SARS-CoV-2 Positivity in Foreign-Born Adults: A Retrospective Study in Verona, Northeast Italy.

We compared SARS-CoV-2 positivity between the foreign-born adult working population and Italians living in the Verona area to investigate whether being a foreign-born adult could confer an increased risk of infection or lead to a diagnostic delay. The present study included 105,774 subjects, aged 18-65 years, tested for SARS-CoV-2 by nasopharyngeal swabs and analyzed at the University Hospital of Verona between January 2020 and September 2022. A logistic regression model was used, controlling for gender, age, time of sampling, and source of referral. A higher proportion of SARS-CoV-2 positivity in Italian (30.09%) than in foreign-born (25.61%) adults was reported, with a higher proportion of SARS-CoV-2 positivity in men than women in both cohorts analyzed. The difference in swab positivity among Italian and foreign-born adults was the highest in people aged 18-29 years (31.5% vs. 23.3%) and tended to disappear thereafter. Swab positivity became comparable between Italian and foreign-born adults during the vaccination campaign. Multivariable analysis confirmed the lower risk of swab positivity among foreign-born adults (OR = 0.85, 95% CI 0.82-0.89). In the Verona area, foreign-born adults showed a lower rate of SARS-CoV-2 positivity than the native population, likely because of underdiagnosis. Hence, public health should increase attention toward these particularly vulnerable populations.

Clinical Performance of Self-Collected Purified Water Gargle for Detection of Influenza a Virus Infection by Real-Time RT-PCR.

Purpose: Self-collected specimens are increasingly being used as alternatives to swab-based methods for the detection of respiratory viruses. While saliva is well accepted, gargle specimens are a potential alternative with characteristics that are more favorable for laboratory handling. This study assessed the performance of gargle specimens in the detection of influenza A viruses (IAVs). Patients and Methods: We performed a prospective head-to-head comparison between combined nasopharyngeal and oropharyngeal swabs (NPS&OPS) and purified water gargle (PWG) among adult outpatients with febrile respiratory symptoms to detect IAVs using real-time RT-PCR during two influenza seasons. Results: During study periods 1 (July 13 to 26, 2022, H3N2 predominated) and 2 (February 25 to March 10, 2023, H1N1 pdm09 predominated), a total of 459 patients were recruited. The overall agreement between the NPS&OPS and PWG was 85.0% (390/459, κ = 0.697), with 88.0% in period 1 and 82.6% in period 2. The detection rate of IAVs in PWG (51.6%, 237/459) was lower than that in NPS&OPS (62.3%, 286/459) (p < 0.0001). The overall sensitivity and specificity were 96.6% (93.7-98.3%) and 100% (97.1-100%) in NPS&OPS and were 80.1% (75.0-84.4%) and 100% (97.1-100%) in PWG, respectively. Among the 227 pairs of concordant positive specimens, cycle threshold (Ct) values were significantly lower in NPS&OPS than in PWG (median Ct values: 24.2, 28.2, p < 0.0001). Conclusion: Although self-collected PWG specimens offer acceptable performance for IAVs molecular testing, NPS&OPS remain a reliable option. Given the convenience of collection, nonviscous gargles are recommended for viral detection during emergencies or under specific conditions.

MOLECULAR DETECTION PROTOCOL OF SARS-COV-2 THROUGH SELF-COLLECTED SALIVA SPECIMENS VERSUS NASOPHARYNGEAL SWABS.

