Ganciclovir Resistance-Linked Mutations in the HCMV Gene: Sanger Sequencing Analysis in Samples from Transplant Recipients at a Tertiary Hospital in Southern Brazil.

Human cytomegalovirus (HCMV) DNAemia remains a significant concern for transplant recipients, largely due to mutations in the viral genome that may lead to antiviral-resistant strains. Mutations in the gene are frequently associated with resistance to ganciclovir (GCV), highlighting the importance of early mutation detection to effectively manage viremia. This study aimed to optimize a Sanger sequencing protocol for analyzing GCV resistance-linked mutations in the HCMV gene from plasma samples of transplant patients treated at Hospital de Clínicas de Porto Alegre, Rio Grande do Sul, Brazil.

Integrated molecular profiling of , mutations, and mismatch repair status in advanced colorectal carcinoma: insights from gender and tumor laterality.

Background: Colorectal carcinoma (CRC) is one of the most frequently diagnosed forms of cancer worldwide. The (, ) and genes encode proteins that are important therapeutic targets for the treatment of CRC and, together with the mismatch repair (MMR) system, are closely related to patient prognosis and survival in advanced CRC. Here we evaluate the mutational profile and the frequency of mutations in the , and genes, along with the expression of MMR in advanced CRC, at a tertiary hospital in southern Brazil.

Challenges to the effectiveness of next-generation sequencing in formalin-fixed paraffin-embedded tumor samples for non-small cell lung cancer.

Introduction: Next-generation sequencing (NGS) of Formalin-Fixed and Paraffin-Embedded (FFPE) specimens is routine in precision oncology practice. However, results are not always conclusive, and it is important to identify which factors may influence FFPE tumor sequencing success.

Materials And Methods: Here, we evaluated the influence of pre-analytical factors on 705 samples of non-small cell lung cancer specimens that underwent NGS testing.

SARS-CoV-2 Variants of Concern: Presumptive Identification via Sanger Sequencing Analysis of the Receptor Binding Domain (RBD) Region of the Gene.

Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via Sanger sequencing of the RBD region and compare the results with data obtained via whole genome sequencing (WGS). Clinical samples (oro/nasopharyngeal) with positive RT-qPCR results for SARS-CoV-2 were used in this study.

Prolonged SARS-CoV-2 Infection and Intra-Patient Viral Evolution in an Immunodeficient Child.

Background: With the progression of the Coronavirus disease pandemic, the number of mutations in the viral genome has increased, showing the adaptive evolution of severe acute respiratory syndrome coronavirus 2 in humans and intensification in transmissibility. Long-term infections also allow the development of viral diversity. In this study, we report the case of a child with severe combined immu presenting a prolonged severe acute respiratory syndrome coronavirus 2 infection.

RT-qPCR half-reaction optimization for the detection of SARS-CoV-2.

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.

SARS-CoV-2 nucleic acid shedding is variable for every person.

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.

Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalisation rate, February 2021, Rio Grande do Sul, Southern Brazil.

The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region's Rio Grande do Sul state, severe COVID-19 case numbers rose 3.

Pooling of samples to optimize SARS-CoV-2 diagnosis by RT-qPCR: comparative analysis of two protocols.

This study has aimed to evaluate the use pool of samples as a strategy to optimize the diagnostic of SARS-CoV-2 by RT-qPCR. A total of 220 naso/orofaryngeal swab samples were collected and tested using two different protocols of sample pooling. Results from protocol A were identical with the individual results.

Comparison of a direct immunofluorescence assay (Oxoid IMAGEN®) and a multiplex RT-PCR DNA microarray assay (CLART® PneumoVir) for the detection of respiratory viruses in hospitalized children.

The objective of this study was to compare the positive detection rates obtained using the Oxoid IMAGEN® direct immunofluorescence assay (designated as IF) with those obtained using the CLART® PneumoVir multiplex RT-PCR DNA microarray assay (designated as RT-PCR) in the diagnosis of respiratory viruses in hospitalized children. This was a retrospective study of 62 individuals < 18 years old who had nasopharyngeal aspirates collected for virus identification in a tertiary university hospital in south Brazil between January 1st, 2014 and December 31st, 2014. All 62 nasopharingeal aspirates were analyzed using both assay methods.

Analysis of Predictive Biomarkers in Patients With Lung Adenocarcinoma From Southern Brazil Reveals a Distinct Profile From Other Regions of the Country.

