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1.
Int J Mol Sci ; 24(11)2023 Jun 03.
Article in English | MEDLINE | ID: covidwho-20233198

ABSTRACT

In this study, the intrinsic surface-enhanced Raman spectroscopy (SERS)-based approach coupled with chemometric analysis was adopted to establish the biochemical fingerprint of SARS-CoV-2 infected human fluids: saliva and nasopharyngeal swabs. The numerical methods, partial least squares discriminant analysis (PLS-DA) and support vector machine classification (SVMC), facilitated the spectroscopic identification of the viral-specific molecules, molecular changes, and distinct physiological signatures of pathetically altered fluids. Next, we developed the reliable classification model for fast identification and differentiation of negative CoV(-) and positive CoV(+) groups. The PLS-DA calibration model was described by a great statistical value-RMSEC and RMSECV below 0.3 and R2cal at the level of ~0.7 for both type of body fluids. The calculated diagnostic parameters for SVMC and PLS-DA at the stage of preparation of calibration model and classification of external samples simulating real diagnostic conditions evinced high accuracy, sensitivity, and specificity for saliva specimens. Here, we outlined the significant role of neopterin as the biomarker in the prediction of COVID-19 infection from nasopharyngeal swab. We also observed the increased content of nucleic acids of DNA/RNA and proteins such as ferritin as well as specific immunoglobulins. The developed SERS for SARS-CoV-2 approach allows: (i) fast, simple and non-invasive collection of analyzed specimens; (ii) fast response with the time of analysis below 15 min, and (iii) sensitive and reliable SERS-based screening of COVID-19 disease.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2/genetics , Saliva/chemistry , Nasopharynx , RNA, Viral/genetics , Spectrum Analysis, Raman , Specimen Handling/methods , COVID-19 Testing
2.
Sex Transm Dis ; 50(6): 323-328, 2023 06 01.
Article in English | MEDLINE | ID: covidwho-20231254

ABSTRACT

BACKGROUND: The prevalence of sexually transmitted infections (STIs) is at an all-time high. Direct-to-consumer STI testing services may help alleviate this undue health burden. These products are sold online and rarely require interaction with a health care professional (HCP). Vendors offer STI self-collection kits or prescriptions for HCP specimen collection. The objective was to understand the scope of direct-to-consumer STI testing services offered and provide recommendations for consumers and industry. METHODS: Seven volunteers searched for "STD tests" on Google from February 1 through March 31, 2021 and shared their top 3 results. The study team extracted data from consumer-facing information on each website. Descriptive statistics and thematic qualitative analyses were performed. RESULTS: Twenty vendors were identified. Most vendors (95%) used Clinical Laboratory Improvement Amendments (CLIA)-certified or College of American Pathologists (CAP) accredited laboratories. Analyses distinguished between STI self-collection kits (n = 9) using independent laboratories and HCP specimen collection (n = 10), which used commercial laboratories (n = 1 offered both). The STI self-collection kits were cheaper per test and bundle on average (eg, $79.00 vs. $106.50 for chlamydia/gonorrhea), and more closely aligned with clinical recommendations compared with the HCP specimen collection options. Websites often contained inaccurate or misleading information (n = 13), often promoting testing outside of the recommendations. CONCLUSIONS: Direct-to-consumer STI testing services are part of an emerging market lacking regulation. Consumers should select vendors offering prescriptions for HCP specimen collection at CAP accredited and CLIA-certified laboratories. Vendors should provide a screening tool to assess individual patient risk prior to test purchase.


