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Mendeley | Further Information

{"title"=>"Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load", "type"=>"journal", "authors"=>[{"first_name"=>"Samuel", "last_name"=>"Alizon", "scopus_author_id"=>"16027863300"}, {"first_name"=>"Viktor", "last_name"=>"von Wyl", "scopus_author_id"=>"21740219900"}, {"first_name"=>"Tanja", "last_name"=>"Stadler", "scopus_author_id"=>"35231151900"}, {"first_name"=>"Roger D.", "last_name"=>"Kouyos", "scopus_author_id"=>"14023112100"}, {"first_name"=>"Sabine", "last_name"=>"Yerly", "scopus_author_id"=>"35228206200"}, {"first_name"=>"Bernard", "last_name"=>"Hirschel", "scopus_author_id"=>"35187033300"}, {"first_name"=>"Jürg", "last_name"=>"Böni", "scopus_author_id"=>"7006574621"}, {"first_name"=>"Cyril", "last_name"=>"Shah", "scopus_author_id"=>"7102026149"}, {"first_name"=>"Thomas", "last_name"=>"Klimkait", "scopus_author_id"=>"7005960625"}, {"first_name"=>"Hansjakob", "last_name"=>"Furrer", "scopus_author_id"=>"35225781600"}, {"first_name"=>"Andri", "last_name"=>"Rauch", "scopus_author_id"=>"35308968700"}, {"first_name"=>"Pietro L.", "last_name"=>"Vernazza", "scopus_author_id"=>"35226022400"}, {"first_name"=>"Enos", "last_name"=>"Bernasconi", "scopus_author_id"=>"7006810424"}, {"first_name"=>"Manuel", "last_name"=>"Battegay", "scopus_author_id"=>"7004770044"}, {"first_name"=>"Philippe", "last_name"=>"Bürgisser", "scopus_author_id"=>"35236352500"}, {"first_name"=>"Amalio", "last_name"=>"Telenti", "scopus_author_id"=>"7006764406"}, {"first_name"=>"Huldrych F.", "last_name"=>"Günthard", "scopus_author_id"=>"7005951278"}, {"first_name"=>"Sebastian", "last_name"=>"Bonhoeffer", "scopus_author_id"=>"7005099220"}], "year"=>2010, "source"=>"PLoS Pathogens", "identifiers"=>{"pmid"=>"24171102", "doi"=>"10.1371/journal.ppat.1001123", "sgr"=>"78149306494", "isbn"=>"2050-084X (Electronic)\\r2050-084X (Linking)", "scopus"=>"2-s2.0-78149306494", "issn"=>"15537366", "pui"=>"359909801"}, "id"=>"38852744-5d00-3d9b-ace9-030c4f5aaef8", "abstract"=>"Developing treatments or vaccines for HIV is challenging because the genetic makeup of the virus is constantly changing in an effort to outwit the human immune system. Moreover, the immune system is highly variable as a result of the long-standing co-evolution of humans and microbes. Each individual will try to oppose the invading virus in a unique way, forcing the virus to acquire specific mutations that can be interpreted as the genetic signature of this one-against-one battle. To explore the influence of co-evolution on HIV, Bartha et al. took samples of both human and viral genomes from 1071 individuals infected with HIV, the AIDS virus, and used genotyping and sequencing technology to obtain a comprehensive description of the genetic variation in both. Computational techniques were then used to search for links between variants in the human DNA sequences and variants in the viral sequences. The most common type of genetic variation found in the human genome is a single nucleotide polymorphism, or SNP for short: a SNP is produced when a single nucleotide – an A, C, G or T – is replaced by a different nucleotide. Bartha et al. found that SNPs within the human DNA sequences in their study were linked to variations in 48 amino acids in HIV. Moreover, all these SNPs were found within a group of genes known as the HLA (human leukocyte antigen) system, which encodes for proteins that play a vital role in the immune response. This work identified the areas of the human genome that put pressure on the AIDS virus, and the regions of the virus that serve to escape human control. The approach developed by Bartha et al. allows the interactions between a microbe and a human host to be studied by looking at the genome of the microbe and the genome of the infected person. It also differentiates host-induced mutations that limit the capacity of the virus to do harm from those that are tolerated by the pathogen. A similar strategy could be used to study other infectious diseases.", "link"=>"http://www.mendeley.com/research/phylogenetic-approach-reveals-virus-genotype-largely-determines-hiv-setpoint-viral-load", "reader_count"=>178, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Librarian"=>1, "Researcher"=>56, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>8, "Student > Master"=>22, "Other"=>11, "Student > Bachelor"=>15, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>8, "Librarian"=>1, "Researcher"=>56, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>36, "Student > Postgraduate"=>8, "Student > Master"=>22, "Other"=>11, "Student > Bachelor"=>15, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Agricultural and Biological Sciences"=>99, "Business, Management and Accounting"=>1, "Chemical Engineering"=>1, "Chemistry"=>1, "Computer Science"=>11, "Engineering"=>3, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>15, "Mathematics"=>3, "Medicine