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1.
Microbiol Spectr ; 10(1): e0245521, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-2193554

ABSTRACT

Containment measures employed during the COVID-19 pandemic included prompt recognition of cases, isolation, and contact tracing. Bilateral nasal (NA) swabs applied to a commercial antigen-based rapid diagnostic test (Ag-RDT) offer a simpler and more comfortable alternative to nasopharyngeal (NP) collection; however, little is known about the sensitivity of this method in an asymptomatic population. Participants in community-based asymptomatic testing sites were screened for SARS-CoV-2 using an Ag-RDT with NP sampling. Positive individuals returned for confirmatory molecular testing and consented to repeating the Ag-RDT using a bilateral NA swab for comparison. Residual test buffer (RTB) from Ag-RDTs was subjected to real-time reverse transcription-PCR (RT-PCR). Of 123,617 asymptomatic individuals, 197 NP Ag-RDT-positive participants were included, with 175 confirmed positive by RT-PCR. Of these cases, 154 were identified from the NA swab collection with Ag-RDT, with a sensitivity of 88.0% compared to the NP swab collection. Stratifying results by RT-PCR cycle threshold demonstrated that sensitivity of the nasal collection method varied based on the cycle threshold (CT) value of the paired RT-PCR sample. RT-PCR testing on the RTB from the Ag-RDT using NP and NA swab collections resulted in 100.0% and 98.7% sensitivity, respectively. NA swabs provide an adequate alternative to NP swab collection for use with Ag-RDT, with the recognition that the test is most sensitive in specimens with high viral loads. With the high sensitivity of RT-PCR testing on RTB from Ag-RDT, a more streamlined approach to confirmatory testing is possible without recollection or use of paired collections strategies. IMPORTANCE Nasal swabbing for SARS-CoV-2 (COVID-19) comes with many benefits but is slightly less sensitive than traditional nasopharyngeal swabbing; however, confirmatory lab-based testing could be performed directly from the residual buffer from either sample type.


Subject(s)
Antigens, Viral/analysis , COVID-19/virology , Carrier State/virology , Nasopharynx/virology , Nose/virology , SARS-CoV-2/isolation & purification , Specimen Handling/methods , Antigens, Viral/genetics , Antigens, Viral/immunology , Asymptomatic Diseases , COVID-19/diagnosis , COVID-19 Serological Testing , Humans , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity
2.
N Z Med J ; 135(1559): 53-58, 2022 Aug 05.
Article in English | MEDLINE | ID: covidwho-2147482

ABSTRACT

AIM: To compare detection of SARS-CoV-2 from paired nasopharyngeal swabs (NPS) and saliva using molecular methods in common use for testing swabs in New Zealand. METHOD: Samples from individuals testing positive for SARS-CoV-2 in Auckland, Wellington and Dunedin were tested at the local laboratories using methods previously established for these sample types. RESULTS: One hundred and ninety-six paired samples from unique individuals were tested, with 46 (23%) positive from either sample type, of which 43/46 (93%) tested positive from NPS, and 42/46 (91%) from saliva, indicating no significant difference in performance between sample types (p=0.69). The average Δ Ct between saliva and nasopharyngeal swabs overall across the sample set was 0.22 cycles, indicating excellent concordance; however, the difference between NPS and saliva collected from the same individual was quite variable with up to 19 cycles difference between the sample types. CONCLUSION: We found that saliva is an equivalent sample type to nasopharyngeal swab for the detection of SARS-CoV-2 in our laboratories using multiple assay combinations and is suitable for use as a diagnostic and surveillance test for selected groups of individuals.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , Clinical Laboratory Techniques/methods , Humans , Nasopharynx , New Zealand , SARS-CoV-2/genetics , Saliva , Specimen Handling/methods
3.
PLoS One ; 17(11): e0278061, 2022.
Article in English | MEDLINE | ID: covidwho-2140683

