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1.
mSphere ; 5(3)2020 06 24.
Article in English | MEDLINE | ID: covidwho-2193484

ABSTRACT

The contamination of patients' surroundings by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains understudied. We sampled the surroundings and the air of six negative-pressure non-intensive care unit (non-ICU) rooms in a designated isolation ward in Chengdu, China, that were occupied by 13 laboratory-confirmed coronavirus disease 2019 (COVID-19) patients who had returned from overseas travel, including 2 asymptomatic patients. A total of 44 of 112 (39.3%) surface samples were positive for SARS-CoV-2 as detected by real-time PCR, suggesting extensive contamination, although all of the air samples were negative. In particular, in a single room occupied by an asymptomatic patient, four sites were SARS-CoV-2 positive, highlighting that asymptomatic COVID-19 patients do contaminate their surroundings and impose risks for others with close contact. Placement of COVID-19 patients in rooms with negative pressure may bring a false feeling of safety, and the importance of rigorous environment cleaning should be emphasized.IMPORTANCE Although it has been well recognized that the virus SARS-CoV-2, the causative agent of COVID-19, can be acquired by exposure to fomites, surprisingly, the contamination of patients' surroundings by SARS-CoV-2 is largely unknown, as there have been few studies. We performed an environmental sampling study for 13 laboratory-confirmed COVID-19 patients and found extensive contamination of patients' surroundings. In particular, we found that asymptomatic COVID-19 patients contaminated their surroundings and therefore imposed risks for other people. Environment cleaning should be emphasized in negative-pressure rooms. The findings may be useful to guide infection control practice to protect health care workers.


Subject(s)
Asymptomatic Infections/epidemiology , Betacoronavirus/isolation & purification , Coronavirus Infections/epidemiology , Environmental Exposure , Environmental Microbiology , Pneumonia, Viral/epidemiology , COVID-19 , Containment of Biohazards/methods , Coronavirus Infections/pathology , Environment , Humans , Pandemics , Pneumonia, Viral/pathology , SARS-CoV-2
2.
J Med Virol ; 93(8): 4748-4755, 2021 08.
Article in English | MEDLINE | ID: covidwho-1610624

ABSTRACT

Respiratory infections are one of the most frequent reasons for medical consultations in children. In low resource settings such as in Lao People's Democratic Republic, knowledge gaps and the dearth of laboratory capacity to support differential diagnosis may contribute to antibiotic overuse. We studied the etiology, temporal trends, and genetic diversity of viral respiratory infections in children to provide evidence for prevention and treatment guidelines. From September 2014 to October 2015, throat swabs and nasopharyngeal aspirates from 445 children under 10 years old with symptoms of acute respiratory infection were collected at the Children Hospital in Vientiane. Rapid antigen tests were performed for influenza A and B and respiratory syncytial virus. Real-time reverse-transcription polymerase chain reactions (RT-PCRs) were performed to detect 16 viruses. Influenza infections were detected with a higher sensitivity using PCR than with the rapid antigen test. By RT-PCR screening, at least one pathogen could be identified for 71.7% of cases. Human rhinoviruses were most frequently detected (29.9%), followed by influenza A and B viruses combined (15.9%). We identify and discuss the seasonality of some of the infections. Altogether these data provide a detailed characterization of respiratory pathogens in Lao children and we provide recommendations for vaccination and further studies.


Subject(s)
Coinfection/epidemiology , Respiratory Tract Infections/epidemiology , Virus Diseases/epidemiology , Viruses/genetics , Acute Disease/epidemiology , Child , Child, Preschool , Coinfection/virology , Female , Humans , Infant , Infant, Newborn , Influenza, Human/diagnosis , Influenza, Human/epidemiology , Influenza, Human/virology , Laos/epidemiology , Male , Prevalence , Respiratory Syncytial Virus Infections/diagnosis , Respiratory Syncytial Virus Infections/epidemiology , Respiratory Syncytial Virus Infections/virology , Respiratory Tract Infections/virology , Viruses/classification , Viruses/isolation & purification
3.
Clin Infect Dis ; 73(11): e3884-e3899, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1561131

ABSTRACT

BACKGROUND: We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset. METHODS: We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool. RESULTS: We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for >14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens. CONCLUSIONS: Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential.


