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1.
Cochrane Database Syst Rev ; 3: CD013705, 2021 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-33760236

RESUMO

BACKGROUND: Accurate rapid diagnostic tests for SARS-CoV-2 infection could contribute to clinical and public health strategies to manage the COVID-19 pandemic. Point-of-care antigen and molecular tests to detect current infection could increase access to testing and early confirmation of cases, and expediate clinical and public health management decisions that may reduce transmission. OBJECTIVES: To assess the diagnostic accuracy of point-of-care antigen and molecular-based tests for diagnosis of SARS-CoV-2 infection. We consider accuracy separately in symptomatic and asymptomatic population groups. SEARCH METHODS: Electronic searches of the Cochrane COVID-19 Study Register and the COVID-19 Living Evidence Database from the University of Bern (which includes daily updates from PubMed and Embase and preprints from medRxiv and bioRxiv) were undertaken on 30 Sept 2020. We checked repositories of COVID-19 publications and included independent evaluations from national reference laboratories, the Foundation for Innovative New Diagnostics and the Diagnostics Global Health website to 16 Nov 2020. We did not apply language restrictions. SELECTION CRITERIA: We included studies of people with either suspected SARS-CoV-2 infection, known SARS-CoV-2 infection or known absence of infection, or those who were being screened for infection. We included test accuracy studies of any design that evaluated commercially produced, rapid antigen or molecular tests suitable for a point-of-care setting (minimal equipment, sample preparation, and biosafety requirements, with results within two hours of sample collection). We included all reference standards that define the presence or absence of SARS-CoV-2 (including reverse transcription polymerase chain reaction (RT-PCR) tests and established diagnostic criteria). DATA COLLECTION AND ANALYSIS: Studies were screened independently in duplicate with disagreements resolved by discussion with a third author. Study characteristics were extracted by one author and checked by a second; extraction of study results and assessments of risk of bias and applicability (made using the QUADAS-2 tool) were undertaken independently in duplicate. We present sensitivity and specificity with 95% confidence intervals (CIs) for each test and pooled data using the bivariate model separately for antigen and molecular-based tests. We tabulated results by test manufacturer and compliance with manufacturer instructions for use and according to symptom status. MAIN RESULTS: Seventy-eight study cohorts were included (described in 64 study reports, including 20 pre-prints), reporting results for 24,087 samples (7,415 with confirmed SARS-CoV-2). Studies were mainly from Europe (n = 39) or North America (n = 20), and evaluated 16 antigen and five molecular assays. We considered risk of bias to be high in 29 (50%) studies because of participant selection; in 66 (85%) because of weaknesses in the reference standard for absence of infection; and in 29 (45%) for participant flow and timing. Studies of antigen tests were of a higher methodological quality compared to studies of molecular tests, particularly regarding the risk of bias for participant selection and the index test. Characteristics of participants in 35 (45%) studies differed from those in whom the test was intended to be used and the delivery of the index test in 39 (50%) studies differed from the way in which the test was intended to be used. Nearly all studies (97%) defined the presence or absence of SARS-CoV-2 based on a single RT-PCR result, and none included participants meeting case definitions for probable COVID-19. Antigen tests Forty-eight studies reported 58 evaluations of antigen tests. Estimates of sensitivity varied considerably between studies. There were differences between symptomatic (72.0%, 95% CI 63.7% to 79.0%; 37 evaluations; 15530 samples, 4410 cases) and asymptomatic participants (58.1%, 95% CI 40.2% to 74.1%; 12 evaluations; 1581 samples, 295 cases). Average sensitivity was higher in the first week after symptom onset (78.3%, 95% CI 71.1% to 84.1%; 26 evaluations; 5769 samples, 2320 cases) than in the second week of symptoms (51.0%, 95% CI 40.8% to 61.0%; 22 evaluations; 935 samples, 692 cases). Sensitivity was high in those with cycle threshold (Ct) values on PCR ≤25 (94.5%, 95% CI 91.0% to 96.7%; 36 evaluations; 2613 cases) compared to those with Ct values >25 (40.7%, 95% CI 31.8% to 50.3%; 36 evaluations; 2632 cases). Sensitivity varied between brands. Using data from instructions for use (IFU) compliant evaluations in symptomatic participants, summary sensitivities ranged from 34.1% (95% CI 29.7% to 38.8%; Coris Bioconcept) to 88.1% (95% CI 84.2% to 91.1%; SD Biosensor STANDARD Q). Average specificities were high in symptomatic and asymptomatic participants, and for most brands (overall summary specificity 99.6%, 95% CI 99.0% to 99.8%). At 5% prevalence using data for the most sensitive assays in symptomatic people (SD Biosensor STANDARD Q and Abbott Panbio), positive predictive values (PPVs) of 84% to 90% mean that between 1 in 10 and 1 in 6 positive results will be a false positive, and between 1 in 4 and 1 in 8 cases will be missed. At 0.5% prevalence applying the same tests in asymptomatic people would result in PPVs of 11% to 28% meaning that between 7 in 10 and 9 in 10 positive results will be false positives, and between 1 in 2 and 1 in 3 cases will be missed. No studies assessed the accuracy of repeated lateral flow testing or self-testing. Rapid molecular assays Thirty studies reported 33 evaluations of five different rapid molecular tests. Sensitivities varied according to test brand. Most of the data relate to the ID NOW and Xpert Xpress assays. Using data from evaluations following the manufacturer's instructions for use, the average sensitivity of ID NOW was 73.0% (95% CI 66.8% to 78.4%) and average specificity 99.7% (95% CI 98.7% to 99.9%; 4 evaluations; 812 samples, 222 cases). For Xpert Xpress, the average sensitivity was 100% (95% CI 88.1% to 100%) and average specificity 97.2% (95% CI 89.4% to 99.3%; 2 evaluations; 100 samples, 29 cases). Insufficient data were available to investigate the effect of symptom status or time after symptom onset. AUTHORS' CONCLUSIONS: Antigen tests vary in sensitivity. In people with signs and symptoms of COVID-19, sensitivities are highest in the first week of illness when viral loads are higher. The assays shown to meet appropriate criteria, such as WHO's priority target product profiles for COVID-19 diagnostics ('acceptable' sensitivity ≥ 80% and specificity ≥ 97%), can be considered as a replacement for laboratory-based RT-PCR when immediate decisions about patient care must be made, or where RT-PCR cannot be delivered in a timely manner. Positive predictive values suggest that confirmatory testing of those with positive results may be considered in low prevalence settings. Due to the variable sensitivity of antigen tests, people who test negative may still be infected. Evidence for testing in asymptomatic cohorts was limited. Test accuracy studies cannot adequately assess the ability of antigen tests to differentiate those who are infectious and require isolation from those who pose no risk, as there is no reference standard for infectiousness. A small number of molecular tests showed high accuracy and may be suitable alternatives to RT-PCR. However, further evaluations of the tests in settings as they are intended to be used are required to fully establish performance in practice. Several important studies in asymptomatic individuals have been reported since the close of our search and will be incorporated at the next update of this review. Comparative studies of antigen tests in their intended use settings and according to test operator (including self-testing) are required.