ABSTRACT

Contaminated surfaces are one of the ways that coronavirus disease 2019 (COVID-19) may be transmitted. SARS-CoV-2 can be detected on environmental surfaces; however, few environmental sampling studies have been conducted in nonclinical settings. The objective of this study was to detect SARS-CoV-2 RNA on environmental surfaces in public areas in Las Vegas, Nevada. In total, 300 surface samples were collected from high-touch surfaces from high-congregate public locations and from a public health facility (PHF) that was visited by COVID-19 patients. Environmental samples were analyzed with quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) using SARS-CoV-2 specific primers and probes for three target genes. Results showed that 31 out of 300 (10.3%) surface samples tested positive for SARS-CoV-2, 24 at the PHF and 7 in high-congregate public locations. Concentrations ranged from 102 to 106 viral particles per 3 ml sample on a wide variety of materials. The data also showed that the N gene assay had greater sensitivity compared to the S and ORF gene assays. Besides frequently touched surfaces, SARS-CoV-2 was detected in restrooms, on floors and surfaces in contact with floors, as well as in a mop water sample. The results of this study describe the extent and distribution of environmental SARS-CoV-2 contamination in public areas in Las Vegas, Nevada. A method using the N gene PCR assay was developed for SARS-CoV-2 environmental monitoring in public areas. Environmental monitoring with this method can determine the specific sites of surface contamination in the community and may be beneficial for prevention of COVID-19 indirect transmission, and evaluation and improvement of infection control practices in public areas, public health facilities, universities, and businesses.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , RNA, Viral/genetics , RNA, Viral/analysis , COVID-19/epidemiology , Specimen Handling , DNA Primers
4.
JMIR Public Health Surveill ; 7(1): e24220, 2021 01 14.
Article in English | MEDLINE | ID: covidwho-2141289

ABSTRACT

BACKGROUND: Real-time polymerase chain reaction using nasopharyngeal swabs is currently the most widely used diagnostic test for SARS-CoV-2 detection. However, false negatives and the sensitivity of this mode of testing have posed challenges in the accurate estimation of the prevalence of SARS-CoV-2 infection rates. OBJECTIVE: The purpose of this study was to evaluate whether technical and, therefore, correctable errors were being made with regard to nasopharyngeal swab procedures. METHODS: We searched a web-based video database (YouTube) for videos demonstrating SARS-CoV-2 nasopharyngeal swab tests, posted from January 1 to May 15, 2020. Videos were rated by 3 blinded rhinologists for accuracy of swab angle and depth. The overall score for swab angle and swab depth for each nasopharyngeal swab demonstration video was determined based on the majority score with agreement between at least 2 of the 3 reviewers. We then comparatively evaluated video data collected from YouTube videos demonstrating the correct nasopharyngeal swab technique with data from videos demonstrating an incorrect nasopharyngeal swab technique. Multiple linear regression analysis with statistical significance set at P=.05 was performed to determine video data variables associated with the correct nasopharyngeal swab technique. RESULTS: In all, 126 videos met the study inclusion and exclusion criteria. Of these, 52.3% (66/126) of all videos demonstrated the correct swab angle, and 46% (58/126) of the videos demonstrated an appropriate swab depth. Moreover, 45.2% (57/126) of the videos demonstrated both correct nasopharyngeal swab angle and appropriate depth, whereas 46.8% (59/126) of the videos demonstrated both incorrect nasopharyngeal swab angle and inappropriate depth. Videos with correct nasopharyngeal swab technique were associated with the swab operators identifying themselves as a medical professional or as an Ear, Nose, Throat-related medical professional. We also found an association between correct nasopharyngeal swab techniques and recency of video publication date (relative to May 15, 2020). CONCLUSIONS: Our findings show that over half of the videos documenting the nasopharyngeal swab test showed an incorrect technique, which could elevate false-negative test rates. Therefore, greater attention needs to be provided toward educating frontline health care workers who routinely perform nasopharyngeal swab procedures.


