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1.
Bioengineering (Basel) ; 9(10)2022 10 18.
Article in English | MEDLINE | ID: covidwho-2081979

ABSTRACT

The outbreak of the monkeypox virus (MPXV) in non-endemic countries is an emerging global health threat and may have an economic impact if proactive actions are not taken. As shown by the COVID-19 pandemic, rapid, accurate, and cost-effective virus detection techniques play a pivotal role in disease diagnosis and control. Considering the sudden multicountry MPXV outbreak, a critical evaluation of the MPXV detection approaches would be a timely addition to the endeavors in progress for MPXV control and prevention. Herein, we evaluate the current MPXV detection methods, discuss their pros and cons, and provide recommended solutions to the problems. We review the traditional and emerging nucleic acid detection approaches, immunodiagnostics, whole-particle detection, and imaging-based MPXV detection techniques. The insights provided in this article will help researchers to develop novel techniques for the diagnosis of MPXV.

2.
ACS ES&T Water ; 2(10):1628-1638, 2022.
Article in English | Web of Science | ID: covidwho-2069856

ABSTRACT

Recent water sector safety concerns during the COVID-19 pandemic highlight the need for industry-focused reviews of emerging pathogens to support evidence-based utility decision-making. Between May 7 and August 20, 2022, more than 41 358 cases of human monkeypox were reported globally from over 87 countries in which the disease is not endemic. Given that the presence and persistence of monkeypox virus (MPXV) in feces, water, and wastewater has not been investigated, we summarize the available evidence on MPXV and related orthopoxviruses to provide sector-wide recommendations and identify knowledge gaps. On the basis of the information available to date, this outbreak is unlikely to pose an exposure and transmission risk from wastewater, biosolids, or water due to the absence of any evidence to date that suggests that infectious MPXV is present in wastewater or biosolids or has caused human cases, clusters, or outbreaks from exposure to these sources. In addition, remaining smallpox vaccine immunity in the population, availability of vaccines and treatments, susceptibility of poxviruses to disinfection (e.g., UV and chlorine), and evidence from health care confirming the efficacy of infection control measures all suggest that current treatment and recommended wastewater worker protection practices are sufficient to protect public and occupational health.

3.
Diagnostics (Basel) ; 12(10)2022 Oct 01.
Article in English | MEDLINE | ID: covidwho-2065754

ABSTRACT

According to the temporary recommendations of the 2021 World Health Organization (WHO), in addition to whole-genome sequencing, laboratories in various countries can also screen for known mutations utilizing targeted RT-PCR-based mutation detection assays. The aim of this work was to generate a laboratory technique to differentiate the main circulating SARS-CoV-2 variants in 2021-2022, when a sharp increase in morbidity was observed with the appearance of the Omicron variant. Real-time PCR methodology is available for use in the majority of scientific and diagnostic institutions in Russia, which makes it possible to increase the coverage of monitoring of variants in the territories of all 85 regions in order to accumulate information for the Central Services and make epidemiological decisions. With the methodology developed by the Central Research Institute of Epidemiology of the Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing (FSSCRP Human Wellbeing) (CRIE), more than 6000 biological samples have been typed, and 7% of samples with the Delta variant and 92% of samples with the Omicron variant have been identified as of 25 August 2022. Reagents for 140,000 definitions have been supplied to regional organizations.

4.
Transbound Emerg Dis ; 69(5): e1338-e1349, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2052987

ABSTRACT

Equine Piroplasmosis (EP) is a tick-borne disease caused by three apicomplexan protozoan parasites, Theileria equi (T. equi), Babesia caballi (B. caballi) and T. haneyi, which can cause similar clinical symptoms. There are five known 18S rRNA genotypes of T. equi group (including T. haneyi) and three of B. caballi. Real-time PCR methods for detecting EP based on 18S rRNA analysis have been developed, but these methods cannot detect all genotypes of EP in China, especially genotype A of T. equi. In this study, a duplex real-time PCR detection method was developed for the simultaneous detection and differentiation of T. equi and B. caballi. The primers and probes for this duplex real-time PCR assay were designed based on the conserved 18S rRNA gene sequences of all genotypes of T. equi and B. caballi including Chinese strain. Double-quenched probes were used in this method, which provide less background and more signal to decrease the number of false positives relative to single-quenched probes. The newly developed real-time PCR assays exhibited good specificity, sensitivity, repeatability and reproducibility. The real-time PCR assays were further validated by comparison with a nested PCR assay and a previous developed real-time PCR for EP and sequencing results in the analysis of 506 clinical samples collected from 2019 to 2020 in eleven provinces and regions of China. Based on clinical performance, the agreements between the duplex real-time PCR assay and the nPCR assay or the previous developed real-time PCR assay were 92.5% (T. equi) and 99.4% (B. caballi) or 87.4% (T. equi) and 97.2% (B. caballi). The detection results showed that the positivity rate of T. equi was 43.87% (222/506) (10 genotype A, 1 genotype B, 4 genotype C, 207 genotype E), while that of B. caballi was 5.10% (26/506) (26 genotype A), and the rate of T. equi and B. caballi co-infection was 2.40% (12/506). The established method could contribute to the accurate diagnosis, pathogenic surveillance and epidemiological investigation of T. equi and B. caballi infections in horses.