Assuntos
Antígenos Virais/análise , /diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Sistemas Automatizados de Assistência Junto ao Leito , /imunologia , Adulto , Infecções Assintomáticas , Viés , Criança , Estudos de Coortes , Reações Falso-Negativas , Reações Falso-Positivas , Humanos , Técnicas de Diagnóstico Molecular/normas , Valor Preditivo dos Testes , Padrões de Referência , Sensibilidade e Especificidade
2.
Vopr Virusol ; 66(1): 17-28, 2021 03 07.
Artigo em Russo | MEDLINE | ID: mdl-33683062

RESUMO

This review presents the basic principles of application of the loop-mediated isothermal amplification (LAMP) reaction for the rapid diagnosis of coronavirus infection caused by SARS-CoV-2. The basic technical details of the method, and the most popular approaches of specific and non-specific detection of amplification products are briefly described. We also discuss the first published works on the use of the method for the detection of the nucleic acid of the SARS-CoV-2 virus, including those being developed in the Russian Federation. For commercially available and published LAMP-based assays, the main analytical characteristics of the tests are listed, which are often comparable to those based on the method of reverse transcription polymerase chain reaction (RT-PCR), and in some cases are even superior. The advantages and limitations of this promising methodology in comparison to other methods of molecular diagnostics, primarily RT-PCR, are discussed, as well as the prospects for the development of technology for the detection of other infectious agents.


