Saliva Swabs Research Articles

P-2171. Comparing Saliva and Nasal Mid-turbinate Swabs for Detection of Respiratory Syncytial Virus (RSV), February 1–April 15, 2024, New Vaccine Surveillance Network

Abstract Background Current diagnostic methods for RSV and other respiratory viruses primarily rely on reverse transcription polymerase chain reaction (RT-PCR) testing of nasopharyngeal (NPS) or nasal mid-turbinate (MTS) swabs. Recent data in adults suggest saliva increases diagnostic yield of RSV. However, the potential of saliva as a specimen type for detecting RSV in children remains understudied. We compared the diagnostic yield of saliva and paired MTS samples for RSV detection in children. Methods Between February 1 to April 15, 2024, a total of 206 paired MTS and saliva samples obtained using the SalivaBio Children’s swab were collected on the same day from subjects under the age of 18 years presenting with acute respiratory illness symptoms. All MTS samples underwent testing using the QIAstat-Dx Respiratory SARS-CoV-2 Panel, which identifies RSV A+B cases. Subsequently, saliva samples from RSV-positive cases identified by MTS testing were extracted using the Kingfisher Apex platform. Positive RSV cases were subtyped by RT-PCR. Results Among 206 paired MTS and saliva specimens tested, RSV A/B was detected in 8 MTS and 7 saliva specimens. Saliva detected RSV A/B in 7 out of 8 (87.5%) samples that tested positive by MTS swabs. Both MTS and saliva tested negative for RSV in 197/206 specimens tested. The median (IQR) Ct values for paired MTS swabs and saliva samples were 25.05 (21.82 – 32.72) and 31.9 (27.45 – 34.48), respectively. The sample missed by saliva had a high Ct value of 36.6. Saliva detected an additional RSV-A positive case with a Ct value of 33.03, which was negative by the MTS swab. Overall concordance of saliva with MTS was 99% (204/206). Conclusion Although the number of RSV detections was low, preliminary findings from this analysis suggest high concordance between MTS and saliva for detection of RSV but that the addition of saliva does not increase diagnostic yield in children. Disclosures Rangaraj Selvarangan, BVSc, PhD, D(ABMM), FIDSA, FAAM, Abbott: Grant/Research Support|Abbott: Honoraria|BioMerieux: Grant/Research Support|Cepheid: Grant/Research Support|Diasorin: Grant/Research Support|GSK: Advisor/Consultant|Hologic: Grant/Research Support|Luminex: Grant/Research Support|Qiagen: Grant/Research Support

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition

Background: In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing’s specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study. Methods: Fourteen participants followed one of three diets—exclusive juice, juice plus food, or plant-based food—for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition. Results: The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance. Conclusions: These findings suggest that short-term juice consumption may negatively affect the microbiota.

Oral microbiota as a biomarker for predicting the risk of malignancy in indeterminate pulmonary nodules: a prospective multicenter study.

Determining the benign or malignant status of indeterminate pulmonary nodules (IPN) with intermediate malignancy risk is a significant clinical challenge. Oral microbiota-lung cancer interactions have qualified oral microbiota as a promising non-invasive predictive biomarker in IPN. Prospectively collected saliva, throat swabs, and tongue coating samples from 1040 IPN patients and 70 healthy controls across three hospitals. Following up, the IPNs were diagnosed as benign (BPN) or malignant pulmonary nodules (MPN). Through 16S rRNA sequencing, bioinformatics analysis, fluorescence in situ hybridization (FISH), and seven machine learning algorithms (support vector machine, logistic regression, naïve bayes, multi-layer perceptron, random forest, gradient-boosting decision tree, and LightGBM), we revealed the oral microbiota characteristics at different stages of HC-BPN-MPN, identified the sample types with the highest predictive potential, constructed and evaluated the optimal MPN prediction model for predictive efficacy, and determined microbial biomarkers. Additionally, based on the SHAP algorithm interpretation of the ML model's output, we have developed a visualized IPN risk prediction system on the web. Saliva, tongue coating, and throat swab microbiotas exhibit site-specific characteristics, with saliva microbiota being the optimal sample type for disease prediction. The saliva-LightGBM model demonstrated the best predictive performance (AUC=0.887, 95%CI: 0.865-0.918), and identified Actinomyces, Rothia, Streptococcus, Prevotella, Porphyromonas, and Veillonella as biomarkers for predicting MPN. FISH was used to confirm the presence of a microbiota within tumors, and external data from a lung cancer cohort, along with three non-IPN disease cohorts, were employed to validate the specificity of the microbial biomarkers. Notably, coabundance analysis of the ecological network revealed that microbial biomarkers exhibit richer interspecies connections within the MPN, which may contribute to the pathogenesis of MPN. This study presents a new predictive strategy for the clinic to determine MPNs from BPNs, which aids in the surgical decision-making for IPN.

