Saliva is superior over nasopharyngeal swab for detecting SARS-CoV2 in COVID-19 patients

SARS-CoV-2 diagnosis in saliva samples: Usefulness and limitations

Saliva samples are important for diagnosis, because they are noninvasive and easy to acquire. The objective of this cross-sectional study was to investigate the value saliva samples have in detecting SARS-CoV-2 in comparison to nasal swabs and a new system named CovidCheck. A standard methodology identified the virus in 185 nasopharyngeal swabs and saliva samples revealing a sensitivity, specificity and positive and negative predictive values of 82,100,100 and 94.67%, respectively for saliva samples. Viral presence in saliva samples with the standard methodology in comparison to the CovidCheck system was evaluated in 67 samples with sensitivity, specificity and positive and negative predictive values of 68, 81, 68 and 81%, respectively. In conclusion, our results highlight the usefulness saliva samples have in detecting respiratory viral infections. However, presence of viral inhibitors and viral load in saliva, and the patient's clinical status should be considered as they might affect amplifying systems results.

Diagnostic performance, stability, and acceptability of self-collected saliva without additives for SARS-CoV-2 molecular diagnosis

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19), leading to a global pandemic. The molecular diagnosis of this virus is mostly performed by collecting upper respiratory samples, which has many disadvantages, including patient discomfort and the need for trained healthcare professionals. Although saliva has emerged as a more comfortable sample, the use of additives to preserve viral RNA is expensive and, in some cases, difficult for self-collection.

METHOD

This study evaluated the diagnostic performance by RT-PCR and stability of self-collected saliva using wide-mouth specimen collection cups without stabilization and/or inactivation buffers for SARS-CoV-2 detection, compared to nasopharyngeal samples and saliva collected with additives. Additionally, the study assessed the acceptability of this sample collection method among participants and healthcare personnel.

RESULTS

The study included 1281 volunteers with a 24.6% positive infection rate. Saliva demonstrated comparable diagnostic performance to nasopharyngeal samples, with a sensitivity of 87.6% and specificity of 99.6%, for a total percent agreement of 96.4%. The study also showed that viral RNA in saliva remained stable for at least 72 h at different temperatures. Notably, saliva samples without additives exhibited a lower RdRp Ct compared to samples with additives, suggesting that the absence of stabilization and/or inactivation buffers does not significantly affect its performance. The study highlighted the acceptability of saliva among patients and healthcare personnel due to its noninvasive nature and ease of collection.

CONCLUSIONS

This research supports the implementation of self-collected saliva as a comfortable and user-friendly alternative sample for SARS-CoV-2 diagnosis.

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.

Dynamic response antibodies SARS-CoV-2 human saliva studied using two-dimensional correlation (2DCOS) infrared spectral analysis coupled with receiver operation characteristics analysis

COVID-19 has affected the entire world due to the rapid spread of SARS-CoV-2, mainly through airborne particles from saliva, which, being easily obtained, help monitor the progression of the disease. Fourier transform infrared (FTIR) spectra combined with chemometric analysis could increase the diagnostic efficiency of the disease. However, two-dimensional correlation spectroscopy (2DCOS) is superior to conventional spectra as it helps to resolve the minute overlapped peaks. In this work, we aimed to use 2DCOS and receiver operating characteristic (ROC) analyses to compare the immune response in saliva associated with COVID-19, which could be important in biomedical diagnosis. FTIR spectra of human saliva samples from male (575) and female (366) patients ranging from 20 to 82 ± 2 years of age were used for the study. Age groups were segregated as G1 (25-40 ± 2 years), G2 (45-60 ± 2 years), and G3 (65-80 ± 2 years). The results of the 2DCOS analysis showed biomolecular changes in response to SARS-CoV-2. 2DCOS analyses of the male G1 + (1579,1644) and -(1531,1598) crossover peaks evidenced changes such as amide I > IgG. Female G1 crossover peaks -(1504,1645), (1504,1545) and -(1391,1645) resulted in amide I > IgG > IgM. The asynchronous spectra in 1300-900 cm-1 of the G2 male group showed that IgM is more important in diagnosing infections than IgA. Female G2 asynchronous spectra -(1027,1242) and + (1068,1176) showed that IgA > IgM is produced against SARS-CoV-2. The G3 male group evidenced antibody changes in IgG > IgM. The absence of IgM in the female G3 population diagnoses a specifically targeted immunoglobulin associated with sex. Moreover, ROC analysis showed sensitivity (85-89 % men; 81-88 % women) and specificity (90-93 % men; 78-92 % women) for the samples studied. The general classification performance (F1 score) of the studied samples is high for the male (88-91 %) and female (80-90 %) populations. This high PPV (positive predictive value) and NPV (negative predictive value) verify our segregation of COVID-19 positive and negative sample groups. Therefore, 2DCOS with ROC analysis using FTIR spectra have the potential for a non-invasive approach to monitoring COVID-19.