Subject(s)
Chlamydia , Gonorrhea , HIV Infections , Sexually Transmitted Diseases , Humans , Sexually Transmitted Diseases/diagnosis , Sexually Transmitted Diseases/prevention & control , Sexually Transmitted Diseases/epidemiology , Gonorrhea/epidemiology , Internet , Specimen Handling/methods , HIV Infections/epidemiology
3.
BMC Pediatr ; 23(1): 201, 2023 04 28.
Article in English | MEDLINE | ID: covidwho-2326720

ABSTRACT

Detection of respiratory viruses requires testing of the upper respiratory tract to obtain specimens for analysis. However, nasal and throat swabs can cause discomfort and procedural anxiety in children. Respiratory sampling methods which are accurate and less invasive are needed. We aim to determine the positive and negative percentage agreement of a novel anterior nasal swab (ANS) compared with the combined throat and anterior nasal swab (CTN), the reference standard, for detection of respiratory viruses. Children 5 - 18 years of age presenting to a tertiary paediatric hospital with respiratory symptoms were tested with both swabs in randomised order. Respiratory samples were tested on a multiplex RT-PCR panel. Viral detections, RT-PCR cycle-threshold values and child/parent/clinician experience of the swab were recorded. There were 157 viral detections from 249 participant CTN swabs. In comparison with the CTN, the overall positive and negative percentage agreement of ANS for detection of respiratory viruses was 96.2% (95% CI, 91.8-98.3%) and 99.8% (95% CI, 99.6-99.9%), respectively. The ANS was "extremely comfortable", or only a "little uncomfortable" for 90% of children compared with 48% for CTN. 202 children (84%) rated the ANS as the preferred swab, and 208 (87%) indicated they would prefer ANS for future testing. The ANS required additional laboratory handling processes compared to the CTN. The ANS has high positive percentage agreement and is comparable to the current standard of care. The high acceptability from the less invasive ANS provides a more comfortable method for respiratory virus testing in children.Trial registrationClinicalTrials.gov ID NCT05043623.


Subject(s)
Viruses , Child , Humans , Multiplex Polymerase Chain Reaction/methods , Pharynx , Prospective Studies , Sensitivity and Specificity , Specimen Handling/methods
4.
Sci Rep ; 13(1): 7174, 2023 05 03.
Article in English | MEDLINE | ID: covidwho-2315869

ABSTRACT

Sample pooling is a promising strategy to facilitate COVID-19 surveillance testing for a larger population in comparison to individual single testing due to resource and time constraints. Increased surveillance testing capacity will reduce the likelihood of outbreaks as the general population is returning to work, school, and other gatherings. We have analyzed the impact of three variables on the effectiveness of pooling test samples: swab type, workflow, and positive sample order. We investigated the performance of several commercially available swabs (Steripack polyester flocked, Puritan nylon flocked, Puritan foam) in comparison to a new injected molded design (Yukon). The bench-top performance of collection swab was conducted with a previously developed anterior nasal cavity tissue model, based on a silk-glycerol sponge to mimic soft tissue mechanics and saturated with a physiologically relevant synthetic nasal fluid spiked with heat-inactivated SARS-CoV-2. Overall, we demonstrated statistically significant differences in performance across the different swab types. A characterization of individual swab uptake (gravimetric analysis) and FITC microparticle release suggests that differences in absorbance and retention drive the observed differences in Ct of the pooled samples. We also proposed two distinct pooling workflows to encompass different community collection modes and analyzed the difference in resulting positive pools as an effect of workflow, swab type, and positive sample order. Overall, swab types with lower volume retention resulted in reduced false negative occurrence, also observed for collection workflows with limited incubation times. Concurrently, positive sample order did have a significant impact on pooling test outcome, particularly in the case of swab type with great volume retention. We demonstrated that the variables investigated here affect the results of pooled COVID-19 testing, and therefore should be considered while designing pooled surveillance testing.