Subject(s)
COVID-19 , Humans , Prospective Studies , RNA, Viral , Reproducibility of Results , SARS-CoV-2 , Serologic Tests
4.
Pan Afr Med J ; 38: 55, 2021.
Article in French | MEDLINE | ID: covidwho-1547713

ABSTRACT

The first outbreak of epidemic respiratory disease due to unknown etiology was reported in the Chinese city of Wuhan December 2019. The World Health Organization (WHO) firstly used the term "new coronavirus 2019" on December 29, 2019. This pandemic, which is currently called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a disease caused by SARS-CoV-2. It was subsequently called coronavirus disease 2019 (COVID-19) by the WHO. The purpose of this study was to determine the prevalence of antibodies against SARS-CoV-2 in all employees of the Nouakchott National Hospital Center (CHN). The study was conducted during the week 20/05/2020 to 27/05/2020. It involved 853 employees of all ranks (doctors, pharmacists, nurses, secretaries, security personnel, administrators...) of whom 504 were male and 331 were female, with a sex ratio of 1,52 with an average age of 39 years, ranging from 20 to 60 years. The screening for IgG and IgM antibodies to SARS-CoV-2 was performed using Biotime (Xiamen Biotime Biotechnology Co., Ltd.) immunochromatographic technique. Out of 835 employees included in our study, 14 were positive (1.67%) of whom 12 had IgM and IgG anti-SARS-CoV-2 antibodies and 2 had isolated IgM. Nasopharyngeal swab polymerase chain reaction (PCR) was performed in these 14 patients and was positive in six. While PCR is the gold standard for the diagnosis of SARS-CoV-2, serological tests for SARS-CoV-2 antibodies, in particular rapid tests (RDTs) are a diagnostic complement to COVID-19. They have the advantage of being easy to realize, of being safe both in the laboratories and outside the laboratories. RDTs enabled us to detect asymptomatic SARS-CoV-2 carriers within CHN employees. This allowed for patients management and isolation to protect patients and their environments.


Subject(s)
COVID-19 Testing , COVID-19/diagnosis , Health Personnel , SARS-CoV-2/isolation & purification , Adult , Antibodies, Viral/blood , COVID-19/epidemiology , Female , Humans , Immunoglobulin G/immunology , Immunoglobulin M/immunology , Male , Mauritania/epidemiology , Middle Aged , Serologic Tests/methods , Young Adult
5.
Clin Infect Dis ; 73(7): e1870-e1877, 2021 10 05.
Article in English | MEDLINE | ID: covidwho-1455249

ABSTRACT

BACKGROUND: We evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface and air contamination during the coronavirus disease 2019 (COVID-19) pandemic in London. METHODS: Prospective, cross-sectional, observational study in a multisite London hospital. Air and surface samples were collected from 7 clinical areas occupied by patients with COVID-19 and a public area of the hospital. Three or four 1.0-m3 air samples were collected in each area using an active air sampler. Surface samples were collected by swabbing items in the immediate vicinity of each air sample. SARS-CoV-2 was detected using reverse-transcription quantitative polymerase chain reaction (PCR) and viral culture; the limit of detection for culturing SARS-CoV-2 from surfaces was determined. RESULTS: Viral RNA was detected on 114 of 218 (52.3%) surfaces and in 14 of 31 (38.7%) air samples, but no virus was cultured. Viral RNA was more likely to be found in areas immediately occupied by COVID-19 patients than in other areas (67 of 105 [63.8%] vs 29 of 64 [45.3%]; odds ratio, 0.5; 95% confidence interval, 0.2-0.9; P = .025, χ2 test). The high PCR cycle threshold value for all samples (>30) indicated that the virus would not be culturable. CONCLUSIONS: Our findings of extensive viral RNA contamination of surfaces and air across a range of acute healthcare settings in the absence of cultured virus underlines the potential risk from environmental contamination in managing COVID-19 and the need for effective use of personal protective equipment, physical distancing, and hand/surface hygiene.


