Peter Simmonds K

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Comprehensive hallmark gene sequence, genomic and structural analysis of Picornavirales viruses clarifies new and existing taxa

The paper genetically classifies 525 Picornavirales genomes and 'picorna-like' viruses using multiple sequence and structural analyses, revealing support for existing families and six novel families, along with 32 new genera.

RNA binding regulation is a new dimension in the type I IFN response

This study identifies RNA-binding proteins regulated by type I IFN, revealing a new layer of antiviral response involving post-translational regulation of RNA binding.

Integrated analysis of protein sequence and structureredefines viral diversity and the taxonomy of the Flaviviridae

The paper redefines the taxonomy of Flaviviridae by integrating protein sequence and structure data, revealing new clades and expanding host range.

C->U transition biases in SARS-CoV-2 - still rampant four years from the start of the COVID-19 pandemic

This study analyzes C->U transition biases in SARS-CoV-2 genomes over four years, finding a consistent rate of C base loss and U accumulation, with most substitutions occurring at non-random sites.

Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data

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

GRAViTy-V2: a grounded viral taxonomy application

GRAViTy-V2 classifies viruses using whole-genome analysis, achieving taxonomic accuracy comparable to expert-curated classifications down to the family level.

Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses

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

Within-host genomics of SARS-CoV-2

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

Mutation bias implicates RNA editing in a wide range of mammalian RNA viruses

The paper identifies a bias toward C->U transitions in RNA viruses, suggesting RNA editing by APOBEC enzymes contributes to sequence diversity and evolution.

Pervasive RNA secondary structure in the genomes of SARS-CoV-2 and other coronaviruses - an endeavour to understand its biological purpose

This study investigates the presence of genome-scale RNA structures in SARS-CoV-2 and other coronaviruses, finding high folding energy differences and rapid evolutionary changes in RNA base pairing.

Impact of virus subtype and host IFNL4 genotype on large-scale RNA structure formation in the genome of hepatitis C virus

The paper examines how HCV virus subtype and host IFNL4 genotype influence genome-scale RNA structure formation and compositional features in HCV.

Interferon lambda 4 impacts broadly on hepatitis C virus diversity.

The paper examines the impact of IFN-lambda4 on HCV diversity using host and viral genetic data from 485 patients, finding that IFN-lambda4 variants influence viral amino acid diversity and load.