RT-PCR para identificação de mutação do receptor do fator de crescimento epidérmico (EGFR) em pacientes com câncer de pulmão de células não pequenas / RT-PCR for identification of epidermal growth factor receptor (EGFR) mutation in patients with non-small cell lung cancer

INTRODUÇÃO: O câncer de pulmão foi o segundo tipo de câncer mais diagnosticado (11,4%) no mundo e a principal causa de morte por câncer (18%) durante o ano de 2020, totalizando 2,2 milhões de novos casos e 1,8 milhões de mortes no ano. Considera-se para fins terapêuticos e prognósticos a divisão em dois principais tipos histológicos: câncer de pulmão células não pequenas células (CPCNP), que representa cerca de 85% de todos os casos de câncer de pulmão, e câncer de pulmão pequenas células (CPPC), associado a aproximadamente 15% dos casos. O comportamento biológico dos tumores malignos pode estar relacionado à expressão molecular, principalmente de proteínas envolvidas no crescimento e sobrevivência celulares, de modo que a segurança e a eficácia do tratamento guardam relação não só com o subtipo histopatológico como também com as características moleculares do tumor. Assim, para melhor direcionamento da terapia (por exemplo, erlotinibe e gefinitibe), torna-se importante diferenciar os subtipos histológicos, e identificar a presença de mutações específicas, como, por exemplo formas alteradas no gene do EGFR, como se recomenda nas Diretrizes Diagnósticas e Terapêuticas do Câncer de Pulmão do Ministério da Saúde. Entretanto, o Ministério da Saúde não recomenda nenhuma técnica específica para identificação de mutação no gene do EGFR, sendo que o rt-PCR é considerado o teste de referência em muitos contextos clínicos e estudos, seguido pelo sequenciamento de nova geração (NGS). PERGUNTA: Em pacientes diagnosticados com CPCNP, qual a acurácia diagnóstica, custoefetividade e impacto orçamentário do diagnóstico molecular por meio da técnica de rtPCR para identificação de mutação do EGFR em comparação ao NGS ou a não realização de rt-PCR? EVIDÊNCIAS CIENTÍFICAS: A revisão sistemática identificou 19 estudos observacionais de acurácia diagnóstica (teste de referência: NGS). A sensibilidade e especificidade do rt-PCR em comparação ao NGS foi de 92,0% e 97,0%, respectivamente. Apenas um estudo reportou dados de sobrevida global para a comparação de rt-PCR positivo e negativo para mutação de EGFR, apresentando uma diferença não significativa estatisticamente, de 19,2 versus 11,6 meses (Log rank p=0,143). Todos os estudos apresentaram ao menos um domínio com alto risco de viés e nenhuma preocupação quanto à aplicabilidade. AVALIAÇÃO ECONÔMICA: Na análise de custo-efetividade/utilidade comparou-se a realização de rt-PCR com a não realização do teste para um horizonte temporal por toda vida. A análise sugere que a realização do rt-PCR de mutação do EGFR para auxiliar na padronização do melhor tratamento de pacientes com CPCNP e sem tratamento prévio na fase metastática, em comparação a não realização do teste, sugere um modesto benefício clínico de 0,043 ano de vida ajustado pela qualidade (QALY) e 0,040 ano de vida (AV) ganho e uma economia de R$ 3.138,25. Portanto, rt-PCR dominou a não realização do teste (razão de custo-efetividade incremental, RCEI, não representada em casos de dominância). Ademais, as análises de sensibilidade determinística revelaram que para QALY e AV, as proporções de pacientes que usam o erlotinibe e gefitinibe são as variáveis que mais impactam na RCEI, seguida pela proporção de resultados positivos obtidos pela rt-PCR de mutação do EGFR. AVALIAÇÃO DE IMPACTO ORÇAMENTÁRIO: Considerando um horizonte temporal de cinco anos, utilizando demanda aferida (dados de APAC de 2015 a 2021) foi estimado o quantitativo de pacientes com carcinoma pulmonar de células não pequenas avançado. Ademais, foi estimada uma taxa de difusão conservadora, tendo um aumento de 10% ao ano para a tecnologia em análise. Desta forma, observou-se que a incorporação do rt-PCR para identificação de mutação do EGFR em pacientes com CPCNP, sem