Abstract B061: Assessing saliva for cancer biomarker discovery: A liquid biopsy approach

Abstract Introduction: Liquid biopsy has been gaining traction as a replacement for invasive tumor biopsies in oncology. Several blood-based in vitro diagnostics have been approved by the FDA and other regulatory agencies, and efforts are being made to validate urine, saliva, and buccal swabs as alternative matrices. The primary aim of this study was to investigate the relative mRNA expression in paired blood and saliva samples from cancer patients and healthy individuals. Methods: We collected matched saliva and blood samples from 35 subjects, comprising 26 patients with prostate, breast, colon, lung, melanoma, and pancreatic cancers, and 9 healthy individuals. Samples were collected using Wren's proprietary stabilization buffer kit, and total RNA extracted by TRIzol-based Qiagen reagents. RNA sequencing (RNA-Seq) was performed on a Novaseq 6000 platform, and data was analyzed using high-performance computing (HPC) with PartekFlow software, employing the BWA aligner (hg38). We focused on comparing gene expression in cancers (as a group) compared to controls. Results: The total number of genes detected in saliva was 3,985, compared to 14,459 genes detected in blood samples. A substantial overlap was observed, with more than 92.8% of saliva-detected genes also found in blood. We also examined housekeeping gene detection in both matrices. In this set of 1,003 housekeeping genes, 30% (n=305) were expressed in both saliva and blood. When we narrowed the scope to only include the 1,154 cancer-related genes as listed by the OncoKB database, 88.3% were detected in saliva and/or blood, with 37.1% of these genes (n=429) were expressed in both saliva and blood. Lastly, we examined a set of 241 cancer-associated biomarkers utilized in RT-PCR-based diagnostic blood assays clinically validated by our laboratory. This subset analysis revealed that 23.2% of these biomarkers were expressed in both saliva and blood. Conclusion: Our data indicate that the majority of mRNA detected in saliva was also detected in blood, with differential expression observed in cancer patients compared to normal controls. Given the relatively high limit of detection (low sensitivity) using RNA-Seq technology compared to PCR and the relatively small number of subjects, the data may suggest that saliva could function as a surrogate biomarker matrix for blood. Citation Format: Srinivas V Koduru, Mark Kidd, Abdel B Halim. Assessing saliva for cancer biomarker discovery: A liquid biopsy approach [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B061.

Relationships of dog behavior and cattle illness signs to dogs’ ability to distinguish between sick and healthy cattle