Subject(s)
COVID-19 , SARS-CoV-2 , Cross-Sectional Studies , Delivery of Health Care , Humans , London/epidemiology , Pandemics , Prospective Studies
6.
Environ Sci Technol ; 55(7): 4174-4182, 2021 04 06.
Article in English | MEDLINE | ID: covidwho-1392752

ABSTRACT

Control technologies to inactivate airborne viruses effectively are needed during the ongoing SARS-CoV-2 pandemic, and to guard against airborne transmitted diseases. We demonstrate that sealed UV-C flow reactors operating with fluences near 253 ± 1 nm of 13.9-49.6 mJ cm-2 efficiently inactivate coronaviruses in an aerosol. For measurements, porcine respiratory coronavirus (PRCV) was nebulized in a custom-built, 3.86 m wind tunnel housed in a biosafety level class II facility. The single pass log10 reduction of active coronavirus was in excess of 2.2 at a flow rate of 2439 L min-1 (13.9 mJ cm-2) and in excess of 3.7 (99.98% removal efficiency) at 684 L min-1 (49.6 mJ cm-2). Because virus titers resulting from sampling downstream of the UV-C reactor were below the limit of detection, the true log reduction is likely even higher than measured. Comparison of virus titration results to reverse transcriptase quantitative PCR and measurement of fluorescein concentrations (doped into the nebulized aerosol) reveals that the reduction in viable PRCV is primarily due to UV-C based inactivation, as opposed to physical collection of virus. The results confirm that UV-C flow reactors can efficiently inactivate coronaviruses through incorporation into HVAC ducts or recirculating air purifiers.


Subject(s)
COVID-19 , Coronavirus , Aerosols , Humans , SARS-CoV-2 , Ultraviolet Rays
8.
Chemistry ; 26(52): 11950-11954, 2020 Sep 16.
Article in English | MEDLINE | ID: covidwho-1384141

ABSTRACT

Thymidine triphosphate bearing benzylidene-tetrahydroxanthylium near-IR fluorophore linked to the 5-methyl group via triazole was synthesized through the CuAAC reaction and was used for polymerase synthesis of labelled DNA probes. The fluorophore lights up upon incorporation to DNA (up to 348-times) presumably due to interactions in major groove and the fluorescence further increases in the single-stranded oligonucleotide. The labelled dsDNA senses binding of small molecules and proteins by a strong decrease of fluorescence. The nucleotide was used as a light-up building block in real-time PCR for detection of SARS-CoV-2 virus.


Subject(s)
COVID-19 , DNA Replication , DNA Probes , Humans , Nucleotides , SARS-CoV-2
9.
Clin Chem ; 66(10): 1349-1350, 2020 10 01.
Article in English | MEDLINE | ID: covidwho-1383204

Subject(s)
COVID-19 , Humans , SARS-CoV-2
10.
J Med Virol ; 2020 Jun 30.
Article in English | MEDLINE | ID: covidwho-1381917