tratamento prévio na fase metastática, pode gerar um incremento de R$ 1.553.250,00 no primeiro ano, chegando a um incremento de R$ 8.193.750,00 no quinto ano de análise (total acumulado de cerca de R$ 24 milhões em cinco anos) em análise que não considera as potenciais economias com a incorporação do teste. Em análise de sensibilidade considerando preço 20% menor, coerente com preço informado por um dos fabricantes contatados, o impacto orçamentário acumulado em cinco anos seria de cerca de R$ 20 milhões. MONITORAMENTO DO HORIZONTE TECNOLÓGICO: No Monitoramento do Horizonte Tecnológico foi encontrada 1 tecnologia, a Allele-Discriminating Priming System (kit - ADPS), da empresa Genecast, sem identificação de licenças sanitárias Anvisa e FDA. CONSIDERAÇÕES FINAIS: A evidência disponível sobre o uso de rt-PCR para identificação de mutação EGFR em comparação ao NGS sugere elevada acurácia do rt-PCR, com sensibilidade e especificidade de 92,0% e 97,0%, respectivamente. A análise de custoefetividade sugere que a realização da rt-PCR de mutação do EGFR em pacientes com CPCNP, em comparação a não realização do teste, é dominante para QALY e AV. A análise de impacto orçamentário da incorporação da rt-PCR de mutação do EGFR em pacientes com CPCNP, no SUS, sugere um incremento de cerca de R$ 21 a 40 milhões em cinco anos de análise, a depender do preço do kit e market share considerado, em análise que não considera a potencial economia com a incorporação do teste. RECOMENDAÇÃO PRELIMINAR DA CONITEC: Os membros do Comitê de Procedimentos e Produtos, presentes na 123ª Reunião Ordinária da Conitec realizada no dia 05 de outubro de 2023, deliberaram por unanimidade que a matéria fosse disponibilizada em consulta pública com recomendação preliminar favorável à incorporação do diagnóstico molecular por meio da técnica de rt-PCR para identificação de mutação do EGFR em pacientes com câncer de pulmão de células não pequenas. CONSULTA PÚBLICA: A consulta pública nº 51 foi realizada entre os dias 12 de dezembro de 2023 e 02 de janeiro de 2024. Foram recebidas 50 contribuições, sendo 6 classificadas como técnico-científicas e 44 como de experiência ou opinião. Todas as contribuições foram favoráveis à incorporação de rt-PCR para identificação de mutação do EGFR em pacientes com CPCNP. Referente às contribuições técnico-científicas, os estudos sugeridos para inclusão no PTC não contemplavam os critérios de elegibilidade da pergunta PIROS e todas as demais contribuições corroboram os resultados apresentados no relatório de recomendação. Quanto às contribuições de experiência e opinião, das 44 recebidas, uma foi desconsiderada por tratar de outra consulta pública. Também foram recebidos dois anexos. As contribuições recebidas e anexos foram submetidos à análise de conteúdo temática. Das 43 contribuições consideradas, todas expressaram concordância em relação à recomendação preliminar da Conitec, portanto, mostraramse favoráveis à incorporação do procedimento em avaliação. Os participantes que tiveram experiência com o rt-PCR relataram como efeitos positivos a importância do uso e acesso ao teste para os pacientes usuários do SUS terem um melhor direcionamento no tratamento do câncer de pulmão de células não pequenas. Enquanto efeitos negativos e dificuldades no uso do rt-PCR, foram apontados a dificuldade no acesso e o custo. RECOMENDAÇÃO FINAL DA CONITEC: Os membros do Comitê de Produtos e Procedimentos presentes na 126ª Reunião Ordinária da Conitec deliberaram, por unanimidade, recomendar a incorporação de rt-PCR para identificação da mutação do receptor do fator de crescimento epidérmico (EGFR) em pacientes com câncer de pulmão de células não pequenas. Foi assinado o Registro de Deliberação nº 876/2024. DECISÃO: e incorporar, no âmbito do Sistema Único de Saúde - SUS, o RT-PCR para identificação de mutação do receptor do fator de crescimento epidérmico (EGFR) em pacientes com câncer de pulmão de células não pequenas, publicada no Diário Oficial da União nº 46, seção 1, página 54, em 07 de março de 2024.

