Evolution and transmission in HIV Steve Paterson Review; Rambaut 2004 Nature Reviews Genetics 5: 52-61 ‘The causes and consequences of HIV evolution’

Slides:

Advertisements

Similar presentations

Antiretroviral Drug Resistance

Advertisements

Antiretroviral Drug Resistance Anna Maria Geretti UCL Medical School & Royal Free Hampstead Medical School, London.

Evoluzione genetica di HIV ed evoluzione clinica della malattia AIDS: due aspetti correlati? Carlo Federico Perno.

Lecture 1 – Introduction and Importance of Systematics

Sanderson The dN/dS ratio on each branch of the primate phylogeny (nonscaled branches) for the S opsin gene (above the branch) and the M/L opsin.

Molecular Clock I. Evolutionary rate Xuhua Xia

Bioe 109 Evolution Summer 2009 Lecture 1: Part II Evolution in action: the HIV virus.

HIV/AIDS as a Microcosm for the Study of Evolution.

Lecture: HIV I.Motivation What can we learn when we apply evolutionary principles to our understanding of the of the HIV epidemic?? Can we use HIV to introduce.

1 Functional prediction in proteins (purifying and positive selection)

Virus Evolution Molecular Epidemiology of Viral Infections Jen-Ren Wang, Ph. D. 王貞仁 Dept. of Medical Laboratory Science and Biotechnology National Cheng.

Materials and Methods Abstract Conclusions Introduction 1. Korber B, et al. Br Med Bull 2001; 58: Rambaut A, et al. Nat. Rev. Genet. 2004; 5:

An Introduction to the HIV Problem Space Oakwood University: Faculty Quantitative Institute Aug. 10–12, 2009.

Retrovirus Biology Immunology/HIV Michael Para, MD 1.

KEY CONCEPT Genetics provides a basis for new medical treatments.

Biology and natural history of the virus

Analysis of HIV Evolution Bobak Seddighzadeh and Kristoffer Chin Department of Biology Loyola Marymount University Bio February 23, 2010.

HIV-1 evolution in response to immune selection pressures

The evolution of HIV Why is HIV fatal?. Lethal strains are favored, due to “Short sighted” evolution within hosts Transmission rate advantages.

Why study evolution?  Best conceptual framework for understanding origins of biodiversity  Adaptations that allow organisms to exploit their environment.

Chapter 26: Phylogeny and the Tree of Life Objectives 1.Identify how phylogenies show evolutionary relationships. 2.Phylogenies are inferred based homologies.

Summary Slide Presentation Are subtype differences important in HIV drug resistance? Lessells RJ, Katzenstein DK, de Oliveira T. Are subtype differences.

Phylogenetic analysis of HIV-1 Gag cleavage sites polymorphism in HIV acutely infected patients Castro E 1,2, Cavassini M 1, Bart PA 2 and Pantaleo G 2.

Ethical issues in research methods: DOs & DON’Ts The Group 2 M. Holm, F. Postma, S. Reddy Vanga, J. Martijn, H. Agic.

Evolution and Human Health. I.Motivation Evolutionary principles can contribute to understanding of origin and treatment of human disease Evolutionary.

PHYLOGENETICS CONTINUED TESTS BY TUESDAY BECAUSE SOME PROBLEMS WITH SCANTRONS.

Lesson 7-3 What are Viruses?

Introduction to Bioinformatics.

Evolution is the unifying concept of biology. Two Central Themes of Biology Adaptation - How and in what ways do organisms function and become better.

Mechanisms of Evolution 16.1 Causes of microevolution.

How Does Antiretroviral Therapy Affect HIV Mutation and Vice Versa? Arlin Toro Devin Iimoto Devin Iimoto.

Evolution and Human Health – Chapter 14 - Flu virus evolution - Antibiotic resistance - Cancer as set of evolving population - Adaptative reasoning and.

Analysis of Recombination in the HIV-1pol Gene Richard Myers Division of Infection and Immunity University College London.