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 Infection-and mRNA Vaccine-induced Humoral Immunity among Schoolchildren in Hawassa, Ethiopia

Background

With the persisting low vaccination intake, particularly in children of low-and middle-income countries (LMICs), seroepidemiological studies are urgently needed to guide and tailor COVID-19 pandemic response efforts in schools and to put mitigation strategies in place for a future post-pandemic resurgence. However, there is limited data on SARS-CoV-2 infection-induced and vaccine-induced humoral immunity in schoolchildren in LMICs, including Ethiopia.

Methods

As the spike receptor binding domain (RBD) is the major target for neutralization antibodies and useful to predict the correlates of protection, we used an in-house anti-RBD IgG ELISA to assess and compare infection-induced antibody response at two-time points and BNT162b2 (BNT) vaccine-induced antibody response at a one-time point in schoolchildren in Hawassa, Ethiopia. In addition, we measured and compared the levels of binding IgA antibodies to spike RBD of SARS-CoV-2 Wild type, Delta, and Omicron variants in a small subset of unvaccinated and BNT-vaccinated schoolchildren.

Results

When we compare SARS-CoV-2 infection-induced seroprevalences among unvaccinated school children (7-19 years) at the two blood sampling points with a 5-month interval, we observed an over 10% increase, from 51.8% (219/419) in the first week of December 2021 (post-Delta wave) to 67.4% (60/89) by the end of May 2022 (post-Omicron wave). Additionally, we found a significant correlation (p = 0.001) between anti-RBD IgG seropositivity and a history of having COVID-19-like symptoms. Compared to the levels of SARS-CoV-2 infection-induced anti-RBD IgG antibodies before vaccination, higher levels of BNT vaccine-induced anti-RBD IgG antibodies were observed even in SARS-CoV-2 infection-naïve schoolchildren of all age groups (p = 0.0001). Importantly, one dose of the BNT vaccine was shown to be adequate to elicit a strong antibody response in schoolchildren with pre-existing anti-RBD IgG antibodies comparable to that of SARS-CoV-2 infection-naive schoolchildren receiving two doses of BNT vaccine, suggesting a single dose administration of the BNT vaccine could be considered for schoolchildren who had prior SARS-CoV-2 infection when a shortage of vaccine supply is a limiting factor to administer two doses irrespective of their serostatus. Despite the small sample size of study participants, the BNT vaccine is shown to be immunogenic and safe for schoolchildren. Irrespective of schoolchildren's vaccination status, we observed a similar pattern of significantly higher levels of IgA antibodies to Delta-RBD than to Omicron-RBD (p < 0.001) in a randomly selected subset of schoolchildren, yet comparable to Wuhan-RBD, suggesting these schoolchildren were more likely to have had SARS-CoV-2 infection with Delta variant. Additionally, we noted a broader IgA antibody reactivity to SARS-CoV-2 variants in vaccinated schoolchildren with prior SARS-CoV-2 infection, supporting the superiority of hybrid immunity.

Conclusion

Our serological data indicate a significant increase in SARS-CoV-2 seroprevalence in children at a post-Omicron five-month follow-up compared to a post-Delta enrolment. Despite the small sample size of study participants, the BNT vaccine is shown to be immunogenic and safe for schoolchildren. Hybrid immunity would likely provide a broader humoral immunity against Wuhan strain, Delta, and Omicron variants than natural infection or vaccination alone does. However, future longitudinal cohort studies in SARS-CoV-2-naïve and COVID-19-recovered schoolchildren receiving the BNT vaccine are needed for a better understanding of the kinetics, breadth, and durability of BNT vaccine-induced multivariant-cross reactive immunity.