Subject(s)
COVID-19 Testing , COVID-19 , Humans , SARS-CoV-2 , COVID-19/diagnosis , COVID-19/epidemiology , Workflow , Specimen Handling/methods
5.
Ann Lab Med ; 43(5): 434-442, 2023 09 01.
Article in English | MEDLINE | ID: covidwho-2297347

ABSTRACT

Background: Nasal swabs and saliva samples are being considered alternatives to nasopharyngeal swabs (NPSs) for detecting severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2); however, few studies have compared the usefulness of nasal swabs, NPSs, and saliva samples for detecting SARS-CoV-2 and other respiratory virus infections. We compared the positivity rates and concentrations of viruses detected in nasal swabs, NPSs, and saliva samples using cycle threshold (Ct) values from real-time PCR tests for respiratory viruses. Methods: In total, 236 samples (48 five-rub and 10 10-rub nasal swabs, 96 NPSs collected using two different products, 48 saliva swabs, and 34 undiluted saliva samples) from 48 patients (34 patients with SARS-CoV-2 and 14 with other respiratory virus infections) and 40 samples from eight healthy controls were obtained. The PCR positivity and Ct values were compared using Allplex Respiratory Panels 1/2/3 and Allplex SARS-CoV-2 real-time PCR. Results: NPSs showed the lowest Ct values (indicating the highest virus concentrations); however, nasal and saliva samples yielded positive results for SARS-CoV-2 and other respiratory viruses. The median Ct value for SARS-CoV-2 E gene PCR using nasal swab samples collected with 10 rubs was significantly different from that obtained using nasal swabs collected with five rubs (Ct=24.3 vs. 28.9; P=0.002), but not from that obtained using NPSs. Conclusions: Our results confirm that the NPS is the best sample type for detecting respiratory viruses, but nasal swabs and saliva samples can be alternatives to NPSs. Vigorously and sufficiently rubbed nasal swabs can provide SARS-CoV-2 concentrations similar to those obtained with NPSs.


Subject(s)
COVID-19 , Viruses , Humans , SARS-CoV-2 , COVID-19/diagnosis , Saliva , Nasopharynx , Real-Time Polymerase Chain Reaction , Specimen Handling/methods
6.
Front Public Health ; 11: 1066934, 2023.
Article in English | MEDLINE | ID: covidwho-2305065

ABSTRACT

A nasopharyngeal swab (NPS) is the most frequently collected sample type when molecular diagnosis of respiratory viruses, including SARS CoV-2, is required. An optimal collection technique would provide sufficient sample quality for the diagnostic process and would minimize the discomfort felt by the patient. This study compares a simplified NPS collection procedure with only one rotation of the swab to a more standard procedure with five rotations. Swabs were collected from 76 healthy volunteers by the same healthcare professional on 2 consecutive days at a similar hour to minimize variability. The number of Ubiquitin C copy number per sample was measured by real-time quantitative PCR and patient discomfort was assessed by questionnaire. No statistically significant difference (p = 0.15) was observed in the Ubiquitin C copy number per sample between a NPS collected with one rotation (5.2 ± 0.6 log UBC number copies/sample) or five rotations (5.3 ± 0.5 log UBC number copies/sample). However, a statistically significant difference was observed in discomfort between these two procedures, the second being much more uncomfortable. Additional analysis of the results showed a weak correlation between discomfort and the number of human cells recovered (Spearman's rho = 0.202) and greater discomfort in younger people. The results of this study show that a NPS collected with one slow rotation has the same quality as a NPS collected with five rotations. However, the collection time is shorter and, most importantly, less unpleasant for patients.


Subject(s)
COVID-19 , Humans , Ubiquitin C , Nasopharynx , SARS-CoV-2 , Specimen Handling/methods
7.
J Ayub Med Coll Abbottabad ; 34(4): 817-822, 2022.
Article in English | MEDLINE | ID: covidwho-2273733

