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.

Abstract INTRODUCTION: Considering the persistent positivity on RT-qPCR tests, the results of SARS-CoV-2 were monitored to evaluate the viral RNA shedding period. METHODS: Between March and June 2020, the sequential results of 29 healthcare workers’ were monitored using RT-qPCR. RESULTS: More than 50% of the individuals remained RT-qPCR positive after 14 days. Furthermore, this is the first study to describe positive RT-qPCR for SARS-CoV-2 in a healthcare worker with mild symptoms 95 days after the first positive test. CONCLUSIONS: Sequential RT-qPCR results were heterogeneous, and the viral RNA shedding period is unique for each person.

ABSTRACT The objective of this study was to investigate the effects of slaughter body weight (SW) on the performance, carcass characteristics, and meat quality of Jersey bulls in feedlots from weaning to slaughter. Eighteen Jersey bulls (125.7±15.9 kg; 5±0.6 months old) were used in the study. The treatments corresponded to three slaughter-weights: L360 – light weight, SW of 360 kg, M390 – medium weight, SW of 390 kg, and H420 – heavy weight, SW of 420 kg (n = 6/treatment); the animals were slaughtered at 368, 392, and 422 kg, respectively. The average daily gain was not influenced by SW. The M390 and H420 groups remained in feedlot, on average, 6 and 51 d longer, respectively, to reach a similar SW in relation to the L360 group. The increase in SW did not influence dry matter intake. However, the L360 group exhibited greater dry matter intake relative to body weight compared with the other two groups (29 vs. 26 g/kg). The increase in SW resulted in heavier and longer carcasses, with higher hot carcass yields. However, animals with greater SW had lower fat thickness. In addition, the increase in SW led to greater pistol cut, bone, and muscle weight for the carcasses. Although the meat color of Jersey bulls was darker in the H420 group, the meat was considered softer and more palatable by the consumer panel compared with the meat from the L360 group. The L360 group exhibited less fluid loss during thawing and cooking. Shear force measured by Warner Blatzer Shear was lower for H420. Animals slaughtered in the L390 group had an intermediate carcass weight, similar carcass yield, better cover fat and meat quality (color and shear) than animals slaughtered in the H420. Combining these factors with a shorter feedlot time compared with that of heavier animals, the SW of feedlot Jersey bulls is recommended at 390 kg.

ABSTRACT Group B Streptococcus is a causative agent of invasive neonatal infections. Maternal colonization by Streptococcus agalactiae is a necessary condition for vertical transmission, with efficient screening of pregnant women playing an essential role in the prevention of neonatal infections. In this study, we aimed to compare the performance of conventional polymerase chain reaction and real-time PCR assays as screening methods for S. agalactiae in pregnant women against the microbiological culture method considered as the gold-standard. A total of 130 samples from pregnant women were analyzed for sensitivity, specificity, positive predictive value, and negative predictive value. Statistical analysis was performed using the SPSS software, version 20.0. The verified colonization rate was 3.8% with the gold-standard, 17.7% with conventional PCR assay, and 29.2% with the real-time PCR test. The trials with conventional PCR and real-time PCR had a sensitivity of 100% and a specificity of 85.6% and 73.6%, respectively. The real-time PCR assay had a better performance compared to the gold-standard and a greater detection rate of colonization by S. agalactiae compared to conventional PCR assay. With its quick results, it would be suitable for using in routine screenings, contributing to the optimization of preventive approaches to neonatal S. agalactiae infection.

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.

Abstract The objective of this work was to produce protein hydrolysates from by-products of the Nile tilapia fileting process, and to assess the effects of different hydrolysis times on the antioxidant activity of the hydrolysed animal-based protein, in free form and incorporated into a food matrix. Gutted tilapia heads and carcasses were hydrolysed by Alcalase® for different hydrolysis times producing six hydrolysates. The protein content, degree of hydrolysis, reverse-phase high-performance liquid chromatography, and antioxidant activity by the ORAC, FRAP and TEAC methods were analysed. Three mini-hamburger formulations were produced and the lipidic oxidation of mini-hamburger was determined by TBARS. The protein contained in the residue was completely recovered in the process. The hydrolysates varied in their degree of hydrolysis, but presented similar levels of antioxidant activity. In the mini-hamburgers the hydrolysate was capable of delaying oxidation after 7 days of storage. Hydrolysis of tilapia processing by-products produced peptides may be used in the formulation of functional foods.