Peripheral blood parameters for predicting PICU admission and mechanical ventilation in pediatric inpatients with human parainfluenza virus-induced pneumonia

Human parainfluenza viruses (hPIVs)-induced pneumonia is an important cause of pediatric hospitalization, and some develop severe pneumonias requiring pediatric intensive care unit (PICU) admission and mechanical ventilation (MV). The aim of this study is to investigate the value of peripheral blood (PB) parameters available on admission in predicting the need for PICU admission and MV due to pneumonia caused by hPIVs. A total of 331 cases including 277 (83.69%) on the general ward (GW) and 54 (16.31%) on the PICU were enrolled between January 2016 and June 2021. Of 54 patients admitted to the PICU, 24 patients (7.25%) received MV, whereas 30 (9.06%) did not. For both the PICU and GW groups, infants accounted for the highest proportion while school children had the lowest. Compared with the GW group, the PICU group had significantly higher rates of premature birth, fatigue, sore throat, headache, chest pain, tachypnea, dyspnea, and underlying diseases including congenital tracheal stenosis, congenital heart disease (CHD), metabolic disorder, and neurological disorder (ND), but significant lower proportion of exclusive breastfeeding and Z-scores for weight-for-height, weight-for-age, height-for-age, and body-mass-index (BMI)-for-age (BMIZ). Higher levels of some leukocyte differential counts (LDC)-related parameters including counts of neutrophil (N), ratios of neutrophil-to-lymphocyte ratio (NLR), derived neutrophils/(leukocytes minus neutrophils) ratio (dNLR), and platelet-to-lymphocyte ratio (PLR), lower levels of some other LDC-related parameters including lymphocyte (L) and monocyte (M) counts, ratios of lymphocyte-to-monocyte ratio (LMR), lymphocyte-to-C-reactive protein ratio, and prognostic nutritional index (PNI), and lower levels of PB protein (PBP)-related parameters including red blood cell (RBC), hemoglobin, total protein (TP), and serum albumin were observed in the PB of patients in the PICU compared with those in the GW. Notably, higher PLR level and two comorbidities including CHD and ND were identified as independent risk factors for PICU admission, while lower PNI level as well as smaller numbers of RBC and L as good predictors. Low levels of TP might be a useful predictor of the need for MV. Overall, the relative contributions of LDC- and PBP-related factors for accurate identification of patients required PICU admission accounted for 53.69% and 46.31%, respectively. Thus, determination of whether a patient with hPIVs-induced pneumonia is admitted to PICU involves consideration of both the LDC- and PBP-related parameters.

Efficacy Validation of SARS-CoV-2-Inactivation and Viral Genome Stability in Saliva by a Guanidine Hydrochloride and Surfactant-Based Virus Lysis/Transport Buffer

To enhance biosafety and reliability in SARS-CoV-2 molecular diagnosis, virus lysis/transport buffers should inactivate the virus and preserve viral RNA under various conditions. Herein, we evaluated the SARS-CoV-2-inactivating activity of guanidine hydrochloride (GuHCl)- and surfactant (hexadecyltrimethylammonium chloride (Hexa-DTMC))-based buffer, Prep Buffer A, (Precision System Science Co., Ltd., Matsudo, Japan) and its efficacy in maintaining the stability of viral RNA at different temperatures using the traditional real-time one-step RT-PCR and geneLEAD VIII sample-to-result platform. Although Prep Buffer A successfully inactivated SARS-CoV-2 in solutions with high and low organic substance loading, there was considerable viral genome degradation at 35 °C compared with that at 4 °C. The individual roles of GuHCl and Hexa-DTMC in virus inactivation and virus genome stability at 35 °C were clarified. Hexa-DTMC alone (0.384%), but not 1.5 M GuHCl alone, exhibited considerable virucidal activity, suggesting that it was essential for potently inactivating SARS-CoV-2 using Prep Buffer A. GuHCl and Hexa-DTMC individually reduced the viral copy numbers to the same degree as Prep Buffer A. Although both components inhibited RNase activity, Hexa-DTMC, but not GuHCl, directly destroyed naked viral RNA. Our findings suggest that samples collected in Prep Buffer A should be stored at 4 °C when RT-PCR will not be performed for several days.

