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

Analyzing factors affecting positivity in drive-through COVID-19 testing: a cross-sectional study

BACKGROUND

Demand for COVID-19 testing prompted the implementation of drive-through testing systems. However, limited research has examined factors influencing testing positivity in this setting.

METHODS

From October 2020 to March 2023, a total of 1,341 patients, along with their clinical information, were referred from local clinics to the Sasebo City COVID-19 drive-through PCR center for testing. Association between clinical information or factors related to the drive-through center and testing results was analyzed by Fisher's exact test and logistic regression models.

RESULTS

Individuals testing positive exhibited higher frequencies of upper respiratory symptoms; cough (OR 1.5 (95% CI 1.2-1.8), p < 0.001, q = 0.005), sore throat (OR 2.4 (95% CI 1.9-3.0), p < 0.001, q < 0.001), runny nose (OR 1.4 (95% CI 1.1-1.8), p = 0.002, q = 0.009), and systemic symptoms; fever (OR 1.5 (95% CI 1.1-2.0), p = 0.006, q = 0.02), headache (OR 1.9 (95% CI 1.4-2.5), p < 0.001, q < 0.001), and joint pain (OR 2.7 (95% CI 1.8-4.1), p < 0.001, q < 0.001). Conversely, gastrointestinal symptoms; diarrhea (OR 0.2 (95% CI 0.1-0.4), p < 0.001, q < 0.001) and nausea (OR 0.3 (95% CI 0.1-0.6), p < 0.001, q < 0.001) were less prevalent among positives. During omicron strain predominant period, higher testing positivity rate (OR 20 (95% CI 13-31), p < 0.001) and shorter period from symptom onset to testing (3.2 vs. 6.0 days, p < 0.001) were observed compared to pre-omicron period. Besides symptoms, contact history with infected persons at home (OR 4.5 (95% CI 3.1-6.5), p < 0.001, q < 0.001) and in office or school (OR 2.9 (95% CI 2.1-4.1), p < 0.001, q < 0.001), as well as the number of sample collection experiences by collectors (B 7.2 (95% CI 2.8-12), p = 0.002) were also associated with testing results.

CONCLUSIONS

These findings underscore the importance of factors related to drive-through centers, especially contact history interviews and sample collection skills, for achieving higher rates of COVID-19 testing positivity. They also contribute to enhanced preparedness for next infectious disease pandemics.

Applications of SARS-CoV-2 serological testing: impact of test performance, sample matrices, and patient characteristics

Laboratory testing has been a key tool in managing the SARS-CoV-2 global pandemic. While rapid antigen and PCR testing has proven useful for diagnosing acute SARS-CoV-2 infections, additional testing methods are required to understand the long-term impact of SARS-CoV-2 infections on immune response. Serological testing, a well-documented laboratory practice, measures the presence of antibodies in a sample to uncover information about host immunity. Although proposed applications of serological testing for clinical use have previously been limited, current research into SARS-CoV-2 has shown growing utility for serological methods in these settings. To name a few, serological testing has been used to identify patients with past infections and long-term active disease and to monitor vaccine efficacy. Test utility and result interpretation, however, are often complicated by factors that include poor test sensitivity early in infection, lack of immune response in some individuals, overlying infection and vaccination responses, lack of standardization of antibody titers/levels between instruments, unknown titers that confer immune protection, and large between-individual biological variation following infection or vaccination. Thus, the three major components of this review will examine (1) factors that affect serological test utility: test performance, testing matrices, seroprevalence concerns and viral variants, (2) patient factors that affect serological response: timing of sampling, age, sex, body mass index, immunosuppression and vaccination, and (3) informative applications of serological testing: identifying past infection, immune surveillance to guide health practices, and examination of protective immunity. SARS-CoV-2 serological testing should be beneficial for clinical care if it is implemented appropriately. However, as with other laboratory developed tests, use of SARS-CoV-2 serology as a testing modality warrants careful consideration of testing limitations and evaluation of its clinical utility.

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.

Oral SARS-CoV-2 host responses predict the early COVID-19 disease course

Objectives

Oral fluids provide ready detection of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses. This study sought to determine relationships between oral virus, oral anti-SARS-CoV-2-specific antibodies, and symptoms.

Methods

Saliva/throat wash (saliva/TW) were collected from asymptomatic and symptomatic, nasopharyngeal (NP) SARS-CoV-2 RT-qPCR+, subjects (n=47). SARS-CoV-2 RT-qPCR, N-antigen detection by immunoblot and lateral flow assay (LFA) were performed. RT-qPCR targeting viral subgenomic RNA (sgRNA) was sequence confirmed. SARS-CoV-2-anti-S protein RBD LFA assessed IgM and IgG responses. Structural analysis identified host salivary molecules analogous to SARS-CoV-2-N-antigen. Statistical analyses were performed.