Dogs are highly successful at detecting disease using olfaction; however, performance varies among dogs. Training detection dogs represents a substantial investment of time and resources; thus, identifying behavioral markers of a successful detection dog and factors that affect dog performance is needed. In a previous study, one of four dogs was able to distinguish between nasal and saliva swabs from healthy cattle and cattle undergoing an inflammatory response at a rate greater than chance, with 73 % accuracy. The present study evaluated how dogs’ accuracy changed throughout training and testing, whether dogs’ responses were related to illness signs present in cattle, and whether dogs’ accuracy was related to their own behavior on a per-trial and per-sample basis. Trial number, or the order of a detection trial within a 20-trial training or test session, was slightly positively correlated with accuracy for one dog. Sample number, the order in which the dogs encountered samples, was slightly positively correlated with per-session accuracy for all dogs. Dog accuracy declined across training sessions that used the same sample (F4381 = 3.48, P = 0.01), suggesting a deterioration in sample quality over time. Among the clinical illness signs measured in cattle, the strongest association demonstrated that greater changes in cattle body temperature were positively associated with dog accuracy (r = 0.32, P < 0.01). During training and testing, positive (sickness-model), negative (healthy) and blank (unscented) samples were presented at equal rates. Dogs spent more time sniffing and made more visits to investigate the positive samples than negative samples, and spent more time sniffing and made more visits to negative samples than blank samples, indicating that less time was required for dogs to rule out unscented stations than to distinguish between cattle swabs. Visits to the negative sample and visits to the positive sample were negatively (r = −0.581, P < 0.01) and positively (r = 0.761, P < 0.01) correlated with accuracy, respectively. Increased latency to search was negatively correlated with accuracy (r = −0.10, P < 0.01). This represents another potential behavioral marker of successful detection dogs.

Detection of Epstein‒Barr virus DNA methylation as tumor markers of nasopharyngeal carcinoma patients in saliva, oropharyngeal swab, oral swab, and mouthwash.

Saliva biopsy of nasopharyngeal carcinoma (NPC) has been developed in our latest study, indicating the application of oral sampling in NPC detection. Further exploration of the potential for self-sampling from the oral cavity is necessary. A total of 907 various samples from oral cavity, including saliva (n=262), oropharyngeal swabs (n=250), oral swabs (n=210), and mouthwash (n=185), were collected. Epstein‒Barr virus (EBV) DNA methylation at the 12,420bp CpG site in EBV genome from the repeat-copy W promoter (Wp) region and at the 11,029bp CpG site in the single-copy C promoter (Cp) region were simultaneously detected in these samples. A significant increase in EBV methylation, no matter at Wp or Cp region, was found in all types of samples from NPC patients. However, EBV DNA methylation in saliva and oropharyngeal swab showed a better diagnostic performance in detecting NPC. The combination of these two sample types and two markers could help to improve the detection of NPC. Our study further explored the optimal self-sampling methods and detection target in the detection of NPC and may facilitate the application of EBV DNA methylation detection in a home-based large-scale screening of NPC.

Hearing Screening for Congenital CytoMegaloVirus-Exploring Parents' Experiences of Completing Targeted Congenital Cytomegalovirus Screening at the Time of Their Infants' Newborn Hearing Screening.

Background/Objectives: Congenital cytomegalovirus (cCMV) is the leading infectious cause of sensorineural hearing loss and neurodevelopmental disabilities, with prompt detection (<21 days of life) required to enable accurate diagnosis and anti-viral treatment where clinically appropriate. International guidelines recommend cCMV screening for infants who do not pass their Universal Newborn Hearing Screening (UNHS). This study aimed to explore parental experiences of targeted cCMV screening through the UNHS in Victoria, Australia between 2019 and 2020 (HearS-cCMV study). Methods: A qualitative study comprising 18 semi-structured interviews with parents who took saliva swabs from their infants who did not pass their UNHS. A maximum variation sampling strategy was used with data analysed using thematic analysis. Results: Four themes described 18 parents' experiences of cCMV screening: (1) parents' lack of CMV awareness prior to cCMV screening; (2) overall positive experience; (3) varied understanding of CMV post screening; and (4) parents were glad to screen their infant for cCMV. Enablers of targeted cCMV screening included the swab being simple and non-invasive, being easier to complete in the hospital than at home, and the screening being well delivered by the staff. Barriers included a potential increase in anxiety, especially with false positives, and the timing of cCMV screening coinciding with their infant not passing UNHS being difficult for some parents. Conclusions: Parent experiences of targeted cCMV screening were positive. Increasing public knowledge of cCMV and training staff members to complete the CMV swab would reduce the risk of false positives and associated parental anxiety. This would facilitate successful routine targeted cCMV screening.