Background: Several reports have shown that saliva specimen is an excellent alternative biofluid sample for SARS-CoV-2 detection. We conducted this study, in order to assess the sensitivity and specificity of using saliva self-collected by adult and pediatric patients, as a biological sample for RT-PCR diagnosis. Aims: The present study was carried out to assess the sensitivity and specificity of using saliva self-collected from adult and pediatric patients, as a biological sample for RT-qPCR diagnosis. Methods: In this study, 50 symptomatic patients and 40 asymptomatic subjects (adult and pediatric) were enrolled between September 2020 and November 2020 at the Department of Infectious Diseases, Bejaia University Hospital (CHU), and tested simultaneously for the sensitivity and specificity of the SARS-CoV-2 viral genome by RT-PCR on both nasopharyngeal swabs NP swab and saliva samples. Results: Our RT-qPCR results revealed that saliva samples showed the highest sensitivity (95% CI [27.67, 29.82]) followed by a nasopharyngeal swab for symptomatic (95% CI [29.64, 31.49]) as well as for asymptomatic adult patients. Moreover, the saliva of symptomatic and asymptomatic patients was monitored, and the presence of viral RNA was detected in >95% of the asymptomatic patients as well as the symptomatic patients. Surprisingly, the Ct values of ORF1ab and N genes are highly lower in nasopharyngeal swabs compared to saliva. Indeed, the mean difference note that for the ORF1ab gene and N gene, the mean of difference in ΔCt value were respectively 3.683 and 3.578. Together, including symptomatic and asymptomatic subjects, the overall agreement between the saliva sample and the nasopharyngeal is about 84%. Conclusion: The sensitivity of saliva samples remains acceptable; it may still be a viable option in locations where laboratory facilities are lacking for diagnostic purposes in the early phase of the disease.

Detection of infectious SARS-CoV-2 in ocular samples is linked to viral load in the nasopharynx.

Introduction: SARS-CoV-2 is known to infect respiratory tissue cells. However, less is known about infection of ocular tissue and potential infectivity of lacrimal fluid. With this study, we want to compare viral loads in eye and nasopharyngeal swabs and analyze these for infectious virus. Methods: Between May 2020 and April 2021 ocular and nasopharyngeal swabs were collected from 28 SARS-CoV-2 infected patients treated on the corona virus disease 2019 (COVID-19)-ward of the University Hospital of Innsbruck, Austria. Samples with PCR detectable SARS-CoV-2 were analyzed via whole genome sequencing and an attempt was made to isolate infectious virus. Results: At the time point of sample collection, 22 individuals were still PCR positive in nasopharyngeal samples and in 6 of these patients one or both ocular samples were additionally positive. CT-values in eyes were generally higher compared to corresponding nasopharyngeal samples and we observed a tendency for lower CT-values, i.e. increased viral load, in nasopharyngeal swabs of individuals with at least one infected eye, compared to those where ocular samples were PCR negative. Ocular and nasopharyngeal sequences from the same patient were assigned to the same variant, either the D614G or the Alpha variant. Infectious virus was successfully isolated from 9 nasopharyngeal swabs, however only from one of the seven PCR positive ocular samples. Conclusion: We could detect SARS-CoV-2 in eyes of some of the infected patients albeit at lower levels compared to nasopharyngeal swabs. However, our results also indicate that lacrimal fluid might be infectious in patients with high viral load.

Comparing Polymerase Chain Reaction Testing of Nasopharyngeal Swab and Lower Respiratory Tract Specimens for the Diagnosis of Pneumocystis jirovecii Pneumonia.

Using nasopharyngeal (NP) swab samples instead of lower respiratory tract specimens for polymerase chain reaction (PCR) to diagnose Pneumocystis jirovecii pneumonia (PJP) may be better tolerated and improve diagnostic accessibility. In this 2-year Australian retrospective cohort study of patients with clinically suspected PJP, P jirovecii PCR on NP swab samples had perfect specificity but low sensitivity (0.66).

Utility of Rapid Nasopharyngeal Swab for Respiratory Pathogens in the Diagnosis of Viral Infections in Children Hospitalized with Fever: A Prospective Validation Study to Improve Antibiotic Use.

Introduction: Fever is among the most common reason for medical assessment and antibiotic prescription in practice. The aim of this study was to evaluate positive and negative predictive values of rapid nasopharyngeal swabs for respiratory pathogens to discriminate viral from bacterial infections. Methods: We prospectively tested children with signs and/or symptoms of infections (e.g., fever, cough, wheezing, suspected urinary tract infection) admitted to a paediatric department. Following discharge, clinical phenotypes were assigned defining a cohort of children having probable/certain viral infection, probable/certain bacterial infection, other inflammatory conditions or healthy controls. Results: In this study, 190 children were enrolled (50.5% females, median age 30.5 (8-86) months). In total, 102 patients (53.7%) were affected by respiratory viral infections, 16 (8.4%) by bacterial infections, 29 (15.3%) were healthy controls and 43 (22.6%) were affected by another pathological condition manifested with fever. In total, 84.3% of patients classified as viral infection tested positive for viruses, compared with 18.8% of patients with bacterial infection (p < 0.001), 18.6% of patients with other condition (p < 0.001) and 17.2% of control patients (p < 0.001). The positive predictive value of NPSs in the diagnosis of viral infection was 88.6% and the negative predictive value was 75.0%. Conclusion: Our findings suggest that rapid NPS tests for respiratory viruses are a useful tool to confirm viral infections in children with fever and improve antibiotic use.