Viruses Big Questions: What is a virus? How does a virus function?

Phylogenetics: The “E” word in disguise Keith A. Crandall, Brigham Young University

Examining the Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Examining Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano Bioinformatics Laboratory Loyola.

SC.912.L Mutations 2. Genetic Recombination (sexual reproduction)

“Neutralizing Antibodies Derived from the B Cells of 1918 Influenza Pandemic Survivors” (Yu et. al) Daniel Greenberg.

Evolutionary Medicine 2015 UNM Evolutionary Medicine Joe Alcock MD MS Department of Emergency Medicine Adjunct, Dept. Biology.

Lecture 13 Immunology and disease: parasite antigenic diversity.

Human survivorship Developed Developing Bob May (2007), TREE 22:

Examining Genetic Similarity and Difference of the Three Progressor Groups at the First and Middle Visits Nicole Anguiano BIOL398: Bioinformatics Laboratory.

Immune system. Human immunodeficiency virus (HIV)

Viral evolution and adaption

Molecular coevolution Steve Paterson. Host-parasite interactions Drive diversity within species Drive divergence between species.

Human survivorship Developed Developing Bob May (2007), TREE 22:

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

Data analyses Course code: ZOO560 Week 3

The HIV Genome Is A Busy Place

Big Questions: What is a virus? How does a virus function?

Immunology and disease: parasite antigenic diversity

From Health and Medical Geography, 4th edition, by Emch, Root, & Carrel. Copyright 2017 by The Guilford Press.

KEY CONCEPT Genetics provides a basis for new medical treatments.

Big Questions: What is a virus? How does a virus function?

Jean-Michel Pawlotsky, MD, PhD Clinics in Liver Disease

Big Questions: What is a virus? How does a virus function?

KEY CONCEPT Genetics provides a basis for new medical treatments.

KEY CONCEPT Genetics provides a basis for new medical treatments.

T. M. Walker, M. Merker, T. A. Kohl, D. W. Crook, S. Niemann, T. E. A

Predicting the Onset of AIDS

S. Borrell, S. Gagneux Clinical Microbiology and Infection

Aim What happens when a bacteria or virus mutates?

M.W. Borgdorff, D. van Soolingen Clinical Microbiology and Infection

Evolution and transmission in HIV

KEY CONCEPT Genetics provides a basis for new medical treatments.

KEY CONCEPT Genetics provides a basis for new medical treatments.

Phylogenetic and convergence analyses of rpoB mutations.

Phylogenetic tree of Mycoplasmagenitalium-positive samples using dual locus sequence typing. Phylogenetic tree of Mycoplasmagenitalium-positive samples.

KEY CONCEPT Genetics provides a basis for new medical treatments.

Presentation transcript:

Evolution and transmission in HIV Steve Paterson Review; Rambaut 2004 Nature Reviews Genetics 5: ‘The causes and consequences of HIV evolution’

Use phylogenies to follow infection HIV is an RNA virus, with a high mutation rate mutates over course of infection

HIV

HIV Gag gene polymorphism

Phylogenetic tree should mirror contact structure of infection

Molecular epidemiology of HIV in Edinburgh HIV mutates as passes from one individual to next Use substitutions to build phylogenies and track pattern of infection

HIV phylogeny Holmes et al (1994) J. Inf. Diseases 171:45-53

Oliveira et al (2006) Nature. 444,

Origins of HIV Rambaut 2004 Nature Reviews Genetics 5: HIV-1 HIV-2

Origins of HIV-1

Within host evolution of HIV high rate of mutation –(0.2 errors/genome) high rate of replication –(gen. time = 2.5 days, virions/day) natural selection –immune selection –genetic drift

Genetic diversity of HIV Rambaut (2004) Nature Reviews Genetics 5, 52-61

Evolution of drug resistance in HIV

env gene blue sites = +ve seln. Ross (2002) J. Virol. 76 : CTL escape Long-livedShort-lived Immune pressure, effective at driving amino-acid change in long-lived patients?