Results

At baseline, LFA-detected N-antigen was immunoblot-confirmed in 82% of TW. However, only 3/17 were saliva/TW qPCR+. Sixty percent of saliva and 83% of TW demonstrated persistent N-antigen at 4 weeks. N-antigen LFA signal in three negative subjects suggested potential cross-detection of 4 structurally analogous salivary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms). At entry, symptomatic subjects demonstrated replication-associated sgRNA junctions, were IgG+ (94%/100% in saliva/TW), and IgM+ (75%/63%). At 4 weeks, SARS-CoV-2 IgG (100%/83%) and IgM (80%/67%) persisted. Oral IgG correlated 100% with NP+PCR status. Cough and fatigue severity (p=0.0008 and 0.016), and presence of nausea, weakness, and composite upper respiratory symptoms (p=0.005, 0.037 and 0.017) were negatively associated with oral IgM. Female oral IgM levels were higher than male (p=0.056).

Conclusion

Important to transmission and disease course, oral viral replication and persistence showed clear relationships with select symptoms, early Ig responses, and gender during early infection. N-antigen cross-reactivity may reflect mimicry of structurally analogous host proteins.

Comparing SARS-CoV-2 Viral Load in Human Saliva to Oropharyngeal Swabs, Nasopharyngeal Swabs, and Sputum: A Systematic Review and Meta-Analysis

A systematic review and meta-analysis were conducted to investigate the SARS-CoV-2 viral load in human saliva and compared it with the loads in oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, the salivary viral loads of symptomatic and asymptomatic COVID-19 patients were compared. Searches were conducted using four electronic databases: PubMed, Embase, Scopus, and Web of Science, for studies published on SARS-CoV-2 loads expressed by CT values or copies/mL RNA. Three reviewers evaluated the included studies to confirm eligibility and assessed the risk of bias. A total of 37 studies were included. Mean CT values in saliva ranged from 21.5 to 39.6 and mean copies/mL RNA ranged from 1.91 × 101 to 6.98 × 1011. Meta-analysis revealed no significant differences in SARS-CoV-2 load in saliva compared to oropharyngeal swabs, nasopharyngeal swabs, and sputum. In addition, no significant differences were observed in the salivary viral load of symptomatic and asymptomatic COVID-19 patients. We conclude that saliva specimen can be used as an alternative for SARS-CoV-2 detection in oropharyngeal swabs, nasopharyngeal swabs, and sputum.

Oral SARS-CoV-2 host responses predict the early COVID-19 disease course

Objectives

Oral fluids provide ready detection of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and host responses. This study sought to determine relationships between oral virus, oral anti-SARS-CoV-2-specific antibodies, and symptoms.

Methods

Saliva/throat wash (saliva/TW) were collected from asymptomatic and symptomatic, nasopharyngeal (NP) SARS-CoV-2 RT-qPCR+, subjects (n=47). SARS-CoV-2 RT-qPCR, N-antigen detection by immunoblot and lateral flow assay (LFA) were performed. RT-qPCR targeting viral subgenomic RNA (sgRNA) was sequence confirmed. SARS-CoV-2-anti-S protein RBD LFA assessed IgM and IgG responses. Structural analysis identified host salivary molecules analogous to SARS-CoV-2-N-antigen. Statistical analyses were performed.

Results

At baseline, LFA-detected N-antigen was immunoblot-confirmed in 82% of TW. However, only 3/17 were saliva/TW qPCR+. Sixty percent of saliva and 83% of TW demonstrated persistent N-antigen at 4 weeks. N-antigen LFA signal in three negative subjects suggested potential cross-detection of 4 structurally analogous salivary RNA binding proteins (alignment 19-29aa, RMSD 1-1.5 Angstroms). At entry, symptomatic subjects demonstrated replication-associated sgRNA junctions, were IgG+ (94%/100% in saliva/TW), and IgM+ (75%/63%). At 4 weeks, SARS-CoV-2 IgG (100%/83%) and IgM (80%/67%) persisted. Oral IgG correlated 100% with NP+PCR status. Cough and fatigue severity (p=0.0008 and 0.016), and presence of nausea, weakness, and composite upper respiratory symptoms (p=0.005, 0.037 and 0.017) were negatively associated with oral IgM. Female oral IgM levels were higher than male (p=0.056).

Conclusion

Important to transmission and disease course, oral viral replication and persistence showed clear relationships with select symptoms, early Ig responses, and gender during early infection. N-antigen cross-reactivity may reflect mimicry of structurally analogous host proteins.

