Judith Breuer

The paper identifies a mechanism by which REP/CAP contaminants arise in rAAV gene therapy through P5 promoter-mediated incorporation during manufacturing.

This study compares how VZV and HSV-1 interact with epidermal differentiation in primary human keratinocytes, showing that viral replication is restricted in differentiated cells, with VZV more affected than HSV-1.

This study evaluates antiviral drug synergy and mutational signatures of RdRp inhibitors against RSV and hPIV in epithelial cell models and primary airway cultures.

The paper identifies manufacturing plasmid sequences and disrupted vector genomes in liver tissue from a patient with AAV gene therapy-related hepatitis.

Castanet is a pipeline for analyzing multi-pathogen enrichment sequencing data, providing accurate consensus sequences and metrics for pathogen detection and quantification.

This study compares metagenomics and targeted approaches for virus detection, finding that targeted methods improve sensitivity while untargeted ONT offers better specificity.

HerpesDRG provides a database and tools for drug resistance mutation analysis in human herpesviruses using genotype-phenotype literature.

This study analyzes genomic variation in Chlamydia trachomatis serovars A and B from Gambian trachoma-endemic villages to understand strain diversification and evolutionary pressures.

This study demonstrates that clinical metagenomics improves diagnostic outcomes for undiagnosed complex paediatric neurological cases, particularly in immunocompromised patients.

This paper evaluates a whole genome sequence report form (SRF) used to change infection prevention behaviors in UK hospitals during the pandemic, finding it supported key theoretical mechanisms and intervention functions.

The paper identifies a viral signature from HCMV genes associated with poor outcomes in immunocompromised patients, using deep sequencing and machine learning.

AYUKA is a fast, reliable viral genotyping tool using whole genome sequencing that requires no pre-processing and provides quality control metrics and genotype identification.

The paper explores the acceptability of rapid whole genome sequencing for managing nosocomial SARS-CoV-2 infections through interviews with healthcare professionals.

The paper introduces a sequence-weighting method for linkage disequilibrium calculations to reduce sampling bias by giving more weight to underrepresented sequences.

The paper investigates how human genetic variation influences Epstein-Barr virus (EBV) sequence diversity by analyzing paired viral and human genomic data from HIV-coinfected individuals.

The paper shows that HIV-positive mothers have compartmentalized CMV genotypes, with three infants transmitting a single closely related maternal cervix strain, and identifies gene similarities linked to tissue-tropism and immunomodulation.

The paper analyzes genomic variation in Chlamydia trachomatis from Ethiopia to assess its role in continued transmission after SAFE interventions.

This paper introduces HaROLD, a method for haplotype reconstruction from longitudinal viral sequencing data using co-varying variant frequencies, showing high accuracy with synthetic datasets.

Three multiplex tiling protocols using a single primer set recover long amplicons of SARS-CoV-2 directly from clinical sample total RNA for sequencing on Nanopore, Illumina, or Sanger platforms.

This study compares whole genome sequencing of Mycobacterium tuberculosis directly from sputum to sequencing from culture, finding greater genetic diversity in sputum-derived samples.

The paper identifies and characterizes a unique VZV latency transcript (VLT) that represses the viral transactivator gene ORF61 during latency, unifying VZV latency with other herpesviruses.