Assuntos
/métodos , Técnicas de Diagnóstico Molecular/normas , Técnicas de Amplificação de Ácido Nucleico/normas , RNA Viral/genética , /genética , Artefatos , /normas , Primers do DNA/genética , Primers do DNA/metabolismo , Sondas de DNA/genética , Sondas de DNA/metabolismo , Humanos , Kit de Reagentes para Diagnóstico , Sensibilidade e Especificidade
3.
J Med Microbiol ; 70(3)2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33704042

RESUMO

At present, the available point of care (POC) molecular assays for hepatitis C are not considered as true POC due to sample collection and processing requiring minimal laboratory infrastructure. A new POC Xpert HCV VL Fingerstick (Xpert FS) precludes such requirements where specimen collected by simple fingerstick can be loaded directly into the test cartridge with results available within 60 min. The present study compared the performance of this assay for HCV RNA quantitation using both capillary whole blood (CWB) and venous whole blood (VWB) with plasma HCV RNA performed on Abbott Real Time HCV PCR. CWB via fingerstick and VWB via venipuncture collected from serologically confirmed HCV-infected participants were loaded into Xpert HCV VL WB for viral load estimation. Simultaneously Abbott Real Time HCV PCR assay was also performed using plasma (reference method). Among the enrolled participants (n=157), the mean age was 46.22±14.79 years and 63 % were male. HCV RNA was detected in 100 cases (63.7 %), median 5.69 (IQR: 5.00-6.32)log10IU ml-1 on the reference method. Xpert FS showed 100 % sensitivity and specificity using both CWB and VWB. The median viral loads detected in CWB and VWB were 5.52 (IQR: 4.59-6.15) and 5.48 (IQR: 4.61-6.07)log10IU ml-1, respectively. Xpert FS offers potential as true POC enabling accurate diagnosis in a single patient visit to the health-care facility, hence may reduce the number of dropouts with a confirmed diagnosis. However, further real-time studies with larger sample size are warranted.


Assuntos
Coleta de Amostras Sanguíneas/métodos , Hepacivirus/isolamento & purificação , Hepatite C/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Testes Imediatos , Adulto , Feminino , Hepacivirus/genética , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/normas , Testes Imediatos/normas , RNA Viral/sangue , RNA Viral/genética , Sensibilidade e Especificidade , Fatores de Tempo , Carga Viral
4.
Virchows Arch ; 478(2): 153-190, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33604759

RESUMO

A European consensus conference on endometrial carcinoma was held in 2014 to produce multidisciplinary evidence-based guidelines on selected questions. Given the large body of literature on the management of endometrial carcinoma published since 2014, the European Society of Gynaecological Oncology (ESGO), the European SocieTy for Radiotherapy & Oncology (ESTRO) and the European Society of Pathology (ESP) jointly decided to update these evidence-based guidelines and to cover new topics in order to improve the quality of care for women with endometrial carcinoma across Europe and worldwide. ESGO/ESTRO/ESP nominated an international multidisciplinary development group consisting of practicing clinicians and researchers who have demonstrated leadership and expertise in the care and research of endometrial carcinoma (27 experts across Europe). To ensure that the guidelines are evidence-based, the literature published since 2014, identified from a systematic search was reviewed and critically appraised. In the absence of any clear scientific evidence, judgment was based on the professional experience and consensus of the development group. The guidelines are thus based on the best available evidence and expert agreement. Prior to publication, the guidelines were reviewed by 191 independent international practitioners in cancer care delivery and patient representatives. The guidelines comprehensively cover endometrial carcinoma staging, definition of prognostic risk groups integrating molecular markers, pre- and intra-operative work-up, fertility preservation, management for early, advanced, metastatic, and recurrent disease and palliative treatment. Principles of radiotherapy and pathological evaluation are also defined.


Assuntos
Carcinoma/terapia , Neoplasias do Endométrio/terapia , Oncologia/normas , Biomarcadores Tumorais/genética , Biópsia/normas , Carcinoma/genética , Carcinoma/patologia , Neoplasias do Endométrio/genética , Neoplasias do Endométrio/patologia , Medicina Baseada em Evidências/normas , Feminino , Humanos , Técnicas de Diagnóstico Molecular/normas , Estadiamento de Neoplasias/normas , Valor Preditivo dos Testes , Medição de Risco , Fatores de Risco , Resultado do Tratamento
5.
Biomacromolecules ; 22(3): 1231-1243, 2021 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-33539086

