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SERIES EDITORS
D. ROLLINSON
Department of Zoology
The Natural History Museum
London, UK

S. HAY
Malaria Public Health and
Epidemiology Group
Centre for Geographic Medicine
KEMRI/University of Oxford/
Wellcome Trust Collaborative
Programme
Nairobi, Kenya

EDITORIAL BOARD
M. COLUZZI
Department of Public Health Sciences, Section of Parasitology
‘Ettore Biocca’ ‘Sapienza – Università di Roma’ 00185 Roma, Italia

C. COMBES
Laboratoire de Biologie Animale, Université de Perpignan, Centre
de Biologie et d’Ecologie Tropicale et Méditerranéenne, 66860
Perpignan Cedex, France

D. D. DESPOMMIER
Division of Tropical Medicine and Environmental Sciences,
Department of Microbiology, Columbia University, New York,
NY 10032, USA

J. J. SHAW
Instituto de Ciências Biomédicas, Universidade de São Paulo,
05508-990, Cidade Universitária, São Paulo, SP, Brazil

K. TANABE
Laboratory of Malariology, International Research Center of
Infectious Diseases. Research Institute for Microbial Diseases,
Osaka University, Suita, 565-0871. Japan
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 CONTRIBUTORS

Shelley A. Adamo
Department of Psychology, Dalhousie University, Halifax, Canada.
Irka Bargielowski
Division of Biology, Imperial College London, United Kingdom.
Marı́a-Gloria Basáñez
Department of Infectious Disease Epidemiology, Imperial College
London, London, United Kingdom; Associate researcher of Centro
Amazónico para Investigación y Control de Enfermedades Tropicales
(CAICET) ‘‘Simón Bolı́var’’, Estado Amazonas, Venezuela.
David G. Biron
PIAF, UMR 547 INRA/Université Blaise-Pascal, Clermont-Ferrand,
France.
Thomas S. Churcher
Department of Infectious Disease Epidemiology, Imperial College
London, London, United Kingdom.
Keith G. Davies
Plant Pathology and Microbiology, Rothamsted Research, Harpenden,
United Kingdom.
Alison M. Dunn
Institute of Integrative and Comparative Biology, Faculty of Biological
Sciences, University of Leeds, United Kingdom.
Paul W. Ewald
Department of Biology and the Program on Disease Evolution, University
of Louisville, Louisville, KY, USA.
Alan Fenwick
Department of Infectious Disease Epidemiology, Faculty of Medicine,
St Mary’s Campus Imperial College, Paddington, United Kingdom.
Philip J. R. Goulder
Department of Paediatrics, University of Oxford, Peter Medawar Building
for Pathogen Research, Oxford, United Kingdom; Partners AIDS Research
Center, Massachusetts General Hospital, Charlestown, Boston, MA, USA;

ix
x Contributors

HIV Pathogenesis Programme, The Doris Duke Medical Research Institute,

University of KwaZulu-Natal, Durban, South Africa.
Marı́a-Eugenia Grillet
Laboratorio de Biologı́a de Vectores, Instituto de Zoologı́a Tropical,
Universidad Central de Venezuela, Caracas, Venezuela; Associate
researcher of Centro Amazónico para Investigación y Control de Enferme-
dades Tropicales (CAICET) ‘‘Simón Bolı́var’’, Estado Amazonas, Venezuela.
Present address: Department of Ecology and Evolutionary Biology,
University of Toronto, Toronto, ON, Canada.
Katrin Hammerschmidt
Department of Animal and Plant Sciences, The University of Sheffield,
Sheffield, United Kingdom.
David Hughes
Department of Organismal Biology, University of Harvard, Cambridge,
MA, USA; School of Biosciences, University of Exeter, Exeter, UK.
Hilary Hurd
Institute for Science and Technology in Medicine, Centre for Applied
Entomology and Parasitology, School of Life Sciences, Keele University,
United Kingdom.
Jacob C. Koella
Division of Biology, Imperial College London, United Kingdom.
Joachim Kurtz
University of Münster, Institute for Evolution and Biodiversity, Münster,
Germany.
Thierry Lefèvre
Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724,
Montpellier, France.
Lena Lorenz
Division of Biology, Imperial College London, United Kingdom.
Fiona Mathews
University of Exeter, Hatherly Laboratories, Exeter, United Kingdom.
Philippa C. Matthews
Department of Paediatrics, University of Oxford, Peter Medawar Building
for Pathogen Research, Oxford, United Kingdom.
Dorothée Missé
Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724,
Montpellier, France.
 Contributors xi