Subject(s)
COVID-19 Testing/methods , Nasopharynx/virology , SARS-CoV-2/isolation & purification , Social Media , Specimen Handling/methods , Video Recording , Diagnostic Errors/prevention & control , Humans , Real-Time Polymerase Chain Reaction
5.
J Nippon Med Sch ; 89(5): 500-505, 2022 Nov 09.
Article in English | MEDLINE | ID: covidwho-2117697

ABSTRACT

BACKGROUND: Nasopharyngeal swabs (NPS) are generally used as specimen samples for antigen qualitative tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The principle of the reaction to the antigen protein is the same when saliva is used, and saliva samples were reported to be as accurate as NPS for real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) testing to identify SARS-CoV-2. Unlike NPS collection, self-collected saliva does not expose healthcare workers to the risk of infection. In this study, we evaluated the feasibility of using saliva samples for a SARS-CoV-2 antigen qualitative test (TA2107SA) under development. METHODS: Saliva samples were collected from patients with confirmed or suspected COVID-19 infection and analyzed. The sensitivity, specificity, and concordance index of the antigen qualitative test were calculated using an RT-qPCR test as reference. RESULTS: Saliva samples were collected from 105 patients. The mean interval from onset to specimen collection was 5.7 days. The mean cycle threshold (Ct) value of RT-qPCR was 31.3. The sensitivity, specificity, and concordance index were 70.7%, 100%, and 0.85, respectively. In 33 patients with Ct values <30, the results of both the RT-qPCR and antigen tests were positive. The sensitivity of the saliva-based TA2107SA SARS-CoV-2 antigen qualitative test was slightly lower than that of the conventional antigen qualitative test using NPS samples from the same patient. CONCLUSION: Saliva-based antigen qualitative tests for SARS-CoV-2 are an alternative option during a pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , COVID-19/diagnosis , Saliva , Feasibility Studies , Pandemics , Specimen Handling , Sensitivity and Specificity
6.
PLoS One ; 17(11): e0277367, 2022.
Article in English | MEDLINE | ID: covidwho-2109332

ABSTRACT

The use of a non-invasive fluorescence in situ hybridization (FISH)-based method on saliva for the detection of SARS-CoV-2 is evaluated in a proof-of-concept study and thereafter utilized in an outpatient setting with the Biotrack-MED® analyzer. For a proof-of-concept study, saliva samples were obtained from 28 persons with mild or moderate COVID-19-related symptoms who were tested RT-PCR positive or negative for SARS-CoV-2. In an outpatient setting, 972 individual saliva samples were utilized. All saliva samples were FISHed with a Cy3-labeled SARS-CoV-2-specific DNA probe and were analyzed manually by fluorescence microscopy (proof-of-concept) or with the SARS-CoV-2 application of the Biotrack-MED® analyzer, a semi-autonomous multi-sample filter cytometer. The proof-of-concept study showed a sensitivity of 96.0% and a specificity of 98.5% and is therefore comparable to the RT-PCR analysis of nasopharyngeal swabs. The outpatient setting showed a sensitivity of 90.9% and a specificity of 94.5% and seems therefore a valid assay for the detection of SARS-CoV-2 in individuals that are healthy, mild or moderate symptomatic. In conclusion, the method evaluated in this study, the FISH-based SARS-CoV-2 application of the Biotrack-MED® analyzer, is a sensitive and reliable assay for the detection of SARS-CoV-2 in the general population.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Saliva/chemistry , COVID-19/diagnosis , In Situ Hybridization, Fluorescence , RNA, Viral/genetics , RNA, Viral/analysis , Nasopharynx , Specimen Handling/methods
7.
PLoS One ; 17(11): e0271860, 2022.
Article in English | MEDLINE | ID: covidwho-2109301

ABSTRACT

Detection of SARS-CoV-2 has created an enormous workload for laboratories worldwide resulting in a restriction at the time of massive testing. Pool testing is a strategy that reduces time and costs. However, beyond the detection of infectious diseases in blood banks, this approach is rarely implemented in routine laboratories. Therefore, what was learned from the SARS-CoV-2 pool testing should represent an opportunity to increase diagnostic capabilities. The present work, carried out in the context of a diagnostic laboratory of a public hospital during the COVID-19 pandemic, represents a contribution to this end. The main limitation of pool testing is the risk of false negatives that could have been identified by individual tests. These limitations are the dilution of samples with a low virus load during pooling and that the integrity of the sample may be affected by the quality of the sample collection. Fortunately, both limitations coincide with the main strengths of droplet digital PCR (ddPCR). ddPCR is a third-generation PCR that splits the amplification into thousands of droplets that work in parallel, increasing sensitivity and resistance to inhibitors. Therefore, ddPCR is particularly useful for pool testing. Here we show how to factor between test sensitivity and savings in test time and resources. We have identified and optimized critical parameters for pool testing. The present study, which analyzed 1000 nasopharyngeal samples, showed that the pool testing could detect even a single positive sample with a CT value of up to 30 in pools of 34 samples. This test was performed using three different standard extraction methods, the simplest being heating only, which resulted in substantial savings of extraction reagents in addition to PCR reagents. Moreover, we show that pooling can be extended to use saliva, which is less invasive and allows self-collection, reducing the risk for health personnel.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Pandemics , COVID-19/diagnosis , COVID-19 Testing , Specimen Handling/methods , Real-Time Polymerase Chain Reaction/methods , Sensitivity and Specificity
8.
Curr Microbiol ; 79(12): 396, 2022 Nov 09.
Article in English | MEDLINE | ID: covidwho-2103868