Subject(s)
Babesia , Babesiosis , Cattle Diseases , Horse Diseases , Theileria , Theileriasis , Animals , Babesia/genetics , Babesiosis/diagnosis , Babesiosis/epidemiology , Babesiosis/parasitology , Cattle , Horse Diseases/diagnosis , Horse Diseases/epidemiology , Horse Diseases/parasitology , Horses , RNA, Ribosomal, 18S/genetics , Real-Time Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/veterinary , Reproducibility of Results , Theileria/genetics , Theileriasis/diagnosis , Theileriasis/epidemiology , Theileriasis/parasitology
5.
Front Bioeng Biotechnol ; 10: 996456, 2022.
Article in English | MEDLINE | ID: covidwho-2043419

ABSTRACT

A portable nucleic acid detection (PNAD) system based on real-time polymerase chain reaction (real-time PCR) has been developed for point-of-care testing (POCT) of infectious disease pathogens. In order to achieve "sample-in, result-out" while keeping the system compact, the hardware system integrates optical, thermal and motion control modules in a limited space for nucleic acid extraction, purification, amplification and detection. Among these hardware modules, the fluorescence module is one of the most important modules, because its performance directly affects the accuracy and sensitivity of the testing results. In this paper, a miniaturized, high-sensitivity and integrated dual-channel fluorescence module have been proposed for the homemade PNAD system. Based on the principle of confocal optical path, two group of excitation-emission optical paths of different wavelengths are integrated in a small space. In terms of circuitry, a current-light dual negative feedback light emitting diode (LED) drive circuit is applied to improve the stability of the excited light source. All optical and electronic components are integrated in a metal box of 55 mm × 45 mm × 15 mm, that helps miniaturize the detection system. Two different modules have been assembled to fit various fluorescent dyes or probes with the set of excitation and emission as follow: module 1#: 470 nm/525 nm, 570 nm/630 nm; module 2#: 520 nm/570 nm, 630 nm/690 nm. Finally, hepatitis B virus (HBV) concentration gradient detection and multiplex detection of different gene targets of SARS-CoV-2 are carried out on the PNAD system equipped with these two fluorescence modules for evaluating their performances. Compared with the commercial real-time PCR instrument, our fluorescence module has good stability and detection sensitivity.

6.
Methods Protoc ; 5(5)2022 Sep 21.
Article in English | MEDLINE | ID: covidwho-2043870

ABSTRACT

RT-PCR tests have become the gold standard for detecting the SARS-CoV-2 virus in the context of the COVID-19 pandemic. Because of the extreme number of cases in periodic waves of infection, there is a severe financial and logistical strain on diagnostic laboratories. For this reason, alternative implementations and validations of academic protocols that employ the lowest cost and the most widely available equipment and reagents found in different regions are essential. In this study, we report an alternative implementation of the EUA 2019-nCoV CDC assay which uses a previously characterized duplex PCR reaction for the N1 and RNAse P target regions and an additional uniplex reaction for the N2 target region. Taking advantage of the Abbott m2000 Sample Preparation System and NEB Luna Universal Probe One-Step RT-qPCR kit, some of the most widely available and inexpensive nucleic acid extraction and amplification platforms, this modified test shows state-of-the-art analytical and clinical sensitivities and specificities when compared with the Seegene Allplex-SARS-CoV-2 assay. This implementation has the potential to be verified and implemented by diagnostic laboratories around the world to guarantee low-cost RT-PCR tests that can take advantage of widely available equipment and reagents.