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

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

Salivary SARS-CoV-2 RNA for diagnosis of COVID-19 patients: a systematic revisew and meta-analysis of diagnostic accuracy

Accurate, self-collected, and non-invasive diagnostics are critical to perform mass-screening diagnostic tests for COVID-19. This systematic review with meta-analysis evaluated the accuracy, sensitivity, and specificity of salivary diagnostics for COVID-19 based on SARS-CoV-2 RNA compared with the current reference tests using a nasopharyngeal swab (NPS) and/or oropharyngeal swab (OPS). An electronic search was performed in seven databases to find COVID-19 diagnostic studies simultaneously using saliva and NPS/OPS tests to detect SARS-CoV-2 by RT-PCR. The search resulted in 10,902 records, of which 44 studies were considered eligible. The total sample consisted of 14,043 participants from 21 countries. The accuracy, specificity, and sensitivity for saliva compared with the NPS/OPS was 94.3% (95%CI= 92.1;95.9), 96.4% (95%CI= 96.1;96.7), and 89.2% (95%CI= 85.5;92.0), respectively. Besides, the sensitivity of NPS/OPS was 90.3% (95%CI= 86.4;93.2) and saliva was 86.4% (95%CI= 82.1;89.8) compared to the combination of saliva and NPS/OPS as the gold standard. These findings suggest a similarity in SARS-CoV-2 RNA detection between NPS/OPS swabs and saliva, and the association of both testing approaches as a reference standard can increase by 3.6% the SARS-CoV-2 detection compared with NPS/OPS alone. This study supports saliva as an attractive alternative for diagnostic platforms to provide a non-invasive detection of SARS-CoV-2.

SARS-CoV-2 RT-qPCR Ct values in saliva and nasopharyngeal swab samples for disease severity prediction

Background

Comparison of clinical value of RT-qPCR-based SARS-CoV-2 tests performed on saliva samples (SSs) and nasopharyngeal swab samples (NPSs) for prediction of the COVID-19 disease severity.

Methods

Three paired SSs and NPSs collected every 3 days from 100 hospitalised COVID-19 patients during 2020 Jul-2021 Jan were tested by RT-qPCR for the original SARS-CoV-2 virus and compared to 150 healthy controls. Cases were divided into mild+moderate (Cohort I, N = 47) and severe disease (Cohort II, N = 53) cohorts and compared.

Results

SARS-CoV-2 was detected in 65% (91/140) vs. 53% (82/156) of NPSs and 49% (68/139) vs. 48% (75/157) of SSs collected from Cohort I and II, respectively, resulting in the total respective detection rates of 58% (173/296) vs. 48% (143/296) (P = 0.017). Ct values of SSs were lower than those of NPSs (mean Ct = 28.01 vs. 30.07, P = 0.002). Although Ct values of the first SSs were significantly lower in Cohort I than in Cohort II (P = 0.04), it became negative earlier (mean 11.7 vs. 14.8 days, P = 0.005). Multivariate Cox proportional hazards regression analysis showed that Ct value ≤30 from SSs was the independent predictor for severe COVID-19 (HR = 10.06, 95% CI: 1.84-55.14, P = 0.008).

Conclusion

Salivary RT-qPCR testing is suitable for SARS-CoV-2 infection control, while simple measurement of Ct values can assist in prediction of COVID-19 severity.

Accuracy of saliva for SARS-CoV-2 detection in outpatients and their household contacts during the circulation of the Omicron variant of concern

BACKGROUND

While nasopharyngeal (NP) swabs are considered the gold standard for severe acute respiratory coronavirus 2 (SARS-CoV-2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) detection, several studies have shown that saliva is an alternative specimen for COVID-19 diagnosis and screening.

METHODS

To analyze the utility of saliva for the diagnosis of COVID-19 during the circulation of the Omicron variant, participants were enrolled in an ongoing cohort designed to assess the natural history of SARS-CoV-2 infection in adults and children. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and Cohen's kappa coefficient were calculated to assess diagnostic performance.

RESULTS

Overall, 818 samples were collected from 365 outpatients from January 3 to February 2, 2022. The median age was 32.8 years (range: 3-94 years). RT-PCR for SARS-CoV-2 was confirmed in 97/121 symptomatic patients (80.2%) and 62/244 (25.4%) asymptomatic patients. Substantial agreement between saliva and combined nasopharyngeal/oropharyngeal samples was observed with a Cohen's kappa value of 0.74 [95% confidence interval (CI): 0.67-0.81]. Sensitivity was 77% (95% CI: 70.9-82.2), specificity 95% (95% CI: 91.9-97), PPV 89.8% (95% CI: 83.1-94.4), NPV 87.9% (95% CI: 83.6-91.5), and accuracy 88.5% (95% CI: 85.0-91.4). Sensitivity was higher among samples collected from symptomatic children aged three years and older and adolescents [84% (95% CI: 70.5-92)] with a Cohen's kappa value of 0.63 (95% CI: 0.35-0.91).

