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Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies

Venturini, Cristina; Pang, Juanita; Tamuri, Asif U; Roy, Sunando; Atkinson, Claire; Griffiths, Paul; Breuer, Judith; (2022) Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies. Virus Evolution , Article veac093. 10.1093/ve/veac093. (In press). Green open access

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Abstract

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We illustrate HaROLD on both RNA and DNA viruses with synthetic Illumina paired read data created from mixed human cytomegalovirus and norovirus genomes, and clinical datasets of human cytomegalovirus and norovirus samples, demonstrating high accuracy, especially when longitudinal samples are available.

Type: Article
Title: Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/ve/veac093
Publisher version: https://doi.org/10.1093/ve/veac093
Language: English
Additional information: © The Author(s) 2022. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
URI: https://discovery.ucl.ac.uk/id/eprint/10157171
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