RESUMO

Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a rapid and inexpensive isothermal alternative to the current gold standard reverse transcription quantitative polymerase chain reaction (RT-qPCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, unlike RT-qPCR, there are no consensus detection regions or optimal RT-LAMP methods, and most protocols do not include internal controls to ensure reliability. Naked RNAs, plasmids, or even RNA from infectious COVID-19 patients have been used as external positive controls for RT-LAMP assays, but such reagents lack the stability required for full-process control. To overcome the lack of proper internal and external positive controls and the instability of the detection RNA, we developed virus-like particles (VLPs) using bacteriophage Qß and plant virus cowpea chlorotic mottle virus (CCMV) for the encapsidation of target RNA, namely a so-called SARS-CoV-2 LAMP detection module (SLDM). The target RNA is a truncated segment of the SARS-CoV-2 nucleocapsid (N) gene and human RNase P gene (internal control) as positive controls for RT-qPCR and RT-LAMP. Target RNAs stably encapsidated in Qß and CCMV VLPs were previously shown to function as full-process controls in RT-qPCR assays, and here we show that SLDMs can fulfill the same function for RT-LAMP and swab-to-test (direct RT-LAMP with heat lysis) assays. The SLDM was validated in a clinical setting, highlighting the promise of VLPs as positive controls for molecular assays.


Assuntos
Bromovirus , Técnicas de Diagnóstico Molecular/normas , Técnicas de Amplificação de Ácido Nucleico/normas , /genética , Bromovirus/química , Bromovirus/genética , /genética , Humanos
6.
Int J Mol Sci ; 22(3)2021 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-33503982

RESUMO

Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.


Assuntos
Biomarcadores Tumorais , Testes Genéticos/métodos , MicroRNAs/genética , Neoplasias/diagnóstico , Neoplasias/genética , Ácidos Nucleicos Livres , MicroRNA Circulante , Regulação Neoplásica da Expressão Gênica , Testes Genéticos/normas , Humanos , Biópsia Líquida/métodos , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Diagnóstico Molecular/normas , Prognóstico
7.
Viruses ; 12(12)2020 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-33334037

RESUMO

Recent outbreaks of African swine fever virus (ASFV) have seen the movement of this virus into multiple new regions with devastating impact. Many of these outbreaks are occurring in remote, or resource-limited areas, that do not have access to molecular laboratories. Loop-mediated isothermal amplification (LAMP) is a rapid point of care test that can overcome a range of inhibitors. We outline further development of a real-time ASFV LAMP, including field verification during an outbreak in Timor-Leste. To increase field applicability, the extraction step was removed and an internal amplification control (IAC) was implemented. Assay performance was assessed in six different sample matrices and verified for a range of clinical samples. A LAMP detection limit of 400 copies/rxn was determined based on synthetic positive control spikes. A colourmetric LAMP assay was also assessed on serum samples. Comparison of the LAMP assay to a quantitative polymerase chain reaction (qPCR) was performed on clinical ASFV samples, using both serum and oral/rectal swabs, with a substantial level of agreement observed. The further verification of the ASFV LAMP assay, removal of extraction step, implementation of an IAC and the assessment of a range of sample matrix, further support the use of this assay for rapid in-field detection of ASFV.


Assuntos
Vírus da Febre Suína Africana/genética , Febre Suína Africana/epidemiologia , Febre Suína Africana/virologia , Surtos de Doenças , Técnicas de Diagnóstico Molecular , Técnicas de Amplificação de Ácido Nucleico , Febre Suína Africana/diagnóstico , Vírus da Febre Suína Africana/isolamento & purificação , Animais , Feminino , Masculino , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Diagnóstico Molecular/normas , Técnicas de Amplificação de Ácido Nucleico/métodos , Técnicas de Amplificação de Ácido Nucleico/normas , Reação em Cadeia da Polimerase em Tempo Real , Sensibilidade e Especificidade , Suínos , Viremia
8.
PLoS One ; 15(12): e0244023, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33347478