External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021.

INTRODUCTION: Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. METHODS: In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/µL, positive sample B with 5 copies/µL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/µL was prepared using a simulated saliva sample. RESULTS: Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. CONCLUSIONS: The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.

Cycle threshold values of SARS-CoV-2 RNA in conjunctival swabs and nasopharyngeal secretions: a comparative study from a tertiary care center in India.

PURPOSE: To detect the viral RNA load of SARS-CoV-2 in conjunctival swabs of COVID-19 patients, and compare with nasopharyngeal swabs. METHODS: Conjunctival swabs of COVID-19 patients (with PCR positive nasopharyngeal swabs) were subjected to quantitative reverse transcription-polymerase chain reaction (RT-PCR) for detection of SARS-CoV-2 RNA. The cycle threshold (Ct) values of Open Reading Frame 1 (ORF 1 Ab gene) and nucleoprotein (N gene) PCRs were used to assess the viral RNA load, and compare them with the baseline values of nasopharyngeal swabs. RESULTS: Of 93 patients, 17 (18.27%) demonstrated SARS-CoV-2 RNA in conjunctival swabs. Baseline nasopharyngeal swabs were collected at a median of 2 days; while, the conjunctival swabs were collected at median 7 days, from onset of illness (p < 0.001). Despite a significant delay in conjunctival swab collection than nasopharyngeal swabs, the Ct values (ORF or N gene PCRs) were comparable between nasopharyngeal swab and conjunctival swab samples. Subsequently, during the recovery period, in four of these 17 patients (with conjunctival swab positivity), when the second nasopharyngeal swab was 'negative', the conjunctival swab was 'positive'. CONCLUSION: The conjunctival swabs demonstrated SARS-CoV-2 RNA in 17 (18.27%) of 93 COVID-19 patients. Our results may suggest a delayed or a prolonged shedding of the virus/viral RNA on the ocular surface than in nasopharyngeal mucosa.

Comparison of influenza viral load in nasopharyngeal and midturbinate swabs.

Different specimen types are used for influenza diagnosis but comparative data for viral loads from different swab types are limited. We compared influenza viral loads (determined by quantitative reverse transcription polymerase chain reaction [RT-PCR]) in 93 paired midturbinate and nasopharyngeal swab aliquots from influenza infected patients enrolled in a phase 3 randomized-controlled study with the objective of maximizing the number of swabs available for sequence analysis. Midturbinate swabs yielded a 53% lower viral load versus nasopharyngeal swabs, and this difference was similar for influenza A and B. These data suggest that nasopharyngeal swabs might be preferred in diagnostic settings when obtaining higher viral load is important.

The effect of the distraction methods used before the COVID-19 test on the fear and anxiety levels of children: a RCT study.

The current study aimed to investigate the effect of the distraction methods employed before nasopharyngeal swab sampling from children within the scope of the COVID test on their anxiety and fear levels. The study was an RCT with parallel groups conducted according to the CONSORT statement at the pediatric emergency unit of a hospital in Turkey. Children aged 5-10 years were randomized into three groups: Kaleidoscope, Visual Illusion Cards, and control. Data were collected by the researchers using the Descriptive Characteristics Form, the Children's Anxiety Meter-State, and the Children's Fear Scale. According to the reports of the children, the parents, and the nurse, the mean anxiety score and the mean fear score in the experimental groups were significantly lower after the nasopharyngeal swab procedure compared to the control group (p < .05). Fear and anxiety were observed less in the visual illusion cards group and the kaleidoscope group.

SalivaDirect: an alternative to a conventional RNA extraction protocol for molecular detection of SARS-CoV-2 in a clinical setting.

IMPORTANCE: Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.

Comparison of "hock-a-loogie" saliva versus nasopharyngeal and oropharyngeal swabs for detecting common respiratory pathogens.