ABSTRACT

Shipment of COVID-19 specimens within the country or overseas at long distances requires cold chain facility using dry ice and triple packing to prevent the risk of COVID-19 infection to the personnel involved in sample transport. The present study aimed to utilize FTA card technology as an alternate means of sample transport and storage across the country. Twenty-one SARS-CoV-2 lab confirmed samples with different Ct value (High, medium & low) were used to detect viral load in samples loaded on FTA card and further compared with VTM samples. The SARS-CoV-2 RNA was detected by rRT-PCR after storing for 14 days at 4 °C and 37 °C. The present study evaluated the utility of FTA cards for preserving the SARS CoV-2 RNA for 14-day period. A significant difference (P < 0.05) was observed in the cycle threshold (ΔCt 4-5) values obtained from FTA and VTM viral samples but it did not affect the positivity. The SARS-CoV-2 RNA could be recovered efficiently from FTA sample stored at 4 °C and 37 °C for 14 days. Thus, FTA cards could be an alternate option for transporting the samples at ambient temperature for a long time.


Subject(s)
COVID-19 , Specimen Handling , Humans , RNA, Viral/genetics , SARS-CoV-2/genetics , COVID-19/diagnosis , Refrigeration
9.
Indian J Pathol Microbiol ; 65(4): 907-910, 2022.
Article in English | MEDLINE | ID: covidwho-2100023

ABSTRACT

Context: COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an emerging pandemic that is rapidly spreading with more than 114 million confirmed cases and 2.5 million deaths by far. Nasopharyngeal swab (NPS) in VTM has been used as the gold standard respiratory specimen for SARS-CoV-2 reverse-transcriptase real-time PCR (rRT-PCR) tests. But now the virus can also be detected in other clinical specimens like bronchoalveolar lavage, sputum, saliva, throat swab, blood, and stool specimens. Aims: The aim of this study was to determine the diagnostic potential of saliva as a sample in comparison to NPS for detection of SARS-CoV-2 by rRT-PCR. Settings and Design: A cross-sectional study was conducted among 256 paired samples (NPS and Saliva) received in the Department of Microbiology, SMS Medical College, Jaipur over a period of 2 months. Methods and Material: NPS from individuals were collected in a sterile tube containing Viral Transport Medium™. Before swab collection, whole saliva was collected by spitting from the suspected patient into a sterile container. Both were stored at room temperature and transferred to the diagnostic laboratory within four hours of collection where extraction was done using Perkin Elmer chemagic extractor and rRT- PCR was performed using NIV, Pune mastermix. Results: Sensitivity, specificity, PPV, and NPV of RT-PCR for the diagnosis of COVID-19 in saliva were 84.26%, 100%, 100%, and 54.05%, respectively. The accuracy of detection of COVID-19 by saliva samples compared to the routinely used NPS samples (considered as the standard reference) for RT PCR was 86.72%. Conclusions: Our results show that saliva as a reliable sample type for SARS-CoV-2 detection.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Reverse Transcriptase Polymerase Chain Reaction , COVID-19/diagnosis , Saliva , Cross-Sectional Studies , Nasopharynx , India , Specimen Handling/methods
13.
Sci Rep ; 12(1): 17080, 2022 Oct 12.
Article in English | MEDLINE | ID: covidwho-2062258