RESUMO

BACKGROUND: PCR is more sensitive than immunofluorescence assay (IFA) for detection of Pneumocystis jirovecii. However, PCR cannot always distinguish infection from colonization. This study aimed to compare the performance of real-time PCR and IFA for diagnosis of P. jirovecii pneumonia (PJP) in a real-world clinical setting. METHODS: A retrospective cohort study was conducted at a 1,300-bed hospital between April 2017 and December 2018. Patients whose respiratory sample (bronchoalveolar lavage or sputum) were tested by both Pneumocystis PCR and IFA were included. Diagnosis of PJP was classified based on multicomponent criteria. Sensitivity, specificity, 95% confidence intervals (CI), and Cohen's kappa coefficient were calculated. RESULTS: There were 222 eligible patients. The sensitivity and specificity of PCR was 91.9% (95% CI, 84.0%-96.7%) and 89.7% (95% CI, 83.3%-94.3%), respectively. The sensitivity and specificity of IFA was 7.0% (95% CI, 2.6%-14.6%) and 99.2% (95% CI, 95.6%-100.0%), respectively. The percent agreement between PCR and IFA was 56.7% (Cohen's kappa -0.02). Among discordant PCR-positive and IFA-negative samples, 78% were collected after PJP treatment. Clinical management would have changed in 14% of patients using diagnostic information, mainly based on PCR results. CONCLUSIONS: PCR is highly sensitive compared with IFA for detection of PJP. Combining clinical, and radiological features with PCR is useful for diagnosis of PJP, particularly when respiratory specimens cannot be promptly collected before initiation of PJP treatment.


Assuntos
Imunofluorescência/métodos , Técnicas de Diagnóstico Molecular/métodos , Pneumonia por Pneumocystis/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/métodos , Adulto , Idoso , Líquido da Lavagem Broncoalveolar/microbiologia , Feminino , Imunofluorescência/normas , Humanos , Masculino , Pessoa de Meia-Idade , Técnicas de Diagnóstico Molecular/normas , Pneumocystis/genética , Pneumocystis/isolamento & purificação , Pneumocystis/patogenicidade , Pneumonia por Pneumocystis/microbiologia , Reação em Cadeia da Polimerase em Tempo Real/normas , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Escarro/microbiologia
9.
Western Pac Surveill Response J ; 11(1): 41-46, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32963890

RESUMO

Problem: Emerging bacterial antimicrobial (antibiotic) resistance (AMR) is a global threat to human health. However, most lower income countries do not have microbiological diagnostic testing for prompt, reliable confirmation of bloodstream infection and identification of AMR. Context: Clinicians in Pacific island nations are increasingly challenged by patients who have infection due to antimicrobial-resistant bacteria. Treatment of infection remains empirical because of a lack of diagnostic testing capacity and may follow guidelines that were formulated without reference to local measures of AMR prevalence. There is limited understanding among clinicians of microbiology testing and test interpretation. Action: Examine the lessons learnt from pilot laboratory development programmes in two Pacific island nations that focused on establishing standard procedures for micrological diagnostics and antimicrobial susceptibility testing (AST) and on improving the training of clinicians to increase their use of laboratory services. Outcome: The pilot programmes addressed a range of logistical difficulties and evaluated two blood culture systems. They also examined and improved internal QC implementation and evaluated the prevalence of AMR. Discussion: Continued development of microbiological diagnostic capability in the Pacific region is paramount. Pacific Island nations need to develop the capability of at least one central laboratory to culture AMR pathogens and subject them to quality-controlled AST or arrange for suitable referral to a nearby country. Discussion: This study demonstrated a persistently high prevalence of three major bacterial STIs across four countries in WHO's Western Pacific Region during nearly two decades. Further strengthening of strategies to control and prevent STIs is warranted.


Assuntos
Antibacterianos/farmacologia , Técnicas Bacteriológicas/normas , Farmacorresistência Bacteriana , Testes de Sensibilidade Microbiana/normas , Técnicas de Diagnóstico Molecular/normas , Humanos , Ilhas do Pacífico , Projetos Piloto , Controle de Qualidade
10.
J Virol Methods ; 285: 113970, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32920028

RESUMO

The global COVID-19 pandemic has led to the rapid development of tests for detection of SARS-CoV-2. Studies are required to assess the relative performance of different assays. Here, we compared the performance of two commercial assays, the cobas® SARS-CoV-2 (Roche Diagnostics) and Xpert® Xpress SARS-CoV-2 (Cepheid®) tests, and a laboratory developed RT-PCR test adapted for use on the Hologic® Panther Fusion® (Hologic®) instrument as well as Bio-Rad and QIAGEN real-time PCR detection systems. Performance characteristics for each test were determined by testing clinical specimens and reference material. All assays detect the pan-Sarbecovirus E (envelope structural protein) gene plus a SARS-CoV-2-specific target. The limit of detection for the E gene target varied from ∼2 copies/reaction to >30 copies/reaction. Due to assay-specific differences in sample processing and nucleic acid extraction, the overall analytical sensitivity ranged from 24 copies/mL specimen to 574 copies/mL specimen. Despite these differences, there was 100 % agreement between the commercial and laboratory developed tests. No false-negative or false-positive SARS-CoV-2 results were observed and there was no cross-reactivity with common respiratory viruses, including endemic coronaviruses.