Evaluating diagnostic accuracy of an RT-PCR test for the detection of SARS-CoV-2 in saliva

Background and objectiveSaliva has been proposed as a potential more convenient, cost-effective, and easier sample for diagnosing SARS-CoV-2 infections, but there is limited knowledge of the impact of saliva volumes and stages of infection on its sensitivity and specificity.MethodsIn this study, we assessed the performance of SARS-CoV-2 testing in 171 saliva samples from 52 mostly mildly symptomatic patients (aged 18 to 70 years) with a positive reference standard result at screening. The samples were collected at different volumes (50, 100, 300, and 500 µl of saliva) and at different stages of the disease (at enrollment, day 7, 14, and 28 post SARS-CoV-2 diagnosis). Imperfect nasopharyngeal (NP) swab nucleic acid amplification testing was used as a reference. We used a logistic regression with generalized estimating equations to estimate sensitivity, specificity, PPV, and NPV, accounting for the correlation between repeated observations.ResultsThe sensitivity and specificity values were consistent across saliva volumes. The sensitivity of saliva samples ranged from 70.2% (95% CI, 49.3–85.0%) for 100 μl to 81.0% (95% CI, 51.9–94.4%) for 300 μl of saliva collected. The specificity values ranged between 75.8% (95% CI, 55.0–88.9%) for 50 μl and 78.8% (95% CI, 63.2–88.9%) for 100 μl saliva compared to NP swab samples. The overall percentage of positive results in NP swabs and saliva specimens remained comparable throughout the study visits. We observed no significant difference in cycle number values between saliva and NP swab specimens, irrespective of saliva volume tested.ConclusionsThe saliva collection offers a promising approach for population-based testing.

Development of a multiplex PCR assay and quantification of microbial markers by ddPCR for identification of saliva and vaginal fluid

The identification of biological fluids at crime scenes contributes to crime scene reconstruction and provides investigative leads. Traditional methods for body fluid identification are limited in terms of sensitivity and are mostly presumptive. Emerging methods based on mRNA and DNA methylation require high quality template source. An exploitable characteristic of body fluids is their distinct microbial profiles allowing for the discrimination of body fluids based on microbiome content. Microbial DNA is highly abundant within the body, robust and stable and can persist in the environment long after human DNA has degraded. 16S rRNA sequencing is the gold standard for microbial analysis; however, NGS is costly, and requires intricate workflows and interpretation. Also, species level resolution is not always achievable. Based on the current challenges, the first objective of this study was to develop a multiplex conventional PCR assay to identify vaginal fluid and saliva by targeting species-specific 16S rRNA microbial markers. The second objective was to employ droplet digital PCR (ddPCR) as a novel approach to quantify bacterial species alone and in a mixture of body fluids. Lactobacillus crispatus and Streptococcus salivarius were selected because of high abundance within vaginal fluid and saliva respectively. While Fusobacterium nucleatum and Gardnerella vaginalis, though present in healthy humans, are also frequently found in oral and vaginal infections, respectively. The multiplex PCR assay detected L. crispatus and G. vaginalis in vaginal fluid while F. nucleatum and S. salivarius was detected in saliva. Multiplex PCR detected F. nucleatum, S. salivarius and L. crispatus in mixed body fluid samples while, G. vaginalis was undetected in mixtures containing vaginal fluid. For samples exposed at room temperature for 65 days, L. crispatus and G. vaginalis were detected in vaginal swabs while only S. salivarius was detected in saliva swabs. The limit of detection was 0.06 copies/µl for F. nucleatum (2.5 ×10−9 ng/µl) and S. salivarius (2.5 ×10−6 ng/µl). L. crispatus and G. vaginalis had detection limits of 0.16 copies/µl (2.5 ×10−4 ng/µl) and 0.48 copies/µl (2.5 ×10−7 ng/µl). All 4 bacterial species were detected in mixtures and aged samples by ddPCR. No significant differences were observed in quantity of bacterial markers in saliva and vaginal fluid. The present research reports for the first time the combination of the above four bacterial markers for the detection of saliva and vaginal fluid and highlights the sensitivity of ddPCR for bacterial quantification in pure and mixed body fluids.