Performance Characteristics of Real-Time PCRs for African Swine Fever Virus Genome Detection-Comparison of Twelve Kits to an OIE-Recommended Method.

African swine fever (ASF) is a major threat to pig production, and real-time PCR (qPCR) protocols are an integral part of ASF laboratory diagnosis. With the pandemic spread of ASF, commercial kits have risen on the market. In Germany, the kits have to go through an approval process and thus, general validation can be assumed. However, they have never been compared to each other. In this study, 12 commercial PCR kits were compared to an OIE-recommended method. Samples representing different matrices, genome loads, and genotypes were included in a panel that was tested under diagnostic conditions. The comparison included user-friendliness, internal controls, and the time required. All qPCRs were able to detect ASFV genome in different matrices across all genotypes and disease courses. With one exception, there were no significant differences when comparing the overall mean. The overall specificity was 100% (95% CI 87.66-100), and the sensitivity was between 95% and 100% (95% CI 91.11-100). As can be expected, variability concerned samples with low genome load. To conclude, all tests were fit for purpose. The test system can therefore be chosen based on compatibility and prioritization of the internal control system.

The selection and identification of compound housekeeping genes for quantitative real-time polymerase chain reaction analysis in rat fetal kidney.

During quantitative real-time polymerase chain reaction (RT-qPCR) data analysis, the selection of optimal housekeeping gene is necessary to ensure the accuracy of results. It is noteworthy that housekeeping genes commonly used in adult studies may not be applicable for fetus. However, the stability analysis of housekeeping gene in fetal kidney has not been reported. This study intends to screen the applicable compound housekeeping genes in rat fetal kidney. In this study, eight housekeeping genes used in kidney studies based on literature reports (GAPDH, ACTB, 18S, HPRT, YWHAZ, HMBS, PPIA, and TBP) were selected as the research object. Their expression levels in the rat fetal kidney in physiological condition and the intrauterine growth retardation (IUGR) model induced by prenatal dexamethasone exposure (PDE) (0.2 mg/kg·day from gestation Days 9 to 20) was measured. Furthermore, these eight housekeeping genes were used to conduct relative quantitative analysis of nephrin expression in the fetal kidney in PDE-induced IUGR model, to compare the influence of choosing different housekeeping gene on data analysis of nephrin expression and to verify the reliability of selected compound housekeeping genes. In this study, stable housekeeping genes of fetal kidney tissues in PDE-induced IUGR model were identified: ACTB, GAPDH, TBP, and HMBS for males; ACTB, YWHAZ, and GAPDH for females. Besides, our results suggest that ACTB + GAPDH were the best compound housekeeping genes for normalization analysis in male fetal kidney studies, and ACTB + YWHAZ in females. This study will provide an experimental evidence basis for the selection of housekeeping genes in the RT-qPCR experiment in renal development toxicology-related models.

Culture-Independent Detection of Poliovirus in Stool Samples by Direct RNA Extraction.

Laboratory surveillance for poliovirus (PV) relies on virus isolation by cell culture to identify PV in stool specimens from acute flaccid paralysis (AFP) cases. Although this method successfully identifies PV, it is time-consuming and necessitates the additional biorisk of growing live virus in an increasingly polio-free world. To reduce the risk of culturing PV, the Global Polio Laboratory Network (GPLN) must switch to culture-independent diagnostic methods with sensitivity at least equivalent to that of cell culture procedures. Five commercial nucleic acid extraction kits and one enrichment method were tested for PV extraction efficiency. RNA yield was measured using real-time reverse transcription (RT)-PCR. Based on greater RNA yield, compared with the other kits, the Quick-RNA viral kit was selected for further testing and was optimized using an RNA extraction procedure for stool suspensions. RNA extraction was retrospectively tested with 182 stool samples that had previously tested positive for PVs, in parallel with the standard GPLN virus isolation algorithm. After virus isolation or RNA extraction, real-time RT-PCR assays were performed. RNA extraction was significantly more sensitive than virus isolation (McNemar's test, P < 0.001). Thereafter, the RNA extraction method was tested in parallel for 202 prospective samples; RNA extraction and virus isolation were not significantly different from each other (McNemar's test, P = 0.13). Direct RNA extraction was noninferior to current cell culture methods for detecting PV in stool samples. Our results show that direct RNA extraction can make downstream manipulation safer and can reduce the risk of accidental posteradication viral release. The method is amenable to implementation in a wide variety of polio laboratories. IMPORTANCE Successfully identifying poliovirus from acute flaccid paralysis (AFP) cases is a vital role of the Global Polio Laboratory Network to achieve the goals of the Global Polio Eradication Initiative. Currently, laboratory surveillance relies on virus isolation by cell culture to test for PV present in stool samples. Although this method can identify polioviruses, laboratories must switch to culture-independent methods to reduce the risk associated with growing live viruses in a soon-to-be polio-free world. By implementing this streamlined method, in combination with real-time RT-PCR, laboratories can quickly screen for and type polioviruses of programmatic importance to support the final stages of global polio eradication.