Assuntos
Betacoronavirus , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Técnicas de Diagnóstico Molecular , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia , Kit de Reagentes para Diagnóstico , Betacoronavirus/genética , Betacoronavirus/imunologia , Técnicas de Laboratório Clínico/métodos , Técnicas de Laboratório Clínico/normas , Humanos , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Diagnóstico Molecular/normas , Pandemias , Kit de Reagentes para Diagnóstico/normas , Sensibilidade e Especificidade
11.
Proc Natl Acad Sci U S A ; 117(37): 22727-22735, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32868442

RESUMO

The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per µL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.


Assuntos
Infecções por Coronavirus/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Pneumonia Viral/diagnóstico , Testes Imediatos/normas , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Betacoronavirus/genética , Betacoronavirus/patogenicidade , Humanos , Limite de Detecção , Técnicas de Diagnóstico Molecular/instrumentação , Técnicas de Diagnóstico Molecular/normas , Mucosa Nasal/virologia , Pandemias , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa/instrumentação , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Smartphone
12.
J Clin Virol ; 130: 104567, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32750665

RESUMO

BACKGROUND: A major expansion in SARS CoV-2 testing is urgently needed. Saliva is an attractive option as an alternative for nasopharyngeal swabs (NPS), since saliva can be self-collected, is non-invasive, and sample quality is not dependent on the expertise of the collector. OBJECTIVE: To compare SARS CoV-2 positivity on paired NPS and saliva samples. STUDY DESIGN: NPS and paired saliva samples were prospectively collected from symptomatic outpatients suspected of having COVID-19 and were tested by real-time RT-PCR. RESULTS: In total, 35/124 (26.6 %) samples were RT-PCR positive, with 33/35 positive by NPS (sensitivity = 94.3 % (95 % CI 81.4%-99.0%)) and 30/35 by pure saliva (sensitivity = 85.7 % (95 % CI 70.6%-93.7%)), for an overall agreement of 117/124 (94.4 %). The median cycle threshold value was significantly lower for NPS than for saliva (p = 0.0331). A third or more of pure saliva samples from symptomatic patients were thick, stringy, and difficult to pipet. CONCLUSIONS: Real-time RT-PCR of pure saliva had an overall sensitivity for SARS CoV-2 RNA detection of 85.7 % when compared to simultaneously collected NPS. Our study highlighted the need to optimize collection and processing before saliva can be used for high volume testing.


Assuntos
Infecções por Coronavirus/diagnóstico , Técnicas de Diagnóstico Molecular/normas , Pneumonia Viral/diagnóstico , RNA Viral/análise , Saliva/virologia , Betacoronavirus , Técnicas de Laboratório Clínico , Humanos , Nasofaringe/virologia , Pacientes Ambulatoriais , Pandemias , Estudos Prospectivos , Reação em Cadeia da Polimerase em Tempo Real , Manejo de Espécimes
13.
Genes (Basel) ; 11(8)2020 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-32824573

RESUMO

The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/diagnóstico , Genoma Viral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Técnicas de Diagnóstico Molecular/métodos , Pneumonia Viral/diagnóstico , Sequenciamento Completo do Genoma/métodos , Betacoronavirus/patogenicidade , Infecções por Coronavirus/virologia , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Técnicas de Diagnóstico Molecular/normas , Pandemias , Pneumonia Viral/virologia , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Sequenciamento Completo do Genoma/normas
14.
J Clin Microbiol ; 58(11)2020 10 21.
Artigo em Inglês | MEDLINE | ID: mdl-32817231

