Evidence map›Paper›PMID 27725301›Full record

ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2016

Genomic diversity and phylogenetic relationships of human papillomavirus 16 (HPV16) in Nepal.

Robert Makowsky, Pema Lhaki, Howard W Wiener, Madhav P Bhatta, Michael Cullen, Derek C Johnson, Rodney T Perry, Mingma Lama, Joseph F Boland, Meredith Yeager and 3 more

Open access · greenAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.7field-weighted citation impact, top 25% of its field
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

5 citing papers in PubMed, 11 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 6 institutions in 2 countries.

Robert MakowskyDepartment of Biostatistics, School of Public Health, University of Alabama at Birmingham, AL, USA.
Pema LhakiNFCC International, Kathmandu, Nepal.
Howard W WienerDepartment of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA.
Madhav P BhattaDepartment of Biostatistics, Environmental Health Sciences, and Epidemiology, College of Public Health, Kent State University, OH, USA.
Michael CullenDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA.
Derek C JohnsonDepartment of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA.
Rodney T PerryDepartment of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA.
Mingma LamaNFCC International, Kathmandu, Nepal.
Joseph F BolandDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA.
Meredith YeagerDivision of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA.
Sarita GhimireCancer Screening Center, Nepal Cancer Care Foundation, Lalitpur, Nepal.
Thomas R BrokerDepartment of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
Sadeep ShresthaDepartment of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA. Electronic address: sshrestha@uab.edu.
University of Alabama at Birmingham · USFrederick National Laboratory for Cancer Research · USKent State University · USLeidos (United States) · USNational Cancer Institute · USNepal Cancer Hospital and Research Center · NP

Funding

Cancer Prevention & Control Training ProgramR25CA047888 · NCI · UNIVERSITY OF ALABAMA AT BIRMINGHAM · PI DEMARK-WAHNEFRIED, WENDY, MENESES, KAREN M · 1988 to 2016
$11.2M
NCI NIH HHS R25 CA047888
6 · The paper itself

Abstract

OBJECTIVES/

backgroundSequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects.

methodsDNA was isolated from exfoliated cervical cells from 17 individuals in Nepal who were previously identified to be HPV16-positive. A custom HPV16 Ion Ampliseq panel of multiplexed degenerate primers was designed that generated 47 overlapping amplicons and covered 99% of the viral genome for all known HPV16 variant lineages. All sequence data were processed through a custom quality control and analysis pipeline of sequence comparisons and phylogenetic analysis.

resultsThere were high similarities across the genomes, with two major indels observed in the non-coding region between E5 and L2. Compared to the PAVE reference HPV16 genome, there were up to 9, 4, 38, 27, 8, 7, 52, and 32 nucleotide variants in the E6, E7, E1, E2, E4, E5, L2, and L1 genes in the Nepalese samples, respectively. Based on sequence variation, HPV16 from Nepal falls across the A, C, and D lineages in this study. We found no evidence of genetic distinctness between HSIL and non-HSIL subjects.

conclusionsThe evolutionary and pathological characteristics of the representative HPV16 genomes from Nepal seem similar to results from other parts of the world and provide the basis for further studies.

Indexed as

Cervix UteriCohort StudiesFemaleGenome, ViralHuman papillomavirus 16HumansMolecular EpidemiologyNepalPapillomavirus InfectionsPhylogenyUterine DiseasesHPV16 lineageHPV16 sequenceHSILNepalPhylogenetic tree

Identifiers

PMID27725301
PMCPMC5136510
OpenAlexW2528460278

What OpenQuestion holds

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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.