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1.
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
2.
JMIR Public Health Surveill ; 7(9): e31930, 2021 09 17.
Article in English | MEDLINE | ID: covidwho-2141353

ABSTRACT

This report aimed to provide an overview of the epidemiological situation of COVID-19 in Morocco and to review the actions carried out as part of the national response to this pandemic. The methodology adopted was based on literature review, interviews with officials and actors in the field, and remote discussion workshops with a multidisciplinary and multisectoral working group. Morocco took advantage of the capacities already strengthened within the framework of the application of the provisions of the International Health Regulations (IHR) of 2005. A SWOT analysis made it possible to note that an unprecedented political commitment enabled all the necessary means to face the pandemic and carry out all the response activities, including a campaign of relentless communication. Nevertheless, and despite the efforts made, the shortage of human resources, especially those qualified in intensive care and resuscitation, has been the main drawback to be addressed. The main lesson learned is a need to further strengthen national capacities to prepare for and respond to possible public health emergencies and to embark on a process overhaul of the health system, including research into innovative tools to ensure the continuity of the various disease prevention and control activities. In addition, response to a health crisis is not only the responsibility of the health sector but also intersectoral collaboration is needed to guarantee an optimal coordinated fight. Community-oriented approaches in public health have to be strengthened through more participation and involvement of nongovernmental organizations (NGOs) and civil society in operational and strategic planning.


Subject(s)
COVID-19/prevention & control , Public Health/methods , COVID-19/epidemiology , COVID-19 Testing/methods , COVID-19 Testing/standards , Humans , Morocco/epidemiology , Public Health/statistics & numerical data , Quarantine/psychology , Quarantine/standards , Workforce/standards
3.
Nature ; 611(7936): 570-577, 2022 11.
Article in English | MEDLINE | ID: covidwho-2106425

ABSTRACT

Expanding our global testing capacity is critical to preventing and containing pandemics1-9. Accordingly, accessible and adaptable automated platforms that in decentralized settings perform nucleic acid amplification tests resource-efficiently are required10-14. Pooled testing can be extremely efficient if the pooling strategy is based on local viral prevalence15-20; however, it requires automation, small sample volume handling and feedback not available in current bulky, capital-intensive liquid handling technologies21-29. Here we use a swarm of millimetre-sized magnets as mobile robotic agents ('ferrobots') for precise and robust handling of magnetized sample droplets and high-fidelity delivery of flexible workflows based on nucleic acid amplification tests to overcome these limitations. Within a palm-sized printed circuit board-based programmable platform, we demonstrated the myriad of laboratory-equivalent operations involved in pooled testing. These operations were guided by an introduced square matrix pooled testing algorithm to identify the samples from infected patients, while maximizing the testing efficiency. We applied this automated technology for the loop-mediated isothermal amplification and detection of the SARS-CoV-2 virus in clinical samples, in which the test results completely matched those obtained off-chip. This technology is easily manufacturable and distributable, and its adoption for viral testing could lead to a 10-300-fold reduction in reagent costs (depending on the viral prevalence) and three orders of magnitude reduction in instrumentation cost. Therefore, it is a promising solution to expand our testing capacity for pandemic preparedness and to reimagine the automated clinical laboratory of the future.


Subject(s)
Automation , COVID-19 Testing , Magnets , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , Robotics , SARS-CoV-2 , Humans , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing/methods , Molecular Diagnostic Techniques/economics , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/economics , Nucleic Acid Amplification Techniques/methods , Pandemics/prevention & control , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Algorithms , Automation/economics , Automation/methods , Robotics/methods , Indicators and Reagents/economics
11.
Environ Microbiol ; 24(10): 4725-4737, 2022 10.
Article in English | MEDLINE | ID: covidwho-2001574

ABSTRACT

SARS-CoV-2 diagnosis is a cornerstone for the management of coronavirus disease 2019 (COVID-19). Numerous studies have assessed saliva performance over nasopharyngeal sampling (NPS), but data in young children are still rare. We explored saliva performance for SARS-CoV-2 detection by RT-PCR according to the time interval from initial symptoms or patient serological status. We collected 509 NPS and saliva paired samples at initial diagnosis from 166 children under 12 years of age (including 57 children under 6), 106 between 12 and 17, and 237 adults. In children under 12, overall detection rate for SARS-CoV-2 was comparable in saliva and NPS, with an overall agreement of 89.8%. Saliva sensitivity was significantly lower than that of NPS (77.1% compared to 95.8%) in pre-school and school-age children but regained 96% when considering seronegative children only. This pattern was also observed to a lesser degree in adolescents but not in adults. Sensitivity of saliva was independent of symptoms, in contrary to NPS, whose sensitivity decreased significantly in asymptomatic subjects. Performance of saliva is excellent in children under 12 at early stages of infection. This reinforces saliva as a collection method for early and unbiased SARS-CoV-2 detection and a less invasive alternative for young children.