CONCLUSIONS

Saliva is a reliable fluid for detecting SARS-CoV-2, especially in symptomatic children and adolescents during the circulation of the Omicron variant.

Impact of DHCWs' Safety Perception on Vaccine Acceptance and Adoption of Risk Mitigation Strategies

OBJECTIVES

To estimate the association between safety perception on vaccine acceptance and adoptions of risk mitigation strategies among dental health care workers (DHCWs).

METHODS

A survey was emailed to DHCWs in the New Jersey area from December 2020 to January 2021. Perceived safety from regular SARS-CoV-2 testing of self, coworkers, and patients and its association with vaccine hesitancy and risk mitigation were ascertained. Risk Mitigation Strategy (RiMS) scores were computed from groupings of office measures: 1) physical distancing (reduced occupancy, traffic flow, donning of masks, minimal room crowding), 2) personal protective equipment (fitted for N95; donning N95 masks; use of face shields; coverings for head, body, and feet), and 3) environmental disinfection (suction, air filtration, ultraviolet, surface wiping).

RESULTS

SARS-CoV-2 testing of dental professionals, coworkers, and patients were perceived to provide safety at 49%, 55%, and 68%, respectively. While dentists were least likely to feel safe with regular self-testing for SARS-CoV-2 (P < 0.001) as compared with hygienists and assistants, they were more willing than hygienists (P = 0.004; odds ratio, 1.79 [95% CI, 1.21 to 2.66]) and assistants (P < 0.001; odds ratio, 3.32 [95% CI, 1.93 to 5.71]) to receive the vaccine. RiMS scores ranged from 0 to 19 for 467 participants (mean [SD], 10.9 [2.9]). RiMS scores did not significantly differ among groups of DHCWs; however, mean RiMS scores were higher among those who received or planned to receive the COVID-19 vaccine than those with who did not (P = 0.004). DHCWs who felt safer with regular testing had greater RiMS scores than those who did not (11.0 vs. 10.3, P = 0.01).

CONCLUSIONS

Understanding DHCWs' perception of risk and safety is crucial, as it likely influences attitudes toward testing and implementation of office risk mitigation policies. Clinical studies that correlate risk perception and RiMS with SARS-CoV-2 testing are needed to demonstrate the effectiveness of RiMS in dental care settings.

KNOWLEDGE TRANSFER STATEMENT

Educators, clinicians, and policy makers can use the results of this study when improving attitudes toward testing and implementation of risk mitigation policies within dental offices, for current and future pandemics.

Quantitative analysis of different respiratory specimens on two automated test systems for detection of SARS-CoV-2 RNA

Molecular testing of SARS-CoV-2 RNA is essential during the pandemic. Here, we compared the results of different respiratory specimens including anterior nasal swabs, pharyngeal swabs, saliva swabs, and gargle lavage samples to nasopharyngeal swabs on two automated SARS-CoV-2 test systems. Samples were collected and tested simultaneously from a total of 36 hospitalized symptomatic COVID-19 patients. Detection and quantification of SARS-CoV-2 was performed on cobas®6800 (Roche) and NeuMoDx™ (Qiagen) systems. Both assays showed reliable detection and quantification of SARS-CoV-2 RNA, with nasopharyngeal swabs showing the highest sensitivity. SARS-CoV-2 RNA concentrations in other respiratory specimens were lower (mean 2.5 log10 copies/ml) or even undetectable in up to 20%. These data clearly indicate that not all respiratory materials are equally suitable for the management of hospitalized patients, especially, in the late phase of COVID-19, when the viral phase subsides and inflammation becomes the predominant factor, making detection of even lower viral loads increasingly important.

Omicron Wave SARS-CoV-2 Diagnosis: Evaluation of Saliva, Anterior Nasal, and Nasopharyngeal Swab Samples

The Omicron variant differs from earlier strains of SARS-CoV-2 in the way it enters host cells and grows in vitro. We therefore reevaluated its diagnosis using saliva, nasopharyngeal swab (NPs), and anterior nasal swab (ANs) specimens from 202 individuals (64.9% symptomatic) tested at the Toulouse University Hospital SARS-CoV-2 drive-through testing center. All tests were done with the Thermo Fisher TaqPath COVID-19 reverse transcription-PCR (RT-PCR) kit. Overall, 92 subjects (45.5%) had one or more positive specimens. Global sensitivities of saliva, NPs, and ANs were 94.6%, 90.2%, and 82.6%, respectively. Saliva provided significantly greater sensitivity among symptomatic patients tested within 5 days of symptom onset (100%) than did ANs (83.1%) or NPs (89.8%). We obtained follow-up samples for 7/20 individuals with discordant results. Among them, 5 symptomatic patients were diagnosed positive on saliva sample only, soon after symptom onset; NPs and ANs became positive only later. Thus, saliva samples are effective tools for the detection of the Omicron variant. In addition to its many advantages, such as improved patient acceptance and reduced cost, saliva sampling could help limit viral spread through earlier viral detection. IMPORTANCE Diagnostic testing for SARS-CoV-2 is an essential component of the global strategy for the prevention and control of COVID-19. Since the beginning of the pandemic, numerous studies have evaluated the diagnostic sensitivity of different respiratory and oral specimens for SARS-CoV-2 detection. The pandemic has been since dominated by the emergence of new variants, the latest being the Omicron variant characterized by numerous mutations and changes in host tropism in vitro that might affect the diagnostic performance of tests depending on the sampling location. In this prospective study, we evaluated the clinical performance of NPs, ANs, and saliva for SARS-CoV-2 diagnosis during the Omicron wave. Our results highlight the effectiveness of saliva-based RT-PCR for the early detection of the Omicron variant. These findings may help to refine guidelines and support the use of a highly sensitive diagnostic method that allows earlier diagnosis, when transmission is the most critical.