Rebecca P. Payne
Department of Paediatrics, University of Oxford, Peter Medawar Building
for Pathogen Research, Oxford, United Kingdom.
Julia G. Prado
Department of Paediatrics, University of Oxford, Peter Medawar Building
for Pathogen Research, Oxford, United Kingdom.
Judith E. Smith
IICB, Faculty of Biological Sciences, Leeds University, Leeds, United
Kingdom.
Frédéric Thomas
Génétique et Evolution des Maladies Infectieuses, UMR CNRS/IRD 2724,
Montpellier, France; Institut de recherche en biologie végétale, Départe-
ment de sciences biologiques Université de Montréal, Montréal, Québec,
Canada.
 PREFACE
This thematic volume of Advances in Parasitology was conceived as a result
of a symposium held at the Linnaean Society in the autumn of 2007, for
which I had the pleasure to convene together with Dr David Rollinson, to
mark the tercentenary of Linnaeus’s birth in combination with the Cente-
nary celebrations of both Imperial College and the Royal Society of Tropi-
cal Medicine and Hygiene. The symposium was extremely successful and
highly attended, and we were delighted that almost every speaker was
willing to subsequently contribute their papers to this volume.
Dobzhansky wrote in his famous essay, ‘‘Nothing in biology makes
sense except in the light of evolution’’, yet this truth so often appears to be
ignored within the medical and biomedical disciplines. Evolution and co-
evolution are the foundations of biology, and biology is the foundation of
medicine and public health. For example, co-evolution has epidemiologi-
cal implications, particularly in the context of emerging and re-emerging
diseases. If co-evolution imposes constraints on susceptibility and patho-
genicity, those constraints may no longer hold when new host-parasite
associations emerge or ancient associations are disrupted, affecting both
the magnitude and severity of disease outbreaks. There may also be
indirect effects of changes in the range of parasites to which a host
population is exposed through altering the selection pressures on existing
parasites. Likewise, altering host genetics, especially by selective breeding
for resistance to a particular parasite, could also affect selection pres-
sures on other parasites. Understanding how parasites respond to
evolved changes in host characteristics may also provide a good model
for their all too apparent potential to respond to other kinds of change,
such as the use of new drugs or vaccines to combat disease. Evolutionary
theory has, therefore, an important role to play in both the interpretation
of host and parasite dynamics and the design and application of disease
control programmes.
This volume brings together a range of articles from scientists from
different fields of research and/or disease control, but with a common
interest in studying the biology of a variety of parasitic (in its broadest
sense) diseases. In so doing, we aim to present what evolutionary think-
ing can contribute to an integrated understanding of the processes shap-
ing host-parasite interactions and control.
The volume starts with a selection of papers on viruses, which,
although not always classified as parasites in the strictest sense, can in
fact be termed the ‘ultimate parasite’. The paper by Rebecca Payne and
colleagues illustrates how the human immunodeficiency virus (HIV)

xiii
xiv Preface

epidemic, of current key concern in terms of global health, also provides a

rare opportunity to examine in detail the initial stages of a host-pathogen
co-evolutionary struggle in humans. In particular, the role of human
leukocyte antigen (HLA) class I and the cytotoxic T-lymphocyte (CTL)
response in controlling HIV replication is described (which may also help
explain how some individuals are able to elicit long-term control (>25
years) of HIV replication during the course of natural infection), as is the
extent to which HIV has already adapted to those HLA class I molecules
and those CTL responses that are most effective in viral suppression. It
becomes evident that viral mutations that enable HIV to evade the CTL
response are already accumulating in populations where the selecting
HLA molecules are highly prevalent, indicating the dynamic and shifting
nature of the battle currently being played out between HIV and human
populations. Indeed, the sequence variation observed at a population level
is not random variation, but appears to be the consequence of Darwinian
selection operating in the context of the host immune response. As a result,
HIV may be predicted to become adapted at a population level to those
immune responses currently identified as mediating control, which is
clearly a major anxiety in relation to vaccine design and future control.
Host-viral interactions are also the focus of Paul Ewald’s paper, in
particular the role they may play in human cancers. Infectious causation
of human cancer was generally considered non-existent during the first
half of the 20th Century, and later reported only as noteworthy exceptions
to the general rule. Indeed, by the mid-1970s, only one human cancer was
widely acknowledged to be caused by uni-cellular or sub-cellular para-
sites, that of endemic Burkitt’s lymphoma, potentially in response to
co-infection of Plasmodium falciparum with Epstein Barr Virus (EBV).
However, with, in part, the current growing recognition of the molecular
mechanisms of pathogen-induced oncogenesis, this paper describes how
pathogens, particularly viruses, either alone or in synergy with other
infectious agents, may be major initiators of oncogenesis for many, if
not most, cancers, with the traditional mutation-driven processes becom-
ing dominant only after this initiation. Many supporting key examples are
presented, such as, for instance, the mouse mammary tumour virus
(MMTV), a causative agent of some human breast cancers. Because can-
cers are so devastating and their treatment is often both gruelling and
marginally effective, a solid record of preventing infection-induced
cancers demands that the full spectrum of infectious causation of cancers
be characterised and accurately understood. Now about 15–20% of all
human cancer are accepted by the World Health Organization as being
caused by parasitism and it is likely that such cases will become more and
more apparent.
The role of parasites in a range of chronic conditions is followed in the
paper by Thierry Lefèvre and colleagues, when considering the diversity
 Preface xv

