HIV-1 genotypic resistance testing using single molecule real-time sequencing.

Background: HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available in many virology laboratories.

Objectives: To evaluate the diagnostic performance of Long-Read Single Molecule Real-time (SMRT) sequencing (Sequel, PacBio) for HIV-1 polymerase genotyping.

Study Design: 111 prospective clinical samples (83 plasma and 28 leukocyte-enriched blood fraction) were analyzed for routine HIV-1 resistance genotyping using Sanger sequencing, Vela NGS, and SMRT sequencing.

BK Viremia and Viruria Does Not Depend on the Type of Double-J Stent Used During Kidney Transplantation.

Objectives: BK virus is a major cause of chronic renal allograft failure.Transplant ureteral stent use has been reported as a risk factorfor BK virus infection. Recently, the use of a new type of ureteral stent (Magnetic Black Star) was reported in kidney transplant recipients.

Evaluation of an automated platform for the detection of HEV RNA in plasma and stool.

Introduction: We evaluated the performance of the automated Altostar HEV RNA platform for detecting HEV RNA.

Methods And Results: Clinical performance was determined by testing 81 plasma samples and 10 fecal samples manually quantified previously with the Realstar RT-PCR assay using the Magnapure instrument for extraction. The assays were concordant for 79/81 plasma samples (97.

Human papillomavirus testing using HPV APTIMA® assay and an external cellularity control in self-collected samples.

In cervical cancer screening programs, the detection of high-risk human papillomavirus (HR-HPV) is now widely implemented on physician-collected samples and has expanded to include self-collected samples. The use of a cellularity control (CC) is needed to reduce false-negative HPV results. An external mRNA CC for the HPV APTIMA® assay was assessed for its analytical performance and the results were compared with both cervix cytobrush samples taken by physicians and self-collected vaginal samples from 148 women.

Acute hepatitis E in French patients and neurological manifestations.

Objectives: Hepatitis E virus (HEV) is a major cause of acute hepatitis worldwide. However, our understanding of the source of contamination is incomplete and the frequency of neurological manifestations in still unknown.

Methods: 200 eligible cases reported to the French National Reference Center from January 2015 to December 2015 were prospectively included in this case-control study (1 case: 1 control, matched for sex, age and area of living) to investigate the risk of infection.

A fully automated system using transcription-mediated amplification for the molecular diagnosis of hepatitis E virus in human blood and faeces.

Background And Objectives: We evaluated the performance of the Procleix HEV RNA assay implemented on the Panther automated platform for detecting HEV RNA.

Study Design And Results: Analytical specificity was 100% and there was no cross contamination, as assessed by assaying 122 plasma samples from HEV RNA-negative blood donors. The limits of detection were determined by Probit analysis with the WHO HEV standard (HEV subtype 3a) and subtype 3f and 3c reference strains.

Performance comparison of deep sequencing platforms for detecting HIV-1 variants in the pol gene.

The present study compares the performances of an in-house sequencing protocol developed on MiSeq, the Sanger method, and the 454 GS-FLX for detecting and quantifying drug-resistant mutations (DRMs) in the human immunodeficiency virus polymerase gene (reverse transcriptase [RT] and protease [PR]). MiSeq sequencing identified all the resistance mutations detected by bulk sequencing (n = 84). Both the MiSeq and 454 GS-FLX platforms identified 67 DRMs in the RT and PR regions, but a further 25 DRMs were identified by only one or other of them.

Direct-acting antivirals and hepatitis B virus (HBV) reactivation in co-infected HBV/HCV kidney-transplant recipients.

Direct-acting agents (DAAs) are highly efficient at treating hepatitis C virus (HCV) infections after kidney transplantation. Although drug agencies have recently warned of the risk of hepatitis B virus (HBV) reactivation after patients have received DAAs, reports have discrepant results in HBsAg-positive and HBsAg-negative patients. We report on 3 cases of HBV reactivation that were detected after achieving a DAA-associated sustained virological response in 3 kidney-transplant recipients initially HBsAg-negative.

HIV-1 genotypic resistance testing using the Vela automated next-generation sequencing platform.

Objectives: To evaluate the diagnostic performance of the Vela next-generation sequencing (NGS) system in conjunction with the Sentosa SQ HIV Genotyping Assay for genotyping HIV-1.

Methods: Plasma RNA was extracted and templates prepared with the Sentosa SX instrument before sequencing the HIV-1 polymerase on the Sentosa SQ301 Sequencer (PGM IonTorrent). The Vela NGS System was compared with direct sequencing and the 454 GS-FLX (Roche) and MiSeq (Illumina) systems for genotypic resistance testing on clinical samples.

A European multicenter study on the analytical performance of the VERIS HBV assay.

Background: Hepatitis B viral load monitoring is an essential part of managing patients with chronic Hepatits B infection. Beckman Coulter has developed the VERIS HBV Assay for use on the fully automated Beckman Coulter DxN VERIS Molecular Diagnostics System. OBJECTIVES: To evaluate the analytical performance of the VERIS HBV Assay at multiple European virology laboratories.

Impact of Human Immunodeficiency Virus Type 1 Minority Variants on the Virus Response to a Rilpivirine-Based First-line Regimen.

Background: Minority resistant variants of human immunodeficiency virus type 1 (HIV-1) could influence the virological response to treatment based on nonnucleoside reverse transcriptase inhibitors (NNRTIs). Data on minority rilpivirine-resistant variants are scarce. This study used next-generation sequencing (NGS) to identify patients harboring minority resistant variants to nucleos(t)ide reverse transcriptase inhibitors and NNRTIs and to assess their influence on the virological response (VR).