and Dentistry"=>25, "Sports and Recreations"=>1, "Physics and Astronomy"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>3, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>25}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Mathematics"=>{"Mathematics"=>3}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}, "Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>99}, "Computer Science"=>{"Computer Science"=>11}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>15}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>4, "Japan"=>1, "United Kingdom"=>4, "Portugal"=>1, "Switzerland"=>1, "Spain"=>1, "India"=>1, "Saudi Arabia"=>1, "Netherlands"=>1, "Belgium"=>1, "Brazil"=>2, "South Africa"=>2, "France"=>1, "Germany"=>1}, "group_count"=>4}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/411905", "https://ndownloader.figshare.com/files/411999"], "description"=>"<div><p>HIV virulence, i.e. the time of progression to AIDS, varies greatly among patients. As for other rapidly evolving pathogens of humans, it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown. We apply the phylogenetic comparative approach (PCA) to estimate the heritability of a trait from one infection to the next, which indicates the control of the virus genotype over this trait. The idea is to use viral RNA sequences obtained from patients infected by HIV-1 subtype B to build a phylogeny, which approximately reflects the transmission chain. Heritability is measured statistically as the propensity for patients close in the phylogeny to exhibit similar infection trait values. The approach reveals that up to half of the variance in set-point viral load, a trait associated with virulence, can be heritable. Our estimate is significant and robust to noise in the phylogeny. We also check for the consistency of our approach by showing that a trait related to drug resistance is almost entirely heritable. Finally, we show the importance of taking into account the transmission chain when estimating correlations between infection traits. The fact that HIV virulence is, at least partially, heritable from one infection to the next has clinical and epidemiological implications. The difference between earlier studies and ours comes from the quality of our dataset and from the power of the PCA, which can be applied to large datasets and accounts for within-host evolution. The PCA opens new perspectives for approaches linking clinical data and evolutionary biology because it can be extended to study other traits or other infectious diseases.</p></div>", "links"=>[], "tags"=>["phylogenetic", "reveals", "genotype", "determines", "hiv", "set-point", "viral"], "article_id"=>141368, "categories"=>["Neuroscience", "Cell Biology", "Cancer", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Samuel Alizon", "Viktor von Wyl", "Tanja Stadler", "Roger D. Kouyos", "Sabine Yerly", "Bernard Hirschel", "Jürg Böni", "Cyril Shah", "Thomas Klimkait", "Hansjakob Furrer", "Andri Rauch", "Pietro L. Vernazza", "Enos Bernasconi", "Manuel Battegay", "Philippe Bürgisser", "Amalio Telenti", "Huldrych F. Günthard", "Sebastian Bonhoeffer"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1001123.s001", "https://dx.doi.org/10.1371/journal.ppat.1001123.s002"], "stats"=>{"downloads"=>17, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Phylogenetic_Approach_Reveals_That_Virus_Genotype_Largely_Determines_HIV_Set_Point_Viral_Load/141368", "title"=>"Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-30 00:22:48"}
• {"files"=>["https://ndownloader.figshare.com/files/826798"], "description"=>"<p>20 phylogenies are simulated to model the evolution of an infection trait in a case where heritability is set to a given value. Phylogenetic signal ( in black and in red) is then estimated on each tree using only 128 leaves to account for incomplete sampling. The box plot shows the median values, the three quartiles and the outliers. The dashed line shows . The slope is (p-value and adjusted ) for and of (p-value and adjusted ) for .</p>", "links"=>[], "tags"=>["evolutionary", "processes"], "article_id"=>497139, "categories"=>["Neuroscience", "Plant Biology", "Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Samuel Alizon", "Viktor von Wyl", "Tanja Stadler", "Roger D. Kouyos", "Sabine Yerly", "Bernard Hirschel", "Jürg Böni", "Cyril Shah", "Thomas Klimkait", "Hansjakob Furrer", "Andri Rauch", "Pietro L. Vernazza", "Enos Bernasconi", "Manuel Battegay", "Philippe Bürgisser", "Amalio Telenti", "Huldrych F. Günthard", "Sebastian Bonhoeffer"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1001123.g002", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_signal_estimated_for_evolutionary_processes_with_known_heritability_/497139", "title"=>"Phylogenetic signal estimated for evolutionary processes with known heritability.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-30 01:58:59"}