Assessing a chip based rapid RTPCR test for SARS CoV-2 detection (TrueNat assay): A diagnostic accuracy study.

COVID-19 testing is required before admission of a patient in the hospitals, invasive procedures, major and minor surgeries etc. Real Time Polymerase chain reaction is the gold standard test for the diagnosis, but requires well equipped biosafety laboratory along with trained manpower. In this study we have evaluated the diagnostic accuracy of novel TrueNat molecular assay for detecting SARS CoV-2. TrueNat is a chip-based real time PCR test and works on portable, light weight, battery powered equipment and can be used in remote areas with poor infrastructure. In this study 1807 patients samples were collected for both TrueNat and RTPCR COVID-19 testing during study period. Of these 174 (9.7%) and 174 (15%) were positive by RTPCR and TrueNat respectively and taking results of RTPCR as gold standard TrueNat test showed a sensitivity, specificity and diagnostic accuracy of 69.5, 90.9% and 89.2% respectively. It can be concluded that TrueNat is a simple, easy to use, good rapid molecular diagnostic test for diagnosis of COVID-19 especially in resource limited settings and will prove to be a game changer of molecular diagnostics in future.

Diagnostic performance of the Abbott RealTime MTB assay for tuberculosis diagnosis in people living with HIV.

Strengthening tuberculosis diagnosis is an international priority and the advocacy for multi-disease testing devices raises the possibility of improving laboratory efficiency. However, the advantages of centralized platforms might not translate into real improvements under operational conditions. This study aimed to evaluate the field use of the Abbott RealTime MTB (RT-MTB) and Xpert MTB/RIF assays, in a large cohort of HIV-positive and TB presumptive cases in Southern Mozambique. Over a 6-month period, 255 HIV-positive TB presumptive cases were consecutively recruited in the high TB/HIV burden district of Manhiça. The diagnostic performance of both assays was evaluated against two different reference standards: a microbiological gold standard (MGS) and a composite reference standard (CRS). Results from the primary analysis (MGS) showed improved sensitivity (Se) and reduced specificity (Sp) for the Abbott RT-MTB assay compared to the Xpert MTB/RIF (RT-MTB Se: 0.92 (95% CI: 0.75;0.99) vs Xpert Se: 0.73 (95% CI: 0.52;0.88) p value = 0.06; RT-MTB Sp: 0.80 (0.72;0.86) vs Xpert Sp: 0.96 (0.92;0.99) p value < 0.001). The lower specificity may be due to cross-reactivity with non-tuberculous mycobacteria (NTMs), the detection of non-viable MTBC, or the identification of true TB cases missed by the gold standard.

Reacción cadena polimerasa en tiempo real para detección del virus papiloma humano (VPH) cáncer de cérvix / Real-time polymerase chain reaction for detection of human papillomavirus (HPV) cervical cancer