Subject(s)
COVID-19 Testing , COVID-19 , SARS-CoV-2 , Saliva , Adolescent , Adult , Child , Child, Preschool , Humans , Clinical Laboratory Techniques/methods , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing/methods , Nasopharynx/virology , Saliva/virology , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification
12.
BMC Infect Dis ; 22(1): 697, 2022 Aug 18.
Article in English | MEDLINE | ID: covidwho-1993335

ABSTRACT

BACKGROUND: High cost of commercial RNA extraction kits limits the testing efficiency of SARS-CoV-2. Here, we developed a simple nucleic acid extraction method for the detection of SARS-CoV-2 directly from nasopharyngeal swab samples. METHODS: A pH sensitive dye was used as the end point detection method. The obvious colour changes between positive and negative reactions eliminates the need of other equipment. RESULTS: Clinical testing using 260 samples showed 92.7% sensitivity (95% CI 87.3-96.3%) and 93.6% specificity (95% CI 87.3-97.4%) of RT-LAMP. CONCLUSIONS: The simple RNA extraction method minimizes the need for any extensive laboratory set-up. We suggest combining this simple nucleic acid extraction method and RT-LAMP technology as the point-of care diagnostic tool.


Subject(s)
COVID-19 Testing , COVID-19 , Molecular Diagnostic Techniques , Nucleic Acid Amplification Techniques , SARS-CoV-2 , COVID-19/diagnosis , COVID-19/virology , COVID-19 Testing/methods , Humans , Molecular Diagnostic Techniques/methods , Nasopharynx/virology , Nucleic Acid Amplification Techniques/methods , Point-of-Care Systems , RNA, Viral/analysis , RNA, Viral/genetics , RNA, Viral/isolation & purification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
13.
BMC Public Health ; 22(1): 1220, 2022 06 20.
Article in English | MEDLINE | ID: covidwho-1962795

ABSTRACT

BACKGROUND: COVID-19 self-testing (ST) is an innovative strategy with the potential to increase the access and uptake of testing and ultimately to limit the spread of the virus. To maximize the uptake and reach of this promising strategy and inform intervention development and scale up, research is needed to understand the acceptability of and willingness to use this tool. This is vital to ensure that Black/African Americans are reached by the Biden-Harris Administration's free national COVID-19 ST program. This study aimed to explore the acceptability and recommendations to promote and scale-up the uptake of COVID-19 ST among Black/African Americans. METHODS: We conducted a cross-sectional qualitative study using a semi-structured questionnaire to assess barriers and facilitators to the uptake of COVID-19 ST among a convenience sample of 28 self-identified Black/African Americans from schools, community centers, and faith-based institutions in Ohio and Maryland. Inductive content analysis was conducted to identify categories and subcategories related to acceptability and recommendations for implementing and scaling up COVID-19 ST in communities. RESULTS: Participants perceived COVID-19 self-testing as an acceptable tool that is beneficial to prevent transmission and address some of the barriers associated with health facility testing, such as transportation cost and human contact at the health facility. However, concerns were raised regarding the accurate use of the kits and costs. Recommendations for implementing and scaling up COVID-19 ST included engagement of community stakeholders to disseminate information about COVID-19 self-testing and creating culturally appropriate education tools to promote knowledge of and clear instructions about how to properly use COVID-19 ST kits. Based on these recommendations, the COVID-19 STEP (Self-Testing Education and Promotion) Project is being developed and will involve engaging community partners such as barbers, church leaders, and other community-based organizations to increase the uptake and use of free COVID-19 ST kits among Black/African Americans. CONCLUSION: Findings showed that most participants considered COVID-19 ST valuable for encouraging COVID-19 testing. However, cost and accuracy concerns may pose barriers. Future work should consider implementing interventions that leverage the benefits of COVID-19 ST and further assess the extent to which these identified facilitators and barriers may influence COVID-19 ST uptake.