Self-collection of saliva samples has attracted considerable attention in recent years, particularly during the coronavirus disease 2019 pandemic. However, studies investigating the detection of other common respiratory pathogens in saliva samples are limited. In this study, nasopharyngeal swabs (NPS), oropharyngeal swabs (OPS), and "hock-a-loogie" saliva (HLS) were collected from 469 patients to detect 13 common respiratory pathogens. Overall positivity rates for NPS (66.1 %), HLS (63.5 %), and OPS (57.8 %) were statistically different (P = 0.028), with an overall concordance of 72.7 %. Additionally, detection rates for NPS (85.9 %) and HLS (83.2 %) for all pathogens were much higher than for OPS (73.3 %). Coronavirus and human rhinovirus were most frequently detected pathogens in NPS (P < 0.001). Mycoplasma pneumoniae was significantly more prevalent in the HLS group (P = 0.008). In conclusion, NPS was a reliable sample type for detecting common respiratory pathogens. HLS was more easily collected and can be used in emergencies or specific conditions. Mixed NPS/OPS and NPS/HLS specimens have the potential to improve detection rates, although OPS testing alone has a relatively high risk for missed detection.

Analysis of a direct access testing system for the detection of SARS-CoV-2 in the paediatric population attending school.

Background: During the COVID-19 pandemic, the paediatric population plays a minor role in the spread of the SARS-CoV-2 virus. However, in order to keep schools open and reduce SARS-CoV spreading, it is necessary to identify and isolate early SARS-CoV-2 positive paediatric patients even if they are asymptomatic. The aim of this study was to describe a setting for SARS-CoV 2 testing based on the spontaneous presentation of paediatric patients attending school without a medical prescription and explore its appropriateness. Study design: Cross-sectional study. Methods: The study performed between September 2020 and March 2021 among a sample of 13,283 paediatric patients who underwent a swab in four different hospital settings (school hot spot, emergency department, day hospital setting and hospital wards). For each patients we collected: date of swab execution, type of swab, execution setting of the swab, result of the swab, information about community spread of the virus in the 14 days prior to the swab execution, sex and age. Results: In our sample, females accounted for 45.8%. The median age was 6.8 years (IQR 3.0-11.2) and the most frequent age category was between 6 and 11 years (27.9%). At multivariable models with a swab tested positive as outcome. The swabs executed in all the hospital settings had a lower likelihood of resulting positive compared with the school hot spot setting. Compared with adolescents aged between 14 and 19 years old, new-borns below 3 months (adjOR 1.83, 95% C.I. 1.14-3) and patients aged between 11 and 14 years old (adjOR 1.32, 95% C.I. 1.07-1.63) reported a higher probability of a swab tested positive. Instead, children aged between 3 months and 3 years (adjOR 0.77, 95% C.I. 0.61-0.96) and children aged between 3 years and 6 years (adjOR 0.66, 95% C.I. 0.53-0.83) were less likely to result positive. The higher was the mean of pooled Rt in the 14 days preceding the swab, the higher was the likelihood of resulting positive (adjOR 1.75, 95% C.I. 1.53-1.99). Conclusion: In conclusion, we found a high incidence of paediatric patients positive to the test for the detection of SARS-CoV-2 at the school hot spot compared with other settings during the period of observation. The free access modality to the nasopharyngeal swab was effective in identifying patients with COVID-19. Public health authorities should implement these testing modality in order to help reduce the spread of SARS-CoV-2 in school settings.

Deep Neural Network-Based Visual Feedback System for Nasopharyngeal Swab Sampling.