ABSTRACT

Palatine tonsils have been observed to harbor several distinct respiratory and herpesviruses in separate studies. In this study, the presence of these viruses in palatine tonsils was comprehensively studied in both children and adults. A cross-sectional analysis of 181 patients (median age 22 years; range, 2.6-66) operated for a benign tonsillar disease was conducted. Real-time polymerase chain reaction was performed to detect 27 distinct viruses in all: eight human herpesviruses, 16 respiratory viruses, parvo B19, and polyoma BK/JC viruses. Clinical characteristics of the patients and underlying conditions were evaluated. In total, 92% of patients had virus detected in tonsils (Epstein-Barr virus 72%, human herpesvirus 7, and 6B 54% and 16%, respectively, enterovirus 18%, parvovirus B19 7% and the rest <4%). No herpes simplex virus 2, varicella zoster virus, polyoma JC virus, parainfluenza-, metapneumo-, or coronaviruses were found. Enterovirus was more common in children and was frequently observed in the presence of HHV6B. None of the viruses showed a positive association to the tonsillar disease. Respiratory symptoms were not associated with the prevalence of viruses. This study comprehensively reports a cross-sectional view of intratonsillar virus infections in elective tonsillectomy patients in a wide age range cohort. Tonsils are a major virus reservoir for distinct herpes and respiratory viruses without a positive association with tonsillar disease or respiratory symptoms.

12.
Sci Rep ; 11(1): 4499, 2021 02 24.
Article in English | MEDLINE | ID: covidwho-1383120

ABSTRACT

The purpose of the study was to compare clinical characteristics and mortality among adults infected with human coronaviruses (HCoV) 229E and OC43. We conducted a retrospective cohort study of adults (≥ 18 years) admitted to the ward of a university teaching hospital for suspected viral infection from October 2012 to December 2017. Multiplex real-time polymerase chain reaction (PCR) was used to test for respiratory viruses. Multivariate logistic regression was used to compare mortality among patients with HCoV 229E and HCoV OC43 infections. The main outcome was 30-day all-cause mortality. Of 8071 patients tested, 1689 were found to have a respiratory virus infection. Of these patients, 133 had HCoV infection, including 12 mixed infections, 44 HCoV 229E infections, and 77 HCoV OC43 infections. HCoV 229E infections peaked in January and February, while HCoV OC43 infections occurred throughout the year. The 30-day all-cause mortality was 25.0% among patients with HCoV 229E infection, and 9.1% among patients with HCoV OC43 infection (adjusted odds ratio: 3.58, 95% confidence interval: 1.19-10.75). Infections with HCoVs 229E and OC43 appear to have different seasonal patterns, and HCoV 229E might be more virulent than HCoV OC43.


Subject(s)
Coronavirus 229E, Human/genetics , Coronavirus Infections/mortality , Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Aged , Coinfection/mortality , Coinfection/virology , Female , Hospitalization , Humans , Male , Middle Aged , Real-Time Polymerase Chain Reaction/methods , Respiratory Tract Infections/mortality , Respiratory Tract Infections/virology , Retrospective Studies
14.
APMIS ; 129(7): 393-400, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1388189

ABSTRACT

The SARS-CoV-2 pandemic has created an urgent need for diagnostic tests to detect viral RNA. Commercial RNA extraction kits are often expensive, in limited supply, and do not always fully inactivate the virus. Together, this calls for the development of safer methods for SARS-CoV-2 extraction that utilize readily available reagents and equipment present in most standard laboratories. We optimized and simplified a RNA extraction method combining a high molar acidic guanidinium isothiocyanate (GITC) solution, phenol and chloroform. First, we determined the GITC/RNA dilution thresholds compatible with an efficient two-step RT-qPCR for B2M mRNA in nasopharyngeal (NP) or oropharyngeal (OP) swab samples. Second, we optimized a one-step RT-qPCR against SARS-CoV-2 using NP and OP samples. We furthermore tested a SARS-CoV-2 dilution series to determine the detection threshold. The method enables downstream detection of SARS-CoV-2 by RT-qPCR with high sensitivity (~4 viral RNA copies per RT-qPCR). The protocol is simple, safe, and expands analysis capacity as the inactivated samples can be used in RT-qPCR detection tests at laboratories not otherwise classified for viral work. The method takes about 30 min from swab to PCR-ready viral RNA and circumvents the need for commercial RNA purification kits.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , RNA, Viral/isolation & purification , SARS-CoV-2/isolation & purification , Specimen Handling/methods , Humans , Reagent Kits, Diagnostic
15.
J AOAC Int ; 104(4): 872-888, 2021 Aug 20.
Article in English | MEDLINE | ID: covidwho-1387921

