooling strategy. Overall, 400 distinct pools were generated and, within 24 h after swab collection, five positive samples were identified. Out of them, four were confirmed by using a commercially available kit suitable for in vitro diagnostic use (IVD). High accuracy, sensitivity and specificity were also determined by comparing our results with a reference IVD assay for all deconvoluted samples. Overall, we conducted 463 analyses instead of 1195, reducing testing resources by more than 60% without lengthening diagnosis time and without significant losses in sensitivity, suggesting that our strategy was successful in recognizing positive cases in a community of asymptomatic individuals with minor requirements of reagents and time when compared to normal testing procedures.

Coronavirus Disease 2019 in Children

Since its appearance in Wuhan in mid-December 2019, acute respiratory syndrome coronavirus 2 (SARS-CoV-2) related 19 coronavirus disease (COVID-19) has spread dramatically worldwide. It soon became apparent that the incidence of pediatric COVID-19 was much lower than the adult form. Morbidity in children is characterized by a variable clinical presentation and course. Symptoms are similar to those of other acute respiratory viral infections, the upper airways being more affected than the lower airways. Thus far, over 90% of children who tested positive for the virus presented mild or moderate symptoms and signs. Most children were asymptomatic, and only a few cases were severe, unlike in the adult population. Deaths have been rare and occurred mainly in children with underlying morbidity. Factors as reduced angiotensin-converting enzyme receptor expression, increased activation of the interferon-related innate immune response, and trained immunity have been implicated in the relative resistance to COVID-19 in children, however the underlying pathogenesis and mechanism of action remain to be established. While at the pandemic outbreak, mild respiratory manifestations were the most frequently described symptoms in children, subsequent reports suggested that the clinical course of COVID-19 is more complex than initially thought. Thanks to the experience acquired in adults, the diagnosis of pediatric SARS-CoV-2 infection has improved with time. Data on the treatment of children are sparse, however, several antiviral trials are ongoing. The purpose of this narrative review is to summarize current understanding of pediatric SARS-CoV-2 infection and provide more accurate information for healthcare workers and improve the care of patients.