7.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(12):1500-1508, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040500

ABSTRACT

Based on the M gene sequence of TGEV and PEDV and VP2 gene sequence of PoRV, the optimal reaction system and amplification procedure were established by optimizing primer, probe concentration and annealing temperature, and the Quantitative PCR method of TaqMan probes for three viruses is successfully established. On this basis, after further optimization of conditions, a triple real-time fluorescent quantitative PCR method for detecting TGEV, PEDV, and PoRV was established. The detection sensitivity of this method for TGEV, PEDV, and PoRV were 2.49 copies/ L, 4.36 copies/ L, and 4.96 copies/ L respectively. The maximum value of CV in repeated trials detected by TGEV, PEDV and PoRV were 2.5%, 3.8%, 4.3%, and the maximum value of CV in repeated trials between groups were 3.7%, 3.4%, 3.2%, which are no more than 5%.indicating that the established method has good reproducibility. Using this method to detect PRV, PCV1, and PRRSV virus samples, there is no cross-reaction, indicating that the method is specific. Using the established method to detect 40 clinical diseases, the samples were tested, and the positive rates of TGEV, PEDV, and PoRV were 5%, 30%, and 12.5%respectively. The mixed infection rate of TGEV and PEDV was 2.5%, the mixed infection rate of PEDV and PoRV was 5%. The results of the multiple fluorescence quantitative PCR method are consistent with those of the detection of a single fluorescent RT-PCR method, indicating that the established method has good clinical application value.

8.
Chinese Veterinary Science / Zhongguo Shouyi Kexue ; 50(11):1373-1378, 2020.
Article in Chinese | CAB Abstracts | ID: covidwho-2040499

ABSTRACT

In order to build a specific, sensitive and rapid detection method for PAstV3 detection, the PAstVB gene sequences in Genbank were used and the conserved region in ORFlb was selected to design specific primers and TaqMan probe. Clinical stool samples were collected and preliminary detected by this newly established real-time RT-PCR method after reaction systems and conditions optimization. This detection method established in this study has a good linear relationship with the standard curve, with R2 value up to 0.9971. The sensitivity is 100 times higher than conventional PCR method, The variation co-efficient of in-batch and inter-batch repeatability test is less than 2.0%, indicating good repeatability. The detection results of Clinical samples showed that the positive rate of this method is higher than conventional PCR method. The establishment of this method provides a rapid detection means for PAstV3 laboratory diagnosis and epidemiological investigation.

9.
Acta Microbiologica Sinica ; 8:3152-3165, 2022.
Article in Chinese | CAB Abstracts | ID: covidwho-2040441

ABSTRACT

Objective: To identify the key host protein that can regulate the replication of porcine epidemic diarrhea virus (PEDV).

10.
Chinese Journal of Virology ; 36(6):1171-1176, 2020.
Article in Chinese | GIM | ID: covidwho-2040435

ABSTRACT

Coronavirus disease 2019 (COVID-19) is caused by infection by SARS-COV-2.. The main clinical manifestations are fever, cough, fatigue, respiratory distress, and even death. The virus is highly contagious, spreads mainly through droplets, and has wrought havoc upon human health, national economies, and public-health systems worldwide. The clinical diagnosis is based mainly on clinical manifestations, computed tomography of the chest, and laboratory examinations. For the latter, real-time fluorescent reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and genome sequencing are the "gold standard" for the diagnosis. Choosing a rapid and efficient method for pathogen detection has a key role in improving the diagnosis rate, cure rate, as well as reducing morbidity and mortality. Compared with genome sequencing, RT-qPCR has the advantages of simple operation and short cycle, which is particularly important for the diagnosis of SARS-CoV-2. Here, we review the sensitivity, specificity, and practicality of different methods of RT-qPCR for detection of the nucleic acids of SARS-CoV-2, and provide a reference for clinicians to choose more efficient detection methods for nucleic acids.

11.
Sri Lankan Journal of Infectious Diseases ; 12(2), 2022.
Article in English | CAB Abstracts | ID: covidwho-2040070

ABSTRACT

Real time RT-PCR is considered as the gold standard test to detect COVID-19. The use of sample pooling strategy increases testing capacity and spares resources. However, the effectiveness of sample pooling should be evaluated in the setting before being implemented. Forty five samples including 20 high positives (Ct<20), 20 low positives (Ct 20-40) and 05 negative samples were used to prepare 1:1, 1:3 and 1:5 simulated sample pools which were then subjected to viral RNA extraction followed by real time RT-PCR. Sensitivity and specificity of sample pooling technique in the detection of SARS-CoV-2 RNA was 100% without significant variation of Ct values. According to our results, pooling of up to 6 samples will not have an effect on the final result in clinical samples and hence can be adopted in the given context for the diagnosis of COVID-19 by RT-PCR.