ABSTRACT

BACKGROUND: The Eurofins GeneScan Technologies' VIRSeek SARS-CoV-2 Mplex kit is a RT (reverse transcription) real-time polymerase chain reaction (RT-qPCR) assay for the detection of two targets on the N-gene (nucleocapsid) of SARS-CoV-2. An extraction control, that allows monitoring of the extraction procedure and PCR inhibition, is included. OBJECTIVE: In silico analysis and wet testing showed inclusivity and exclusivity of the assay. The complete workflow starting from surface swabbing (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS-CoV-2 Mplex), and evaluation with FastFinder was validated in comparison to the CDC method for detection of SARS-CoV-2 on stainless steel. METHOD: In silico analysis was performed by using the MFOLD online program. The matrix study was performed for stainless steel inoculated with SARS-CoV-2 isolated from the first documented US case of a traveler from Wuhan, China. RESULTS: For inclusivity, 15 764 sequences were analyzed and all mismatches (0.37% of the sequences had single mismatches) were considered non-critical. Cross reactivity for closely related viruses and background organisms was performed, resulting in correct exclusion of all. No significant differences were observed for the probability of detection (POD) study when comparing to the CDC method. CONCLUSIONS: Results of the inclusivity and exclusivity study show that the assay is specific for detection of SARS-CoV-2. The POD study showed no statistically significant difference compared to the CDC reference method, results were identical for the uninoculated and the high level. For the fractional recovery level, the candidate method detected 9/17 samples leading to a POD of 0.47, the reference method detected 11/20 samples leading to a POD of 0.55. HIGHLIGHT: The complete workflow starting from swabbing of the surface (VIRSeek PATHOSwab kit), RNA extraction (VIRSeek RNAExtractor), RT-PCR (VIRSeek SARS CoV-2 Mplex) and evaluation with FastFinder was validated in comparison to the US Centers for Disease Control and Prevention method for detection of SARS-CoV-2 on Stainless Steel.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Sensitivity and Specificity , Stainless Steel
17.
Gynecol Endocrinol ; 37(2): 157-161, 2021 Feb.
Article in English | MEDLINE | ID: covidwho-1376255

ABSTRACT

In patients with endometriosis, ectopic endometrial tissues can escape from immune system control and survive in other tissues. The pathophysiology of endometriosis is still not fully understood. In this study, we aimed to clarify the pathophysiology of endometriosis, which is thought to be a benign but infiltrative cancer type, which has many similarities with cancer biology by determining PD-1 expression in patients with endometriosis. In this study, n = 73 cases who underwent surgery or examination at the Obstetrics and Gynecology Clinic of Sivas Cumhuriyet University Faculty of Medicine and diagnosed as endometriosis in the biopsy material taken with the pre-diagnosis of endometriosis constituted the patient group. The control group consisted of n = 64 healthy subjects without concomitant malignancy or chronic inflammatory disease. Venous whole blood samples were obtained from the study groups. PD-1 and PD-L1 levels were determined by the ELISA method from serum and plasma samples. PD-1 gene expression level was determined by RT-PCR. The PD-1 level was found to be approximately 350 ± 150 ng/L and 45 ± 17 ng/L in endometriosis and control group, respectively. While the PD-L1 level was approximately 760 ± 108 ng/L in the patients, this level was 140 ± 14 ng/L in the controls. According to the RT-PCR results, the expression of the PD-1 gene 10 times higher compared to the controls. Conclusion: The identified increase of PD-1 levels and gene expression in endometriosis groups show that immunotherapy may be used in the treatment of endometriosis.