During the 2019 coronavirus disease pandemic, robotic-based systems for swab sampling were developed to reduce burdens on healthcare workers and their risk of infection. Teleoperated sampling systems are especially appreciated as they fundamentally prevent contact with suspected COVID-19 patients. However, the limited field of view of the installed cameras prevents the operator from recognizing the position and deformation of the swab inserted into the nasal cavity, which highly decreases the operating performance. To overcome this limitation, this study proposes a visual feedback system that monitors and reconstructs the shape of an NP swab using augmented reality (AR). The sampling device contained three load cells and measured the interaction force applied to the swab, while the shape information was captured using a motion-tracking program. These datasets were used to train a one-dimensional convolution neural network (1DCNN) model, which estimated the coordinates of three feature points of the swab in 2D X-Y plane. Based on these points, the virtual shape of the swab, reflecting the curvature of the actual one, was reconstructed and overlaid on the visual display. The accuracy of the 1DCNN model was evaluated on a 2D plane under ten different bending conditions. The results demonstrate that the x-values of the predicted points show errors of under 0.590 mm from P0, while those of P1 and P2 show a biased error of about -1.5 mm with constant standard deviations. For the y-values, the error of all feature points under positive bending is uniformly estimated with under 1 mm of difference, when the error under negative bending increases depending on the amount of deformation. Finally, experiments using a collaborative robot validate its ability to visualize the actual swab's position and deformation on the camera image of 2D and 3D phantoms.

Comparative study on Saliva and Nasopharyngeal swabs and the outcome of RT-PCR test in patients with mild symptoms of SARS-CoV-2 / Estudio comparativo de muestras de saliva y nasofaríngeas y el resultado de la prueba RT-PCR en pacientes con síntomas leves de SARS-CoV-2

Aim A simple and reliable method for diagnosing COVID 19 infections is the needed. The role of saliva in the transmission of the infection has already been established. Method Saliva and nasopharyngeal swabs from patients suspected to have COVID 19 infections were taken simultaneously, and the results of the RT-PCR were compared. Result Total 405 samples were collected, of which 250 males and 155 females. In the 391 samples included for analysis, 370 (94.63%) samples were found to have concordance results, and 21 (5.37%) samples had discordant results. Conclusion The use of saliva to diagnose COVID 19 infection is reliable, and its use can be recommended. (AU)

Objetivo Un método simple y confiable para diagnosticar infecciones por COVID 19 es necesario. Ya se ha establecido el papel de la saliva en la transmisión de la infección. Método Se tomaron simultáneamente hisopos de saliva y nasofaríngeos de pacientes con sospecha de infección por COVID 19 y se compararon los resultados de la RT-PCR. Resultado Se recogieron 405 muestras, de las cuales 250 hombres y 155 mujeres. En las 391 muestras incluidas para el análisis, se encontró que 370 (94,63%) muestras tenían resultados de concordancia y 21 (5,37%) muestras tenían resultados discordantes. Conclusión El uso de la saliva para diagnosticar la infección por COVID 19 es confiable y se puede recomendar su uso. (AU)

Pre-Pandemic Distribution of Bacterial Species in Nasopharyngeal Swab Specimens from Pediatric and Adult Patients Detected via RT-PCR Using the Allplex Respiratory Panel.

Background: Recently, panel-based molecular diagnostics for the simultaneous detection of respiratory viruses and bacteria in nasopharyngeal swab (NPS) specimens have been highlighted. We identified the distribution of bacterial species in NPS specimens collected from pediatric and adult patients by employing RT-PCR (Allplex respiratory panel 4, RP4, Seegene) to estimate its applicability in a panel-based assay for detecting respiratory viruses. Methods: We used 271 and 173 NPS specimens from pediatric and adult patients, respectively. The results of the Allplex RP4 panel using NPS (NPS-RP4) from adult patients were compared with those of the Seeplex PneumoBacter ACE Detection assay (Seegene), which used sputum for testing (sputum-Seeplex). Results: A total of 147 specimens (54.2%) were positive for the NPS-RP4 panel in pediatric patients. There were 94, 77, 10, 3, 3, and 2 specimens that were positive for Haemophilus influenzae (HI), Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP), Chlamydia pneumoniae (CP), Bordetella pertussis (BP), and B. parapertussis (BPP), respectively. Among 173 adult patients, 39 specimens (22.5%) were positive in the NPS-RP4. Thirty specimens were positive for HI, and 13 were positive for SP. One specimen tested positive for both MP and Legionella pneumophila (LP). CP, BP, and BPP results were all negative. However, 126 specimens (72.8%) had positive results with sputum-Seeplex (99 SP, 59 HI, three LP, and two MP), and the overall percentage of agreement between the two assays was 39.3% in the adult patients. Conclusions: Bacterial species in NPS from more than half of pediatric patients were detected. Performing the Allplex RP4 assay with NPS revealed additional respiratory bacteria that are not detected in current clinical practices, which do not include bacterial testing, demanding the use of sputum specimens. However, the use of NPS showed low agreement with standard assays using sputum in adult patients. Thus, more research is needed to develop a reliable RT-PCR method using NPS specimens in adult patients.