ABSTRACT

The coronavirus disease caused by the SARS-CoV-2 virus has affected people worldwide for more than two years. Here we present a new diagnostic method based on nonlinear dielectric spectroscopy to detect the presence of the SARS-CoV-2 virus in swab samples. A known current is injected into the virus sample suspension, and the biomarker is the third harmonic detected in the power spectrum of the recorded signal. Computational modeling of harmonic production supports the hypothesis of ion channels (the E-protein) with nonlinear current-voltage characteristics being present on the virus envelope as a possible origin of harmonics. The developed system is able to distinguish between positive and negative samples with 5-10 dBc (decibels relative to the carrier) higher third harmonic ratios in positive samples, in agreement with the computational estimation. Our early results demonstrate that this method can detect the virus in solution. This is the first time harmonic signatures are used to detect SARS-CoV-2 in swab samples.


Subject(s)
Biosensing Techniques , COVID-19 , COVID-19/diagnosis , Dielectric Spectroscopy , Humans , SARS-CoV-2 , Specimen Handling
14.
Viruses ; 14(9)2022 08 27.
Article in English | MEDLINE | ID: covidwho-2055387

ABSTRACT

Universal antiretroviral therapy (ART, "treat all") was recommended by the World Health Organization in 2015; however, HIV-1 transmission is still ongoing. This study characterizes the drivers of HIV transmission in the "treat all" era. Demographic and clinical information and HIV pol gene were collected from all newly diagnosed cases in Shenyang, the largest city in Northeast China, during 2016 to 2019. Molecular networks were constructed based on genetic distance and logistic regression analysis was used to assess potential transmission source characteristics. The cumulative ART coverage in Shenyang increased significantly from 77.0% (485/630) in 2016 to 93.0% (2598/2794) in 2019 (p < 0.001). Molecular networks showed that recent HIV infections linked to untreated individuals decreased from 61.6% in 2017 to 28.9% in 2019, while linking to individuals with viral suppression (VS) increased from 9.0% to 49.0% during the same time frame (p < 0.001). Undiagnosed people living with HIV (PLWH) hidden behind the links between index cases and individuals with VS were likely to be male, younger than 25 years of age, with Manchu nationality (p < 0.05). HIV transmission has declined significantly in the era of "treat all". Undiagnosed PLWH may drive HIV transmission and should be the target for early detection and intervention.


Subject(s)
HIV Infections , HIV-1 , China/epidemiology , Female , Genes, pol , HIV Infections/diagnosis , HIV Infections/drug therapy , HIV Infections/epidemiology , HIV-1/genetics , Humans , Male , Specimen Handling
15.
PLoS One ; 17(9): e0275201, 2022.
Article in English | MEDLINE | ID: covidwho-2054361

ABSTRACT

Molecular diagnostic testing has played a critical role in the global response to the novel Coronavirus disease (COVID-19) pandemic, since its first outbreak in late 2019. At the inception of the COVID-19 pandemic, nasopharyngeal swab sample analysis for COVID-19 diagnosis using the real-time polymerase chain reaction (RT-PCR) technique was the most widely used. However, due to the high cost and difficulty of sample collection, the number of available sample types for COVID-19 diagnosis is rapidly increasing, as is the COVID-19 diagnostic literature. The use of nasal swabs, saliva, and oral fluids as viable sample options for the effective detection of SARS-CoV-2 has been implemented successfully in different settings since 2020. These alternative sample type provides a plethora of advantages including decreasing the high exposure risk to frontline workers, enhancing the chances of home self-sampling, reducing the cost, and significantly increasing testing capacity. This study sought to ascertain the effectiveness of Saliva samples as an alternative for COVID-19 diagnosis in Nigeria. Demographic data, paired samples of Nasopharyngeal Swab and Drooling Saliva were obtained from 309 consenting individuals aged 8-83 years presenting for COVID-19 testing. All samples were simultaneously assayed for the detection of SARS-CoV-2 RdRp, N, and E genes using the GeneFinder™ COVID-19 Plus RT-PCR test kit. Out of 309 participants, only 299 with valid RT-PCR results comprising 159 (53.2%) males and 140 (46.8%) females were analyzed in this study using the R Statistical package. Among the 299 samples analyzed, 39 (13.0%) had SARS-CoV-2 detected in at least one specimen type. Both swabs and saliva were positive in 20 (51.3%) participants. Ten participants (25.6%) had swab positive/saliva-negative results and 9 participants (23.1%) had saliva positive/swab-negative results. The percentage of positive and negative agreement of the saliva samples with the nasopharyngeal swab were 67% and 97% respectively with positive and negative predictive values as 69% and 96% respectively. The findings indicate that drooling saliva samples have good and comparable diagnostic accuracy to the nasopharyngeal swabs with moderate sensitivities and high specificities.