and evolution of manipulative strategies in host-parasite interactions. In

this case the altered behaviour of the host is a phenotype of the parasite
and is controlled by the parasite’s genes, and hence may be termed part
of the parasite’s ‘extended phenotype’. In this review the authors examine
the mechanisms by which parasites are known to control the behaviour
of their hosts and describe novel methodologies for future research, such
as the need for more molecular and specifically proteomic techniques for
determining the genetic basis of manipulation. The authors propose that
parasites do not necessarily manipulate the brain of their hosts in the way
a puppeteer controls a puppet, delicately tweaking only those neural
circuits responsible for specific behavioural traits. Instead they suggest
that certain parasites appear to strike the host’s brain with a number of
diffuse and widespread effects, some of which induce changes in host
behaviour. A range of examples are described, such as the case of the
contrasting pathological phenotypes (aggressive vs. paralytic forms) dis-
played in human rabies between individuals, even following bites and
hence viral ‘strain’ from the same rabid dog, thereby implying a differen-
tial role of the host immune response in enabling such virally altered host
behaviour. The authors also highlight how, in the vast majority of cases,
our level of understanding of such host-parasite interactions is far from
complete, despite the fact that parasites are believed by some (admittedly
non-parasitologists) to be simple organisms.
Hilary Hurd’s paper on the evolutionary drivers of parasite-induced
changes in host life-history traits continues and expands upon several of
the general themes raised in the preceding papers. Key concepts under
consideration here relate to whether changes in host reproductive fitness
are by-products of infection, parasite manipulations, host adaptations,
mafia-like strategies and/or host compensatory responses. Her paper
focuses on the reproductive fitness of insect hosts and vectors, in particu-
lar that of tapeworms and beetles and malaria infections in anopheline
mosquitoes. Evidence is put forward for both a manipulator molecule of
parasite origin and for host-initiated regulation. This paper again high-
lights how it is imperative that evolutionary theories must now be sup-
ported by empirical evidence gained from studying the molecular,
biochemical and physiological mechanisms underlying changes in host
life-history traits, ideally using organisms that have evolved together and
that are in their natural environment.
Katrin Hammerschmidt and Joachim Kurtz’s paper considers host-
parasite interactions in parasites with complex life cycles, and hence those
that require two or more consecutive invertebrate and vertebrate hosts.
Despite the fact that so many parasites, including those of profound
medical and veterinary importance, have complex life cycles, our under-
standing of the evolution of complex life cycles is currently still in its
infancy. This paper describes in detail recent research into the
xvi Preface