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.

Direct Nasal Swab for Rapid Test and Saliva as an Alternative Biological Sample for RT-PCR in COVID-19 Diagnosis

Accurate and early diagnoses are prerequisites for prompt treatment. For coronavirus disease 2019 (COVID-19), it is even more crucial. Currently, choice of methods include rapid diagnostic tests and reverse transcription polymerase chain reaction (RT-PCR) using samples mostly of respiratory origin and sometimes saliva. We evaluated two rapid diagnostic tests with three specimen types using viral transport medium (VTM) containing naso-oropharyngeal (NOP) swabs, direct nasal and direct nasopharyngeal (NP) samples from 428 prospective patients. We also performed RT-PCR for 428 NOP VTM and 316 saliva samples to compare results. The sensitivity of the SD Biosensor Standard Q COVID-19 antigen (Ag) test kit drastically raised from an average of 65.55% (NOP VTM) to 85.25% (direct nasal samples), while RT-PCR was the gold standard. For the CareStart kit, the sensitivity was almost similar for direct NP swabs; the average was 84.57%. The specificities were ≥95% for both SD Biosensor Standard Q and CareStart COVID-19 Ag tests in all platforms. The kits were also able to detect patients with different variants as well. Alternatively, RT-PCR results from saliva and NOP VTM samples showed high sensitivities of 96.45% and 95.48% with respect to each other as standard. The overall results demonstrated high performance of the rapid tests, indicating the suitability for regular surveillance at clinical facilities when using direct nasal or direct NP samples rather than NOP VTM. Additionally, the analysis also signifies not showed that RT-PCR of saliva can be used as an choice of method to RT-PCR of NOP VTM, providing an easier, non-invasive sample collection method. IMPORTANCE There are several methods for the diagnosis of coronavirus disease 2019 (COVID-19), and the choice of methods depends mostly on the resources and level of sensitivity required by the user and health care providers. Still, reverse transcription polymerase chain reaction (RT-PCR) has been chosen as the best method using direct naso-oropharyngeal swabs. There are also other methods of fast detection, such as rapid diagnostic tests (RDTs), which offer result within 15 to 20 min and have become quite popular for self-testing and in the clinical setting. The major drawback of the currently used RT-PCR method is compliance, as it may cause irritation, and patients often refuse to test in such a way. RDTs, although inexpensive, suffer from low sensitivity due to technical issues. In this article, we propose saliva as a noninvasive source for RT-PCR samples and evaluate various specimen types at different times after infection for the best possible output from COVID-19 rapid tests.

The Oral Cavity Potentially Serving as a Reservoir for SARS-CoV-2 but Not Necessarily Facilitating the Spread of COVID-19 in Dental Practice

Intraoral tissues, secretions, and microenvironments may provide severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with the conditions necessary for viral cellular entry and inhabitation. The aim of the present study is to overview the oral cavity that potentially serves as a reservoir for SARS-CoV-2, and then discuss the possibility that such oral cavity facilitates the spread of coronavirus disease 2019 (COVID-19) in dental practice. Articles were retrieved from PubMed/Medline, LitCovid, ProQuest, Google Scholar, and preprint medRxiv databases. Results of the literature search indicated that SARS-CoV-2 host cell entry-relevant receptor and virus/cell membrane fusion mediators are expressed in major and minor salivary glands, tongue, taste bud, periodontal tissue, and dental pulp, which would be a target and reservoir for SARS-CoV-2. SARS-CoV-2 is present in saliva and gingival crevicular fluid of COVID-19 patients. These secretions would contaminate dental aerosol and droplet with SARS-CoV-2. SARS-CoV-2 inhabits periodontal pocket, gingival sulcus, and dental caries lesion, which could provide SARS-CoV-2 with a habitat. SARS-CoV-2 ribonucleic acid is preserved in dental calculus, which may inform of the previous infection with SARS-CoV-2. Despite involvement of the oral cavity in SARS-CoV-2 transmission and infection, to date, there have been no clusters of COVID-19 in dental practice. Dental settings are much less likely to facilitate the spread of COVID-19 compared with general medical settings, which may be explained by the situation of dentistry that the number of patients to visit dental offices/clinics was decreased during the COVID-19 pandemic, the characteristics of dentistry that dental professionals have maintained high awareness of viral infection prevention, adhered to a strict protocol for infection control, and been using personal protective equipment for a long time, the experimental results that dental devices generate only small amounts of aerosol responsible for the airborne viral transmission, irrigant from the dental unit contributes to the aerosol microbiota much rather than saliva, and the commonly used evacuation or suction system effectively reduces aerosol and droplet generation, and the possibility that human saliva exhibits the antiviral activity and the property to inhibit SARS-CoV-2 infection. It is considered that dental treatment and oral health care can be delivered safely in the COVID-19 era.

