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Scientific Reports Feb 2022The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection...
The ongoing SARS-CoV-2 pandemic and subsequent demand for viral testing has led to issues in scaling diagnostic lab efforts and in securing basic supplies for collection and processing of samples. This has motivated efforts by the scientific community to establish improved protocols that are more scalable, less resource intensive, and less expensive. One such developmental effort has resulted in an assay called "Swab-Seq", so named because it was originally developed to work with dry nasal swab samples. The existing gold standard test consists of RNA extracted from a nasopharyngeal (NP) swab that is subjected to quantitative reverse transcription polymerase chain reaction (qRT-PCR). Swab-Seq adapts this method to a next-generation sequencing readout. By pairing this modification with extraction-free sampling techniques, Swab-Seq achieves high scalability, low cost per sample, and a reasonable turnaround time. We evaluated the effectiveness of this assay in a community surveillance setting by testing samples collected from both symptomatic and asymptomatic individuals using the traditional NP swab. In addition, we evaluated extraction-free sampling techniques (both saliva and saline mouth gargle samples). We found the assay to be as clinically sensitive as the qRT-PCR assay, adaptable to multiple sample types, and able to easily accommodate hundreds of samples at a time. We thus provide independent validation of Swab-Seq and extend its utility regarding sample type and sample stability. Assays of this type greatly expand the possibility of routine, noninvasive, repeated testing of asymptomatic individuals suitable for current and potential future needs.
Topics: COVID-19
PubMed: 35197492
DOI: 10.1038/s41598-022-06901-5 -
Biomedicines Feb 2022The aim of this study was to compare the test results from patients who, within a short timescale, have been tested for COVID-19 using both a pharyngeal swab and...
The aim of this study was to compare the test results from patients who, within a short timescale, have been tested for COVID-19 using both a pharyngeal swab and tracheal secretion. Data were collected from the database of AUH, from patients hospitalized between 1 March 2020 and 1 March 2021 who, due to symptoms of COVID-19, were tested by a pharyngeal swab and by tracheal secretion. We found great agreement between oropharyngeal swab and tracheal secretion RT-PCR testing for the diagnosis of COVID-19, with 98.5% of double tests being concordant and only 1.5% being discordant. This finding may advocate a single-test strategy being either an oropharyngeal swab RT-PCR testing or tracheal secretion, although this study revealed 15.9% false negative oropharyngeal swabs.
PubMed: 35203697
DOI: 10.3390/biomedicines10020488 -
Journal of Infection and Chemotherapy :... Jul 2021Rapid antigen detection (RAD) tests are convenient tools for detecting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinics, and testing using...
INTRODUCTION
Rapid antigen detection (RAD) tests are convenient tools for detecting the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinics, and testing using saliva samples could decrease the risk of infection during sample collection. This study aimed to assess the accuracy of the SARS-CoV-2 RAD for testing of nasopharyngeal swab specimens and saliva samples in comparison with the RT-PCR tests and viral culture for detecting viable virus.
METHODS
One hundred seventeen nasopharyngeal swab specimens and 73 saliva samples with positive results on RT-PCR were used. Residual samples were assayed using a commercially available RAD test immediately, and its positivity was determined at various time points during the clinical course. The concordance between 54 nasopharyngeal swab samples and saliva samples that were collected simultaneously was determined. Viral culture was performed on 117 samples and compared with the results of the RAD test.
RESULTS
The positive rate of RAD test using saliva samples was low throughout the clinical course. Poor concordance was observed between nasopharyngeal swab specimens and saliva samples (75.9%, kappa coefficient 0.310). However, a substantially high concordance between the RAD test and viral culture was observed in both nasopharyngeal swab specimens (86.8%, kappa coefficient 0.680) and saliva samples (95.1%, kappa coefficient 0.643).
CONCLUSIONS
The sensitivity of the SARS-CoV-2 RAD test was insufficient, particularly for saliva samples. However, a substantially high concordance with viral culture suggests its potential utility as an auxiliary test for estimating SARS-CoV-2 viability.
Topics: COVID-19; Humans; Nasopharynx; Reverse Transcriptase Polymerase Chain Reaction; SARS-CoV-2; Saliva
PubMed: 33934920
DOI: 10.1016/j.jiac.2021.04.010 -
Frontiers in Microbiology 2021Enteric fever is a severe systemic infection caused by serovar Typhi (ST) and serovar Paratyphi A (SPA). Detection of ST and SPA in wastewater can be used as a...
Development of Moore Swab and Ultrafiltration Concentration and Detection Methods for Typhi and Paratyphi A in Wastewater and Application in Kolkata, India and Dhaka, Bangladesh.