ABSTRACT

BACKGROUND: We tested the utility of mini-pool PCR testing for the rational use of PCR consumables in screening for CoViD-19. METHODS: After pilot experiments, 3-samples pool size was selected. One step RT-PCR was performed. The samples in the mini-pool having COVID gene amplification were tested individually. RESULTS: 1548 samples tested in 516 mini-pools resulted 396 mini-pools as negative and 120 as positive. Upon individual testing, 110 samples tested positive and 9 were inconclusive. 876 PCR reactions were performed to test 1548 samples, saving 43% PCR reagents. Centres with low prevalence resulted in most saving on reagents (50%), while centres with high prevalence resulted in more test reactions. Testing of individual samples resulted in delays in reporting. CONCLUSIONS: Pooling can increase lab capacity, however, pooling delays results and cause degradation of samples.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , COVID-19/epidemiology , SARS-CoV-2/genetics , COVID-19 Testing , Pakistan/epidemiology , Specimen Handling/methods , Polymerase Chain Reaction , Sensitivity and Specificity , RNA, Viral
8.
PLoS One ; 18(3): e0282853, 2023.
Article in English | MEDLINE | ID: covidwho-2278548

ABSTRACT

Cervical cancer screening rates are declining in the US, with persistent disparities among vulnerable populations. Strategies to better reach under-screened communities are needed. The COVID pandemic sparked major shifts in healthcare delivery, including the accelerated development and adoption of rapid diagnostic testing, broadened access to remote care, and growing consumer demand for self-testing, which could be leveraged for cervical cancer. Rapid tests for the detection of Human Papillomavirus (HPV) have the potential to improve cervical cancer screening coverage, and if coupled with patient-collected cervicovaginal samples, create an opportunity for self-testing. The objectives of this study were: 1) to examine whether COVID influenced clinician perspectives of rapid testing as a screening modality; and 2) to assess clinician awareness, perceived benefits and limitations, and willingness to adopt point-of-care HPV testing, patient self-sampling, and rapid HPV self-testing with self-collected samples. The methodology adopted consisted of an online cross-sectional survey (n = 224) and in-depth interviews (n = 20) were conducted with clinicians who perform cervical cancer screening in Indiana, ranked in the top ten states for cervical cancer mortality and with marked disparities across socio-demographic groups. The main findings show that about half the clinicians reported that the COVID pandemic had influenced their views on rapid testing as a screening modality both positively (greater public acceptability of rapid testing and impact on patient care) and negatively (concerns regarding accuracy of rapid tests). The majority of clinicians (82%) were willing to adopt rapid HPV testing at the point-of-care, while only 48% were willing to adopt rapid HPV self-testing with self-collected samples. In-depth interviews revealed provider concerns around patients' ability to collect their own sample, report results correctly, and return to the clinic for follow-up and other preventive care. Addressing clinician concerns about self-sampling and rapid HPV testing, such as ensuring that rapid tests include sample adequacy controls, is necessary to mitigate barriers to adoption for cervical cancer screening.


Subject(s)
COVID-19 , Papillomavirus Infections , Uterine Cervical Neoplasms , Female , Humans , Uterine Cervical Neoplasms/diagnosis , Uterine Cervical Neoplasms/epidemiology , Uterine Cervical Neoplasms/prevention & control , Human Papillomavirus Viruses , Vaginal Smears/methods , Early Detection of Cancer/methods , Cross-Sectional Studies , Papillomaviridae , COVID-19/diagnosis , COVID-19/epidemiology , Specimen Handling/methods , Mass Screening/methods , Self Care , Patient Acceptance of Health Care
9.
PLoS One ; 18(3): e0282976, 2023.
Article in English | MEDLINE | ID: covidwho-2283300

ABSTRACT

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.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2/genetics , Saliva/chemistry , RNA, Viral/genetics , RNA, Viral/analysis , Cross-Sectional Studies , Ethiopia/epidemiology , COVID-19 Testing , Clinical Laboratory Techniques/methods , Specimen Handling/methods , Nasopharynx
10.
Acta Virol ; 67(1): 3-12, 2023.
Article in English | MEDLINE | ID: covidwho-2253310