O objetivo deste experimento foi avaliar as características da carcaça de bezerros holandeses terminados em confinamento ou em pastagem com suplementação e abatidos com diferentes pesos de abate. Os animais confinados foram alimentados com volumoso e concentrado comercial, na proporção de 40:60, sendo a silagem de milho utilizada como volumoso. O delineamento experimental foi o inteiramente casualizado, em arranjo fatorial 2x4 (dois sistemas de terminação x quatro pesos de abate). Os animais foram abatidos à medida que atingiam os pesos de abate pré-determinados (140, 180, 220 e 260kg). O sistema de acabamento não teve influência sobre o peso e rendimento de carcaça quente e fria e as perdas de carcaça, mas os animais confinados apresentaram maior espessura de gordura. Animais confinados apresentaram melhor conformação, comparados com os terminados em pastagem. À medida que aumentou o peso de abate, houve crescimento linear para peso de carcaça quente e fria, rendimento de carcaça quente e fria, conformação, medidas métricas e peso dos cortes comerciais da carcaça. O percentual do corte traseiro decresceu com o aumento do peso de abate, enquanto que a espessura de gordura apresentou resposta quadrática. Os sistemas de abate apresentaram rendimento de carcaça semelhante. As características da carcaça melhoram com o aumento do peso de abate, mas, em percentagem, são semelhantes

Introduction This study reports the pediatric epidemiology of respiratory syncytial virus (RSV), influenza (IF), parainfluenza (PIV), and adenovirus (ADV) at Hospital de Clínicas de Porto Alegre. Methods Cases of infection, hospitalizations in intensive care units (ICUs), nosocomial infections, and lethality rates were collected from 2007 to 2010. Results RSV accounted for most nosocomial infections. Intensive care units admission rates for ADV and RSV infections were highest in 2007 and 2010. During 2008-2009, H1N1 and ADV had the highest ICU admission rates. ADV had the highest fatality rate during 2007-2009. Conclusions Each virus exhibited distinct behavior, causing hospitalization, outbreaks, or lethality.

Introduction Herpes simplex virus (HSV) and varicella zoster virus (VZV) are responsible for a variety of human diseases, including central nervous system diseases. The use of polymerase chain reaction (PCR) techniques on cerebrospinal fluid samples has allowed the detection of viral DNA with high sensitivity and specificity. Methods Serial dilutions of quantified commercial controls of each virus were subjected to an in-house nested-PCR technique. Results The minimum detection limits for HSV and VZV were 5 and 10 copies/µL, respectively. Conclusions The detection limit of nested-PCR for HSV and VZV in this study was similar to the limits found in previous studies.

Burkholderia cenocepacia may cause serious infections in patients with cystic fibrosis, and this microorganism can be highly transmissible. Pulsed-field gel electrophoresis is widely used to study the dynamics of strain spread in cystic fibrosis patients. The aim of this work was to perform pulsed-field gel electrophoresis-based molecular typing of B. cenocepacia isolates to evaluate the epidemiology of this species at our hospital. A total of 28 isolates from 23 cystic fibrosis patients were analyzed. Initially, we compared isolates obtained from the same patient at different periods of time. We then compared the pulsed-field gel electrophoresis profiles of 15 IIIA isolates, and in a third analysis, evaluated the genetic profile of 8 IIIB isolates from different patients. The pulsed-field gel electrophoresis profiles of isolates from the same patient indicated that they are genetically indistinguishable. Analysis of isolates from different patients revealed the presence of multiple clonal groups. These results do not indicate cross-transmission of a unique clone of B. cenocepacia among cystic fibrosis patients, although this has been observed in some patients. Our findings highlight the importance of adequate patient follow-up at cystic fibrosis centers and adherence to management and segregation measures in cystic fibrosis patients colonized with B. cenocepacia.