Enteric fever is a severe systemic infection caused by serovar Typhi (ST) and serovar Paratyphi A (SPA). Detection of ST and SPA in wastewater can be used as a surveillance strategy to determine burden of infection and identify priority areas for water, sanitation, and hygiene interventions and vaccination campaigns. However, sensitive and specific detection of ST and SPA in environmental samples has been challenging. In this study, we developed and validated two methods for concentrating and detecting ST/SPA from wastewater: the Moore swab trap method for qualitative results, and ultrafiltration (UF) for sensitive quantitative detection, coupled with qPCR. We then applied these methods for ST and SPA wastewater surveillance in Kolkata, India and Dhaka, Bangladesh, two enteric fever endemic areas. The qPCR assays had a limit of detection of 17 equivalent genome copies (EGC) for ST and 25 EGC for SPA with good reproducibility. In seeded trials, the Moore swab method had a limit of detection of approximately 0.05-0.005 cfu/mL for both ST and SPA. In 53 Moore swab samples collected from three Kolkata pumping stations between September 2019 and March 2020, ST was detected in 69.8% and SPA was detected in 20.8%. Analysis of sewage samples seeded with known amount of ST and SPA and concentrated via the UF method, followed by polyethylene glycol precipitation and qPCR detection demonstrated that UF can effectively recover approximately 8, 5, and 3 log cfu of seeded ST and SPA in 5, 10, and 20 L of wastewater. Using the UF method in Dhaka, ST was detected in 26.7% (8/30) of 20 L drain samples with a range of 0.11-2.10 log EGC per 100 mL and 100% (4/4) of 20 L canal samples with a range of 1.02-2.02 log EGC per 100 mL. These results indicate that the Moore swab and UF methods provide sensitive presence/absence and quantitative detection of ST/SPA in wastewater samples.
PubMed: 34335510
DOI: 10.3389/fmicb.2021.684094 -
A comparison of swab types on sample adequacy, suspects comfort and provider preference in COVID-19.American Journal of Otolaryngology 2021This study was aimed to compare the virological, suspect reported outcomes and provider preferences during COVID-19 swab taking procedure used for sampling. (Comparative Study)
Comparative Study
AIM
This study was aimed to compare the virological, suspect reported outcomes and provider preferences during COVID-19 swab taking procedure used for sampling.
METHODS
The COVID-19 suspects are subjected to nasopharyngeal (NP) and oropharyngeal (OP) swabs for testing. Two types of swabs (Nylon and Dacron) are used for sample collection. Prospectively each suspect's response is collected and assessed for self-reported comfort level. The provider's experience with each suspect and virological outcomes recorded separately. The sample adequacy was compared based on swab types and demographic characteristics.
RESULTS
A total of 1008 COVID-19 suspects were considered for comparison of various outcomes. Dacron and flocked Nylon swab sticks are used for taking 530 and 478 samples, respectively. Suspects who underwent the procedure using Nylon swabs were six times more likely to have pain/discomfort compared to when Dacron swab was used (Adj RR (95% CI: 6.76 (3.53 to 13, p=0.0001))). The providers perceived six times more resistance with the Nylon swabs compared to Dacron Swabs (Adj RR (95% CI: 5.96 (3.88 to 9.14, p=0.0001))). The pediatric population had a higher rate of blood staining in Dacron swab [Dacron 66 (80.5%); Nylon 51 (54.8%) p=0.0001]. The sample adequacy rate and laboratory positivity rate were not significantly different from each other.
CONCLUSIONS
Given the comparable virological outcomes, the difference in suspect and providers comfort should drive swab selection based on characteristics of the suspects. The bulbous Nylon swab caused more pain/discomfort in adults compared to Dacron.
Topics: Adolescent; Adult; Attitude of Health Personnel; COVID-19 Testing; Child; Child, Preschool; Female; Humans; Infant; Infant, Newborn; Male; Middle Aged; Nasopharynx; Nylons; Oropharynx; Patient Comfort; Polyethylene Terephthalates; Prospective Studies; Specimen Handling; Young Adult
PubMed: 33418177
DOI: 10.1016/j.amjoto.2020.102872 -
Indian Journal of Ophthalmology Dec 2021To evaluate the presence of SARS-CoV-2 RNA in the conjunctival swab sample of positive confirmed COVID-19 patients and to find out its association with comorbidity and... (Observational Study)
Observational Study
Detection of SARS-CoV-2 RNA in a conjunctival swab sample in real-time-polymerase chain reaction positive COVID-19 patients and its association with comorbidity and severity at a designated COVID-19 hospital in Central India.
PURPOSE
To evaluate the presence of SARS-CoV-2 RNA in the conjunctival swab sample of positive confirmed COVID-19 patients and to find out its association with comorbidity and severity of COVID-19 disease.