Predictors of SARS-CoV-2 RNA From Nasopharyngeal Swabs and Concordance With Other Compartments in Nonhospitalized Adults With Mild to Moderate COVID-19

Background

Identifying characteristics associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding may be useful to understand viral compartmentalization, disease pathogenesis, and risks for viral transmission.

Methods

Participants were enrolled August 2020 to February 2021 in ACTIV-2/A5401, a placebo-controlled platform trial evaluating investigational therapies for mild-to-moderate coronavirus disease 2019 (COVID-19), and underwent quantitative SARS-CoV-2 RNA testing on nasopharyngeal and anterior nasal swabs, oral wash/saliva, and plasma at entry (day 0, pretreatment) and days 3, 7, 14, and 28. Concordance of RNA levels (copies/mL) across compartments and predictors of nasopharyngeal RNA levels were assessed at entry (n = 537). Predictors of changes over time were evaluated among placebo recipients (n = 265) with censored linear regression models.

Results

Nasopharyngeal and anterior nasal RNA levels at study entry were highly correlated (r = 0.84); higher levels of both were associated with greater detection of RNA in plasma and oral wash/saliva. Older age, White non-Hispanic race/ethnicity, lower body mass index (BMI), SARS-CoV-2 immunoglobulin G seronegativity, and shorter prior symptom duration were associated with higher nasopharyngeal RNA at entry. In adjusted models, body mass index and race/ethnicity associations were attenuated, but the association with age remained (for every 10 years older, mean nasopharyngeal RNA was 0.27 log10 copies/mL higher; P < .001). Examining longitudinal viral RNA levels among placebo recipients, women had faster declines in nasopharyngeal RNA than men (mean change, -2.0 vs -1.3 log10 copies/mL, entry to day 3; P < .001).

Conclusions

SARS-CoV-2 RNA shedding was concordant across compartments. Age was strongly associated with viral shedding, and men had slower viral clearance than women, which could explain sex differences in acute COVID-19 outcomes.

Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals.

METHODS

Between October 2020 and July 2021, we sequenced 4439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral RNA burden and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals.

RESULTS

The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about 3 months (104 ± 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, 3 of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad viral RNA copy number values during acute infection (interquartile range, 1.2-8.64 Log copies/mL), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies/mL, P < .00001). Nevertheless, 49% to 50% of all breakthroughs, and 56% to 60% of Delta-infected breakthroughs exhibited viral RNA levels above the transmissibility threshold (4 Log copies/mL) irrespective of time after vaccination.

CONCLUSIONS

Delta infection transmissibility and general viral RNA quantification patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should specifically address whether extra vaccine doses curb breakthrough contribution to epidemic spread.

Favipiravir, lopinavir-ritonavir, or combination therapy (FLARE): A randomised, double-blind, 2 × 2 factorial placebo-controlled trial of early antiviral therapy in COVID-19

BACKGROUND

Early antiviral treatment is effective for Coronavirus Disease 2019 (COVID-19) but currently available agents are expensive. Favipiravir is routinely used in many countries, but efficacy is unproven. Antiviral combinations have not been systematically studied. We aimed to evaluate the effect of favipiravir, lopinavir-ritonavir or the combination of both agents on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral load trajectory when administered early.