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring in air traffic is important in the prevention of the virus spreading from abroad. The gold standard for SARS-CoV-2 detection is RT-qPCR; however, for early and low viral load detection, a much more sensitive method, such as droplet digital PCR (ddPCR), is required. Our first step was to developed both, ddPCR and RT-qPCR methods, for sensitive SARS-CoV-2 detection. Analysis of ten swab/saliva samples of five Covid-19 patients in different stages of disease showed positivity in 6/10 samples with RT-qPCR and 9/10 with ddPCR. We also used our RT-qPCR method for SARS-CoV-2 detection without the need of RNA extraction, obtaining results in 90-120 minutes. We analyzed 116 self-collected saliva samples from passengers and airport staff arriving from abroad. All samples were negative by RT-qPCR, while 1 was positive, using ddPCR. Lastly, we developed ddPCR assays for SARS-CoV-2 variants identification (alpha, beta, gamma, delta/kappa) that are more economically advantageous when compared to NGS. Our findings demonstrated that saliva samples can be stored at ambient temperature, as we did not observe any significant difference between a fresh sample and the same sample after 24 hours (p = 0.23), hence, saliva collection is the optimal route for sampling airplane passengers. Our results also showed that droplet digital PCR is a more suitable method for detecting virus from saliva, compared to RT-qPCR. Keywords: COVID-19; RT-PCR; ddPCR; SARS-CoV-2; nasopharyngeal swab; saliva.


Subject(s)
Air Travel , COVID-19 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , COVID-19 Testing , Sensitivity and Specificity , Polymerase Chain Reaction , RNA, Viral/genetics , Saliva/chemistry , Specimen Handling/methods
11.
Int J Mol Sci ; 24(5)2023 Mar 02.
Article in English | MEDLINE | ID: covidwho-2252658

ABSTRACT

To compare the detection of the SARS-CoV-2 Omicron variant in nasopharyngeal-swab (NPS) and oral saliva samples. 255 samples were obtained from 85 Omicron-infected patients. SARS-CoV-2 load was measured in the NPS and saliva samples by using Simplexa™ COVID-19 direct and Alinity m SARS-CoV-2 AMP assays. Results obtained with the two diagnostic platforms showed very good inter-assay concordance (91.4 and 82.4% for saliva and NPS samples, respectively) and a significant correlation among cycle threshold (Ct) values. Both platforms revealed a highly significant correlation among Ct obtained in the two matrices. Although the median Ct value was lower in NPS than in saliva samples, the Ct drop was comparable in size for both types of samples after 7 days of antiviral treatment of the Omicron-infected patients. Our result demonstrates that the detection of the SARS-CoV-2 Omicron variant is not influenced by the type of sample used for PCR analysis, and that saliva can be used as an alternative specimen for detection and follow-up of Omicron-infected patients.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , Saliva , COVID-19 Testing , Clinical Laboratory Techniques/methods , Specimen Handling/methods , Nasopharynx
12.
J Biomol Tech ; 33(3)2022 10 15.
Article in English | MEDLINE | ID: covidwho-2251033

ABSTRACT

Background: Supply chain disruptions during the COVID-19 pandemic have affected the availability of components for specimen collection kits to detect SARS-CoV-2. Plastic injection molding offers a rapid and cheap method for mass production of swabs for upper respiratory tract sampling. Local production of virus transport medium increases flexibility to assemble sample collection kits if the medium provides appropriate stability for SARS-CoV-2 detection. Methods: A locally produced virus transport medium and a novel injection molded plastic swab were validated for SARS-CoV-2 detection by reverse-transcription quantitative polymerase chain reaction. Both components were compared to standard counterparts using viral reference material and representative patient samples. Results: Clinical testing showed no significant differences between molded and flocked swabs. Commercial and in-house virus transport media provided stable test results for over 40 days of specimen storage and showed no differences in test results using patient samples. Conclusions: This collection kit provides new supply chain options for SARS-CoV-2 testing.