RESUMO

The coronavirus disease (COVID-19) pandemic has placed the clinical laboratory and testing for SARS-CoV-2 front and center in the worldwide discussion of how to end the outbreak. Clinical laboratories have responded by developing, validating, and implementing a variety of molecular and serologic assays to test for SARS-CoV-2 infection. This has played an essential role in identifying cases, informing isolation decisions, and helping to curb the spread of disease. However, as the demand for COVID-19 testing has increased, laboratory professionals have faced a growing list of challenges, uncertainties, and, in some situations, controversy, as they have attempted to balance the need for increasing test capacity with maintaining a high-quality laboratory operation. The emergence of this new viral pathogen has raised unique diagnostic questions for which there have not always been straightforward answers. In this commentary, the author addresses several areas of current debate, including (i) the role of molecular assays in defining the duration of isolation/quarantine, (ii) whether the PCR cycle threshold value should be included on patient reports, (iii) if specimen pooling and testing by research staff represent acceptable solutions to expand screening, and (iv) whether testing a large percentage of the population is feasible and represents a viable strategy to end the pandemic.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Pneumonia Viral/diagnóstico , Betacoronavirus/genética , Betacoronavirus/imunologia , Serviços de Laboratório Clínico/normas , Infecções por Coronavirus/prevenção & controle , Humanos , Programas de Rastreamento , Pessoal de Laboratório Médico/normas , Técnicas de Diagnóstico Molecular/normas , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Reação em Cadeia da Polimerase/normas , Quarentena/normas , Sensibilidade e Especificidade , Manejo de Espécimes
15.
Int J Mol Sci ; 21(16)2020 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-32784770

RESUMO

Sensitive molecular assays are critical for coronavirus disease 2019 (COVID-19) diagnosis. Here, we designed and evaluated two single-tube nested (STN) real-time RT-PCR assays, targeting SARS-CoV-2 RdRp/Hel and N genes. Both STN assays had a low limit of detection and did not cross react with other human coronaviruses and respiratory viruses. Using 213 initial respiratory specimens from suspected COVID-19 patients, the sensitivity of both the STN COVID-19-RdRp/Hel and the STN COVID-19-N assays was 100% (99/99), while that of the comparator non-nested N assay was 95% (94/99). Among 108 follow-up specimens from confirmed COVID-19 patients who tested negative by the non-nested COVID-19-RdRp/Hel assay, 28 (25.9%) were positive for SARS-CoV-2 by the STN COVID-19-RdRp/Hel or the STN COVID-19-N assay. To evaluate the performance of our novel STN assays in pooled specimens, we created four sample pools, with each pool consisting of one low positive specimen and 49 negative specimens. While the non-nested COVID-19-RdRp/Hel assay was positive in only one of four sample pools (25%), both of the STN assays were positive in two of four samples pools (50%). In conclusion, the STN assays are highly sensitive and specific for SARS-CoV-2 detection. Their boosted sensitivity offers advantages in non-traditional COVID-19 testing algorithms such as saliva screening and pooled sample screening during massive screening.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/virologia , Técnicas de Diagnóstico Molecular/métodos , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase em Tempo Real/métodos , Betacoronavirus/patogenicidade , Infecções por Coronavirus/diagnóstico , Humanos , Técnicas de Diagnóstico Molecular/normas , Proteínas do Nucleocapsídeo/genética , Pandemias , Fosfoproteínas , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase em Tempo Real/normas , Mucosa Respiratória/virologia , Sensibilidade e Especificidade , Proteínas não Estruturais Virais/genética
17.
J Clin Lab Anal ; 34(10): e23507, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32754967

RESUMO

BACKGROUND: Reverse transcription-polymerase chain reaction (RT-PCR) is an extremely common clinical method for detecting pathogens, particularly for emerging infectious diseases such as the new coronavirus disease (COVID-19). Currently, detection of the RNA from the novel coronavirus SARS-CoV-2 is the gold standard for establishing a COVID-19 diagnosis. This study evaluates the characteristic performance of the analytical system in a clinical laboratory. METHODS: A commercial SARS-CoV-2 RNA RT-PCR Kit used in a clinical laboratory is assessed based on ISO 15189 verification requirements. A multiple real-time RT-PCR assay for the RdRP, N, and E genes in SARS-CoV-2 is verified. RESULTS: The analytical system exhibits good analytical sensitivity (1000 copies/mL) and specificity (100%); however, the values of 86.7% and 100% for analytical accuracy deserved attention, compared with two other types of methods. Overall, the kit is potentially useful for SARS-CoV-2 diagnostic testing and meets the verification requirements. CONCLUSION: Compliance with international standards, such as ISO 15189, is valuable for clinical laboratories and for improving laboratory medicine quality and safety. Normalization is essential for obtaining reliable results from the SARS-CoV-2 RNA RT-PCR assay. This study aims to develop an improved SARS-CoV-2 verification framework compared with traditional molecular diagnostic methods, given the urgency of implementing new assays in clinical laboratories.