METHODS AND FINDINGS

We conducted a Phase 2, proof of principle, randomised, placebo-controlled, 2 × 2 factorial, double-blind trial of ambulatory outpatients with early COVID-19 (within 7 days of symptom onset) at 2 sites in the United Kingdom. Participants were randomised using a centralised online process to receive: favipiravir (1,800 mg twice daily on Day 1 followed by 400 mg 4 times daily on Days 2 to 7) plus lopinavir-ritonavir (400 mg/100 mg twice daily on Day 1, followed by 200 mg/50 mg 4 times daily on Days 2 to 7), favipiravir plus lopinavir-ritonavir placebo, lopinavir-ritonavir plus favipiravir placebo, or both placebos. The primary outcome was SARS-CoV-2 viral load at Day 5, accounting for baseline viral load. Between 6 October 2020 and 4 November 2021, we recruited 240 participants. For the favipiravir+lopinavir-ritonavir, favipiravir+placebo, lopinavir-ritonavir+placebo, and placebo-only arms, we recruited 61, 59, 60, and 60 participants and analysed 55, 56, 55, and 58 participants, respectively, who provided viral load measures at Day 1 and Day 5. In the primary analysis, the mean viral load in the favipiravir+placebo arm had changed by -0.57 log10 (95% CI -1.21 to 0.07, p = 0.08) and in the lopinavir-ritonavir+placebo arm by -0.18 log10 (95% CI -0.82 to 0.46, p = 0.58) compared to the placebo arm at Day 5. There was no significant interaction between favipiravir and lopinavir-ritonavir (interaction coefficient term: 0.59 log10, 95% CI -0.32 to 1.50, p = 0.20). More participants had undetectable virus at Day 5 in the favipiravir+placebo arm compared to placebo only (46.3% versus 26.9%, odds ratio (OR): 2.47, 95% CI 1.08 to 5.65; p = 0.03). Adverse events were observed more frequently with lopinavir-ritonavir, mainly gastrointestinal disturbance. Favipiravir drug levels were lower in the combination arm than the favipiravir monotherapy arm, possibly due to poor absorption. The major limitation was that the study population was relatively young and healthy compared to those most affected by the COVID-19 pandemic.

CONCLUSIONS

At the current doses, no treatment significantly reduced viral load in the primary analysis. Favipiravir requires further evaluation with consideration of dose escalation. Lopinavir-ritonavir administration was associated with lower plasma favipiravir concentrations.

TRIAL REGISTRATION

Clinicaltrials.gov NCT04499677 EudraCT: 2020-002106-68.

Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from saliva

Polymerase chain reaction (PCR) has proven to be the gold-standard for SARS-CoV-2 detection in clinical settings. The most common approaches rely on nasopharyngeal specimens obtained from swabs, followed by RNA extraction, reverse transcription and quantitative PCR. Although swab-based PCR is sensitive, swabbing is invasive and unpleasant to administer, reducing patient compliance for regular testing and resulting in an increased risk of improper sampling. To overcome these obstacles, we developed a non-invasive one-step RT-qPCR assay performed directly on saliva specimens. The University of Nottingham Asymptomatic Testing Service protocol simplifies sample collection and bypasses the need for RNA extraction, or additives, thus helping to encourage more regular testing and reducing processing time and costs. We have evaluated the assay against the performance criteria specified by the UK regulatory bodies and attained accreditation (BS EN ISO/IEC 17,025:2017) for SARS-CoV-2 diagnostic testing by the United Kingdom Accreditation Service. We observed a sensitivity of 1 viral copy per microlitre of saliva, and demonstrated a concordance of > 99.4% between our results and those of other accredited testing facilities. We concluded that saliva is a stable medium that allows for a highly precise, repeatable, and robust testing method.

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.

Positivity rates of SAR-CoV-2 infection in orthodontic patients at the orthodontic clinic, University of Illinois Chicago