12.
Clin Chim Acta ; 536: 104-111, 2022 Nov 01.
Article in English | MEDLINE | ID: covidwho-2031182

ABSTRACT

Over the past two years, SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) infection has spread globally causing multi-organ disease and severely impacting the healthcare systems of all countries. Accordingly, the development of easy-to-access diagnostic devices has become essential to limit the effect of the virus worldwide. Real-Time PCR is considered the gold standard to identify SARS-CoV-2 infection due to high sensitivity, affordability, and capacity to detect low viral loads at early disease stage. Advances in lab on a chip technology has led to the development of some Point-of-Care (POC) devices using Real-Time PCR and approved by the United States Food and Drug Administration. We provide an overview on recently developed POC tests for the rapid diagnosis of COVID-19 infection. Practical applications of miniaturized devices based on viral genome amplification as well as favorable features such as reduced sample processing time, ease of use by non-specialized personnel, and the potential of PCR-based POC technologies will be highlighted and reviewed.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Testing , Humans , Point-of-Care Systems , Point-of-Care Testing , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , Sensitivity and Specificity
13.
Jurnal Berkala Epidemiologi / Periodic Epidemiology Journal ; 10(1):48-57, 2022.
Article in English | CAB Abstracts | ID: covidwho-2026037

ABSTRACT

Background: Coronavirus 2019 (COVID-19) is a global pandemic with various clinical manifestations and is affected by multifactor. Epidemiological data of COVID-19 in Indonesia, especially in Surabaya have not been well established yet. Purpose: This study aims to provide the COVID-19 patients profile in Surabaya City, Indonesia. Method: The study data were retrospectively collected from electrical medical records in Primasatya Husada Citra (PHC) Hospital of Surabaya, one of the referral hospitals for COVID-19 in Surabaya. Descriptive and Spearman correlation statistics were done for data analysis.

14.
Front Microbiol ; 13: 935688, 2022.
Article in English | MEDLINE | ID: covidwho-2022791

ABSTRACT

Persistent infection and prolonged shedding of human bocavirus 1 (HBoV1) in children have been reported, and the role of HBoV1 as a sole causative pathogen in acute respiratory infection (ARI) is yet to be established. While the reported prevalence of HBoV infection varies due to different detection methods and sampling criteria, determining the viral and bacterial etiology of HBoV infection using multiplex real-time PCR is yet to be reported. Herein, we aimed to further explore the pathogenicity of HBoV in patients with ARI by screening the viral and bacterial infections in children with ARI in Qingdao and comparing the epidemiological, clinical characteristics, and etiological results. Human bocavirus was identified in 28.1% of the samples, and further sequencing analysis of the detected HBoV confirmed 96.4% as HBoV1. The rate of HBoV as a single viral infection was 75%, and the rate of coinfection with bacteria was 66.1%, suggesting the need for continued monitoring of HBoV in children with ARIs. Clinical characterization suggested that HBoV infection may affect the function of organs, such as the liver, kidney, and heart, and the blood acid-base balance. Additionally, it is essential to promote awareness about the importance of disinfection and sterilization of the hospital environment and standardizing operations. The interactions between HBoV and other pathogens remain to be investigated in further detail in the future.