Subject(s)
COVID-19 , Sialorrhea , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , Female , Humans , Male , Nasopharynx , Pandemics , RNA-Dependent RNA Polymerase , SARS-CoV-2/genetics , Saliva , Specimen Handling/methods
17.
JAMA ; 328(10): 935-940, 2022 09 13.
Article in English | MEDLINE | ID: covidwho-2047345

ABSTRACT

Importance: Despite the expansion of SARS-CoV-2 testing, available tests have not received Emergency Use Authorization for performance with self-collected anterior nares (nasal) swabs from children younger than 14 years because the effect of pediatric self-swabbing on SARS-CoV-2 test sensitivity is unknown. Objective: To characterize the ability of school-aged children to self-collect nasal swabs for SARS-CoV-2 testing compared with collection by health care workers. Design, Setting, and Participants: Cross-sectional study of 197 symptomatic children and adolescents aged 4 to 14 years old. Individuals were recruited based on results of testing in the Children's Healthcare of Atlanta system from July to August 2021. Exposures: Children and adolescents were given instructional material consisting of a short instructional video and a handout with written and visual steps for self-swab collection. Participants first provided a self-collected nasal swab. Health care workers then collected a second specimen. Main Outcomes and Measures: The primary outcome was SARS-CoV-2 detection and relative quantitation by cycle threshold (Ct) in self- vs health care worker-collected nasal swabs when tested with a real-time reverse transcriptase-polymerase chain reaction test with Emergency Use Authorization. Results: Among the study participants, 108 of 194 (55.7%) were male and the median age was 9 years (IQR, 6-11). Of the 196 participants, 87 (44.4%) tested positive for SARS-CoV-2 and 105 (53.6%) tested negative by both self- and health care worker-collected swabs. Two children tested positive by self- or health care worker-collected swab alone; 1 child had an invalid health care worker swab. Compared with health care worker-collected swabs, self-collected swabs had 97.8% (95% CI, 94.7%-100.0%) and 98.1% (95% CI, 95.6%-100.0%) positive and negative percent agreement, respectively, and SARS-CoV-2 Ct values did not differ significantly between groups (mean [SD] Ct, self-swab: 26.7 [5.4] vs health care worker swab: 26.3 [6.0]; P = .65). Conclusions and Relevance: After hearing and seeing simple instructional materials, children and adolescents aged 4 to 14 years self-collected nasal swabs that closely agreed on SARS-CoV-2 detection with swabs collected by health care workers.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , COVID-19/diagnosis , COVID-19 Testing , Child , Child, Preschool , Cross-Sectional Studies , Female , Health Personnel , Humans , Male , Specimen Handling/methods
18.
Int J Mol Sci ; 23(18)2022 Sep 14.
Article in English | MEDLINE | ID: covidwho-2039870

ABSTRACT

Body fluid identification at crime scenes can be crucial in retrieving the appropriate evidence that leads to the perpetrator and, in some cases, the victim. For this purpose, immunochromatographic tests are simple, fast and suitable for crime scenes. The potential sample is retrieved with a swab, normally a cotton swab, moistened in a specific buffer. Nonetheless, there are other swab types available, which have been proven to be efficient for DNA isolation and analysis. The aim of this study is to evaluate the efficiency of different swab types for body fluid identification as well as DNA isolation and characterization. Fifty microliters of human saliva were deposited in three different types of fabric (denim, cotton, and polyester). After 24 h at room temperature, samples were recovered by applying three different swab types, and the tests were performed. Subsequently, total DNA was recovered from the sample buffer. Cotton swabs performed worse in denim and cotton fabrics in both immunochromatography tests and DNA yield. No differences were observed for polyester. In contrast, and except for two replicates, it was possible to obtain a full DNA profile per fabric and swab type, and to identify the mtDNA haplogroup. In this paper, the impact of swab types on body fluid identification through the application of immunochromatographic tests is analyzed for the first time. This work corroborates previous research related to the influence of swab types in nuclear DNA isolation and characterization.