Subject(s)
African Americans , COVID-19 Testing , Self-Testing , African Americans/psychology , COVID-19/diagnosis , COVID-19/ethnology , COVID-19 Testing/methods , Cross-Sectional Studies , Humans
14.
Sci Rep ; 12(1): 12612, 2022 07 23.
Article in English | MEDLINE | ID: covidwho-1956424

ABSTRACT

Saliva has been demonstrated as feasible alternative to naso-oropharyngeal swab (NOS) for SARS-CoV-2 detection through reverse transcription quantitative/real-time polymerase chain reaction (RT-qPCR). This study compared the diagnostic agreement of conventional NOS, saliva with RNA extraction (SE) and saliva without RNA extraction (SalivaDirect) processing for RT-qPCR in identifying SARS-CoV-2. All techniques were also compared, as separate index tests, to a composite reference standard (CRS) where positive and negative results were defined as SARS-CoV-2 detection in either one or no sample, respectively. Of 517 paired samples, SARS-CoV-2 was detected in 150 (29.01%) NOS and 151 (29.21%) saliva specimens. The saliva-based tests were noted to have a sensitivity, specificity and accuracy (95% confidence interval) of 92.67% (87.26%, 96.28%), 97.55% (95.40%, 98.87%) and 96.13% (94.09%, 97.62%), respectively, for SE RT-qPCR and 91.33% (85.64%, 95.30%), 98.91% (97.23%, 99.70%) and 96.71% (94.79%, 98.07%), respectively, for SalivaDirect RT-qPCR compared to NOS RT-qPCR. Compared to CRS, all platforms demonstrated statistically similar diagnostic performance. These findings suggest that both conventional and streamlined saliva RT-qPCR are at least non-inferior to conventional NOS RT-qPCR in detecting SARS-CoV-2.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Nasopharynx/virology , RNA, Viral/analysis , SARS-CoV-2/isolation & purification , Saliva/virology , Clinical Laboratory Techniques/methods , Cross-Sectional Studies , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Saliva/chemistry , Sensitivity and Specificity , Specimen Handling/methods
15.
PLoS One ; 17(3): e0264929, 2022.
Article in English | MEDLINE | ID: covidwho-1938420

ABSTRACT

BACKGROUND: People experiencing homelessness who live in congregate shelters are at high risk of SARS-CoV2 transmission and severe COVID-19. Current screening and response protocols using rRT-PCR in homeless shelters are expensive, require specialized staff and have delays in returning results and implementing responses. METHODS: We piloted a program to offer frequent, rapid antigen-based tests (BinaxNOW) to residents and staff of congregate-living shelters in San Francisco, California, from January 15th to February 19th, 2021. We used the Reach-Effectiveness-Adoption-Implementation-Maintenance (RE-AIM) framework to evaluate the implementation. RESULTS: Reach: We offered testing at ten of twelve eligible shelters. Shelter residents and staff had variable participation across shelters; approximately half of eligible individuals tested at least once; few tested consistently during the study. Effectiveness: 2.2% of participants tested positive. We identified three outbreaks, but none exceeded 5 cases. All BinaxNOW-positive participants were isolated or left the shelters. Adoption: We offered testing to all eligible participants within weeks of the project's initiation. Implementation: Adaptations made to increase reach and improve consistency were promptly implemented. Maintenance: San Francisco Department of Public Health expanded and maintained testing with minimal support after the end of the pilot. CONCLUSION: Rapid and frequent antigen testing for SARS-CoV2 in homeless shelters is a viable alternative to rRT-PCR testing that can lead to immediate isolation of infectious individuals. Using the RE-AIM framework, we evaluated and adapted interventions to enable the expansion and maintenance of protocols.