15.
Viruses ; 14(8)2022 08 19.
Article in English | MEDLINE | ID: covidwho-2010309

ABSTRACT

Porcine viral diarrhea diseases affect the swine industry, resulting in significant economic losses. Porcine epidemic diarrhea virus (PEDV) genotypes G1 and G2, and groups A and C of the porcine rotavirus, are major etiological agents of severe gastroenteritis and profuse diarrhea, particularly among piglets, with mortality rates of up to 100%. Based on the high prevalence rate and frequent co-infection of PEDV, RVA, and RVC, close monitoring is necessary to avoid greater economic losses. We have developed a multiplex TaqMan probe-based real-time PCR for the rapid simultaneous detection and differentiation of PEDV subtypes G1 and G2, RVA, and RVC. This test is highly sensitive, as the detection limits were 20 and 100 copies/µL for the G1 and G2 subtypes of PEDV, respectively, and 50 copies/µL for RVA and RVC, respectively. Eighty-eight swine clinical samples were used to evaluate this new test. The results were 100% in concordance with the standard methods. Since reassortment between porcine and human rotaviruses has been reported, this multiplex test not only provides a basis for the management of swine diarrheal viruses, but also has the potential to impact public health as well.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Rotavirus , Swine Diseases , Animals , Coronavirus Infections/veterinary , Diarrhea/diagnosis , Diarrhea/veterinary , Porcine epidemic diarrhea virus/genetics , Porcine epidemic diarrhea virus/isolation & purification , Real-Time Polymerase Chain Reaction/methods , Real-Time Polymerase Chain Reaction/veterinary , Rotavirus/genetics , Rotavirus/isolation & purification , Sensitivity and Specificity , Swine , Swine Diseases/virology
16.
Biosensors (Basel) ; 12(9)2022 Sep 01.
Article in English | MEDLINE | ID: covidwho-2009947

ABSTRACT

The COVID-19 pandemic poses a threat to global health. Due to its high sensitivity, specificity, and stability, real-time fluorescence quantitative (real-time PCR) detection has become the most extensively used approach for diagnosing SARS-CoV-2 pneumonia. According to a report from the World Health Organization, emerging and underdeveloped nations lack nucleic acid detection kits and polymerase chain reaction (PCR) instruments for molecular biological detection. In addition, sending samples to a laboratory for testing may result in considerable delays between sampling and diagnosis, which is not favorable to the timely prevention and control of new crown outbreaks. Concurrently, there is an urgent demand for accurate PCR devices that do not require a laboratory setting, are more portable, and are capable of completing testing on-site. Hence, we report on HDLRT-qPCR, a new, low-cost, multiplexed real-time fluorescence detection apparatus that we have developed for on-site testing investigations of diverse diseases in developing nations. This apparatus can complete on-site testing rapidly and sensitively. The entire cost of this instrument does not exceed USD 760. In order to demonstrate the applicability of our PCR instrument, we conducted testing that revealed that we achieved gradient amplification and melting curves comparable to those of commercially available equipment. Good consistency characterized the testing outcomes. The successful detection of target genes demonstrates the reliability of our inexpensive PCR diagnostic technique. With this apparatus, there is no need to transport samples to a central laboratory; instead, we conduct testing at the sampling site. This saves time on transportation, substantially accelerates overall testing speed, and provides results within 40 min.


Subject(s)
COVID-19 , Nucleic Acids , COVID-19/diagnosis , COVID-19 Testing , Clinical Laboratory Techniques/methods , Humans , Pandemics , Real-Time Polymerase Chain Reaction/methods , Reproducibility of Results , SARS-CoV-2/genetics , Sensitivity and Specificity
17.
Water Air Soil Pollut ; 233(9): 372, 2022.
Article in English | MEDLINE | ID: covidwho-2007220

ABSTRACT

The COVID-19 pandemic affected human life at every level. In this study, we analyzed genetic markers (N and ORF1ab, RNA genes) of SARS-CoV-2 in domestic wastewaters (DWW) in San Justo City (Santa Fe, Argentina), using reverse transcription-quantitative real-time PCR. Out of the 30 analyzed samples, 30% were positive for SARS-CoV-2 RNA. Of the total positive samples, 77% correspond to untreated DWW, 23% to pre-chlorination, and no SARS-CoV-2 RNA was registered at the post-chlorination sampling site. The viral loads of N and OFR1ab genes decreased significantly along the treatment process, and the increase in the number of viral copies of the N gene could anticipate, by 6 days, the number of clinical cases in the population. The concentration of chlorine recommended by the WHO (≥ 0.5 mg L-1 after at least 30 min of contact time at pH 8.0) successfully removed SARS-CoV-2 RNA from DWW. The efficiency of wastewater-based epidemiology (WBE) confirms the need to control and increase DWW treatment systems on a regional and global scale. This work could contribute to building a network for WBE to monitor SARS-CoV-2 in wastewaters during the pandemic waves and the epidemic remission phase. Supplementary Information: The online version contains supplementary material available at 10.1007/s11270-022-05772-w.

