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2000 Biocomputing 2001  
A new algorithm for inferring the evolution of within-host viral sequences is presented.  ...  The algorithm is applied to a data set of the V3 region of the HIV-1 envelope genes sequenced at different years after the infection of a single patient.  ...  Acknowledgments We thank three anonymous reviewers for giving us very helpful comments. This study was supported by a grant to women researcher to F. Ren from ESSO SEKIYU K.K. Japan.  ... 
doi:10.1142/9789814447362_0057 fatcat:uwdqkatoobco3an5cygjli4gwi

Reconstruction and Analysis of Within-host Longitudinal HIV-1 Evolution by a Distance-based Sequential-linking Algorithm

Soichi Ogishima, Fengrong Ren, Hiroshi Tanaka
2001 Chem-Bio Informatics Journal  
We applied this new algorithm to a data of the V3 region of the HIV-1 envelope genes sequenced at different years after the infection of a single patient.  ...  In this study we develop a new phylogenetic method to describe within-host (patient) viral evolution. Our method accommodates ordinary phylogenetic tree with viral evolution.  ...  This study is supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.  ... 
doi:10.1273/cbij.1.73 fatcat:lnvv5uvz5rgorfjp4jhc5kmizy

A Sequential-Linking Method for Analysis of Within-Host Viral Evolution

Fengrong Ren, Soichi Ogishima, Hiroshi Tanaka
2000 Genome Informatics Series  
We applied the method to a data set of the V3 region of HIV-1 envelope gene and carried out a detailed analysis of viral evolution.  ...  In this study, we develop a new method to detect when the neutral and adaptive evolution occur in the process of within-host viral evolution, and to reconstruct a longitudinal phylogenetic tree using sequential  ... 
doi:10.11234/gi1990.11.408 fatcat:5an4na5ervexboki6cikjxbo7q

Towards a new paradigm linking virus molecular evolution and pathogenesis: experimental design and phylodynamic inference

Melissa M Norström, Annika C Karlsson, Marco Salemi
2012 The New Microbiologica  
Phylogenetic analysis has become a powerful tool for the investigation of evolution at a molecular level.  ...  This review focuses specifically on experimental and data assembling strategies that are required to test multi-level phylodynamic hypotheses, ranging from intra-host viral evolution to population dynamics  ...  (A) Intrahost evolution data set using a sub- Towards a new paradigm linking virus molecular evolution and pathogenesis 107 FIGURE 5 -Example of phylogeny patterns in HIV-1 intra-and inter- host evolution  ... 
pmid:22707126 fatcat:g3hf2m4s5jf4rpyweorkehpphq

The Specificity and Polymorphism of the MHC Class I Prevents the Global Adaptation of HIV-1 to the Monomorphic Proteasome and TAP

Boris Schmid, Can Keşmir, Rob J. de Boer, Douglas F. Nixon
2008 PLoS ONE  
We estimate that upon transmission of a virus to a new host 39%-66% of the mutations that caused epitope precursor escapes are released from immune selection pressure.  ...  To assess whether viruses exploit this apparent vulnerability, we study the evolution of HIV-1 with bioinformatic tools that allow us to predict CTL epitopes, and quantify the frequency and accumulation  ...  We would like to thank Alan Perelson for hosting us and Bette Korber and Karina Yusim for the productive discussions during the early stages of this research.  ... 
doi:10.1371/journal.pone.0003525 pmid:18949050 pmcid:PMC2569417 fatcat:2mq63fzyyfgnph7qsuc7pzuv34

The intra-host evolutionary and population dynamics of human immunodeficiency virus type 1: a phylogenetic perspective

Marco Salemi
2013 Infectious Disease Reports  
of HIV-1 intra-host genealogies inferred from longitudinally sampled viral sequences; HIV-1 intra-host sub-population structure; the potential relationship between viral evolutionary rate and disease  ...  The intra-host evolutionary and population dynamics of the human immunodeficiency virus type 1 (HIV-1), the cause of the acquired immunodeficiency syndrome, have been the focus of one of the most extensive  ...  Review HIV-1 intra-host effective population size and metapopulation structure Strong evidence for the importance of selection on HIV-1 intra-host evolution is also provided by studies on the total viral  ... 
doi:10.4081/idr.2013.s1.e3 pmid:24470967 pmcid:PMC3892624 fatcat:zr5julqxqrfpnajrqg6vnzceum

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan, Christophe Fraser
2012 PLoS Computational Biology  
At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry.  ...  We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data.  ...  Contributed reagents/ materials/analysis tools: LCS EMB DEM HS ABvW. Wrote the paper: AFYP.  ... 
doi:10.1371/journal.pcbi.1002753 pmid:23133358 pmcid:PMC3486858 fatcat:4a2qeabbabf3jhp36so7g6uvlq

MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies

Patricia Buendia, Giri Narasimhan
2004 Proceedings. IEEE Computational Systems Bioinformatics Conference  
A new computational method to study within-host viral evolution is explored to better understand the evolution and pathogenesis of viruses.  ...  We test our algorithm using extensive simmulations and apply it to a set of HIV sequence data isolated from one patient over a period of ten years.  ...  Introduction The processes involved in intra-host (within a single host or patient) and inter-host evolution are strikingly different for retroviruses such as HIV [12] .  ... 
pmid:16448005 pmcid:PMC3195421 fatcat:cgoioromonesboepgf3mnx6tmy

The complexities of genome analysis, the Retroid agent perspective

M. A. McClure
2000 Bioinformatics  
of information within and between organisms.  ...  A description of these complexities is presented as a three parameter conceptual framework that considers type, size, and mechanism of events that contribute to the evolution of genes, genomes, and organisms  ...  Angela Baldo and King Jordan, and Seanna Corro, Julianna Hudak, and Ben Sutter for discussion and critical reading of the manuscript.  ... 
doi:10.1093/bioinformatics/16.2.79 pmid:10842727 fatcat:ygzxwii6snbfpls3z3ycoxdtcy

A Generalized Entropy Measure of Within-Host Viral Diversity for Identifying Recent HIV-1 Infections

Julia Wei Wu, Oscar Patterson-Lomba, Vladimir Novitsky, Marcello Pagano
2015 Medicine  
We analyzed HIV gag sequences from a cohort in Botswana. Fortytwo subjects newly infected by HIV-1 Subtype C were followed through 500 days post-seroconversion.  ...  Using sliding window analysis, we screened for genetic regions within gag that best differentiate recent versus chronic infections.  ...  Seage III for helpful discussions. We thank the study participants.  ... 
doi:10.1097/md.0000000000001865 pmid:26496342 pmcid:PMC4620842 fatcat:gc7kt4k33rgfrotnzwli42gyhy

Impact of Clinical Parameters in the Intrahost Evolution of HIV-1 Subtype B in Pediatric Patients: A Machine Learning Approach

Patricia Rojas Sánchez, Alberto Cobos, Marisa Navaro, José Tomas Ramos, Israel Pagán, África Holguín
2017 Genome Biology and Evolution  
The best-predictor variables for HIV-1B evolutionary parameters were the age of HIV-1 diagnosis for d, the age at first antiretroviral treatment for d N and the year of HIV-1 diagnosis for d s .  ...  Determining the factors modulating the genetic diversity of HIV-1 populations is essential to understand viral evolution.  ...  We thank CoRISPE and the professionals responsible for the routine resistance testing in the participant hospitals for providing epidemiological-clinical data and pol sequences of enrolled patients when  ... 
doi:10.1093/gbe/evx193 pmid:29044435 pmcid:PMC5647794 fatcat:qgnjykv2hzgrddkngjg5rmezge

Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies

Yaakov Maman, Uri Hershberg, Yoram Louzoun
2014 Immunogenetics  
favorable form when the threat is removed (i.e., in a new host).  ...  of selection during viral evolution.  ...  A paired t test was used for HIV versus SIV protein conservation. A chi-squared test was used for the analysis of the codon bias and mutation rates.  ... 
doi:10.1007/s00251-014-0811-4 pmid:25376343 fatcat:xzcdhhtjbredlczxxfxunpzyiq

HIV Whole-Genome Sequencing Now: Answering Still-Open Questions

Karin J. Metzner, Y.-W. Tang
2016 Journal of Clinical Microbiology  
Diversity, evolution, and epidemiology of HIV are directly relevant to HIV transmission and pathogenesis; hence, they play a key role in antiretroviral treatment and vaccine design.  ...  Global HIV whole-genome sequencing would provide a treasure chest of data to answer many questions still open in these fields.  ...  Support for this article was provided by, the Swiss Initiative in Systems Biology (MRD-Project HIV-X).  ... 
doi:10.1128/jcm.03265-15 pmid:26791367 pmcid:PMC4809914 fatcat:ldr255p4uvetfdkaouaawu7yhq

An exploratory algorithm to identify intra-host recombinant viral sequences

Marco Salemi, Rebecca R. Gray, Maureen M. Goodenow
2008 Molecular Phylogenetics and Evolution  
The results show that our procedure can be a valuable exploratory tool for detection of recombinant sequences before phylogenetic analysis, and also suggest that HIV-1 recombination in vivo is far more  ...  More problematic is the identification of recombinants among closely related sequences such as a viral population within a host.  ...  Holloway University Chair for AIDS Research (M.M.G).  ... 
doi:10.1016/j.ympev.2008.08.017 pmid:18801446 pmcid:PMC2615825 fatcat:tss4e3bcxjajhg7u3ad6sscnvq

Molecular Evolution: The HIV Envelope Protein

Brian Rybarczyk
2008 Evolution: Education and Outreach  
enters the host, will affect the rate of V1/V2 evolution.  ...  The activity will provide students a hands-on experience working with actual scientific data to elucidate the molecular evolution of the virus during the infection of a host.  ... 
doi:10.1007/s12052-007-0023-6 fatcat:am464xugpnf4xlejor6xn3ln54
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