Subject(s)
COVID-19 , Neoplasms , Humans , SARS-CoV-2 , COVID-19 Testing , Pandemics , Nasopharynx/chemistry , Specimen Handling/methods , Culture Media , RNA, Viral
14.
J Infect Chemother ; 29(6): 586-591, 2023 Jun.
Article in English | MEDLINE | ID: covidwho-2266830

ABSTRACT

BACKGROUND: In the context of the coronavirus disease 2019 (COVID-19) pandemic, a rapid and reliable point-of-care test is an essential tool for controlling the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In particular, an immunochromatography test (ICT) that uses saliva specimens for rapid antigen detection not only reduces the risk of secondary infections but also reduces the burden on medical personnel. METHODS: The newly developed salivary antigen test kit "Inspecter Kowa® SARS-CoV-2" is an ICT to which saliva specimens can be directly applied. We evaluated its usefulness in comparison with reverse transcription quantitative PCR (RT-qPCR) and the Espline® SARS-CoV-2 Kit for the detection of SARS-CoV-2 using nasopharyngeal swab specimens. In this study, 140 patients with suspected symptomatic COVID-19 who visited our hospital were enrolled, and nasopharyngeal swab and saliva specimens were collected after they consented to participate in the study. RESULTS: Inspector Kowa SARS-CoV-2 was positive in 45 of 61 (73.8%) saliva that were positive by RT-qPCR and the Espline® SARS-CoV-2 Kit was also positive in 56 of 60 (93.3%) Np swabs that were positive by RT-qPCR. Good antigen detection was achieved by ICT with saliva and nasopharyngeal swab specimens when viral load was ≥105 copies/mL, whereas detection sensitivity was low when viral load was <105 copies/mL, especially in saliva specimens. CONCLUSION: This ICT for the detection of SARS-CoV-2 salivary antigen is an attractive tool that does not require specialized equipment and allows patients to perform the entire process from sample collection to self-diagnose and to reduce the burden on medical care during a pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19 Testing , Saliva , Clinical Laboratory Techniques/methods , Specimen Handling/methods , Nasopharynx
15.
Transl Neurodegener ; 12(1): 13, 2023 03 16.
Article in English | MEDLINE | ID: covidwho-2257673

ABSTRACT

Nasal swabs are non-invasive testing methods for detecting diseases by collecting samples from the nasal cavity or nasopharynx. Dysosmia is regarded as an early sign of coronavirus disease 2019 (COVID-19), and nasal swabs are the gold standard for the detection. By nasal swabs, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids can be cyclically amplified and detected using real-time reverse transcriptase-polymerase chain reaction after sampling. Similarly, olfactory dysfunction precedes the onset of typical clinical manifestations by several years in prion diseases and other neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. In neurodegenerative diseases, nasal swab tests are currently being explored using seed amplification assay (SAA) of pathogenic misfolded proteins, such as prion, α-synuclein, and tau. These misfolded proteins can serve as templates for the conformational change of other copies from the native form into the same misfolded form in a prion-like manner. SAA for misfolded prion-like proteins from nasal swab extracts has been developed, conceptually analogous to PCR, showing high sensitivity and specificity for molecular diagnosis of degenerative diseases even in the prodromal stage. Cyclic amplification assay of nasal swab extracts is an attractive and feasible method for accurate and non-invasive detection of trace amount of pathogenic substances for screening and diagnosis of neurodegenerative disease.


Subject(s)
COVID-19 , Multiple System Atrophy , Prions , Humans , COVID-19/diagnosis , SARS-CoV-2 , Specimen Handling/methods , COVID-19 Testing
16.
J Virol Methods ; 316: 114713, 2023 06.
Article in English | MEDLINE | ID: covidwho-2255829