INTRODUCCIÓN: El cáncer de cérvix ha ocupa el primer lugar en las neoplasias con mayor número de casos nuevos registrados en el INEN durante los últimos 10 años. - El virus del papiloma humano (VPH) es fundamental para el desarrollo de neoplasias de cuello uterino y puede detectarse en el 99,7% de los cánceres de cuello uterino. - PCR y captura de híbridos (CH2) son dos técnicas aprobadas nacional y mundialmente para el diagnóstico de VPH. - El diagnóstico por PCR tiene la ventaja de diferenciar oncogenes de alto grado, especialmente 16 y 18 para VPH, en comparación con CH2. METODOLOGÍA: Se revisó literatura existente respecto a la técnica de diagnóstico por PCR para VPH. Se encontró una revisión sistemática y tres estudios clínicos primario. DISCUSIÓN: Ambas pruebas tienen una concordancia mayor del 80%, sin embargo, la prueba PCR diferencia los subtipos oncogénicos y no oncogénicos. - La evidencia es discordante, respecto a la sensibilidad y especificad de las pruebas de PCR y CH2, pues estas varían según la prevalencia de la enfermedad y la población evaluada. Sin embargo, muestra mayor especificidad para PCR. - En el Perú se realizan detección de VPH con PCR-TR. Las agencias reguladoras como la FDA han aprobado el uso de esta tecnología en diferentes plataformas de diagnóstico, así como el MINSA aprobado el uso de diagnóstico de VPH con técnicas moleculares. - Para la implementación de esta nueva tecnología se debe contar con los reactivos, profesional médico capacitado para la lectura de los resultados y contar con el personal médico que atienda a quienes den positivo a la prueba de VPH. - Se sugiere el uso de PCR-TR para el diagnóstico de VPH en el INEN. CONCLUSIONES: El virus del papiloma humano (VPH) es fundamental para el desarrollo de neoplasias de cuello uterino y puede detectarse en el 99,7% de los cánceres de cuello uterino. PCR y captura de híbridos (CHII) son dos técnicas aprobadas nacional y mundialmente para el diagnóstico de VPH. El diagnóstico por PCR tiene la ventaja de diferenciar oncogenes de alto grado, especialmente 16 y 18 para VPH, en comparación con CHII. Se revisó literatura existente respecto a la técnica de diagnóstico por PCR para VPH. Se encontró una revisión sistemática y algunos estudios clínicos primario. Ambas pruebas tienen una concordancia mayor del 80%, sin embargo, la prueba PCR diferencia los subtipos oncogénicos y no oncogénicos. La evidencia es discordante, respecto a la sensibilidad y especificad de las pruebas de PCR y CHII. Sin embargo, muestra mayor especificidad para PCR.

Implementation of an open-source robotic platform for SARS-CoV-2 testing by real-time RT-PCR.

The current global pandemic due to the SARS-CoV-2 has pushed the limits of global health systems across all aspects of clinical care, including laboratory diagnostics. Supply chain disruptions and rapidly-shifting markets have resulted in flash-scarcity of commercial laboratory reagents; this has motivated health care providers to search for alternative workflows to cope with the international increase in demand for SARS-CoV-2 testing. The aim of this study is to present a reproducible workflow for real time RT-PCR SARS-CoV-2 testing using OT-2 open-source liquid-handling robots (Opentrons, NY). We have developed a framework that includes a code template which is helpful for building different stand-alone robotic stations, capable of performing specific protocols. Such stations can be combined together to create a complex multi-stage workflow, from sample setup to real time RT-PCR. Using our open-source code, it is easy to create new stations or workflows from scratch, adapt existing templates to update the experimental protocols, or to fine-tune the code to fit specific needs. Using this framework, we developed the code for two different workflows and evaluated them using external quality assessment (EQA) samples from the European Molecular Genetics Quality Network (EMQN). The affordability of this platform makes automated SARS-CoV-2 PCR testing accessible for most laboratories and hospitals with qualified bioinformatics personnel. This platform also allows for flexibility, as it is not dependent on any specific commercial kit, and thus it can be quickly adapted to protocol changes, reagent, consumable shortages, or any other temporary material constraints.

Accurate Measurement of Cellular and Cell-Free Circulating Mitochondrial DNA Content from Human Blood Samples Using Real-Time Quantitative PCR.

Changes in circulating mitochondrial DNA (mtDNA) are widely used to indicate mitochondrial dysfunction in common non-genetic diseases where mitochondrial dysfunction may play a role. However, the methodology being used is not always specific and reproducible, and most studies use whole blood rather than evaluating cellular and cell-free mtDNA separately. Cellular mtDNA is contained within the mitochondrion and encodes vital subunits of the OXPHOS machinery. Conversely, cell-free mtDNA can have harmful effects, triggering inflammatory responses and potentially contributing to pathogenic processes. In this chapter, we describe a protocol to accurately measure the amount of cellular and cell-free human mtDNA in peripheral blood. Absolute quantification is carried out using real-time quantitative PCR (qPCR) to quantify cellular mtDNA, measured as the mitochondrial genome to nuclear genome ratio (designated the Mt/N ratio) in whole blood and peripheral blood mononuclear cells (PBMCs) and the number of mtDNA copies per µL in plasma and serum. We describe how to (1) separate whole blood into PBMCs, plasma, and serum fractions, (2) prepare DNA from each of these fractions, (3) prepare dilution standards for absolute quantification, (4) carry out qPCR for either relative or absolute quantification from test samples, (5) analyze qPCR data, and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use and can be modified to quantify mtDNA from other body fluids, human cells, and tissues.

A Prospective Evaluation of the Analytical Performance of GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B.