Feasibility, performances and predictive value of congenital CMV neonatal screening on saliva swabs

BackgroundEarly diagnosis of congenital CMV infection (cCMVI) allows for early intervention and follow-up to detect delayed hearing loss. While CMV PCR in urine is the gold standard for cCMVI diagnosis, saliva testing is often performed. ObjectivesOur aim was to determine (i) if swab saliva sampling needed standardization, (ii) if a threshold value in “virus copies per million cells (Mc)” in saliva samples could improve clinical specificity, and (iii) to establish a correlation between viral load in saliva and symptomatology/outcome of cCMVI. Materials and methodsIn our institution, universal newborn screening is performed on saliva swabs at delivery or until day 3 of life. If positive, CMV PCR in urine is done within 2 weeks to confirm or exclude cCMVI. ResultsCell quantification showed that saliva swab sampling was well performed as 95.4 % samples had more than 100 cells/10 µL. There was a good correlation between saliva viral load in copies/mL and in copies/Mc (Pearson's r = 0.96, p < 0.0001). However, threshold values, established to determine a viral load level at which we could confidently identify infected newborns, did not improve positive predictive value (21.8 % for copies/mL and 21 % for copies/Mc vs 25.4 % without threshold) but instead reduced sensitivity (88 % and 85% vs 100 % without threshold). Samples collected on day 2 or 3 had better positive predictive value (38.7 %) compared to those collected on day 1 (23.8 %). Symptomatology at birth was not significantly associated with viral load in saliva at diagnosis. However, sequelae occurrence was associated with viral load in saliva (copies/Mc). DiscussionOur results confirm that saliva swab is a suitable sample for universal neonatal screening. However, identifying newborns that will develop sequelae remains an issue in the management of cCMVI.

Integrated Antigenic and Nucleic Acid Detection in Single Virions and Extracellular Vesicles with Viral Content.

Virion-mediated outbreaks are imminent and despite rapid responses, continue to cause adverse symptoms and death. Therefore, tunable, sensitive, high-throughput assays are needed to help diagnose future virion-mediated outbreaks. Herein, it is developed a tunable in situ assay to selectively enrich virions and extracellular vesicles (EVs) and simultaneously detect antigens and nucleic acids at a single-particle resolution. The Biochip Antigen and RNA Assay (BARA) enhanced sensitivities compared to quantitative reverse-transcription polymerase chain reaction (qRT-PCR), enabling the detection of virions in asymptomatic patients, genetic mutations in single virions, and enabling the continued long-term expression of viral RNA in the EV-enriched subpopulation in the plasma of patients with post-acute sequelae of the coronavirus disease of 2019 (COVID-19). BARA revealed highly accurate diagnoses of COVID-19 by simultaneously detecting the spike glycoprotein and nucleocapsid-encoding RNA in saliva and nasopharyngeal swab samples. Altogether, the single-particle detection of antigens and viral RNA provides a tunable framework for the diagnosis, monitoring, and mutation screening of current and future outbreaks.

Persistent feline coronavirus infection in a cat with cardiac and gastrointestinal signs

Background Feline coronavirus infection causes feline infectious peritonitis in a subset of cats, but can also result in persistent infection. The tissue reservoirs of feline coronavirus and the role of viral persistence in pathogenesis are poorly understood. Aims This study aimed to identify sites of feline coronavirus persistence in a naturally infected cat, identify disease correlates and characterise within-host viral evolution. Methods The study followed a 5-year-old Bengal cat for 6 years and collected non-invasive samples, including faeces and conjunctival, oropharyngeal and saliva swabs. At 11-years-old, the patient was euthanised as a result of respiratory distress, and tissue samples were collected. The authors used hybridisation capture and next-generation sequencing methodologies focused on the feline coronavirus S gene, along with RNA in-situ hybridisation. Results During the study, the patient was diagnosed with inflammatory bowel disease, alimentary small cell lymphoma, chronic rhinitis and mitral valve regurgitation. Feline coronavirus was detected in the nasal cavity, intestine, faeces and conjunctiva in 2017, and in the intestine, faeces and heart in 2022. Sequence analysis showed that the virus adapted to tissue reservoirs over time. Conclusions This study identifies potential feline coronavirus reservoirs. The relationship of persistent feline coronavirus infection to chronic conditions warrants further investigation.

