Abstract INTRODUCTION: The main laboratory test for the diagnosis of coronavirus disease 2019 (COVID-19) is the reverse transcription real-time polymerase chain reaction (RT-qPCR). However, RT-qPCR is expensive because of the number of tests required. This study aimed to evaluate an alternative to the RT-qPCR approach for the detection of sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is half of the total volume currently recommended by the US Centers for Disease Control and Prevention. METHODS: The analytical limit of detection (LoD) and the reaction efficiency using half volumes of the RT-qPCR assay were evaluated for the N1 and N2 regions using a synthetic control RNA. A panel of 76 SARS-CoV-2-positive and 26 SARS-CoV-2-negative clinical samples was evaluated to establish clinical sensitivity and specificity. RESULTS: The RT-qPCR assay efficiency was 105% for the half and standard reactions considering the N2 target and 84% (standard) and 101% (half) for N1. The RT-qPCR half-reaction LoD for N1 and N2 were 20 and 80 copies/µL, respectively. The clinical sensitivity and specificity were 100%. The half reaction presented a decrease of up to 5.5 cycle thresholds compared with standard RT-qPCR. CONCLUSIONS: The use of the RT-qPCR half-reaction proved feasible and economic for the detection of SARS-CoV-2 RNA.

Resumo Introdução: A infecção pelo vírus BK (BKV) em pacientes de transplante renal pode levar a disfunção do aloenxerto renal e perda do enxerto. A determinação precisa da carga viral do BKV é fundamental para prevenir a nefropatia associada ao BKV (BKVAN), mas o ponto de corte de melhor valor preditivo para BKVAN ainda é foco de debates. Objetivo: Avaliar o desempenho de um teste de qPCR comercial e outro desenvolvido internamente para detecção quantitativa de vírus BK em receptores de transplante renal. Métodos: O presente estudo prospectivo incluiu receptores de transplante renal de dois grandes hospitais universitários no Brasil. Os pacientes foram testados para infecção por BKV a cada três meses no primeiro ano pós-transplante com um teste comercial de reação em cadeia de polimerase quantitativa em tempo real (qPCR) e outro desenvolvido internamente. A presença de BKVAN foi confirmada com base na histopatologia. A área sob a curva para o qPCR plasmático foi determinada a partir da análise da característica de operação do receptor. Resultados: Um total de 200 pacientes foram incluídos. Cinquenta e oito por cento eram do sexo masculino, 19,5% tinham diabetes mellitus e 82% tiveram seus rins transplantados de doadores falecidos. Viremia de BKV foi detectada em 32,5% dos pacientes e oito (4%) foram diagnosticados com BKVAN. BKVAN foi associada a viremia de 4,1 log cópias/mL usando o kit comercial. O corte para o ensaio interno foi de 6,1 log cópias/mL. A linearidade entre o kit comercial e o ensaio interno foi R2 = 0,83. Conclusão: Nosso estudo demonstrou uma acentuada variabilidade na carga viral de BKV quando diferentes metodologias de qPCR foram utilizadas. O ensaio interno de qPCR mostrou-se clinicamente útil, além de ser uma opção menos onerosa em relação aos kits comerciais de qPCR. Há uma necessidade urgente de se definir padrões de BKV para a comunidade internacional.

Abstract Introduction: BK virus (BKV) infection in renal transplant patients may cause kidney allograft dysfunction and graft loss. Accurate determination of BKV viral load is critical to prevent BKV-associated nephropathy (BKVAN) but the cut-off that best predicts BKVAN remains controversial. Objective: To evaluate the performance of a commercial and an in-house qPCR test for quantitative detection of BK virus in kidney transplant recipients. Methods: This was a prospective study with kidney transplant recipients from two large university hospitals in Brazil. Patients were screened for BKV infection every 3 months in the first year post-transplant with a commercial and an in-house real time polymerase chain reaction (qPCR) test. BKVAN was confirmed based on histopathology. The area under the curve for plasma qPCR was determined from receiver operating characteristic analysis. Results: A total of 200 patients were enrolled. Fifty-eight percent were male, 19.5% had diabetes mellitus, and 82% had the kidney transplanted from a deceased donor. BKV viremia was detected in 32.5% and BKVAN was diagnosed in 8 patients (4%). BKVAN was associated with viremia of 4.1 log copies/mL, using a commercial kit. The cut-off for the in-house assay was 6.1 log copies/mL. The linearity between the commercial kit and the in-house assay was R2=0.83. Conclusion: Our study shows that marked variability occurs in BKV viral load when different qPCR methodologies are used. The in-house qPCR assay proved clinically useful, a cheaper option in comparison to commercial qPCR kits. There is an urgent need to make BKV standards available to the international community.