BACKGROUND: Molecular tests are the mainstay of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, their accessibility can be limited by the long examination time and inability to evaluate multiple samples at once. OBJECTIVE: This study evaluated the analytical performance of the newly developed rapid molecular assays GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B. METHOD: This prospective study was conducted between 14 December 2020 and 9 January 2021 at a polymerase chain reaction (PCR) center. Samples were collected from the nasopharynx with flocked swabs. Molecular tests were performed with the GENECUBE® system and reference reverse transcription (RT)-PCR, and the results of the two assays were compared. RESULT: Among 1065 samples, 81 (7.6%) were positive for SARS-CoV-2 on the reference RT-PCR. Three showed discordance between GENECUBE® HQ SARS-CoV-2 and the reference RT-PCR; the total, positive, and negative samples of concordance for the two assays were 99.7%, 100%, and 99.7%, respectively. All discordant cases were positive with GENECUBE® HQ SARS-CoV-2 and negative with the reference RT-PCR. SARS-CoV-2 was detected in all three samples using another molecular assay for SARS-CoV-2. For GENECUBE® FLU A/B, the total, positive, and negative samples of concordance for the two assays were 99.5%, 100%, and 99.1%. CONCLUSION: The GENECUBE® HQ SARS-CoV-2 and GENECUBE® FLU A/B demonstrated sufficient analytical performance to detect SARS-CoV-2 and influenza virus A/B.

Comparative practicability and analytical performances of Credo VitaPCR™ Flu A&B and Cepheid Xpert® Xpress Flu/RSV platforms.

To compare the practicability (usability and satisfaction) and analytical performances of VitaPCR™ Flu A&B Assay (Credo Diagnostics Biomedical Pte. Ltd., Singapore, Republic of Singapore) and Xpert® Xpress Flu/RSV kit (Cepheid, Sunnyvale, USA), two rapid point-of-care (POC) nucleic acid amplification tests (NAATs) by reference to multiplex RT-PCR for respiratory viruses. Nasopharyngeal swabs (n=117) were collected from patients with influenza-like illness in Paris, France. Thawed specimens were further analyzed with both NAATs. The usability was comparable for both NAATs. Satisfaction questionnaire was better for the VitaPCR™ platform for the short time of test result in 20 minutes. Both NAATs showed comparable sensitivities (VitaPCRTM: 95.0%; Xpert® Xpress: 97.5%) and specificities (100%) for influenza A/B RNA detection, with excellent reliability and accuracy between both NAATs. Both VitaPCR™ and Xpert® Xpress NAATs can be implemented in hospital setting as POC NAATs to rapidly detect influenza A/B RNA in symptomatic patients.

Ultra-precise quantification of mRNA targets across a broad dynamic range with nanoreactor beads.

Precise quantification of molecular targets in a biological sample across a wide dynamic range is a key requirement in many diagnostic procedures, such as monitoring response to therapy or detection of measurable residual disease. State of the art digital PCR assays provide for a dynamic range of four orders of magnitude. However digital assays are complex and require sophisticated microfluidic tools. Here we present an assay format that enables ultra-precise quantification of RNA targets in a single measurement across a dynamic range of more than six orders of magnitude. The approach is based on hydrogel beads that provide for microfluidic free compartmentalization of the sample as they are used as nanoreactors for reverse transcription, PCR amplification and combined real time and digital detection of gene transcripts. We have applied these nanoreactor beads for establishing an assay for the detection and quantification of BCR-ABL1 fusion transcripts. The assay has been characterized for its precision and linear dynamic range. A comparison of the new method against conventional real time RT-PCR analysis (reference method) with clinical samples from patients with chronic myeloid leukemia (CML) revealed excellent concordance with Pearsons correlation coefficient of 0.983 and slope of 1.08.

Analytic Sensitivity of 3 Nucleic Acid Detection Assays in Diagnosis of SARS-CoV-2 Infection.

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and it is unclear how available assays compare. METHODS: For the Abbott RealTime SARS-CoV-2 assay (m2000; Abbott Molecular), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from 8538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of 2 other assays with more rapid turnaround times [Cepheid Xpert Xpress (GeneXpert; Cepheid); n = 27] and a laboratory developed test on the Luminex ARIES system [ARIES LDT (Luminex); n = 50] as a function of virus concentrations, from which we projected their false-negative rates in our patient population. RESULTS: SARS-CoV-2 was detected in 27% (95% CI: 26%-28%) of all specimens. Estimated viral concentrations were widely distributed, and 17% (95% CI: 16%-19%) of positive individuals had viral concentrations <845 copies/mL. Positive percent agreement was strongly related to viral concentration, and reliable detection (i.e., ≥95%) was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false-negative rates of 4% (95% CI: 0%-21%) and 27% (95% CI: 11%-46%), respectively. CONCLUSIONS: Substantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with less analytic sensitivity.