Subject(s)
DNA Fingerprinting , Specimen Handling , DNA Fingerprinting/methods , DNA, Mitochondrial/analysis , Humans , Polyesters , Saliva/chemistry , Specimen Handling/methods
19.
Microbiol Spectr ; 10(5): e0142222, 2022 Oct 26.
Article in English | MEDLINE | ID: covidwho-2038249

ABSTRACT

We examined the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcription-PCR (RT-PCR) of side-by-side saliva and oropharyngeal swab (OPS) samples from 639 symptomatic and asymptomatic subjects, of which 47 subjects were found to be positive for SARS-CoV-2 in the OPS or saliva sample or both. It was found that the detection rate (93.6% for both OPS and saliva) as well as the sensitivity and specificity were comparable between the two sampling methods in this cohort. The sensitivity was 0.932 (95% confidence interval [CI], 0.818 to 0.977) and the specificity was 0.995 (95% CI, 0.985 to 0.998), both for saliva when OPS sampling was used as the reference and for OPS when saliva was used as the reference. Furthermore, the Cohen's kappa value was 0.926 (95% CI, 0.868 to 0.985), indicating strong agreement between the two sampling methods. In addition, the viral RNA stability in pure saliva and saliva mixed with preservation buffers was examined following storage at room temperature and at 4°C. It was found that pure saliva kept the viral RNA stable for 9 days at both temperatures and that the type of preservation buffer can either enhance or reduce the stability of the RNA. We conclude that self-administered saliva sampling is an attractive alternative to oropharyngeal swabbing for SARS-CoV-2 detection, and it might be useful in large-scale testing. IMPORTANCE It is not inconceivable that we will witness recurring surges of COVID-19 before the pandemic finally recedes. It is therefore still relevant to look for feasible, simple, and flexible screening methods so that schools, workplaces, and communities in general can avoid lockdowns. In this work, we analyzed two different sampling methods: oropharyngeal swabs and saliva collection. Oropharyngeal swabs must be collected by trained health personnel at clinics, whereas self-assisted saliva collection can be performed at any given location. It was found that the two sampling methods were comparable. Saliva sampling is a simple method that allows easy mass testing using minimal resources from the existing health care system, and this method may therefore prove to be an effective tool for containing the COVID-19 pandemic.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Pandemics , COVID-19/diagnosis , COVID-19 Testing , Saliva , RNA, Viral , Communicable Disease Control , Specimen Handling/methods
20.
APMIS ; 130(11): 671-677, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2032363

ABSTRACT

The present study was conducted to compare the performance of patient self-collected oral swab (OS) with healthcare worker (HCW)-collected nasopharyngeal swab (NPS) for SARS-CoV-2 detection by reverse transcription polymerase chain reaction (RT-PCR) in real-world setting. Paired OS and NPS were collected from 485 consecutive individuals presenting with symptoms of coronavirus disease-19 (COVID-19) or asymptomatic contacts of COVID-19 cases. Both specimens were processed for RT-PCR and cycle threshold (Ct) value for each test was obtained. Positive percent agreement (PPA), negative percent agreement (NPA), overall percent agreement (OPA) and kappa were calculated for OS RT-PCR compared with NPS RT-PCR as reference. A total of 116/485 (23.9%) participants were positive by NPS RT-PCR. OS had PPA of 71.6%, NPA of 98.8%, OPA of 92.4% and kappa of 0.771. Almost all participants (483/485, 99.6%) reported OS as a convenient and comfortable sample for SARS-CoV-2 testing over NPS. All participants with Ct values <25 and majority (90.8%) with Ct values <30 were detected by OS. To conclude, OS self-sampling was preferred in comparison with NPS due the ease and comfort during collection. The performance of OS RT-PCR for SARS-CoV-2 detection, however, was sub-optimal in comparison with NPS RT-PCR.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Testing , Cheek , Health Personnel , Humans , Nasopharynx , SARS-CoV-2/genetics , Specimen Handling , Tongue
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