Evidence map›Paper›PMID 40879819›Full record

ArticleCurrent microbiology2025

Codon Usage Pattern of Papillomavirus E6, E7, and L1 Genes Across Hosts.

Xudong Liu, Kexin Li, Xiaojing Chen, Yaqian Li, Tianshu Sun, Roujie Huang, Yanan Shi, Zilong He, Lei Li

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Article in Current microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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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

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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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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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

9 authors.

Xudong Liu *National Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
Kexin Li *School of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100730, China.
Xiaojing ChenNational Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
Yaqian LiNational Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
Tianshu SunNational Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China.
Roujie HuangDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing, 100730, China.
Yanan ShiBiomedical Engineering Facility of National Infrastructures for Translational Medicine, Peking Union Medical College Hospital, Beijing, 100730, China.
Zilong HeSchool of Engineering Medicine, Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, 100730, China. hezilong@buaa.edu.cn.
Lei LiNational Infrastructures for Translational Medicine, the State Key Laboratory for Complex, Severe, and Rare Diseases, Institute of Clinical Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Shuaifuyuan No. 1, Dongcheng District, Beijing, 100730, China. lileigh@163.com.

Funding

Peking Union Medical College Hospital Young Reserve Talent Development Program UHB12577the CAMS Innovation Fund for Medical Sciences (CIFMS) 2024-I2M-C&T-B-029the National High Level Hospital Clinical Research Funding 2022-PUMCH-B-083the National High Level Hospital Clinical Research Funding 2022-PUMCH-C-010the National High Level Hospital Clinical Research Funding 2022-PUMCH-C-022the National High Level Hospital Clinical Research Funding 2022-PUMCH-D-003the State Key Laboratory for Complex, Severe and Rare Diseases in Peking Union Medical College Hospital, by the Key Research Project of Beijing Natural Science Foundation Z220013
6 · The paper itself

Abstract

This study investigates the codon usage preferences of papillomaviruses across different hosts and examines the evolutionary relationships of key genes (L1, E6, and E7). Complete genome sequences of 86 papillomavirus strains were retrieved from the PaVE database. Phylogenetic trees were constructed using MAFFT and ITOL, and codon usage indices, including RSCU, ENC, CAI, and GC3, were calculated using CodonW. ENC-GC3, Neutrality, and PR2-bias analyses were conducted to explore the factors shaping codon usage patterns. The analyzed genomes were categorized into five groups (Clade1, Clade2, Clade3, Clade4, and Others), exhibiting variations in CAI and ENC values. Phylogenetic analysis revealed three distinct gene clusters. ENC-GC3, Neutrality, and PR2-bias analyses demonstrated that both natural selection and mutation pressure influence codon usage. These findings suggest that codon usage preferences and the evolutionary dynamics of L1, E6, and E7 genes differ across hosts, driven by a combination of selection and mutational forces.

Indexed as

Capsid ProteinsCodon UsageOncogene Proteins, ViralPapillomaviridaePapillomavirus E7 ProteinsCodonEvolution, MolecularGenome, ViralHumansPapillomavirus InfectionsPhylogenySelection, GeneticCapsid ProteinsCodonOncogene Proteins, ViralPapillomavirus E7 Proteins

Identifiers

PMID40879819

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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.