Assuntos
Betacoronavirus/genética , Técnicas de Laboratório Clínico , Infecções por Coronavirus/diagnóstico , Técnicas de Diagnóstico Molecular , Pneumonia Viral/diagnóstico , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Técnicas de Laboratório Clínico/métodos , Técnicas de Laboratório Clínico/normas , Humanos , Limite de Detecção , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Diagnóstico Molecular/normas , Pandemias , Controle de Qualidade , RNA Viral/análise , Reprodutibilidade dos Testes , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas
18.
Exp Parasitol ; 217: 107960, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32755552

RESUMO

Guinea worm Dracunculus medinensis causes debilitating disease in people and is subject to an ongoing global eradication programme. Research and controls are constrained by a lack of diagnostic tools. We developed a specific and sensitive LAMP method for detecting D. medinensis larval DNA in copepod vectors. We were able to detect a single larva in a background of field-collected copepods. This method could form the basis of a "pond-side test" for detecting potential sources of Guinea worm infection in the environment, in copepods, including in the guts of fish as potential transport hosts, enabling research, surveillance and targeting of control measures. The key constraint on the utility of this assay as a field diagnostic, is a lack of knowledge of variation in the temporal and spatial distribution of D. medinensis larvae in copepods in water bodies in the affected areas and how best to sample copepods to obtain a reliable diagnostic sample. These fundamental knowledge gaps could readily be addressed with field collections of samples across areas experiencing a range of worm infection frequencies, coupled with field and laboratory analyses using LAMP and PCR.


Assuntos
Copépodes/parasitologia , Dracunculus/isolamento & purificação , Técnicas de Diagnóstico Molecular/normas , Técnicas de Amplificação de Ácido Nucleico/normas , Tanques/parasitologia , África , Animais , Sequência de Bases , Gatos , Copépodes/genética , Primers do DNA/química , DNA de Helmintos/isolamento & purificação , Vetores de Doenças , Cães , Dracunculus/genética , Humanos , Papio , Sensibilidade e Especificidade , Fatores de Tempo
19.
Hell J Nucl Med ; 23 Suppl: 8-14, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32860390

RESUMO

On December 2019, a new coronavirus disease (COVID-19) emerged in China and spread worldwide, causing acute severe respiratory syndrome. Due to the increased transmission rate of the virus, it became of great importance the early diagnosis of the disease. The coronavirus pandemic led to the development of numerous tests in order to mass screening population for active viral load and for the identification of antibodies for epidemiological purposes. This review summarizes the different diagnostic tests available to the clinicians for the diagnosis and follow up of the SARS COV-2 infections.


Assuntos
Infecções por Coronavirus/diagnóstico , Técnicas de Diagnóstico Molecular/métodos , Pneumonia Viral/diagnóstico , Radiografia Torácica/métodos , Técnicas de Cultura de Células/métodos , Infecções por Coronavirus/sangue , Infecções por Coronavirus/diagnóstico por imagem , Humanos , Imunoensaio/métodos , Imunoensaio/normas , Técnicas de Diagnóstico Molecular/normas , Pandemias , Pneumonia Viral/sangue , Pneumonia Viral/diagnóstico por imagem , Radiografia Torácica/normas , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Reação em Cadeia da Polimerase Via Transcriptase Reversa/normas , Sensibilidade e Especificidade , Testes Sorológicos/métodos , Testes Sorológicos/normas
20.
Biotechniques ; 69(3): 178-185, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32635743

RESUMO

Loop-mediated isothermal amplification (LAMP) is a versatile technique for detection of target DNA and RNA, enabling rapid molecular diagnostic assays with minimal equipment. The global SARS-CoV-2 pandemic has presented an urgent need for new and better diagnostic methods, with colorimetric LAMP utilized in numerous studies for SARS-CoV-2 detection. However, the sensitivity of colorimetric LAMP in early reports has been below that of the standard RT-qPCR tests, and we sought to improve performance. Here we report the use of guanidine hydrochloride and combined primer sets to increase speed and sensitivity in colorimetric LAMP, bringing this simple method up to the standards of sophisticated techniques and enabling accurate, high-throughput diagnostics.


Assuntos
Betacoronavirus/isolamento & purificação , Técnicas de Laboratório Clínico/métodos , Guanidina , Técnicas de Diagnóstico Molecular/métodos , Técnicas de Amplificação de Ácido Nucleico/métodos , Técnicas de Laboratório Clínico/normas , Colorimetria , Infecções por Coronavirus/diagnóstico , Humanos , Técnicas de Diagnóstico Molecular/normas , Técnicas de Amplificação de Ácido Nucleico/normas , Fenolsulfonaftaleína
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