immunological interaction of such a parasite, the model tapeworm

Schistocephalus solidus, with its two intermediate hosts, a cyclopoid cope-
pod and the three-spined stickleback. The data presented indicate that
immunological interactions between host(s) and parasite(s) are relevant
factors influencing not only parasite establishment and growth, but
potentially also behavioural manipulation of the hosts. In complement
to the Lefèvre et al. paper above, these authors elaborate upon the
‘‘extended phenotype’’ concept to include the proximate physiological
causes, whereby parasitised hosts can truly be seen as ‘‘deeply modified
organisms’’.
Turning towards more field-based evolutionary and epidemiological
studies, Judith Smith examines one of our most ubiquitous parasites,
Toxoplasma gondii. The paper describes how this parasite’s, again com-
plex, life cycle has become adapted to exploit multiple routes of transmis-
sion through a sexual cycle in the definitive host and asexually in the
intermediate host. While such alternative routes may operate synergisti-
cally to enhance transmission, this paper illustrates how they might also
provide a vehicle for selection, leading to partitioning of strains in the
environment, including potential differences in shifts from sexual to
asexual transmission between epidemiological regions.
Alison Dunn’s review considers the fate of (non-human) parasites
during a biological invasion and their impact on both native and invasive
hosts, asking whether parasites can directly or indirectly mediate inva-
sion success. Using illustrations from a range of studies focusing on
parasitism in amphipod invasions, this paper describes how, for example,
an introduced species may either lose its parasites as a result of the
introduction, introduce novel parasites to hosts in the new range and/or
acquire parasites from its new environment. Furthermore, this paper
highlights how, as a result of local adaptation, parasites tend to have a
differential effect on native versus invading hosts, which will be a key
determinant for the outcome of any invasion and its impact on the
recipient community.
Fiona Mathews’ paper then considers the importance of a detailed
understanding of the ecology of zoonotic diseases in wildlife, both in
terms of predicting their success and managing their control. More than
two-thirds of emerging, or re-emerging, infectious diseases are thought to
originate in wildlife. Despite this, co-ordinated surveillance schemes are
rare, and most efforts at disease control operate at the level of crisis
management. This review examines the pathways linking zoonoses in
wildlife with infection in other hosts, using examples from a range of key
zoonoses including European bat lyssaviruses and bovine tuberculosis.
The paper also describes how, while the vast majority of efforts to control
zoonoses in wildlife hosts rely on culling strategies, the alternative, and
 Preface xvii

potentially more successful, approach is to understand the factors leading

to disease outbreaks in the first place and to manage these instead.
Issues of the importance of understanding host-parasite interactions
for disease control, in this case biocontrol by a bacterium Pasteuria
penetrans, a hyperparasite of root-knot nematodes (Meloidogyne spp.),
are also illustrated in the paper by Keith Davies. It is only relatively
recently with the development of industrialised agriculture that plant
parasitic nematodes have been recognised as an important constraint on
crop production. For the majority of their evolutionary history, plant
parasitic nematodes have been part of a multi-trophic interaction between
their plant host and their natural enemies. This paper discusses the
reasons why bacterium-nematode surface interactions are likely to hold
the key to understanding host-specificity and evolutionary dynamics in
this system, and presents some genomic insights into potential solutions
for future bio-control.
In terms of direct disease control of human parasites (and hence where
public health measures can be seen as a major interaction by a host on
their parasites), Alan Fenwick’s paper documents how recent shifts in
global health policy have led towards the implementation of mass che-
motherapeutic control programmes at the national scale in previously
‘neglected’ countries, such as those within sub-Saharan Africa. However,
while celebrating the rapid success achieved to date by such programmes,
in terms of reduced infection prevalence, intensity and associated human
morbidity, it is acknowledged that evolutionary change in response to
drug selection pressure may be predicted under certain circumstances,
particularly in terms of the development of potential drug resistance.
Theoretical and empirical data gained to date thereby serve to highlight
the importance of careful monitoring and evaluation of parasites and their
hosts whenever and wherever chemotherapy is applied and where para-
site transmission remains.
The paper by Marı́a-Gloria Basáñez and colleagues then focuses on
one of these neglected tropical diseases, onchocerciasis, in relation to its
blackfly (Simulium) vector, with particular reference to the transmission
dynamics, density-dependent interactions, evolutionary implications and
ultimately control of human onchocerciasis. The authors examine evi-
dence to suggest that Onchocerca may exploit interactions to enhance its
transmission and discuss the consequences on onchocerciasis transmis-
sion of local adaptation in Onchocerca-Simulium complexes. Mathematical
models to coalesce and interpret current data and help identify optimal
control strategies are introduced. The authors describe in detail the pros-
pect that drug resistance may potentially become a public health concern,
and how future genetically structured mathematical models combining
population dynamics and genetics may provide insights into evolution-
arily stable strategies for different host-parasite complexes.
xviii Preface