Streptococcus agalactiae or group B Streptococcus (GBS) is one of the most important causal agents of serious neonatal infections. Numerous assays have been evaluated for GBS screening in order to validate a fast and efficient method. The aim of this study was to compare the culture technique (established as the gold standard) with the molecular method of polymerase chain reaction (PCR) with specific primers (atr gene). Two hundred and sixty-three samples were analyzed. Vaginal samples were collected, according to the Centers for Disease Control and Prevention (CDC) recommendations, from women over 35 weeks of pregnancy at Hospital de Clínicas de Porto Alegre (HCPA). Two different extraction methods were tested in all samples collected. PCR technique yielded 71 (26.99%) positive results. Sensitivity and specificity for PCR were 100% and 86.88%, respectively. PCR demonstrated a shorter turnaround time than the culture. The molecular methodology proved to be a useful screening for GBS, allowing effective treatment to be initiated in shorter time to prevent newborn infection.

INTRODUÇÃO: O citomegalovírus humano (HCMV), causador de infecção latente, reativa com frequência em pacientes imunossuprimidos. Portanto, o HCMV permanece uma das infecções mais comuns após transplantes de órgãos sólidos e de células hematopoiéticas resultando em significativa morbidade, perda do enxerto e ocasional mortalidade. Assim, o diagnóstico precoce para uma terapia preventiva é de grande importância. Este estudo visa comparar o desempenho dos métodos PCR qualitativo in-house e antigenemia pp65 para o diagnóstico de infecção por CMV em pacientes imunossuprimidos do Hospital de Clínicas de Porto Alegre. MÉTODOS: O estudo foi realizado em 216 amostras de sangue total (EDTA) coletadas de 85 pacientes, entre agosto de 2006 e janeiro de 2007. RESULTADOS: Dentre as 216 amostras analisadas, 81 (37,5%) amostras apresentaram resultados positivos na PCR, enquanto 48 (22,2%) apresentaram resultados positivos na antigenemia. A sensibilidade, especificidade, valor preditivo positivo e valor preditivo negativo para a PCR, considerando antigenemia como padrão foram 87,5%, 76,8%, 51,8% e 95,5%, respectivamente. CONCLUSÕES: Estes resultados demonstraram que a PCR tem alta sensibilidade e valor preditivo negativo. Consequentemente PCR é especialmente indicada para o diagnóstico inicial de infecção por HCMV. No caso da estratégia de terapia preventiva, a identificação de pacientes com alto risco para a doença por HCMV é fundamental e a PCR pode ser uma ferramenta útil.

INTRODUCTION: Human cytomegalovirus (HCMV) is often reactive in latently infected immunosuppressed patients. Accordingly, HCMV remains one of the most common infections following solid organ and hemopoietic stem cell transplantations, resulting in significant morbidity, graft loss and occasional mortality. The early diagnosis of HCMV disease is important in immunosuppressed patients, since in these individuals, preemptive treatment is useful. The objective of this study was to compare the performance of the in-house qualitative polymerase chain reaction (PCR) and pp65 antigenemia to HCMV infection in immunosuppressed patients in the Hospital de Clínicas of Porto Alegre (HCPA). METHODS: A total of 216 blood samples collected between August 2006 and January 2007 were investigated. RESULTS: Among the samples analyzed, 81 (37.5%) were HCMV-positive by PCR, while 48 (22.2%) were positive for antigenemia. Considering antigenemia as the gold standard, sensitivity, specificity, positive predictive values and negative predictive values for PCR were 87.5%, 76.8%, 51.8% and 95.5% respectively. CONCLUSIONS: These results demonstrated that qualitative PCR has high sensitivity and negative predictive value (NPV). Consequently PCR is especially indicated for the initial diagnosis of HCMV infection. In the case of preemptive treatment strategy, identification of patients at high-risk for HCMV disease is fundamental and PCR can be useful tool.

