P. Simmonds

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.

Understanding off-target growth defects introduced to influenza A virus by synonymous recoding

This study identifies compensatory mutations that cause replication defects in a CpG-enriched influenza A virus, revealing polymerase slippage and type I interferon induction as key mechanisms.

A unified evolutionary framework to reconstruct the viral histories of human, simian, and prosimian immunodeficiency viruses across timescales

This paper reconstructs the evolutionary history of SIVs and pSIVs across timescales using a time-dependent rate model, finding the most recent common ancestor of extant SIVs dates to ~1 million years ago.

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

The paper identifies 11,420 viroid-like circular RNAs across 5,131 metatranscriptomes and 1,344 plant transcriptomes, revealing a five-fold increase in known viroid-like agents and novel ribozyme combinations.

CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy

This paper engineers an influenza A virus with increased CpG content, showing it is attenuated in mice but replication competent in vaccine propagation systems, suggesting a new strategy for live attenuated vaccines.

Seasonal dynamics of the wild rodent faecal virome

This study examines seasonal changes in the virome of wild rodents, finding that many viruses are seasonally transient and linked to host and environmental factors.

Zinc finger antiviral protein (ZAP) activity in mammalian and avian hosts in CpG and UpA-mediated restriction of RNA viruses and investigation of ZAP-mediated shaping of host transcriptome compositions

This study investigates ZAP activity in mammals and birds, finding no evidence that ZAP shapes antiviral gene compositions or impacts virus genome dinucleotide frequencies.

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes

The paper presents 37 new genomes of haloarchaeal tailed viruses, expands their classification into 14 families, and explores their evolution and ecological distribution.

Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses

The paper introduces a mechanistic model explaining time-dependent substitution rate decay in viruses, showing it applies across virus types and revises evolutionary timescales for HCV and sarbecoviruses.

An adaptive compromise - Conflicting evolutionary pressures on arthropod borne Zika virus dinucleotide composition in mammalian hosts and mosquito vectors

This study investigates how Zika virus balances CpG suppression in vertebrate hosts with different compositional needs in mosquito vectors, showing that CpG-high mutants replicate better in mosquitoes and show vaccine potential in mice.

Mutagenesis Mapping of RNA Structures within the Foot-and-Mouth Disease Virus Genome Reveals Functional Elements Localised in the Polymerase (3Dpol) Encoding Region.

The paper identifies three critical RNA structures in the FMDV genome essential for replicon replication, while 42 others are non-essential, suggesting potential targets for vaccine development.

Evaluation of Different PCR Assay Formats for Sensitive and Specific Detection of SARS-CoV-2 RNA

The paper evaluates different PCR formats for SARS-CoV-2 RNA detection, finding that nested PCR with agarose gel electrophoresis is sensitive and specific but has variable sensitivity depending on transcript length.

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent COVID-19 patients.

This study examines T cell immunity in UK COVID-19 patients, finding stronger and broader memory T cell responses in severe cases, with implications for vaccine design.

Association of zinc-finger antiviral protein (ZAP) binding to viral genomic RNA with attenuation of replication of echovirus 7

This study investigates how ZAP binding to viral RNA affects echovirus 7 replication, showing specific dinucleotide recognition and interactions with OAS3 and stress granules.

Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

This study identifies three HCV polymorphisms in NS2 and NS3 proteins associated with sofosbuvir treatment failure using whole genome sequencing of 507 patients.

Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses - causes and consequences for their short and long evolutionary trajectories

This study identifies C->U hypermutation as a major driver of sequence variation in SARS-CoV-2 and other coronaviruses, with implications for their evolutionary dynamics.

Human cytomegalovirus evades ZAP detection by suppressing CpG dinucleotides in the major immediate early genes.

This study shows HCMV evades ZAP detection by suppressing CpG dinucleotides in its IE1 gene, and TRIM25 regulates ZAP isoform expression.

Evolutionary origins of epidemic potential among human RNA viruses

The paper investigates the evolutionary origins of epidemic potential in human RNA viruses, finding that most transmissible lineages evolved from non-human viruses.