Subject(s)
B7-H1 Antigen/blood , Endometriosis/blood , Programmed Cell Death 1 Receptor/blood , Case-Control Studies , Endometriosis/etiology , Female , Humans
18.
J Mol Diagn ; 23(9): 1085-1096, 2021 09.
Article in English | MEDLINE | ID: covidwho-1370607

ABSTRACT

Widespread high-throughput testing for identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by RT-PCR has been a foundation in the response to the coronavirus disease 2019 (COVID-19) pandemic. Quality assurance metrics for these RT-PCR tests are still evolving as testing is widely implemented. As testing increases, it is important to understand performance characteristics and the errors associated with these tests. Herein, we investigate a high-throughput, laboratory-developed SARS-CoV-2 RT-PCR assay to determine whether modeling can generate quality control metrics that identify false-positive (FP) results due to contamination. This study reviewed repeated clinical samples focusing on positive samples that test negative on re-extraction and PCR, likely representing false positives. To identify and predict false-positive samples, we constructed machine learning-derived models based on the extraction method used. These models identified variables associated with false-positive results across all methods, with sensitivities for predicting FP results ranging between 67% and 100%. Application of the models to all results predicted a total FP rate of 0.08% across all samples, or 2.3% of positive results, similar to reports for other RT-PCR tests for RNA viruses. These models can predict quality control parameters, enabling laboratories to generate decision trees that reduce interpretation errors, allow for automated reflex testing of samples with a high FP probability, improve workflow efficiency, and increase diagnostic accuracy for patient care.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , RNA, Viral/isolation & purification , Reverse Transcriptase Polymerase Chain Reaction/methods , Automation, Laboratory , Carrier State/virology , Decision Support Systems, Clinical , False Positive Reactions , High-Throughput Nucleotide Sequencing/methods , Humans , Machine Learning , SARS-CoV-2/genetics , Viral Load , Workflow
19.
J Med Virol ; 93(9): 5655-5659, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1363696

ABSTRACT

The current reliable recommended test for coronavirus disease 2019 (COVID-19) diagnosis is quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Rapid antigen test devices could be useful as they are less expensive, faster without the need of specialized laboratories to perform the test. We report the performances of two rapid immunochromatographic antigen testing devices compared with RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in nasopharyngeal samples. We carried out a lateral-flow tests study on 401 nasopharyngeal swab samples from nonduplicated suspected COVID-19 subjects. An equal volume of universal transport medium tubes-containing samples (dilution ratio = 1:15) were added to the manufacturer's extraction buffer solution (dilution ratio = 1:2) and analyzed on BioSpeedia COVID19Speed-Antigen Test and on Abbott Panbio™ COVID-19 Ag Rapid Test, devices. Qualitative results were compared to those obtained by the RT-qPCR (Allplex™ SARS-CoV-2 Assay Seegene). Based on our data, the overall sensitivity for BioSpeedia and Panbio devices was estimated at 65.5% and 75.0%, respectively. The sensitivity was greater for cycle threshold values less than 25 achieving 90.4 and 96.8 for BioSpeedia and Panbio devices, respectively. A perfect specificity of 100.0% was observed for both devices.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , Antigens, Viral/analysis , Diagnostic Tests, Routine , Humans , Nasopharynx/virology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sensitivity and Specificity
20.
J Med Virol ; 93(9): 5538-5543, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1363694

ABSTRACT

In the current coronavirus disease 2019 (COVID-19) pandemic there is a mass screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) happening around the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite the identification of cases and to facilitate early isolation and control spread. Hence this study evaluates six different rapid nucleic acid detection assays that are commercially available for SARS-CoV-2 virus detection. Nasopharyngeal samples were collected from 4981 participants and were tested for the SARS-CoV-2 virus by the gold standard real-time reverse-transcription polymerase chain reaction (RT-PCR) method and with one of these six rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection. AQ-TOP had the highest sensitivity (98%) and a strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports. Genechecker system, Abbott ID NOW, and Cobas Liat were found to have the best performance and agreement when compared with the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large-scale screening of COVID-19.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , SARS-CoV-2/isolation & purification , COVID-19 Nucleic Acid Testing/instrumentation , COVID-19 Nucleic Acid Testing/standards , Humans , Nasopharynx/virology , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity , United Arab Emirates
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