Impact of antigen test target failure and testing strategies on the transmission of SARS-CoV-2 variants

Population testing remains central to COVID-19 control and surveillance, with countries increasingly using antigen tests rather than molecular tests. Here we describe a SARS-CoV-2 variant that escapes N antigen tests due to multiple disruptive amino-acid substitutions in the N protein. By fitting a multistrain compartmental model to genomic and epidemiological data, we show that widespread antigen testing in the Italian region of Veneto favored the undetected spread of the antigen-escape variant compared to the rest of Italy. We highlight novel limitations of widespread antigen testing in the absence of molecular testing for diagnostic or confirmatory purposes. Notably, we find that genomic surveillance systems which rely on antigen population testing to identify samples for sequencing will bias detection of escape antigen test variants. Together, these findings highlight the importance of retaining molecular testing for surveillance purposes, including in contexts where the use of antigen tests is widespread.

Cohort profile: top the Spread Ottawa (SSO)-a community-based prospective cohort study on antibody responses, antibody neutralisation efficiency and cellular immunity to SARS-CoV-2 infection and vaccination

PURPOSE

To investigate the robustness and longevity of SARS-CoV-2 immune responses conferred by natural infection and vaccination among priority populations such as immunocompromised individuals and people with post-acute sequelae of COVID-19 in a prospective cohort study (Stop the Spread Ottawa-SSO) in adults living in the Ottawa region. In this paper, we describe the study design, ongoing data collection and baseline characteristics of participants.

PARTICIPANTS

Since October 2020, participants who tested positive for COVID-19 (convalescents) or at high risk of exposure to the virus (under surveillance) have provided monthly blood and saliva samples over a 10-month period. As of 2 November 2021, 1026 adults had completed the baseline survey and 976 had attended baseline bloodwork. 300 participants will continue to provide bimonthly blood samples for 24 additional months (ie, total follow-up of 34 months).

FINDINGS TO DATE

The median age of the baseline sample was 44 (IQR 23, range: 18-79) and just over two-thirds (n=688; 67.1%) were female. 255 participants (24.9%) had a history of COVID-19 infection confirmed by PCR and/or serology. Over 600 participants (60.0%) work in high-risk occupations (eg, healthcare, teaching and transportation). 108 participants (10.5%) reported immunocompromising conditions or treatments at baseline (eg, cancer, HIV, other immune deficiency, and/or use of immunosuppressants).

FUTURE PLANS

SSO continues to yield rich research potential, given the collection of pre-vaccine baseline data and samples from the majority of participants, recruitment of diverse subgroups of interest, and a high level of participant retention and compliance with monthly sampling. The 24-month study extension will maximise opportunities to track SARS-CoV-2 immunity and vaccine efficacy, detect and characterise emerging variants, and compare subgroup humoral and cellular response robustness and persistence.

Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test

INTRODUCTION

Nanoparticle-based biosensors (NPBs) are point-of-care diagnostic platforms that can be used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high accuracy.

AREAS COVERED

EBSCOhost Web, Embase, ProQuest, PubMed/MEDLINE, Scopus, Web of Science, and WHO Global Literature on Coronavirus Disease 2019 (COVID-19) were searched for relevant records published from 1 November 2019 to 30 April 2022. Records reporting original data on the accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins from pharyngeal swab specimens were considered. Findings were reported based on the PRISMA 2020 statement. The QUADAS-2 tool was used for assessment of quality and risk of bias among the included studies.

EXPERT OPINION

A total of 50 relevant records were identified, of which 13 were included. The included studies explored the diagnostic performance of 13 clinically applied distinct nanoparticle-based biosensors in a total of 789 pharyngeal swabs collected from 376 COVID-19 patients and 413 otherwise healthy individuals. The mean sensitivity, specificity, and accuracy were 97.07%, 94.43%, and 96.91%, respectively, in comparison to RT-qPCR as the reference test. Considering their ease-of-operation, portability, low-cost manufacturing, NPBs could be considered suitable candidate diagnostic platforms for substituting RT-qPCR.