COVID-19 has impacted and increased risks for healthcare providers, including orthodontists. There is no information regarding the potential transmission risks in the orthodontic community. This study aims to compare the positivity rate of SARS-CoV-2 infection in orthodontic patients at the University of Illinois Chicago (UIC) orthodontic clinic to the positivity rate of the local population in Chicago. All orthodontic patients who sought treatment at the UIC orthodontic clinic from June 16 to October 31, 2021, were invited to participate in the study. Three milliliters of saliva from the participants were collected in the sample collection tubes and subjected to a polymerase chain reaction (PCR) based assay to detect SAR-CoV-2. All participants’ age, sex, history of COVID-19 infection, and vaccination status were recorded. The COVID-19 positivity rates of Chicago, Cook County of Illinois, and the orthodontic clinic at UIC were compared. One thousand four hundred and thirty-seven orthodontic patients aged 6 to 70 years old (41.8% males and 58.2% females) participated in the study. Among all participants, nine participants tested positive for SARS-CoV-2 (5 males and 4 females). During the study, the average COVID-19 positivity rate at the UIC orthodontic clinic was 0.626%. All of the positive participants were asymptomatic, and two of the participants had a history of COVID-19 infection. Among all positive participants, three participants had received complete COVID-19 vaccination. An increased frequency of positive cases at the orthodontic clinic was observed during the time of high positivity rate in Chicago and Cook County. A potential risk of COVID-19 transmission from patients to orthodontic providers remains, even with asymptomatic and vaccinated patients.

Performance of nasopharyngeal swab and saliva in detecting Delta and Omicron SARS-CoV-2 variants

A prospective cohort study was conducted during the Delta and Omicron severe acute respiratory syndrome coronavirus type 2 (SARS‐CoV‐2) epidemic waves from paired nasopharyngeal swab (NPS or NP swab) and saliva samples taken from 624 participants. The study aimed to assess if any differences among participants from both waves could be observed and if any difference in molecular diagnostic performance could be observed among the two sample types. Samples were transported immediately to the laboratory to ensure the highest possible sample quality without any freezing and thawing steps before processing. Nucleic acids from saliva and NPS were prospectively extracted and SARS‐CoV‐2 was detected using a real‐time reverse‐transcription polymerase chain reaction. All observed results were statistically analyzed. Although the results obtained with NP and saliva agreed overall, higher viral loads were observed in NP swabs regardless of the day of specimen collection in both SARS‐CoV‐2 epidemic waves. No significant difference could be observed between the two epidemic waves characterized by Delta or Omicron SARS‐CoV‐2. To note, Delta infection resulted in higher viral loads both in NP and saliva and more symptoms, including rhinorrhea, cough, and dyspnea, whereas Omicron wave patients more frequently reported sore throat. An increase in the mean log RNA of SARS‐CoV‐2 was observed with the number of expressed symptoms in both waves, however, the difference was not significant. Data confirmed that results from saliva were concordant with those from NP swabs, although saliva proved to be a challenging sample with frequent inhibitions that required substantial retesting.

Respiratory viruses among pediatric inpatients with acute lower respiratory tract infections in Jinan, China, 2016-2019

The viral etiologies responsible for acute lower respiratory tract infections (ALRI) are a major cause of pediatric hospitalization, and some develop severe diseases requiring pediatric intensive care unit (PICU) admission. The aim of this study was to determine the prevalence of viruses and risk factors associated with PICU admission among patients hospitalized for ALRI. Nasopharyngeal swabs were collected to detect human rhinovirus (HRV), influenza A and B viruses (IAV, IBV), parainfluenza viruses (PIV), and respiratory syncytial virus (RSV) by reverse transcription-polymerase chain reaction (RT-PCR) and adenovirus (ADV) by PCR. Of the 5590 pediatric inpatients enrolled, respiratory viral infection occurred in 2102 (37.60%) patients, including 1846 (33.02%) single and 256 (4.58%) mixed viral infections. Among the nasopharyngeal swabs from pediatric inpatients, HRV accounted for the highest detection rate (16.48%), followed by PIV (8.35%), RSV (7.41%), ADV (4.63%), IAV (3.51%), and IBV (2.08%). The positive rate of viral tests decreased with increasing age and was higher in males (39.29%) than females (34.67%). The prevalence of viral infection was the highest in winter (41.57%) and lowest in autumn (31.78%). Each virus had a seasonal pattern, with peaks occurring in months of their epidemic seasons. RSV infection and the presence of comorbidities including congenital tracheal stenosis, congenital heart disease, metabolic disorder, immunodeficiency, renal disease, gastrointestinal disease and neurological disorder might be associated with the need for PICU admission. Therefore, this study provides useful information for the prevention and control of virus-related respiratory diseases and the early identification of and the intervention in severe cases. This article is protected by copyright. All rights reserved.