Subject(s)
COVID-19 Serological Testing/methods , COVID-19/diagnosis , Homeless Persons/statistics & numerical data , COVID-19/immunology , COVID-19 Testing/methods , California , Disease Outbreaks/prevention & control , Housing , Humans , Immunologic Tests/methods , Mass Screening/methods , Pilot Projects , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , San Francisco
17.
PLoS One ; 17(2): e0264159, 2022.
Article in English | MEDLINE | ID: covidwho-1910540

ABSTRACT

BACKGROUND: Although serologic tests for COVID-19 diagnosis are rarely indicated nowadays, they remain commercially available and widely used in Brazil. The objective of this study was to evaluate the cost-effectiveness of anti-SARS-CoV-2antibody diagnostic tests for COVID-19 in Brazil. METHODS: Eleven commercially available diagnostic tests, comprising five lateral-flow immunochromatographic assays (LFAs) and six immunoenzymatic assays (ELISA) were analyzed from the perspective of the Brazilian Unified Health System. RESULTS: The direct costs of LFAs ranged from US$ 11.42 to US$ 17.41and of ELISAs, from US$ 6.59 to US$ 10.31. Considering an estimated disease prevalence between 5% and 10%, the anti-SARS-CoV-2 ELISA (IgG) was the most cost-effective test, followed by the rapid One Step COVID-19 Test, at an incremental cost-effectiveness ratio of US$ 2.52 and US$ 1.26 per properly diagnosed case, respectively. Considering only the LFAs, at the same prevalence estimates, two tests, the COVID-19 IgG/IgM and the One Step COVID-19 Test, showed high effectiveness at similar costs. For situations where the estimated probability of disease is 50%, the LFAs are more costly and less effective alternatives. CONCLUSIONS: Nowadays there are few indications for the use of serologic tests in the diagnosis of COVID-19 and numerous commercially available tests, with marked differences are observed among them. In general, LFA tests are more cost-effective for estimated low-COVID-19-prevalences, while ELISAs are more cost-effective for high-pretest-probability scenarios.


Subject(s)
Antibodies, Viral/isolation & purification , COVID-19 Testing/economics , COVID-19/diagnosis , Brazil , COVID-19/virology , COVID-19 Testing/methods , Cost-Benefit Analysis , Humans , Sensitivity and Specificity
18.
J Appl Lab Med ; 7(5): 1175-1188, 2022 09 01.
Article in English | MEDLINE | ID: covidwho-1901194

ABSTRACT

BACKGROUND: COVID-19 is a highly contagious respiratory disease that can be transmitted through human exhaled breath. It has caused immense loss and has challenged the healthcare sector. It has affected the economy of countries and thereby affected numerous sectors. Analysis of human breath samples is an attractive strategy for rapid diagnosis of COVID-19 by monitoring breath biomarkers. CONTENT: Breath collection is a noninvasive process. Various technologies are employed for detection of breath biomarkers like mass spectrometry, biosensors, artificial learning, and machine learning. These tools have low turnaround time, robustness, and provide onsite results. Also, MS-based approaches are promising tools with high speed, specificity, sensitivity, reproducibility, and broader coverage, as well as its coupling with various chromatographic separation techniques providing better clinical and biochemical understanding of COVID-19 using breath samples. SUMMARY: Herein, we have tried to review the MS-based approaches as well as other techniques used for the analysis of breath samples for COVID-19 diagnosis. We have also highlighted the different breath analyzers being developed for COVID-19 detection.


Subject(s)
Breath Tests , COVID-19 Testing , COVID-19 , Biomarkers/analysis , COVID-19/diagnosis , COVID-19 Testing/methods , Humans , Reproducibility of Results
20.
J Korean Med Sci ; 37(21): e168, 2022 May 30.
Article in English | MEDLINE | ID: covidwho-1875391

ABSTRACT

Despite the accuracy of nucleic acid amplification tests (NAATs), rapid antigen tests (RATs) for severe acute respiratory syndrome coronavirus-2 are widely used as point-of-care tests. A total of 282 pairs of reverse transcription-polymerase chain reaction and Standard Q COVID-19 Ag tests were serially conducted for 68 patients every 3-4 days until their discharge. Through a field evaluation of RATs using direct nasopharyngeal swabs, the sensitivities were 84.6% and 87.3% for E and RNA-dependent RNA polymerase (RdRp) genes, respectively, for specimens with cycle thresholds (Cts) < 25. The Ct values of E and RdRp genes for 95% detection rates by RATs were 16.9 and 18.1, respectively. The sensitivity of RAT was 48.4% after the onset of symptoms, which was not sufficient. RAT positivity gradually decreased with increased time after symptom onset and had continuously lower sensitivity than NAATs.


Subject(s)
COVID-19 Testing , COVID-19 , SARS-CoV-2 , Antigens, Viral , COVID-19/diagnosis , COVID-19 Testing/methods , Humans , Nasopharynx , RNA-Dependent RNA Polymerase , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
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