METHODS
We conducted an observational cross-sectional study at a dedicated tertiary COVID-19 hospital in central India for a period of 8 weeks from February 2021to March 2021. We included patients who tested positive for SARS-CoV-2 RNA through nasopharyngeal swab and were above 18 years of age. Swab samples have been collected within 48 h of admission. Conjunctival swab was taken from the lower fornix of both eyes and sent to microbiology laboratory for real-time- polymerase chain reaction (RT-PCR).
RESULTS
Out of 150 patients, conjunctival swab RT-PCR was positive in five patients (3.33%). Two patients had conjunctival manifestations in the form of conjunctivitis but conjunctival swab RT-PCR was negative in those patients. Among the RT-PCR positive patients, two (40%) were from mild, one (20%) was from moderate, and two (40%) were from severe category. No association could be established between conjunctival swab RT-PCR positivity and severity of the disease or associated comorbidity.
CONCLUSION
Our study provides evidence that SARS-CoV-2 RNA could be detected in conjunctival secretions, and though the risk is relatively low, the eye may act as source of transmission. Extra caution should be taken by healthcare workers, and use of proper precautions like face shields and goggles should be encouraged.
Topics: COVID-19; Comorbidity; Conjunctiva; Cross-Sectional Studies; Hospitals; Humans; RNA, Viral; Real-Time Polymerase Chain Reaction; SARS-CoV-2
PubMed: 34827010
DOI: 10.4103/ijo.IJO_1604_21 -
Journal of Medical Virology Jul 2021The aim is to comparatively evaluate the results of simultaneous conjunctiva and oropharynx-nasopharynx (ONP) swabs in patients who had presented to the outpatient... (Comparative Study)
Comparative Study
The aim is to comparatively evaluate the results of simultaneous conjunctiva and oropharynx-nasopharynx (ONP) swabs in patients who had presented to the outpatient department with a suspicion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). An ONP sample was obtained following bilateral conjunctiva swabs in 85 subjects with a contact history or symptoms but unknown SARS-CoV-2 status and with no ocular symptoms or findings. The results were evaluated according to the patient's symptoms and how the swab was taken. The conjunctiva swab was positive in 29 (34.1%) cases and the ONP swab in 20 (23.5%) cases. Both methods produced positive results in 11 (14.1%) cases. The mean cycle threshold (C ) value was 30.15 ± 3.41 in symptomatic cases and 33.62 ± 1.76 in asymptomatic cases (p = .008). The mean C value was 24.37 ± 3.48 when only the ONP swab was positive and 31.22 ± 1.99 when only the conjunctiva swab was positive. In cases that were positive by both methods, the mean C value was 25.21 ± 4.94 for the ONP swab and 30.29 ± 5.05 for the conjunctiva swab. We found higher SARS-CoV-2 detection rates with the conjunctiva swab than the ONP swab in cases with unknown SARS-CoV-2 status in the early period. In addition, the conjunctival viral load seemed to be higher in symptomatic cases than in asymptomatic cases. We, therefore, believe a conjunctiva swab could be an alternative method to detect SARS-CoV-2 at the time of the first presentation to the outpatient department.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; COVID-19; COVID-19 Testing; Conjunctiva; Diagnostic Tests, Routine; Female; Humans; Male; Middle Aged; Nasopharynx; Oropharynx; Prospective Studies; RNA, Viral; Real-Time Polymerase Chain Reaction; SARS-CoV-2; Specimen Handling; Viral Load; Young Adult
PubMed: 33783859
DOI: 10.1002/jmv.26981 -
Iranian Journal of Pharmaceutical... 2020A cleaning validation for a family of compounds utilizing swab sampling and rinse solution procedures, and high performance liquid chromatography for separation and...
Evaluation of Swab and Rinse Sampling Procedures and Recovery Rate Determination in Cleaning Validation Considering Various Surfaces, Amount and Nature of the Residues and Contaminants.
A cleaning validation for a family of compounds utilizing swab sampling and rinse solution procedures, and high performance liquid chromatography for separation and detection of the analytes was performed.Effective parameters on recovery including sampling method, swab characteristics, solvent, swabbing technique, and material substance of product contact surfaces within the manufacturing equipment for swab and rinse sampling method, quantitative cleaning verification method, and active pharmaceutical ingredient (API) level and nature have been studied.The limit of detection and the limit of quantitation for the HPLC method were determined to be 0.0198 µg/mL, and 0.0495 µg/mL of the analyte, respectively. The linearity on replicate injections of the standard prepared in the range of 0.78, 1.55, 3.1, and 6.2 µg/mL, and relative standard deviation (R.S.D.) found to be 1.2, 1.0, 0.9, and 0.6, respectively with correlation coefficient of R = 0.9999. Recovery coverage for each type of surface was acceptable, ranging from 63.88% for swab sampling of stainless steel to 97.85% for rinse sampling of PVC. The acceptance criteria for precision on replicate injections of the analyte prepared in three concentration levels covering the specified range of 50, 100, and 200% was successfully accomplished R.S.D. lower than 15% for recovery results.Thus, choosing the appropriate sampling method, swab type, and surface condition can affect and increase recovery rate determination efficiency.
