Imperial College London
Alternate

DrXavierDidelot

Faculty of Medicine, School of Public Health

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 3622x.didelot

 
 
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Location

 

G30Medical SchoolSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Ortiz:2022:10.1101/2022.06.07.495142,
author = {Ortiz, AT and Kendall, M and Storey, N and Hatcher, J and Dunn, H and Roy, S and Williams, R and Williams, C and Goldstein, RA and Didelot, X and Harris, K and Breuer, J and Grandjean, L},
doi = {10.1101/2022.06.07.495142},
journal = {bioRxiv},
title = {Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.},
url = {http://dx.doi.org/10.1101/2022.06.07.495142},
year = {2022}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
AU  - Ortiz,AT
AU  - Kendall,M
AU  - Storey,N
AU  - Hatcher,J
AU  - Dunn,H
AU  - Roy,S
AU  - Williams,R
AU  - Williams,C
AU  - Goldstein,RA
AU  - Didelot,X
AU  - Harris,K
AU  - Breuer,J
AU  - Grandjean,L
DO  - 10.1101/2022.06.07.495142
PY  - 2022///
TI  - Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks.
T2  - bioRxiv
UR  - http://dx.doi.org/10.1101/2022.06.07.495142
UR  - https://www.ncbi.nlm.nih.gov/pubmed/35702156
ER  -
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