Thushan I. de Silva

Molecular analysis of Lancefield group C/G streptococci causing human infections in Sheffield, UK.

This study performs whole-genome sequencing of Lancefield group C/G streptococci isolates from Sheffield, UK, revealing high genomic diversity, antimicrobial resistance, and persistence within hosts.

Unique nasal cell states induced by common pediatric respiratory viruses

This study maps virus-specific nasal cell states in children using single-cell RNA sequencing and links them to disease severity and asthma risk.

Integrative Mapping of Pre-existing Immune Landscapes for Vaccine Response Prediction

Immunaut identifies distinct immunophenotypic responder groups shaped by baseline immune landscapes using a comprehensive LAIV dataset, advancing precision vaccinology and guiding personalized immunization strategies.

Molecular characterisation of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022-23 UK upsurge

This study characterizes non-invasive Streptococcus pyogenes isolates from a 2022-23 UK scarlet fever upsurge, revealing strain diversity and genomic features associated with different infection types.

How acceptable is rapid whole genome sequencing for infectious disease management in hospitals? Perspectives of those involved in managing nosocomial SARS-CoV-2

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

Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka

The paper analyzes SARS-CoV-2 genomic sequences from Sri Lanka to track lineage prevalence and transmission patterns, finding B.1.411 was dominant until B.1.1.7 replaced it in late 2020.

periscope: Sub-Genomic RNA Identification in SARS-CoV-2 Genomic Sequencing Data

Periscope identifies and quantifies sub-genomic RNAs in SARS-CoV-2 genomic data, detecting canonical and non-canonical sgRNAs with high fidelity.

Altered Subgenomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections

The paper shows that B.1.1.7 SARS-CoV-2 lineage has increased subgenomic RNA expression compared to other lineages, with a noncanonical sgRNA near ORF9b showing a 16-fold increase in median expression.