Author

Ewan W. Smith

MRC University of Glasgow Centre for Virus Research

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Evolutionary Biology· 2 Bioinformatics· 1 Cancer Biology· 1 Genomics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 4 Approach:experimental assay· 2 Organism:human· 2 Research Focus:variant calling· 2 Organism:virus· 2 Assay:whole-genome sequencing· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Christopher J. R. IllingworthiD· 3 shared David L. RobertsoniD· 2 shared Joseph HughesiD· 2 shared Slawomir KubikiD· 2 shared Zhenyu XuiD· 2 shared Adrian Willig· 1 shared Alexandra Saitta· 1 shared Alexandre HarléiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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3 shared papersEvolutionary Biology

Christopher J. R. IllingworthORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

Understanding the emergence of the influenza A/H3N2 K subclade in its historical and evolutionary context

Kieran Dee, Ryan M. Imrie, Oscar A. MacLean, Laura Noelia Mojsiejczuk, Ewan W. Smith, Savitha Raveendran, Kieran lamb, Hanting Chen, Verena Schultz, Z. J. Wang, Sarah K. Walsh, Junsen Zhang, Ed Hutchinson, Brian J. Willett, Emma C. Thomson, , Pablo R. Murcia

The paper investigates the emergence of the influenza A/H3N2 K subclade, finding limited antigenic change and age-dependent vaccine responses, suggesting non-antigenic selection pressures.

bioRxiv · May 24, 2026 · PreprintEvolutionary Biology

CD8scape: an accessible, command-line tool for predicting viral escape from the CD8+ T cell response

Ewan W. Smith, Joseph Hughes, David L. Robertson, Christopher J. R. Illingworth

CD8scape predicts viral escape from CD8+ T cell response using HLA genotype and within-host sequence variation to identify immune escape potential.

bioRxiv · Apr 22, 2026 · PreprintBioinformatics

Variable rates of SARS-CoV-2 evolution in chronic infections

Ewan W. Smith, William L Hamilton, Ben Warne, Elena R Walker, Aminu S. Jahun, Myra D.T. Hosmillo, Ravindra K. Gupta, Ian Goodfellow, Effrossyni Gkrania‐Klotsas, M. Estée Török, Christopher J. R. Illingworth

This study analyzes within-host SARS-CoV-2 evolution in chronic infections, finding variable rates of evolution and evidence of subpopulation structure.

PLoS Pathogens · Apr 28, 2025Peer-reviewedEvolutionary Biology

Critical assay parameters facilitating confident detection of expression changes, fusions and short variants in RNA isolated from tissue

Slawomir Kubik, Izabela Matyszczak, Nicholas R. T. Toda, Elia Magrinelli, Pierre‐Yves Helleboid, Ewan W. Smith, Fedor Bezrukov, Chloe Ryder, Jonathan Lopez, Alexandre Harlé, Zhenyu Xu

The paper identifies critical sequencing parameters for reliable detection of expression changes, fusions, and variants in targeted RNA sequencing of tumor samples.

bioRxiv · Oct 30, 2024 · PreprintCancer Biology

Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples

Slawomir Kubik, Ana Claudia Marques, Xiaobin Xing, Janine Silvery, Claire Bertelli, Flavio De Maio, Spyros Pournaras, Tom Burr, Yannis Duffourd, Helena Siemens, Chakib Alloui, Lin Ye Song, Yvan Wenger, Alexandra Saitta, Morgane Macheret, , Zhenyu Xu

This study provides guidelines for accurate SARS-CoV-2 genotyping using amplicon-based sequencing, showing that at least 1000 viral genomes are needed to reliably detect variants at 10% frequency.

Clinical Microbiology and Infection · Apr 2, 2021Peer-reviewedGenomics