18.
Pravention Und Gesundheitsforderung ; 2022.
Article in English | Web of Science | ID: covidwho-2003758

ABSTRACT

Background. For detection of SARS-CoV-2-infected persons ("severe acute respiratory syndrome coronavirus 2") quantitative Real-Time PCR (qRT-PCR) remains the gold standard. SARS-CoV-2 antigen-detecting rapid diagnostic tests (Ag-RDTs) have the advantage of being fast and simple to use at any location. According to previous studies, Ag-RDTs seem to have poorer sensitivity and specificity. There are currently a few hundred Ag-RDTs available, but many of them have not been independently evaluated. Objectives. Evaluation of diagnostic performance of rapid antigen tests detecting SARS-CoV-2 from 6 different manufacturers. Materials and methods. We performed Ag-RDTS with naso- and oropharnygeal swabs from laboratory routine which had had already resulted in a positive qRT-PCR test. To exclude possible dilution effects when samples were used for a second time, we also performed qRT-PCR analytics for already used samples. The initially measured Ct values could be confirmed. Results. Ag-RDTs showed differences in discrimination between positive and negative results. In samples with lower virus concentrations (Ct value > 30), the results were not reliable and the discrimination between negative and positive results was not unambigious. Conclusions. Ag-RDTs with high sensitivity allow the identification of highly contagious patients anywhere. There are differences between manufacturers which are important when testing patients. An independent transparent evaluation of Ag-RDTs is necessary.

19.
Int J Infect Dis ; 123: 1-8, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2000451

ABSTRACT

OBJECTIVES: The performance of a new point-of-care CE-IVD-marked isothermal lab-on-phone COVID-19 assay was assessed in comparison to a gold standard real-time reverse transcriptase-PCR method. METHODS: The study was conducted following a nonprobability sampling of ≥16-year-old volunteers from three different laboratories, using direct mouthwash (N = 24) or nasopharyngeal (N = 191) clinical samples. RESULTS: The assay demonstrated 95.19% sensitivity and 100% specificity for detection of SARS-CoV-2 in direct nasopharyngeal crude samples and 78.95% sensitivity and 100% specificity in direct mouthwash crude samples. It also successfully detected currently predominant SARS-CoV-2 variants of concern (Beta B.1.351, Delta B.1.617.2, and Omicron B.1.1.529) and demonstrated to be inert against potential cross-reactions of other common respiratory pathogens that cause infections that present similar symptoms to COVID-19. CONCLUSION: This lab-on-phone pocket-sized assay relies on an isothermal amplification of SARS-CoV-2's N and E genes, taking just 50 minutes from sample to result, with only 2 minutes of hands-on time. It presents good performance when using direct nasopharyngeal crude samples, enabling a low-cost, real-time, rapid, and accurate identification of SARS-CoV-2 infections at the point of care, which is important for both clinical management and population screening, as a tool to break the chain of transmission of COVID-19 pandemic, especially in low-resources environments.


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , COVID-19/diagnosis , COVID-19 Testing , Humans , Laboratories , Molecular Diagnostic Techniques/methods , Mouthwashes , Nucleic Acid Amplification Techniques/methods , Pandemics , RNA, Viral/analysis , RNA, Viral/genetics , RNA-Directed DNA Polymerase/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
20.
Diagnostics (Basel) ; 12(8)2022 Aug 18.
Article in English | MEDLINE | ID: covidwho-1997535

ABSTRACT

The demand for assays that can rapidly and accurately detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains high. We evaluated the performance of two rapid real-time reverse transcription polymerase chain reaction (RT-qPCR) assays (STANDARD M10 SARS-CoV-2 and Xpert Xpress SARS-CoV-2) against conventional RT-qPCR assays (STANDARD M nCoV and Allplex SARS-CoV-2) for detecting SARS-CoV-2. A total of 225 swab samples were collected and tested using the four assays. The STANDARD M10 SARS-CoV-2 assay showed 97.4% positive percent agreement (PPA) and 100.0% negative percent agreement (NPA) compared to the STANDARD M nCoV assay and Allplex SARS-CoV-2 assay. STANDARD M10 exhibited high performance except in samples with low viral loads (cycle threshold (Ct) > 30). Xpert Xpress showed PPA and NPA of 100.0% compared to the two conventional RT-qPCR assays. The kappa coefficient (Κ) showed nearly almost perfect agreement between each assay and conventional RT-qPCR assays. The correlations of Ct values between the two rapid RT-qPCR and conventional RT-qPCR assays were >0.8, indicating strong correlations. All included assays could detect SARS-CoV-2 variants, such as the Alpha, Beta, and Gamma variants. The recently developed STANDARD M10 has a shorter turnaround time and random-access detection on automated devices, thereby facilitating efficient testing in emergency settings.

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