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.

SARS-CoV-2 Co-Infections and Recombinations Identified by Long-Read Single-Molecule Real-Time Sequencing.

Co-infection with at least 2 strains of virus is the prerequisite for recombination, one of the means of genetic diversification. Little is known about the prevalence of these events in SARS-CoV-2, partly because it is difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology to sequence whole genomes and targeted regions for haplotyping.

HIV-1 resistance genotyping by ultra-deep sequencing and 6-month virological response to first-line treatment.

Objectives: To evaluate the routine use of the Sentosa ultra-deep sequencing (UDS) system for HIV-1 polymerase resistance genotyping in treatment-naïve individuals and to analyse the virological response (VR) to first-line antiretroviral treatment.

Methods: HIV drug resistance was determined on 237 consecutive samples from treatment-naïve individuals using the Sentosa UDS platform with two mutation detection thresholds (3% and 20%). VR was defined as a plasma HIV-1 virus load <50 copies/mL after 6 months of treatment.

Classification of the Zoonotic Hepatitis E Virus Genotype 3 Into Distinct Subgenotypes.

Hepatitis E virus (HEV) genotype 3 is the most common genotype linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.

Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance.

Background: Patients on antiretroviral therapy could benefit from HIV-1 DNA resistance genotyping for exploring virological failure with low viral load or to guide treatment simplification. Few new generation sequencing data are available.

Objective: To check that the automated deep sequencing Sentosa platform (Vela DX) detected minority resistant variants well enough for HIV DNA genotyping.

Performance of the Xpert HBV Viral Load assay versus the Aptima Quant assay for quantifying hepatitis B virus DNA.

Quantification of HBV DNA is used for initiating and monitoring antiviral treatment. We have evaluated the Xpert HBV Viral Load (VL) assay on the GeneXpert instrument. We estimated its limit of detection to be 7.

Assessment of HIV-1 subtyping for Cameroon strains using phylogenetic analysis of pol gene sequences.

Phylogenetic analysis of human immunodeficiency virus type 1 (HIV-1) pol gene is a useful method for subtyping European strains of HIV-1. The suitability of this method for genetically diverse African strains was evaluated by comparing HIV-1 subtyping of Cameroon strains using a long fragment of the pol gene sequence to the findings obtained using env gene sequences. When the pol gene could not be amplified, the reverse transcriptase (RT) or the protease (PR) genes were used.