The Ability to Detect the COVID-19 Genome Using Saliva Swabs in Comparison with Nasopharyngeal Swabs in Baghdad

Abstract Objective Nasopharyngeal swab (NPS) sampling has been recommended by the World Health Organization (WHO) since the start of the COVID-19 pandemic, and real-time reverse transcription polymerase chain reaction (RT–PCR) is used to detect SARS-CoV- 2, the causative agent of COVID-19. This sampling technique is invasive and causes discomfort to the patient. Saliva swabs (SSs) can be used as an alternative noninvasive method; however, there are limited data confirming its suitability for the diagnosis of COVID-19. The aim of this study was to test the ability to detect COVID-19 using SSs in comparison with NPSs in the Baghdad Alkark sector. Materials and Methods Six hundred and fifty patients were included in this study, and written informed consent was obtained from all the study participants. Paired NPSs and SSs were collected at the same time from each participant between days 3 and 5 after disease initiation. SSs were taken from the sublingual area. An RT‒PCR assay was used to detect the viral ribonucleic acid (RNA) of SARS-CoV-2 for the diagnosis of COVID-19. The chi-squared test was used for data analysis, with p &lt; 0.05 considered significant. Results Out of 650 participants with suspected COVID-19 (313 males and 145 females), 313 were confirmed to be positive for COVID-19 by quantitative RT–PCR (RT‒qPCR) using both samples. The ages ranged between 12 and 85 years, with a mean/standard deviation (SD) of 45.45 (16.62) years. All the cases with positive results using NPSs were also positive when SSs were used. Statistically, there was no significant difference between the two groups (p = 0.347). Conclusion RT‒PCR assays conducted on SSs and NPSs performed similarly, indicating that SSs may be a safe, inexpensive diagnostic sampling method and an effective tool for population screening. We recommend more studies to support this finding.

Corrigendum: The Ability to Detect the COVID-19 Genome Using Saliva Swabs in Comparison with Nasopharyngeal Swabs in Baghdad

Corrigendum: The Ability to Detect the COVID-19 Genome Using Saliva Swabs in Comparison with Nasopharyngeal Swabs in Baghdad

Saliva as a Biological Fluid in SARS-CoV-2 Detection.

The polymerase chain reaction of upper respiratory tract swab samples was established as the gold standard procedure for diagnosing SARS-CoV-2 during the COVID pandemic. However, saliva collection has attracted attention as an alternative diagnostic collection method. The goal of this study was to compare the use of saliva and nasopharyngeal swab (NPS) samples for the detection of SARS-CoV-2. Ninety-nine paired samples were evaluated for the detection of SARS-CoV-2 by saliva and swab for a qualitative diagnosis and quantitative comparison of viral particles. Furthermore, the detection limits for each sample collection technique were determined. The cycle threshold (CT) values of the saliva samples, the vaccination status, and the financial costs associated with each collection technique were compared. The results showed qualitative equivalence in diagnosis (96.96%) comparing saliva and swab collection, although there was low quantitative agreement. Furthermore, the detection limit test demonstrated equivalence for both collection methods. We did not observe a statistically significant association between CT values and vaccination status, indicating that the vaccine had no influence on viral load at diagnosis. Finally, we observed that the use of saliva incurs lower financial costs and requires less use of plastic materials, making it more sustainable. These findings support the adoption of saliva collection as a feasible and sustainable alternative to the diagnosis of COVID-19.