Comparison between Abbott m2000 RealTime and Alinity m STI systems for detection of Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycoplasma genitalium.

The new Abbott Alinity m STI Assay was compared with Abbott m2000 RealTime PCR. For Chlamydia trachomatis, 26 (7.5%) of 347 samples were positive in the Alinity assay and 24 (6.9%) in the m2000 assay. Corresponding figures for Neisseria gonorrhoeae were 23 (6.6%) and 17 (4.9%). For Mycoplasma genitalium, 22 (7.9%) of 279 samples were positive in the Alinity assay and 18 (6.5%) in the m2000 assay, for which DNA extraction was performed on an m2000sp instrument combined with in-house real-time PCR. The Alinity assay has at least the same sensitivity as the m2000 assay. The specificity was evaluated by discrepancy analysis.

Reverse Transcription Recombinase-Aided Amplification Assay With Lateral Flow Dipstick Assay for Rapid Detection of 2019 Novel Coronavirus.

Background: The emerging Coronavirus Disease-2019 (COVID-19) has challenged the public health globally. With the increasing requirement of detection for SARS-CoV-2 outside of the laboratory setting, a rapid and precise Point of Care Test (POCT) is urgently needed. Methods: Targeting the nucleocapsid (N) gene of SARS-CoV-2, specific primers, and probes for reverse transcription recombinase-aided amplification coupled with lateral flow dipstick (RT-RAA/LFD) platform were designed. For specificity evaluation, it was tested with human coronaviruses, human influenza A virus, influenza B viruses, respiratory syncytial virus, and hepatitis B virus, respectively. For sensitivity assay, it was estimated by templates of recombinant plasmid and pseudovirus of SARS-CoV-2 RNA. For clinical assessment, 100 clinical samples (13 positive and 87 negatives for SARS-CoV-2) were tested via quantitative reverse transcription PCR (RT-qPCR) and RT-RAA/LFD, respectively. Results: The limit of detection was 1 copies/µl in RT-RAA/LFD assay, which could be conducted within 30 min at 39°C, without any cross-reaction with other human coronaviruses and clinical respiratory pathogens. Compared with RT-qPCR, the established POCT assay offered 100% specificity and 100% sensitivity in the detection of clinical samples. Conclusion: This work provides a convenient POCT tool for rapid screening, diagnosis, and monitoring of suspected patients in SARS-CoV-2 endemic areas.

Thermal Shift Assay for Exploring Interactions Between Fatty Acid-Binding Protein and Inhibitors.

Thermal shift assay (TSA) is a widely used method in discovering potential compounds (e.g., ligands, inhibitors, and other additives) to the target protein for structural genomics and drug screening in both academia and industry. The presence of sensitive fluorescent dye enables to monitor thermal stability of protein and compounds affecting this stability. By using a conventional real-time PCR instrument, it is determined as a low-cost and high efficacy experiment applied to identify optimal conditions for ligand binds to protein. Fatty acid-binding proteins (FABPs) are small molecular proteins in transporting fatty acids and other lipophilic substances in physiological and pathological responses. This chapter presents a comprehensive workflow to monitor recombinant FABP-compound interactions for an initial screening for inhibitors using TSA with SYPRO Orange dye.

Ultrasensitive monitoring strategy of PCR-like levels for zearalenone contamination based DNA barcode.

BACKGROUND: The ultrasensitive monitoring strategy of zearalenone (ZEN) is essential and desirable for food safety and human health. In the present study, a coupling of gold nanoparticles-DNA barcode and direct competitive immunoassay-based real-time polymerase chain reaction signal amplification (RT-IPCR) for ZEN close to the sensitivity of PCR-like levels is described and evaluated. RESULTS: The RT-IPCR benefited from the use of a DNA barcode and RT-PCR detection strategy, thus resulting in ultrasensitive and simple detection for ZEN. Under the optimal RT-IPCR, the linear range of detection was from 0.5 to 1000 pg mL-1 and the limit of detection was 0.5 pg mL-1 , which was 400-fold lower than the enzyme-linked immunosorbent assay. The detection procedure was simplified and the detection time was shortened. The specificity, accuracy and precision of the RT-IPCR confirmed a high performance. ZEN-positive contamination levels were from 0.056 to 152.12 ng g-1 by the RT-IPCR, which was demonstrated to be highly reliable by liquid chromatography-tandem mass spectrometry. CONCLUSION: The proposed RT-IPCR could be used as an alternative for detecting ZEN with satisfactory ultrasensitivity, simplicity, low cost and high-throughput. The present study could provide a strategy for the ultrasensitive detection of the small molecule with a simple and practical approach, which has significant appeal and application prospects.