• {"files"=>["https://ndownloader.figshare.com/files/826935"], "description"=>"<p>We use two estimators ( and ) that lead to similar results. Significance code for the p-value of the randomisation test for is ‘’ , ‘’ , ‘’ , and ‘n.s.’ indicates that the signal does not differ from that found on a random tree. The are obtained by taking the median value of over 161 trees (see the Methods). We also show the standard deviation in brackets. ‘—’ indicates that the largest tree could not be computed with the Bayesian method because of the large number of patients. is the sample size of each dataset.</p>", "links"=>[], "tags"=>["datasets"], "article_id"=>497283, "categories"=>["Neuroscience", "Plant Biology", "Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Samuel Alizon", "Viktor von Wyl", "Tanja Stadler", "Roger D. Kouyos", "Sabine Yerly", "Bernard Hirschel", "Jürg Böni", "Cyril Shah", "Thomas Klimkait", "Hansjakob Furrer", "Andri Rauch", "Pietro L. Vernazza", "Enos Bernasconi", "Manuel Battegay", "Philippe Bürgisser", "Amalio Telenti", "Huldrych F. Günthard", "Sebastian Bonhoeffer"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1001123.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_signal_in_the_4_datasets_for_the_three_different_traits_/497283", "title"=>"Phylogenetic signal in the 4 datasets for the three different traits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-30 02:01:23"}
• {"files"=>["https://ndownloader.figshare.com/files/826879"], "description"=>"<p>The first line is a regression between log(spVL) and dsCD4. The second line tests if values for a given trait vary across risk groups. OLS is the ordinary generalised least square without phylogenetic correction (a generalised linear model yielded similar results); RegBM indicates a correction based on the tree assuming Brownian motion. SE stands for ‘Standard Error’. For further details, see the Supplementary Methods. Significance code for the p-value of the test is ‘’ , ‘’ , ‘’ and ‘n.s.’ for non sognificant.</p>", "links"=>[], "tags"=>["life-history", "correction", "phylogenetic"], "article_id"=>497226, "categories"=>["Neuroscience", "Plant Biology", "Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Samuel Alizon", "Viktor von Wyl", "Tanja Stadler", "Roger D. Kouyos", "Sabine Yerly", "Bernard Hirschel", "Jürg Böni", "Cyril Shah", "Thomas Klimkait", "Hansjakob Furrer", "Andri Rauch", "Pietro L. Vernazza", "Enos Bernasconi", "Manuel Battegay", "Philippe Bürgisser", "Amalio Telenti", "Huldrych F. Günthard", "Sebastian Bonhoeffer"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1001123.t002", "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regressions_between_life_history_traits_with_and_without_correction_for_phylogenetic_signal_/497226", "title"=>"Regressions between life-history traits with and without correction for phylogenetic signal.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-30 02:00:26"}
• {"files"=>["https://ndownloader.figshare.com/files/826666"], "description"=>"<p><b>A</b>) A phylogeny based on HIV sequences obtained from patients with known set-point viral loads, <b>B</b>) Phylogenetic distance between two tips versus difference in trait value between these two tips (slope and p-value) and <b>C</b>) Distribution of log(spVL) values in the MSM strict dataset. Panel A shows the maximum likelihood phylogenetic tree built with the MSM strict dataset. Squares on the tips of the tree correspond to infected patients. The colour of the squares and the graph on the right indicate the set-point viral load (colours range from blue to red for increasing log(spVL)). The PCA tests the correlation between proximity in the phylogeny and trait values (log(spVL)). The circles on the tree nodes indicate bootstrap values: black is greater than 90%, grey is between 50 and 90% and white is lower than 50%.</p>", "links"=>[], "tags"=>["phylogenies", "MSM"], "article_id"=>497007, "categories"=>["Neuroscience", "Plant Biology", "Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Samuel Alizon", "Viktor von Wyl", "Tanja Stadler", "Roger D. Kouyos", "Sabine Yerly", "Bernard Hirschel", "Jürg Böni", "Cyril Shah", "Thomas Klimkait", "Hansjakob Furrer", "Andri Rauch", "Pietro L. Vernazza", "Enos Bernasconi", "Manuel Battegay", "Philippe Bürgisser", "Amalio Telenti", "Huldrych F. Günthard", "Sebastian Bonhoeffer"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1001123.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Combining_phylogenies_and_trait_values_in_the_MSM_strict_dataset_/497007", "title"=>"Combining phylogenies and trait values in the MSM strict dataset.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-30 01:56:47"}

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Relative Metric

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F1000Prime | Further Information

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