Comparison of Elva Diagnostic SARS-CoV-2 Saliva Nucleic Acid Test Kit with RT-qPCR and Rapid Antigen Tests in COVID-19 Patients

The practical application of the reverse transcription loop-mediated isothermal amplification (RT-LAMP) technique has been confirmed in diagnosing different viral infections. Nevertheless, its accuracy in identifying SARS-CoV-2, particularly in practical clinical situations, has not been thoroughly investigated. This study aims to investigate the sensitivity and specificity of the Elva Diagnostic SARS-CoV-2 Saliva Nucleic Acid Test Kit, utilizing the RT-LAMP and Rapid Antigen Test (RAT) methods for in vitro diagnostic testing, compared to the real-time quantitative polymerase chain reaction (RT-qPCR) method throughout the progression of COVID-19. Method: This study employed an analytical observational diagnostic test at Dr. Soetomo Regional Public Hospital, Surabaya, from March 2022 to May 2022. This research involved 54 samples of saliva and nasopharyngeal swabs obtained from 36 patients confirmed positive for COVID-19 and 18 samples from subjects not confirmed to have COVID-19, tested using the RT-qPCR method. The diagnostic performance of both the RT-LAMP and RAT methods was assessed by calculating their sensitivity and specificity in comparison to RT-qPCR, beginning from the time the patient was confirmed positive for COVID-19. The suitability of each method was analyzed using Cohen’s kappa. The nucleocapsid (N) protein gene from SARS-CoV-2 RNA was detected with RT-LAMP and RAT test kits which showed incompatibilities with the RT-qPCR method (p value 0.308). The positive and negative results with the RT-LAMP and RAT method examinations were similar in number compared to the RT-qPCR method, where the positive results in the RT-LAMP and RAT methods were 2 subjects and the negative results were 52 subjects. Based on the results, only 2 confirmed cases had positive results with RT-LAMP and RAT, which means the sensitivity of both tests is only 5.5% and both are poor screening tests for patients suspected of having COVID-19. In addition, the specificity of RT-qPCR as the gold standard examination method for diagnosing COVID-19 cannot be replaced by the RT-LAMP and RAT methods.

Dogs' ability to detect an inflammatory immune response in cattle via olfaction.

Canine olfaction is a potential means for detection of respiratory disease in beef cattle. In a prior study, two dogs were trained to discriminate between nasal swabs from healthy cattle and cattle that developed Bovine Respiratory Disease. Dogs had some ability to identify samples from BRD-affected cattle, but results were ambiguous. The purpose of this study was to evaluate more dogs using better-controlled training and testing procedures. Nasal and saliva swabs were collected from 96 cattle before and after administering a vaccine to induce an inflammatory immune response. Samples were stored at -80°C for up to 11 months before use, and samples from animals with an elevated body temperature at baseline were omitted. An automated olfactometer apparatus was constructed to improve blinding procedures and reduce opportunities for odor contamination. Four dogs were trained to distinguish between swabs from healthy and sickness-model cattle, including the two dogs from the previous study ("Runnels" and "Cheaps") and two inexperienced dogs ("Molokai" and "Amy"). During a seven-month training period, dogs were exposed to samples from 28 animals. Dogs were tested on 59 sets of unfamiliar samples. Performance varied among dogs (χ2 = 10.48, p = 0.02). Molokai's performance was above chance (0.73 ± 0.06, p = 0.0006), while Amy (0.44 ± 0.06, p = 0.43), Cheaps (0.53 ± 0.07, p = 0.79), and Runnels (0.56 ± 0.06, p = 0.43) did not respond correctly at a rate different from chance. Accuracy did not differ between nasal swabs (0.63 ± 0.08) and saliva swabs (0.53 ± 0.08, χ2 = 0.81, p = 0.37). The results of this study indicate that canine olfaction may be an effective means of detecting illness in beef cattle. However, individual dogs' aptitude for this detection task varies.

Saliva and tongue microbiota in burning mouth syndrome: An exploratory study of potential roles.