Resumo Introdução: Citomegalovírus (CMV) é uma importante causa de infecção viral após o transplante renal. Os métodos diagnósticos presentemente utilizados são a antigenemia pp-65 e os métodos que utilizam a amplificação de ácidos nucléicos pela reação em cadeia da polimerase (PCR) e visam à detecção da replicação viral. Objetivo: O objetivo deste estudo foi avaliar e comparar a incidência de infecção ativa por CMV em pacientes transplantados renais pelos dois métodos e estabelecer a melhor correlação clínico-laboratorial. Métodos: Trinta pacientes transplantados renais seqüenciais em um único centro foram incluídos em um estudo de coorte prospectiva. Amostras de sangue periférico foram coletadas a partir do 15º dia até o 6º mês pós-transplante e avaliadas para replicação de CMV por Antigenemia pp-65 e PCR quantitativo (qPCR). Resultados: Foram analisadas 240 amostras e a incidência de infecção ativa foi similar pelos dois métodos. O tempo médio transcorrido desde o transplante até o primeiro teste com resultado positivo foi quase idêntico entretanto mais amostras tiveram resultado positivo por qPCR do que antigenemia, um comportamento que se manteve quase uniforme ao longo do tempo. Concordância entre os testes foi observada em 217 amostras (90,4%; kappa = 0,529; p < 0,001) e em 25 pacientes (83,3%; kappa = 0,667; p < 0,001). A avaliação dos parâmetros diagnósticos para replicação de CMV revelaram maior sensibilidade para qPCR (82,1%) contra antigenemia (59,0%). PCR quantitativo também foi levemente mais preciso do que antigenemia. Conclusão: Nossos dados demonstram que ambos os métodos são adequados e tem precisão quase equivalente para a detecção da replicação do CMV após o transplante renal. A escolha entre um ou outro deve levar em consideração a demanda, capacidade de execução e custo-efetividade em cada instituição.

Abstract Introduction: Cytomegalovirus (CMV) infection is a main viral infection after kidney transplantation. The diagnostic methods currently employed are pp65 antigenemia and nucleic acid amplification by polymerase chain reaction (PCR) and aim at detecting viral replication. Objective: The goal of this study was to evaluate and compare by both methods the incidence of CMV active infection in kidney transplant patients and to establishthe best clinical-laboratory correlation. Methods: Thirty sequential kidney transplant recipients were enrolled in a single center prospective cohort study. Peripheral blood samples were drawn from day 15 until the 6th month after transplantation and tested for CMV replication by pp65 antigenemia and quantitative PCR assays (qPCR). Results: Two hundred forty samples were analyzed and the incidence of active infection was similar by both methods. Time elapsed to the first positive test was almost identical but more samples tested positive by qPCR than by antigenemia in a behavior that was almost evenly distributed overtime. Agreement between tests was observed in 217 samples (90.4%; kappa = 0.529; p < 0.001) and in 25 patients the tests were concordant (83.3%; kappa = 0.667; p < 0.001). The evaluation of the diagnostic parameters for CMV replication revealed higher sensitivity for the qPCR test (82.1%) against antigenemia (59.0%). Quantitative PCR was also slightly more accurate than antigenemia. Conclusion: Our data demonstrate that both methods are suitable and have almost equivalent accuracy for the detection of post-transplant cytomegalovirus replication. The choice for either test must take in consideration the demand, execution capability and cost-effectiveness at each institution.

Meningitis is a severe and potentially fatal form of tuberculosis. The diagnostic workup involves detection of acid-fast bacilli (AFB) in the cerebrospinal fluid (CSF) by microscopy or culture, however, the difficulty in detecting the organism poses a challenge to diagnosis. The use of the polymerase chain reaction (PCR) in the diagnostic approach to Mycobacterium tuberculosis (MTB) meningitis has been reported as a fast and accurate method, with several commercial kits available. As an alternative, some institutions have been developing inexpensive in house assays. In our institution, we use an in house PCR for tuberculosis. We analyzed the performance of our PCR for the diagnosis of MTB meningitis in 148 consecutive patients, using MTB culture as gold standard. The sensitivity and specificity of CSF PCR for the diagnosis of MTB meningitis was 50% and 98.6% respectively with a concordance with CSF mycobacterial culture of 96% (Kappa=0.52). In contrast to CSF cultures for MTB, our PCR test is a fast, simple and inexpensive tool to diagnose tuberculous meningitis with a performance similar to that obtained with the available commercial kits.