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dc.contributor.authorZhao, Leien
dc.contributor.authorIllingworth, Christopheren
dc.date.accessioned2019-01-22T00:31:11Z
dc.date.available2019-01-22T00:31:11Z
dc.date.issued2019-01-30en
dc.identifier.issn2057-1577
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/288311
dc.description.abstractViruses exist within hosts at large population sizes and are subject to high rates of mutation. As such, viral populations exhibit considerable sequence diversity. A variety of summary statistics have been developed which describe, in a single number, the extent of diversity in a viral population; such measurements allow for the diversities of different populations to be compared, and for the effect of evolutionary forces on a population to be assessed. Here we highlight statistical artefacts underlying some common measures of sequence diversity, whereby variation in the depth of genome sequencing may substantially affect the extent of diversity measured in a viral population, making comparisons of population diversity invalid. Specifically, naive estimation of sequence entropy provides a systematically biased metric, a lower read depth being expected to produce a lower estimate of diversity. The number of polymorphic loci per kilobase of genome is more unpredictably affected by read depth, giving potentially flawed results at lower sequencing depths. We show that the nucleotide diversity statistic p provides an unbiased estimate of diversity in the sense that the expected value of the statistic is equal to the correct value of the property being measured. Our results are of importance for studies interpreting genome sequence data; we describe how diversity may be assessed in viral populations in a fair and unbiased manner.
dc.description.sponsorshipWellcome
dc.format.mediumElectronic-eCollectionen
dc.languageengen
dc.titleMeasurements of intrahost viral diversity require an unbiased diversity metric.en
dc.typeArticle
prism.issueIdentifier1en
prism.publicationDate2019en
prism.publicationNameVirus evolutionen
prism.startingPagevey041
prism.volume5en
dc.identifier.doi10.17863/CAM.35627
dcterms.dateAccepted2018-12-03en
rioxxterms.versionofrecord10.1093/ve/vey041en
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2019-01-30en
dc.contributor.orcidZhao, Lei [0000-0002-6551-2707]
dc.contributor.orcidIllingworth, Christopher [0000-0002-0030-2784]
dc.identifier.eissn2057-1577
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idWellcome Trust (101239/Z/13/Z)
pubs.funder-project-idIsaac Newton Trust (Minute 18.23(i))
cam.orpheus.successMon Jun 08 08:19:42 BST 2020 - The item has an open VoR version.*
rioxxterms.freetoread.startdate2022-01-21


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