INTRODUCTION: Resistance to macrolides, lincosamides and streptogramins B (MLS B antibiotics) in staphylococci may be due to modification in ribosomal target methylase encoded by erm genes. The expression of MLS B resistance lead to three phenotypes, namely constitutive resistance (cMLS B), inducible resistance (iMLS B), and resistance only to macrolides and streptogramins B (MS B). The iMLS B resistance is the most difficult to detect in the clinical laboratory. OBJECTIVE: This study investigated the expression of MLS B resistance and the prevalence of the erm genes among 152 clinical isolates of Staphylococcus aureus and coagulase-negative Staphylococcus (CNS) from Hospital de Clínicas de Porto Alegre. METHODS: Primary MLS B resistance was detected by the disk diffusion method. Isolates with iMLS B phenotype were tested by double-disk induction method. All isolates were tested by a genotypic assay, PCR with specific primers. RESULTS: A total of 46.7% of staphylococci were positive for cMLS B; 3.3% for iMLS B and 3.3% for MS B. One or more erm genes were present in 50.1% of isolates. The gene ermA was detected in 49 isolates, ermC in 29 and ermB in 3. CONCLUSION: The prevalence of the ermA, ermB and ermC genes were 29.6%, 17.1% and 0.66% respectively, and constitutive resistance was the most frequent as compared to the other two phenotypes.

OBJETIVO: Avaliar a correlação entre cifose pós-traumática e função nos pacientes submetidos ao tratamento conservador das fraturas toracolombares do tipo explosão. MÉTODOS: Realizado estudo retrospectivo segundo os critérios de Denis e Magerl classificados como subtipo A3 em 36 pacientes que preencheram o critério de inclusão para esta amostra e submetidos à aplicação de gesso antigravitacional ou órtese toracolombossacra (TLSO). A média de idade dos pacientes estudados foi de 50,83 anos, com mínimo de 13 e máximo de 83 anos, sendo 20 do sexo masculino e 16 do feminino. O resultado do tratamento foi avaliado com base no questionário de qualidade de vida Short Form-36 (SF-36) e nas escalas de dor e trabalho de Denis e o quadro clínico neurológico conforme a classificação de Frankel. A quantificação da dor foi realizada com base na escala visual analógica da dor (EVA) A mensuração da cifose residual foi obtida pelo método de Cobb à admissão e ao final do seguimento. Mostrar o grau maior, menor e a média na admissão e no final do tratamento. RESULTADOS: Foi observada fraca correlação positiva (r = 0,563; p < 0,001) entre a cifose residual e o escore de dor (EVA). Não houve correlação entre cifose final e o SF-36 e as escalas de Denis (p > 0,05). CONCLUSÃO: Não existe evidente relação entre a cifose residual e o desfecho funcional e de sintomas dos pacientes.

OBJECTIVE: To assess the correlation between kyphosis and post-traumatic symptoms in patients undergoing conservative treatment for thoracolumbar burst fractures. METHODS: A retrospective study was carried out with 36 patients meeting the inclusion criteria for this kind of fracture classified as Denis and Magerl's subtype A3 and treated with anti-gravitational casting or TLSO. The mean age of patients was 50.83 years, ranging from 13 to 83 years, being 20 male and 16 female subjects. The treatment outcome was evaluated based on the SF-36 questionnaire, on Denis scores for pain and work and Frankel clinical and neurological scale. The quantification of pain was based on the visual analogue scale for pain. The measurement of the residual kyphosis was obtained by the Cobb method at admission and at the end of the follow-up. RESULTS: A weak positive correlation (r = 0.563; p < 0.001) was found between residual kyphosis and pain score (EVA). No correlation was found between final kyphosis and SF-36 and Denis scores (p > 0.05). CONCLUSION: There is no evident correlation between residual kyphosis, functional outcome and patients' symptoms.