Jacob Koella and colleagues’ paper concludes this volume with a

consideration of novel aspects for control of a major disease of public
health importance, specifically that of microsporidians as so-called ‘evo-
lution-proof’ agents of malaria control. Despite substantial control efforts
control, malaria remains one of our most serious and deadly diseases.
While some of the problems in controlling malaria are socio-economic,
others are biological, in particular those relating to this parasite’s intense
transmission and the emergence and spread of resistance of the malaria
parasites and their mosquito vectors against most of the chemicals used to
attack them. The authors question the potential success of proposed
future malaria control agents. For example, even following the develop-
ment of effective vaccines, subsequent strong novel selective pressures
may be likely to induce the parasite to develop escape-mutants. Indeed,
certain vaccines may even by predicted to lead to more virulent parasites.
Likewise the potential effectiveness of novel genetic strategies, aimed to
use either transformed sterile male mosquitoes or to drive genes for
resistance to infection linked to a transposable element through popula-
tions, is also questioned. New methods for control are therefore desper-
ately needed, although such methods would be useful only if they are
effective (i.e., decrease transmission substantially) and evolutionarily
sustainable (i.e., evolution-proof, in that they prevent evolution from
eroding efficacy). These authors propose microsporidian parasites that
infect mosquitoes as one potentially effective and sustainable agent for
malaria control, and describe in detail a range of recent studies to support
this. The authors conclude that, while the evolution of resistance may be
inevitable, with a solid understanding of the host-parasite systems
involved the failure of control need not be.
Therefore, this collection of papers covers a wide range of systems,
exemplified by a broad spectrum of micro-and macroparasites, impacting
humans, domestic and wild animals, and plants. It illustrates the impor-
tance of evolutionary considerations and concepts, both as thinking tools
for qualitative understanding or as guiding tools for decision making in
major control programmes. We thank the support of the editorial team of
Advances in Parasitology and hope that our readers will enjoy this volume
as much as we have enjoyed preparing it.

JOANNE P. WEBSTER
 CHAPTER 1
HLA-Mediated Control of HIV
and HIV Adaptation to HLA
Rebecca P. Payne,* Philippa C. Matthews,*
Julia G. Prado,* and Philip J. R. Goulder*,†,‡

Contents 1.1. Introduction 2

1.1.1. Epidemiology 2
1.1.2. Control of HIV: Progress and
challenges in therapeutics 2
1.1.3. Control of HIV: Successful immune responses 3
1.2. CD8þ Cytotoxic T Lymphocytes (CTL)
and Control of Viraemia 3
1.3. Disease Outcome Mediated by CTL 5
1.3.1. Effective CTL responses and dominant
role of HLA-B 5
1.3.2. CTL responses targeting HIV Gag 6
1.4. Immune Escape—Viral Escape Mutations from CTL 8
1.4.1. Impact of HIV escape mutations within a host 8
1.4.2. Impact of HIV escape mutations transmitted
to a new host 9
1.5. HIV Evolution and Immune Selection 12
1.5.1. Origin and evolution of HIV 12
1.5.2. HLA footprints and HIV evolution 13
1.6. Summary 14
References 15

* Department of Paediatrics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford,
United Kingdom
{
Partners AIDS Research Center, Massachusetts General Hospital, Charlestown, Boston, MA, USA
{
HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal,
Durban, South Africa

Advances in Parasitology, Volume 68 # 2009 Elsevier Ltd.

ISSN 0065-308X, DOI: 10.1016/S0065-308X(08)00601-5 All rights reserved.

1
2 Rebecca P. Payne et al.

Abstract The human immunodeficiency virus (HIV) epidemic provides a rare

opportunity to examine in detail the initial stages of a host-
pathogen co-evolutionary struggle in humans. The genes encoding
the human leukocyte antigen (HLA) class I molecules have a critical
influence in the success or failure of the immune response against
HIV. The particular HLA class I molecules expressed by each indi-
vidual defines the type of cytotoxic T-lymphocyte (CTL) response
that is made against the virus. This chapter describes the role of
HLA class I and the CTL response in controlling HIV replication, and
discusses the extent to which HIV has already adapted to those
HLA class I molecules and CTL responses that are most effective in
viral suppression. It is evident that viral mutations that enable HIV
to evade the CTL response are indeed already accumulating in
populations where the selecting HLA molecules are highly preva-
lent, indicating the dynamic and shifting nature of the evolutionary
interplay between HIV and human populations.