PubMed: 33680038
DOI: 10.22037/ijpr.2020.1101173 -
The Journal of Antimicrobial... Aug 2021HIV exposure to penile tissues provides a risk of acquisition among men, yet studies evaluating penile antiretroviral (ARV) drug distribution have been lacking. We...
BACKGROUND
HIV exposure to penile tissues provides a risk of acquisition among men, yet studies evaluating penile antiretroviral (ARV) drug distribution have been lacking. We measured ARVs on urethral and glans surface swabs collected following a dose of tenofovir alafenamide, emtricitabine, elvitegravir, darunavir and cobicistat.
METHODS
Thirty-five HIV-negative male participants provided urethral swabs, glans swabs, rectal swabs, blood and urine up to 96 h following a single dose of tenofovir alafenamide/emtricitabine/elvitegravir/cobicistat and darunavir. ARVs were measured by liquid chromatography-mass spectrometry with a lower limit of detection (LOD) of 1 ng/swab for swabs and 10 ng/mL for plasma and urine. Concentrations are reported as median and range.
RESULTS
Urethral swab emtricitabine and darunavir concentrations peaked at 4 h for emtricitabine (36 ng/swab; 3-307 ng/swab) and 8 h for darunavir (25 ng/swab; 2-52 ng/swab). Glans swab emtricitabine and darunavir concentrations peaked 24 h after dosing (emtricitabine 14 ng/swab,
swab; darunavir 6 ng/swab, swab). Estimated peak urethral secretion emtricitabine and darunavir concentrations are between 10 and 20 μg/mL, similar to rectal secretions, 4-fold greater than in plasma, but 2-fold lower than in urine. Tenofovir and elvitegravir were detected on less than 20% of urethral or glans swabs collected within 24 h of dosing. CONCLUSIONS
We document ARV dosing in the urethra and on the glans surface with high drug concentrations noted for emtricitabine and darunavir and lower tenofovir and elvitegravir concentrations. Data suggest a potential protective role of urethral emtricitabine or darunavir against penile HIV acquisition.
Topics: Anti-HIV Agents; Cobicistat; Emtricitabine; HIV Infections; HIV-1; Humans; Male; Pharmaceutical Preparations; Urethra
PubMed: 34007982
DOI: 10.1093/jac/dkab155 -
Frontiers in Immunology 2022Sore throat is a common reason for overuse of antibiotics. The value of inflammatory or biomarkers in throat swab or saliva samples in predicting benefit from...
INTRODUCTION
Sore throat is a common reason for overuse of antibiotics. The value of inflammatory or biomarkers in throat swab or saliva samples in predicting benefit from antibiotics is unknown.
METHODS
We used the 'person-based approach' to develop an online tool to support self-swabbing and recruited adults and children with sore throats through participating general practices and social media. Participants took bacterial and viral swabs and a saliva sponge swab and passive drool sample. Bacterial swabs were cultured for streptococcus (Group A, B, C, F and G). The viral swab and saliva samples were tested using a routine respiratory panel PCR and Covid-19 PCR testing. We used remaining viral swab and saliva sample volume for biomarker analysis using a panel of 13 biomarkers.
RESULTS
We recruited 11 asymptomatic participants and 45 symptomatic participants. From 45 symptomatic participants, bacterial throat swab, viral throat swab, saliva sponge and saliva drool samples were returned by 41/45 (91.1%), 43/45 (95.6%), 43/45 (95.6%) and 43/45 (95.6%) participants respectively. Three saliva sponge and 6 saliva drool samples were of insufficient quantity. Two adult participants had positive bacterial swabs. Six participants had a virus detected from at least one sample (swab or saliva). All of the biomarkers assessed were detectable from all samples where there was sufficient volume for testing. For most biomarkers we found higher concentrations in the saliva samples. Due to low numbers, we were not able to compare biomarker concentrations in those who did and did not have a bacterial pathogen detected. We found no evidence of a difference between biomarker concentrations between the symptomatic and asymptomatic participants but the distributions were wide.
CONCLUSIONS
We have demonstrated that it is feasible for patients with sore throat to self-swab and provide saliva samples for pathogen and biomarker analysis. Typical bacterial and viral pathogens were detected but at low prevalence rates. Further work is needed to determine if measuring biomarkers using oropharyngeal samples can help to differentiate between viral and bacterial pathogens in patients classified as medium or high risk using clinical scores, in order to better guide antibiotic prescribing and reduce inappropriate prescriptions.
Topics: Child; Adult; Humans; Feasibility Studies; COVID-19; Pharyngitis; Streptococcus pyogenes; Anti-Bacterial Agents; Biomarkers
PubMed: 36275691
DOI: 10.3389/fimmu.2022.1016181