Evidence map›Paper›PMID 24146849›Full record

ArticlePloS one2013

Using HSV-1 genome phylogenetics to track past human migrations.

Aaron W Kolb, Cécile Ané, Curtis R Brandt

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 50 papers.

0numbers the graph read from it
0cells of the map it votes in
50citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

50 citing papers in PubMed.

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  17. Coalescing replication compartments provide the opportunity for recombination between coinfecting herpesviruses.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019
    Article
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

3 authors.

Aaron W KolbDepartment of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
Cécile Ané
Curtis R Brandt

Funding

UW Vision Research Core - Administrative CoreP30EY016665 · NEI · UNIVERSITY OF WISCONSIN-MADISON · PI ROBERT W NICKELLS · 2005 to 2026
$12.6M
VIRUS SPECIFIC FACTORS OF HSV TO CORNEAL DISEASER01EY007336 · NEI · UNIVERSITY OF WISCONSIN-MADISON · PI BRANDT, CURTIS R · 1987 to 2008
$1.8M
Virion Sialic Acid and HSV Ocular InfectionR01EY018597 · NEI · UNIVERSITY OF WISCONSIN-MADISON · PI BRANDT, CURTIS R · 2008 to 2011
$1.5M
Virulence Genes in Herpes Simplex Virus Ocular InfectionR01EY023292 · NEI · UNIVERSITY OF WISCONSIN-MADISON · PI BRANDT, CURTIS R · 2013 to 2015
$1.4M
NEI NIH HHS P30 EY016665NEI NIH HHS P30EY016665NEI NIH HHS R01 EY007336NEI NIH HHS R01 EY018597NEI NIH HHS R01EY018597NEI NIH HHS R01 EY023292NEI NIH HHS R01EY07336
6 · The paper itself

Abstract

We compared 31 complete and nearly complete globally derived HSV-1 genomic sequences using HSV-2 HG52 as an outgroup to investigate their phylogenetic relationships and look for evidence of recombination. The sequences were retrieved from NCBI and were then aligned using Clustal W. The generation of a maximum likelihood tree resulted in a six clade structure that corresponded with the timing and routes of past human migration. The East African derived viruses contained the greatest amount of genetic diversity and formed four of the six clades. The East Asian and European/North American derived viruses formed separate clades. HSV-1 strains E07, E22 and E03 were highly divergent and may each represent an individual clade. Possible recombination was analyzed by partitioning the alignment into 5 kb segments, performing individual phylogenetic analysis on each partition and generating a.phylogenetic network from the results. However most evidence for recombination spread at the base of the tree suggesting that recombination did not significantly disrupt the clade structure. Examination of previous estimates of HSV-1 mutation rates in conjunction with the phylogenetic data presented here, suggests that the substitution rate for HSV-1 is approximately 1.38 × 10(-7) subs/site/year. In conclusion, this study expands the previously described HSV-1 three clade phylogenetic structures to a minimum of six and shows that the clade structure also mirrors global human migrations. Given that HSV-1 has co-evolved with its host, sequencing HSV-1 isolated from various populations could serve as a surrogate biomarker to study human population structure and migration patterns.

Indexed as

Human MigrationPhylogenyGenetics, PopulationGenetic VariationGenome, ViralGeographyHerpesvirus 1, HumanHumansLikelihood FunctionsRecombination, GeneticTime Factors

Identifiers

PMID24146849
PMCPMC3797750

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.