ABSTRACT

BACKGROUND: During the course of the COVID-19 pandemic, nasopharyngeal swabs, combined throat and nose swabs and saliva samples have been evaluated for SARS-CoV-2 detection using nucleic acid amplification tests (NAT). Literature on anterior nasal swabs is limited. We investigated a novel anterior nasal swab that has been designed to standardised self-collection, maximise sample uptake and improve user comfort. We used combined throat and nose swabs and neat saliva samples as the comparators. RESULTS: The overall positive percentage agreement between the Rhinoswab™ and the combined throat and nose swab was 95.2 % at day 2 post participant recruitment and 93.3 % on day 4 post participant recruitment. This was favourable to the positive percentage agreement with saliva at the same time points. CONCLUSION: In our study the Rhinoswab™ performed equally well in comparison to a combined throat and nose swab for the laboratory detection of SARS-CoV-2 using nucleic acid amplification techniques.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/diagnosis , Nasopharynx , Pandemics , COVID-19 Testing , Saliva , Specimen Handling/methods
17.
Analyst ; 148(8): 1743-1751, 2023 Apr 11.
Article in English | MEDLINE | ID: covidwho-2258966

ABSTRACT

The necessity for the large-scale screening of viral pathogens has been amply demonstrated during the COVID-19 pandemic. During this time, SARS-CoV-2 nucleic acid pooled testing, such as Dorfman-based group testing, was widely adopted in response to the sudden increased demand for detection. However, the current approach still necessitates the individual retesting of positive pools. Here, we established an efficient method termed the fragment-length identification of pooled nucleic acid samples (FLIPNAS), where all subsamples (n = 8) can be uniquely labelled and tested in a single-time detection among pools of samples. We used a novel and simple design of unique primers (UPs) to generate amplicons of unique lengths after reverse transcription and polymerase chain reaction to reach this aim. As a result, the unique lengths of the amplicons can be recognized and traced back to the corresponding UPs and specific samples. Our results demonstrated that FLIPNAS could recognize one to eight positive subsamples in a single test without retesting positive pools. The system also showed sufficient sensitivity for the mass monitoring of SARS-CoV-2 and no cross-reactivity against three common respiratory diseases. Moreover, the FLIPNAS results of 40 samples with a positive ratio of 7.8% were in 100% agreement with their individual detection results using the gold standard. Collectively, this study shows that the efficiency of nucleic acid pooling detection can be further improved by FLIPNAS, which can speed up testing and mitigate the urgent demand for resources.


Subject(s)
COVID-19 , Humans , COVID-19/diagnosis , SARS-CoV-2 , Pandemics , Specimen Handling/methods , Sensitivity and Specificity
19.
Virol J ; 20(1): 21, 2023 02 06.
Article in English | MEDLINE | ID: covidwho-2232287

ABSTRACT

BACKGROUND: SARS-CoV-2 replicates efficiently in the upper airways of humans and produces high loads of virus RNA and, at least in the initial phase after infection, many infectious virus particles. Studying virus ultrastructure, such as particle integrity or presence of spike proteins, and effects on their host cells in patient samples is important to understand the pathogenicity of SARS-CoV-2. METHODS: Suspensions from swab samples with a high load of virus RNA (Ct < 20) were sedimented by desktop ultracentrifugation and prepared for thin section electron microscopy using a novel method which is described in detail. Embedding was performed in Epon or in LR White resin using standard or rapid protocols. Thin sections were examined using transmission electron microscopy. RESULTS: Virus particles could be regularly detected in the extracellular space, embedded in a background of heterogenous material (e.g. vesicles and needle-like crystals), and within ciliated cells. Morphology (i.e. shape, size, spike density) of virus particles in the swab samples was very similar to particle morphology in cell culture. However, in some of the samples the virus particles hardly revealed spikes. Infected ciliated cells occasionally showed replication organelles, such as double-membrane vesicles. The most common cells in all samples were keratinocytes from the mucosa and bacteria. CONCLUSIONS: The new method allows the ultrastructural visualization and analysis of coronavirus particles and of infected host cells from easy to collect naso/oropharyngeal patient swab samples.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Specimen Handling/methods , Microscopy, Electron, Transmission , RNA
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