1.1. INTRODUCTION

1.1.1. Epidemiology
Since human immunodeficiency virus (HIV) was identified in the early
1980s as the causative agent of acquired immunodeficiency (AIDS), the
number of people living with HIV has relentlessly increased. In 2007,
2.5 million new infections were reported. Since 1981 there have been
an estimated 25 millions deaths (UNAIDS WHO AIDS epidemic
update 2007).

1.1.2. Control of HIV: Progress and challenges in therapeutics

The introduction of anti-retroviral therapy (ART) has resulted in a
decrease in mortality and morbidity among HIV-infected subjects. How-
ever, access to ART is still very limited in most resource-poor countries
where the epicentre of the pandemic is located. Thus, while the prospect
of an effective HIV vaccine remains bleak, it has never been so needed.
The failure, in 2007, of one of the most promising T-cell-based vaccine
candidates, which aimed either to protect against HIV transmission or to
lower viral loads in vaccinees who became infected (Sekaly, 2008;
Steinbrook, 2007; Watkins et al., 2008), has prompted the HIV scientific
community to confront the limitations in our knowledge of what consti-
tutes protective T-cell immunity.
 HIV and HLA 3

There are multiple challenges to creating an effective HIV vaccine that

is able to elicit, what are believed to be, the immune responses likely to
contain HIV, namely, broad neutralising antibodies and strong cytotoxic
T-lymphocyte (CTL) responses. Perhaps the greatest of these challenges is
the sequence variability of HIV, a hallmark of the virus, which results from
the high error rate of the viral reverse transcriptase (Preston et al., 1988).
Thus, from an HIV vaccine perspective, effective immune responses need
to be induced against a vast range of different, albeit closely related,
viruses. In addition, the sequence variation observed at a population
level is not random variation, but is to some extent the consequence of
Darwinian selection operating in the context of the host immune response.
Within a particular infected individual, the virus adapts to the immune
responses generated against it by selecting viral amino acid sequence
changes that reduce immune recognition of HIV and these increase in
frequency, ultimately replacing the wild-type virus. Following transmis-
sion of virus to a new recipient, some of these viral adaptations persist.
In this way, HIV may become adapted at a population level to those
immune responses currently identified as mediating control. This is
clearly a major anxiety in relation to vaccine design.

1.1.3. Control of HIV: Successful immune responses

In spite of the success with which HIV can evade the host immune
response, some individuals are able to elicit long-term control of HIV
replication during the course of natural infection. Individuals infected
more than 25 years ago have been identified, who have levels of plasma
HIV so low that the virus is undetectable by even the most sensitive
assays. It is valuable to understand which immune responses are respon-
sible for controlling HIV replication in this way. This review focuses on
the central role played by T-cell immunity in control of HIV infection.
In particular, we address the impact of viral evasion of CTL (CD8þ T cell)
responses through the selection of mutations that reduce or abrogate the
recognition of virus-infected cells by CTLs—so-called ‘CTL escape’—on
immune control of HIV in the individual, and at a population level.
Finally, we discuss the implications for vaccine design of CTL as a
major driving force of HIV evolution.

1.2. CD8þ CYTOTOXIC T LYMPHOCYTES (CTL)

AND CONTROL OF VIRAEMIA

In the first few weeks of untreated adult HIV infection, the level of viraemia
typically rises to around 107 HIV ribonucleic acid (RNA) copies per milli-
litre (ml) of plasma. This subsequently declines during the following few
4 Rebecca P. Payne et al.