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 for molecular detection of SARS‐CoV ‐2 in preschool and school‐age children

SARS‐CoV‐2 diagnosis is a cornerstone for the management of coronavirus disease 2019 (COVID‐19). Numerous studies have assessed saliva performance over nasopharyngeal sampling (NPS), but data in young children are still rare. We explored saliva performance for SARS‐CoV‐2 detection by RT‐PCR according to the time interval from initial symptoms or patient serological status. We collected 509 NPS and saliva paired samples at initial diagnosis from 166 children under 12 years of age (including 57 children under 6), 106 between 12 and 17, and 237 adults. In children under 12, overall detection rate for SARS‐CoV‐2 was comparable in saliva and NPS, with an overall agreement of 89.8%. Saliva sensitivity was significantly lower than that of NPS (77.1% compared to 95.8%) in pre‐school and school‐age children but regained 96% when considering seronegative children only. This pattern was also observed to a lesser degree in adolescents but not in adults. Sensitivity of saliva was independent of symptoms, in contrary to NPS, whose sensitivity decreased significantly in asymptomatic subjects. Performance of saliva is excellent in children under 12 at early stages of infection. This reinforces saliva as a collection method for early and unbiased SARS‐CoV‐2 detection and a less invasive alternative for young children.

The COVID-19 and TB syndemic: the way forward

Together, SARS-CoV-2 and M. tuberculosis have killed approximately 5.7 million people worldwide over the past 2 years. The COVID-19 pandemic, and the non-pharmaceutical interventions to mitigate COVID-19 transmission (including social distancing regulations, partial lockdowns and quarantines), have disrupted healthcare services and led to a reallocation of resources to COVID-19 care. There has also been a tragic loss of healthcare workers who succumbed to the disease. This has had consequences for TB services, and the fear of contracting COVID-19 may also have contributed to reduced access to TB services. Altogether, this is projected to have resulted in a 5-year setback in terms of mortality from TB and a 9-year setback in terms of TB detection. In addition, past and present TB disease has been reported to increase both COVID-19 fatality and incidence. Similarly, COVID-19 may adversely affect TB outcomes. From a more positive perspective, the pandemic has also created opportunities to improve TB care. In this review, we highlight similarities and differences between these two infectious diseases, describe gaps in our knowledge and discuss solutions and priorities for future research.

3D-printed simulator for nasopharyngeal swab collection for COVID-19

OBJECTIVES

Diagnosis of COVID-19 is essential to prevent the spread of SARS-CoV-2. Nasopharyngeal swabs (NPS) remain the gold standard in screening, although associated with false negative results (up to 30%). We developed a 3D simulator of the nasal and pharyngeal cavities for the learning and improvement of NPS collection.

PATIENTS AND METHODS

Simulator training sessions were carried out in 11 centers in France. A questionnaire assessing the simulator was administered at the end of the sessions. The study population included both healthcare workers (HCW) and volunteers from the general population.

RESULTS

Out of 589 participants, overall satisfaction was scored 9.0 [8.9-9.1] on a scale of 0 to 10 with excellent results in the 16 evaluation items of each category (HCWs and general population, NPS novices and experienced). The simulator was considered very realistic (95%), easy to use (97%), useful to understand the anatomy (89%) and NPS sampling technique (93%). This educational tool was considered essential (93%). Participants felt their future NPS would be more reliable (72%), less painful (70%), easier to perform (88%) and that they would be carried out more serenely (90%). The mean number of NPS conducted on the simulator to feel at ease was two; technical fluency with the simulator can thus be acquired quickly.

CONCLUSION

Our simulator, whose 3D printing can be reproduced freely using a permanent open access link, is an essential educational tool to standardize the learning and improvement of NPS collection. It should enhance virus detection and thus contribute to better pandemic control.

Is saliva collected passively without forceful coughing sensitive to detect SARS-CoV-2 in ambulatory cases? A systematic review

OBJECTIVE

This systematic review was conducted to assess the sensitivity rate of SARS-CoV-2 detection in the saliva of ambulatory asymptomatic and mildly symptomatic patients, with saliva being collected passively without any forceful coughing.

STUDY DESIGN

A literature search was performed from January 2020 to July 2021. Prospective studies excluding letters to editors were included in our review only if saliva and nasopharyngeal samples were collected simultaneously and sensitivity was reported using reverse transcription polymerase chain reaction (RT-PCR) in asymptomatic or mildly symptomatic ambulatory cases.