Excellent Characteristics of Environmentally Friendly 3D-Printed Nasopharyngeal Swabs for Medical Sample Collection.

3D-printed nasopharyngeal swabs for medical sample collection have been manufactured via additive manufacturing (AM), evaluated, and characterized in the present study. A multi-part component of nasopharyngeal swabs was proposed, in which the swab and handle were manufactured separately to reach sustainable production and environmentally friendly products. The swab was investigated using tensile, flexural, surface roughness, dimensional accuracy, and sample collection testing. The influence of printing parameters and post-curing time treatment on the mechanical properties, surface roughness, and dimensional accuracy of 3D-printed nasopharyngeal swabs were also evaluated. The result showed that 3D-printed nasopharyngeal swab shows outstanding tensile strength compared to the commercial flock nasopharyngeal swab. Moreover, the swab neck flexibility test showed that both PLA and dental non-castable 3D-printed nasopharyngeal swabs were able to bend 180°. Subsequently, the surface roughness of 3D-printed nasopharyngeal swab was identic with the commercial flock nasopharyngeal swab. The proposed 3D-printed nasopharyngeal swab design could carry an artificial mucus sample of 141.6 mg at a viscosity of 9455.4 mPa.s. The cost to fabricate a 3D-printed nasopharyngeal swab was estimated at USD0.01-0.02 per swab. 3D-printed nasopharyngeal swab shows potential as a feasible option, greener, less medical waste, and more sustainable.

Termination of paroxysmal supraventricular tachycardia by intranasal swab insertion.

Paroxysmal supraventricular tachycardia (SVT) is a common emergency department presentation. Vagal maneuvers are commonly tried to terminate SVT but are often unsuccessful in terminating the dysrhythmia. The use of adenosine, while often successful, is associated with a number of side effects and is often disliked by patients with recurrent episodes of SVT. We report on a 44-year-old woman with a past medical history of SVT who presented to the emergency department (ED) due to a recurrence of her SVT. The patient had no intravenous access and preferred not to receive adenosine. The patient received intranasal stimulation with a nasopharyngeal swab used for COVID-19 testing for 5-10 s. After less than 10 s, the patient converted to a sinus rhythm. She was successfully discharged from the ED after 1 h of observation and no recurrence of her SVT.

Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2.

PURPOSE: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. METHODS: We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. RESULTS: We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. CONCLUSION: These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.

Assessment of antibodies in the upper and lower human respiratory tract at steady state and after respiratory viral infection.

Objectives: There is an increasing appreciation for the need to study mucosal antibody responses in humans. Our aim was to determine the utility of different types of samples from the human respiratory tract, specifically nasopharyngeal (NP) swabs obtained for diagnostic purposes and bronchoalveolar lavage (BAL) obtained in outpatient and inpatient settings. Methods: We analysed antibody levels in plasma and NP swabs from 67 individuals with acute influenza as well as plasma and BAL from individuals undergoing bronchoscopy, including five control subjects as well as seven moderately and seven severely ill subjects with a respiratory viral infection. Levels of α2-macroglobulin were determined in BAL and plasma to assess plasma exudation. Results: IgG and IgA were readily detectable in BAL and NP swabs, albeit at different ratios, while IgM levels were low. The total amount of antibody recovered from NP swabs varied greatly between study participants. Accordingly, the levels of influenza HA-specific antibodies varied, and individuals with lower amounts of total Ig in NP swabs had undetectable levels of HA-specific Ig. Similarly, the total amount of antibody recovered from BAL varied between study participants. However, severely ill patients showed evidence of increased plasma exudation, which may confound analysis of their BAL samples for mucosal antibodies. Conclusion: Nasopharyngeal swabs collected for diagnostic purposes may have utility in assessing antibodies from the human nasal mucosa, but variability in sampling should be accounted for. BAL samples can be utilised to study antibodies from the lower respiratory tract, but the possibility of plasma exudation should be excluded.