An Ultra-Rapid Real-Time RT-PCR Method Using the PCR1100 to Detect Severe Acute Respiratory Syndrome Coronavirus-2.

The disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Wuhan, China, in December 2019, has rapidly spread worldwide. SARS-CoV-2 is usually detected via real-time reverse-transcription polymerase chain reaction (RT-PCR). However, the increase in specimen load in institutions/hospitals necessitates a simpler detection system. Here, we present an ultra-rapid, real-time RT-PCR assay for SARS-CoV-2 detection using PCR1100 device. Although PCR1100 tests only one specimen at a time, the amplification period is less than 20 min and the sensitivity and specificity match those of conventional real-time RT-PCR performed on large instruments. The method is potentially helpful when daily multiple SARS-CoV-2 testing is needed, for example to confirm virus-free status prior to patient discharge.

Detection of dengue, chikungunya, and Zika RNA in blood donors from Southeast Asia.

BACKGROUND: Chikungunya (CHIKV), dengue (DENV), and Zika (ZIKV) viruses are of concern due to the potential of transfusion transmission in blood, especially in regions such as Southeast Asia where the viruses are endemic. The recent availability of nucleic acid testing (NAT) to screen blood donations on an automated platform provides the opportunity to detect potentially infectious units in asymptomatic donors. STUDY DESIGN AND METHODS: Three thousand blood donations from Vietnam and 6000 from Thailand were screened with a real-time polymerase chain reaction (PCR) test (cobas CHIKV/DENV, Roche Diagnostics, Indianapolis, IN) and equal numbers on cobas Zika (Roche Diagnostics). Reactive samples were tested by alternative NAT with resolution of discordant results by heminested PCR. Throughput of simultaneous testing of the two assays on the cobas 8800 system (Roche Diagnostics) was evaluated. RESULTS: In Vietnam, 9 of 3045 samples were reactive for DENV and all were confirmed, for a prevalence (with 95% confidence interval [CI]) of 0.296% (0.135-0.560). In Thailand, 2 of 6000 samples were reactive for CHIKV, 4 of 6000 for DENV, and 1 of 6005 for ZIKV, and all confirmed. The prevalence of CHIKV is 0.033% (0.004-0.120), DENV 0.067% (0.018-0.171), and ZIKV 0.017% (0.000-0.093). The overall specificity for the cobas CHIKV/DENV and cobas Zika tests was 100% (99.959-100). For the simultaneous assay testing, 960 test results were available in 7 hours and 53 minutes. CONCLUSION: Detection of CHIKV, DENV, and ZIKV RNA in donor samples in Vietnam and Thailand indicate the presence of the virus in asymptomatic blood donors. The cobas 6800/8800 systems (Roche Molecular Systems, Pleasanton, CA) enable screening blood donations in endemic areas for these viruses together or separately.

Simultaneous and accurate visual identification of chicken, duck and pork components with the molecular amplification integrated lateral flow strip.

We propose a visual strategy for simultaneous detection of multiple adulterated components in beef by integration of multiple polymerase chain reaction (mPCR) with the lateral flow strip (LFS). The primer sets for adulterated components are uniquely designed with different nucleic acid tags (NAT), enabling the amplicons with specific wobbled sequences at two opposite ends. The wobbled sequences will precisely hybridize with the pre-immobilized capture probes on T lines (T1, T2 and T3) and C line, contributing to the coloration of LFS. Taking advantages of extraordinary amplification efficiency of PCR and simplicity of LFS, common adulterated components including chicken, duck and pork can be easily detected with LOD as low as 0.01% (wt%), which is comparable to that of quantitative real-time polymerase chain reaction (qPCR) but with more simplified operations and reduced costs. The method can be extended to identification of other components by replacing the functional primer set. This method can be a useful candidate for meat quality control at the resource-limited setups.