RESULTS

A total of 436 studies were assessed; 10 (4 cohorts and 6 cross-sectional) studies met our inclusion criteria. The sensitivity rate of saliva to detect SARS-CoV-2 varied from 85.7% to 98.6% in all except for 3 studies. Lower sensitivity levels were attributed to low viral load (51.9% and 63.8%) or lack of supervision while collecting saliva (66.7%).

CONCLUSIONS

Passively collected saliva in the absence of coughing has a high sensitivity rate to detect SARS-CoV-2 in asymptomatic and mildly symptomatic patients compared with nasopharyngeal swabs. Limitations of previous studies, such as lack of attention to the method of saliva collection, stages, and severity of the disease at the time of sample collection, can be researched in future investigations.

One-Step RT-qPCR for Viral RNA Detection Using Digital Analysis

The rapid detection of viruses is becoming increasingly important to prevent widespread infections. However, virus detection via reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is time-consuming, as it involves independent nucleic acid extraction and complementary DNA synthesis. This process limits the potential for rapid diagnosis and mass analysis, which are necessary to curtail viral spread. In this study, a simple and rapid thermolysis method was developed to circumvent the need for extraction and purification of viral RNA. The developed protocol was applied to one-chip digital PCR (OCdPCR), which allowed thermolysis, RT, and digital PCR in a single unit comprising 20,000 chambers of sub-nanoliter volume. Two viruses such as tobacco mosaic virus and cucumber mosaic virus were tested as model viral particles. First, the temperature, exposure time, and template concentration were optimized against tobacco mosaic viral particles, and the most efficient conditions were identified as 85°C, 5 min, and 0.01 μg/nL with a cycle threshold of approximately 33. Finally, the OCdPCR analysis yielded 1,130.2 copies/µL using 10⁻² μg/nL of viral particles in a 30 min thermolysis-RT reaction at 70°C. This novel protocol shows promise as a quick, accurate, and precise method for large-scale viral analysis in the future.

A Sensitive, Portable Microfluidic Device for SARS-CoV-2 Detection from Self-Collected Saliva

Since the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in December 2019, the spread of SARS-CoV2 infection has been escalating rapidly around the world. In order to provide more timely access to medical intervention, including diagnostic tests and medical treatment, the FDA authorized multiple test protocols for diagnostic tests from nasopharyngeal swab, saliva, urine, bronchoalveolar lavage and fecal samples. The traditional diagnostic tests for this novel coronavirus 2019 require standard processes of viral RNA isolation, reverse transcription of RNA to cDNA, then real-time quantitative PCR with the RNA templates extracted from the patient samples. Recently, many reports have demonstrated a direct detection of SARS-Co-V2 genomic material from saliva samples without any RNA isolation step. To make the rapid detection of SARS-Co-V2 infection more accessible, a point-of-care type device was developed for SARS-CoV-2 detection. Herein, we report a portable microfluidic-based integrated detection-analysis system for SARS-CoV-2 nucleic acids detection directly from saliva samples. The saliva cartridge is self-contained and capable of microfluidic evaluation of saliva, from heating, mixing with the primers to multiplex real-time quantitative polymerase chain reaction, detecting SARS-CoV-2 with different primer sets and internal control. The approach has a detection sensitivity of 1000 copies/mL of SARS-CoV-2 RNA or virus, with consistency and automation, from saliva sample-in to result-out.

SARS-CoV-2 Transmissibility Within Day Care Centers-Study Protocol of a Prospective Analysis of Outbreaks in Germany

Introduction: Until today, the role of children in the transmission dynamics of SARS-CoV-2 and the development of the COVID-19 pandemic seems to be dynamic and is not finally resolved. The primary aim of this study is to investigate the transmission dynamics of SARS-CoV-2 in child day care centers and connected households as well as transmission-related indicators and clinical symptoms among children and adults. Methods and Analysis: COALA ("Corona outbreak-related examinations in day care centers") is a day care center- and household-based study with a case-ascertained study design. Based on day care centers with at least one reported case of SARS-CoV-2, we include one- to six-year-old children and staff of the affected group in the day care center as well as their respective households. We visit each child's and adult's household. During the home visit we take from each household member a combined mouth and nose swab as well as a saliva sample for analysis of SARS-CoV-2-RNA by real-time reverse transcription polymerase chain reaction (real-time RT-PCR) and a capillary blood sample for a retrospective assessment of an earlier SARS-CoV-2 infection. Furthermore, information on health status, socio-demographics and COVID-19 protective measures are collected via a short telephone interview in the subsequent days. In the following 12 days, household members (or parents for their children) self-collect the same respiratory samples as described above every 3 days and a stool sample for children once. COVID-19 symptoms are documented daily in a symptom diary. Approximately 35 days after testing the index case, every participant who tested positive for SARS-CoV-2 during the study is re-visited at home for another capillary blood sample and a standardized interview. The analysis includes secondary attack rates, by age of primary case, both in the day care center and in households, as well as viral shedding dynamics, including the beginning of shedding relative to symptom onset and viral clearance. Discussion: The results contribute to a better understanding of the epidemiological and virological transmission-related indicators of SARS-CoV-2 among young children, as compared to adults and the interplay between day care and households.