Patterns of residual HIV-1 RNA shedding in the seminal plasma of patients on effective antiretroviral therapy.

Background: More and more HIV-1-infected men on effective antiretroviral treatment (ART) have unprotected sex in order to procreate. The main factor influencing transmission is seminal HIV shedding. While the risk of HIV transmission is very low, it is difficult to assess in individuals.

A European multicientre study on the comparison of HBV viral loads between VERIS HBV assay and Roche COBAS TAQMAN HBV test, Abbott RealTime HBV assay, Siemens VERSANT HBV assay, and Qiagen artus HBV RG kit.

Background: Hepatitis B viral load testing is essential to treatment and monitoring decisions in patients with chronic Hepatitis B. Beckman Coulter has developed the VERIS HBV Assay (Veris) for use on the fully automated DxN VERIS Molecular Diagnostics System. OBJECTIVES: To evaluate the clinical performance of the Veris HBV Assay at multiple EU laboratories STUDY DESIGN: Method comparison was performed with a total of 344 plasma specimens from HBV infected patients tested with Veris and COBAS TaqMan HBV Test (Cobas), 207 specimens tested with Veris and RealTime HBV Assay (RealTime), 86 specimens tested with Veris and VERSANT HBV Assay (Versant), and 74 specimens tested with Veris and artus HBV RG PCR kit (artus).

Interlaboratory quality control of total HIV-1 DNA load measurement for multicenter reservoir studies.

Background: Viral reservoirs represent an important barrier to HIV cure. Accurate markers of HIV reservoirs are needed to develop multicenter studies. The aim of this multicenter quality control (QC) was to evaluate the inter-laboratory reproducibility of total HIV-1-DNA quantification.

A European multicientre study on the comparison of HIV-1 viral loads between VERIS HIV-1 Assay and Roche COBAS® TAQMAN® HIV-1 test, Abbott RealTime HIV-1 Assay, and Siemens VERSANT HIV-1 Assay.

Background: Viral load monitoring is essential for patients under treatment for HIV. Beckman Coulter has developed the VERIS HIV-1 Assay for use on the novel, automated DxN VERIS Molecular Diagnostics System. OBJECTIVES: Evaluation of the clinical performance of the new quantitative VERIS HIV-1 Assay at multiple EU laboratories.

Malignancies in hepatitis C virus-positive and -negative kidney transplant recipients: A case-controlled study.

Background: Malignancies and lymphoma are common complications after kidney transplantation. However, no link has been made between the incidence of malignancies and hepatitis C virus (HCV) infection in this setting. This case-controlled study compared the incidence of malignancies, including lymphoma, between kidney transplant (KT) patients with or without HCV replication.

European Multicenter Study on Analytical Performance of Veris HIV-1 Assay.

The analytical performance of the Veris HIV-1 assay for use on the new, fully automated Beckman Coulter DxN Veris molecular diagnostics system was evaluated at 10 European virology laboratories. The precision, analytical sensitivity, performance with negative samples, linearity, and performance with HIV-1 groups/subtypes were evaluated. The precision for the 1-ml assay showed a standard deviation (SD) of 0.

Comparison of Cobas® HPV and Anyplex™ II HPV28 assays for detecting and genotyping human papillomavirus.

Persistent infection with high-risk human papillomavirus (HPV-HR) is a recognized cause of cervical cancer. The aim of this study was to compare analytical and clinical performances of the Cobas® HPV and Anyplex™ II HPV28 assays for HPV detection and genotyping. A total of 94 cervical samples were tested.

A European multicentre study on the comparison of HCV viral loads between VERIS HCV assay and COBAS TaqMan HCV Test and RealTime HCV Assay.

Background: Beckman Coulter has developed the VERIS HCV Assay for use on the new fully automated DxN VERIS Molecular Diagnostic System for HCV viral load monitoring.

Objectives: Evaluate the clinical performance of the new quantitative VERIS HCV Assay.

Study Design: Comparison was performed on 279 plasma specimens from HCV infected patients tested with the VERIS HCV Assay and COBAS Ampliprep/COBAS Taqman HCV Test and 369 specimens tested with the VERIS HCV Assay and RealTime HCV Assay.

Performance comparison of next-generation sequencing platforms for determining HIV-1 coreceptor use.

The coreceptor used by HIV-1 must be determined before a CCR5 antagonist, part of the arsenal of antiretroviral drugs, is prescribed because viruses that enter cells using the CXCR4 coreceptor are responsible for treatment failure. HIV-1 tropism is also correlated with disease progression and so must be determined for virological studies. Tropism can be determined by next-generation sequencing (NGS), but not all of these new technologies have been fully validated for use in clinical practice.

European Multicenter Study on Analytical Performance of DxN Veris System HCV Assay.

The analytical performance of the Veris HCV Assay for use on the new and fully automated Beckman Coulter DxN Veris Molecular Diagnostics System (DxN Veris System) was evaluated at 10 European virology laboratories. Precision, analytical sensitivity, specificity, and performance with negative samples, linearity, and performance with hepatitis C virus (HCV) genotypes were evaluated. Precision for all sites showed a standard deviation (SD) of 0.

HEV infection in French HIV-infected patients.

Objectives: The reported prevalence of anti-hepatitis E virus antibodies in HIV-positive patients from industrialized countries varies greatly. It is also difficult to compare these data with the anti-IgG prevalence in the general population because age and sex are not matched in most studies. Moreover, MSM are at increased risk of viral hepatitis.