Burning mouth syndrome (BMS) is a chronic orofacial pain disorder with unclear etiology, in which the tongue is most commonly affected. This study aims to provide implication of the possible relationship between oral microbiota and the pathogenesis of BMS. Saliva and tongue swabs of 15 primary BMS patients and 10 healthy controls were collected and assessed by 16S rRNA gene amplicon sequencing. The microbiota compositions were compared and bioinformatic analysis was conducted. Differences in microbiota compositions between BMS patients and healthy controls were revealed in both saliva and tongue samples. In saliva, Streptococcus, Rothia, and Neisseria were the predominant genus at the taxonomic level in BMS patients. In tongue samples, Prevotella, Streptococcus, and Neisseria were the dominant genus at thetaxonomic level in BMS patients. LEfSe analysis and linear discriminant analysis score showed that Actinobacteria were the predominant phylum in saliva, and Selenomonas were enriched in the dorsum of the tongue of BMS patients. This study for the first-time reported saliva and tongue microbiota profiles were distinguished from that of healthy controls, indicating a necessity for further research on the possible relationship between oral microbes and the pathogenesis of BMS.

Non-Invasive Specimen Collection in COVID-19 RT-PCR Testing: An Observational Study at an Indonesian Tertiary Hospital

Background: COVID-19 is a disease of SARS-CoV2 beta coronavirus infection. One way to control the progression of COVID-19 symptoms is a rapid and accurate diagnosis. The current gold standard of COVID-19 diagnostic method uses RT-PCR from nasopharyngeal (NP) swabs and sputum specimens. Objective: To assess the efficacy of saliva and rectal swabs as non-invasive alternatives to the conventional nasopharyngeal swab for RTPCR testing in COVID-19 diagnosis, with a focus on the potential benefits for healthcare providers and patient comfort. Methods: This observational study was conducted with 80 confirmed cases at a tertiary hospital in Indonesia, the study compared RTPCR positivity rates among different collection methods. Results: A high positivity rate of 92% for nasopharyngeal swabs, with saliva and rectal swabs yielding 36% and 34%, respectively. Notably, the positivity rates for saliva and rectal samples increased to 60% and 50% when testing occurred between five to seven days post-symptom onset. Crucially, in older patients, both saliva and rectal swabs demonstrated higher positivity rates than in younger patients within the initial four days of symptom onset, with rates of 43% and 17%, respectively. Furthermore, a significant correlation was found between rectal swab positivity on day one and mortality in the older cohort, where lower Ct values on day seven were significantly associated with the deceased group. Conclusion: These findings support the potential of saliva and rectal swabs in predicting disease severity and patient outcomes, suggesting a safer and more convenient testing strategy for COVID- 19.

Evaluation of Oral Microflora-Related to Dental Caries and Salivary pH in type II Diabetic Patients.

Diabetes mellitus is one of the chronic diseases and a group of metabolic disorders characterized by a high blood sugar level over a prolonged period. The present study aimed to evaluate and correlate HbA1c, salivary pH, and oral bacterial microflora (streptococcus and lactobacillus colony-forming unit (CFU)) related to dental caries in normal, controlled, and uncontrolled type II diabetic patients. A total of 90 samples were taken for this study. The HbA1c test was recorded and grouped into three (normal, prediabetic, and diabetic). CFUs (streptococcus and lactobacillus) were evaluated by the spit-and-swab method. Salivary pH was measured with a pH strip with color coding. By using the post hoc test, the P-value was significant. The CFU of streptococcus and lactobacillus in the saliva spit and swab method is statistically significant for P <0.005 and P <0.01 among normal, prediabetic, and diabetic groups. In diabetic patients, there is a higher incidence of dental caries (s.d. 6.7), a higher CFU (s.d. 6194.5) in the bacterial microflora, and a lower salivary pH (s.d. 0.6) than in prediabetic and normal patients. From the present study, we conclude that there is a slight increase in the CFU of Streptococcus mutans in diabetic patients compared to non-diabetic patients. This CFU increase and decrease in salivary PH were strongly associated with increased dental caries in diabetic patients.