Pneumocystis jirovecii pneumonia in breast cancer mimicking SARS-CoV-2 pneumonia during pandemic

Pneumocystis jirovecii pneumonia (PJP) is one of the most common HIV-related opportunistic infection. Apart from HIV patients, subjects treated with an associated therapy of high doses glucocorticoids and immunosuppressive drugs should be considered at risk. SARS-CoV-2 has become worldly known as the responsible of the pandemic that hit the world in late 2019 and that is still ongoing. Italy, and especially Brescia, was one of the area most struck by the pandemic, with a significant number of cases being reported (more than 112,648 as of October 2021). The diagnosis of SARS-CoV-2 is mainly based on RT-PCR assays performed on nasopharyngeal swab, X-ray of the chest and clinical manifestations. We describe two cases of PJP in two immunocompromised patients with breast cancer who were admitted at Spedali Civili of Brescia hospital, Italy, with an initial diagnosis of SARS-CoV-2 pneumonia, despite testing negative to RT-PCR on nasopharyngeal swabs. We also retrospectively reassessed all cases of pneumonia deemed as SARS-CoV-2-related upon admission and then converted to PJP as the final diagnosis. We describe the two following cases to emphasize that clinicians should always be alert about PJP, even during the SARS-CoV-2 pandemic, and avoid focusing on COVID-19 exclusively. PJP should always be considered as a differential diagnosis in patients, particularly if immunosuppressed, with an X-ray or TC of the chest suggestive of interstitial pneumonia and a negative SARS-CoV-2 RT-PCR on nasopharyngeal swabs.

Salivary detection of COVID-19: clinical performance of oral sponge sampling for SARS-CoV-2 testing

BACKGROUND

The current diagnostic standard for coronavirus disease 2019 (COVID-19) is reverse transcriptase-polymerase chain reaction (RT-PCR) testing with nasopharyngeal (NP) swabs. The invasiveness and need for trained personnel make the NP technique unsuited for repeated community-based mass screening. We developed a technique to collect saliva in a simple and easy way with the sponges that are usually used for tamponade of epistaxis. This study was carried out to validate the clinical performance of oral sponge (OS) sampling for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing.

METHODS

Over a period of 22 weeks, we collected prospectively 409 paired NP and OS samples from consecutive subjects presenting to a public community-based free screening centre. Subjects were referred by their attending physician because of recent COVID-19 symptoms (n = 147) or by the contact tracing staff of the French public health insurance because they were considered as close contacts of a laboratory-confirmed COVID-19 case (n = 262).

RESULTS

In symptomatic subjects, RT-PCR SARS-CoV-2 testing with OS showed a 96.5% (95% CI: 89.6-94.8) concordance with NP testing, and a 93.2% (95% CI: 89.1-97.3) sensitivity when using the IdyllaTM platform and a sensitivity of 76.3% (95% CI: 69.4-83.2) on the Synlab Barla laboratory platform. In close contacts the NP-OS concordance (93.8%, 95% CI: 90.9-96.7) and OS sensitivity (71.9%, 95% CI: 66.5-77.3) were slightly lower.

CONCLUSION

These results strongly suggest that OS testing is a straightforward, low-cost and high-throughput sampling method that can be used for frequent RT-PCR testing of COVID-19 patients and mass screening of populations.

Implementation of a pooled surveillance testing program for asymptomatic SARS-CoV-2 infections in K-12 schools and universities

BACKGROUND

The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community.

METHODS

We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5-18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis.

FINDINGS

From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems.

INTERPRETATION

By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty.

FUNDING

Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.

Over- and under-estimation of COVID-19 deaths

The ratio of COVID-19-attributable deaths versus “true” COVID-19 deaths depends on the synchronicity of the epidemic wave with population mortality; duration of test positivity, diagnostic time window, and testing practices close to and at death; infection prevalence; the extent of diagnosing without testing documentation; and the ratio of overall (all-cause) population mortality rate and infection fatality rate. A nomogram is offered to assess the potential extent of over- and under-counting in different situations. COVID-19 deaths were apparently under-counted early in the pandemic and continue to be under-counted in several countries, especially in Africa, while over-counting probably currently exists for several other countries, especially those with intensive testing and high sensitization and/or incentives for COVID-19 diagnoses. Death attribution in a syndemic like COVID-19 needs great caution. Finally, excess death estimates are subject to substantial annual variability and include also indirect effects of the pandemic and the effects of measures taken.