Purpose: Adenocarcinoma is the most common histologic subtype of non-small-cell lung cancer, representing 40% of all diagnoses. Several biomarkers are currently used to determine patient eligibility for targeted treatments, including analysis of molecular alterations in and , as well as programmed death-ligand 1 (PD-L1) protein expression. Epidemiologic data reporting the frequency of these biomarkers in Brazilian patients with lung adenocarcinoma (LUAD) are limited, and existing studies predominantly included patients from the southeast region of the country.

Assessment of Changes in Body Composition During the First Postoperative Year After Bariatric Surgery.

Background: The potential effect of bariatric surgery on weight reduction and improvement of associated comorbidities is known, but the ratio obtained between the components of body weight, including lean body mass, body fat mass, and bone mass, is still not determined. This study aims to verify the changes in body composition during the first year after bariatric surgery.

Methods: We conducted a prospective observational cohort study.

Assessment of conventional PCR and real-time PCR compared to the gold standard method for screening Streptococcus agalactiae in pregnant women.

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.

Quantitative detection of BK virus in kidney transplant recipients: a prospective validation study.

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.

Global respiratory syncytial virus-associated mortality in young children (RSV GOLD): a retrospective case series.

Background: Respiratory syncytial virus (RSV) infection is an important cause of pneumonia mortality in young children. However, clinical data for fatal RSV infection are scarce. We aimed to identify clinical and socioeconomic characteristics of children aged younger than 5 years with RSV-related mortality using individual patient data.

Evaluation of diagnostic tests for cytomegalovirus active infection in renal transplant recipients.

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.

Outbreaks due to Mycobacterium abscessus subsp. bolletii in southern Brazil: persistence of a single clone from 2007 to 2011.

Outbreaks associated with rapidly growing mycobacteria (RGM) have been increasingly reported worldwide, including in Brazil. Among the RGM, the Mycobacterium abscessus complex is the most pathogenic and related to multidrug resistance. The aim of this study was to evaluate the antimicrobial susceptibility and molecular profile of RGM isolates involved in new postsurgical infection outbreaks in Brazil since 2007.

Effects of Lactobacillus rhamnosus GG on hepatic and serum lipid profiles in zebrafish exposed to ethanol.

Zebrafish is a powerful tool in pharmacological research and useful to identify new therapies. Probiotics can offer therapeutic options in alcoholic liver disease. This study was done in two independent experiments: first, we confirmed the intestinal colonization of probiotic Lactobacillus rhamnosus GG (LGG) after ethanol exposure.

Viral epidemiology of respiratory infections among children at a tertiary hospital in Southern Brazil.

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.

Evaluation of respiratory syncytial virus group A and B genotypes among nosocomial and community-acquired pediatric infections in Southern Brazil.

Background: Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract illness in children worldwide. Molecular analyses show two distinct RSV groups (A and B) that comprise different genotypes. This variability contributes to the capacity of RSV to cause yearly outbreaks.

The impact of serum vancomycin levels and minimum inhibitory concentrations of methicillin-resistant Staphylococcus aureus on mortality in patients with nosocomial pneumonia.

Background: Vancomycin is the treatment of choice for methicillin-resistant Staphylococcus aureus (MRSA) infections; however, treatment failure is not uncommon, even when the minimum inhibitory concentration (MIC) of the MRSA strain is within the susceptible range for vancomycin.

Objective: To describe the relationship between molecular markers such as the mecA and agrII genes, serum vancomycin levels and vancomycin MICs, and the 30-day mortality rate of patients with nosocomial MRSA pneumonia in an intensive care unit (ICU).

Methods: The present study was a prospective cohort study including all patients with MRSA hospital-acquired pneumonia or ventilator-associated pneumonia who were admitted to the ICU of a tertiary care hospital between June 2009 and December 2011.

Minimum detection limit of an in-house nested-PCR assay for herpes simplex virus and varicella zoster virus.

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.

Genetic similarity of Burkholderia cenocepacia from cystic fibrosis patients.

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.

Optimization of one-step duplex real-time RT-PCR for detection of influenza and respiratory syncytial virus in nasopharyngeal aspirates.

Viruses are major contributors to acute respiratory infection-related morbidity and mortality worldwide. The influenza (IF) viruses and human respiratory syncytial virus (RSV) play a particularly important role in the etiology of acute respiratory infections. This study sought to standardize a one-step duplex real-time RT-PCR technique to optimize diagnosis of IFA/IFB and RSVA/RSVB infection.