weeks by 102-103 copies per ml of plasma to a relatively stable viral

set-point with a median of around 30,000 copies per ml. The particular
set point established in each individual HIV-infected person is strongly
predictive of the time it will take for that person to progress to AIDS; lower
viral set-points predict slower progression to AIDS and higher viral
set-points predict more rapid progression (Mellors et al., 1996). For
instance, a viral set point of 30,000 copies per ml of plasma is predictive
of AIDS progression in approximately 10 years in the absence of ART.
There are several lines of evidence to indicate the central role of CTL in
control of HIV replication. First, the temporal association between the
appearance of HIV-specific CTL responses and the decrease in viral load
during acute infection suggests the importance of CTL in the establishment
of viral set-point (Borrow et al., 1994; Koup et al., 1994). This observation was
confirmed by studies in the Simian Immunodeficiency Virus (SIV)-macaque
model, in which depletion of circulating CTL with anti-CD8 monoclonal
antibodies resulted in a loss of control of viraemia in both the acute and
chronic phase ( Jin et al., 1999; Matano et al., 1998; Schmitz et al., 1999).
A second line of evidence to support the role of CTL in immune
control of HIV is the association between certain HLA class I molecules
and disease outcome (Carrington and O’Brien 2003; Goulder and Watkins
2008; Kiepiela et al., 2004). CTL are able to recognise HIV-infected target
cells because the infected cells present fragments of HIV proteins in the
peptide-binding groove of cell-surface HLA class I molecules. Recogni-
tion of the HIV peptide/HLA complex on the target cell, by the T-cell
receptor (TCR) of the CTL results in the release of cytokines, chemokines
and molecules, such as perforin and granzymes, that affect the rapid lysis
and apoptosis of the infected target cell. The HLA region, which is
situated on the short arm of chromosome 6, is the most polymorphic of
the entire human genome (Mungall et al., 2003). This extraordinary diver-
sity ensures that a wide range of pathogen-derived proteins can be pre-
sented for recognition by CTL. The disease outcome from HIV, and other
infectious diseases that are contained by CTL, is thus critically dependent
on the particular protein fragments presented by HLA class I molecules.
Which HIV proteins form successful targets for CTL and which form
apparently useless targets for CTL is further discussed below.
In the context of HIV, the reason that different HLA molecules can be
associated with particular disease outcomes may be due to differences in the
peptide-binding groove of the HLA molecules and hence the different
fragments of HIV peptides that are presented for recognition by CTL. For
example, HLA-B*57, which is associated with successful control of HIV
infection, typically binds peptides that carry either a tryptophan or a
phenylalanine (both large, hydrophobic residues) at the carboxy-terminus
of the peptide. HLA-B*27, also associated with slow progression, only binds
peptides that carry an arginine at position 2 (Marsh et al., 2000).
 HIV and HLA 5

A third line of evidence suggesting the importance of CTL in control of

HIV infection is the demonstration that the selection of particular CTL
escape mutations can precipitate loss of immune control (Barouch et al.,
2002; Feeney et al., 2004; Goulder et al., 1997). Taken together, and as
discussed further below, these studies indicate the strong causal link
connecting particular HLA molecules and the resulting CTL responses
with effective control of HIV replication.

1.3. DISEASE OUTCOME MEDIATED BY CTL

1.3.1. Effective CTL responses and dominant role of HLA-B
The association between HIV immune control and expression of certain
HLA class I molecules is most striking for alleles located in the HLA-B
locus. For example, HLA-B*27, HLA-B*57 and HLA-B*51 have been asso-
ciated with successful control of HIV infection whereas HLA-B alleles
such as HLA-B*5802 and HLA-B*3502 have been associated with rapid
disease progression (Honeyborne et al., 2007; Kiepiela et al., 2004; Leslie
et al., 2006; O’Brien et al., 2001). The HLA-B locus is the most polymorphic
of the three major HLA class I loci, with 817 alleles described compared
with 486 HLA-A alleles and 263 HLA-C alleles (IGTM/HLA database).
Indeed, the HLA-B locus is the most polymorphic region in the entire
human genome reflecting the fact that this is a site of exceptionally strong
balancing selection (Belich et al., 1992; Watkins et al., 1992) and the vital
role played by HLA-B in immune protection from pathogens whose
control is dependent upon CTL.
The mechanism by which particular HLA-B alleles mediate viral con-
trol of HIV provides a crucial clue to understanding which CTL responses
need to be induced by an effective HIV vaccine. Recent studies have
suggested that a critical factor linking these protective HLA-B alleles is
the fact that they all present epitopes from within the HIV Gag protein,
whereas HLA alleles associated with a lack of immune control present no,
or few, Gag epitopes (Matthews et al., 2008). Indeed, several population
studies of HIV infection have shown that an increased breadth of
Gag-specific CD8þ T-cell responses correlates with decreased viral load,
irrespective of HLA type, while no correlation has been observed for
non-Gag-specific responses (Edwards et al., 2002; Geldmacher et al.,
2007; Honeyborne et al., 2007; Kiepiela et al., 2007; Klein et al., 1995;
Masemola et al., 2004; Novitsky et al., 2003; Riviere et al., 1989, 1995,
Zuniga et al., 2006). Studies of immune control of SIV in several different
macaque models also suggest a key role for Gag as an immune target
(Goulder and Watkins, 2008). In short, a broad Gag-specific CTL response
6 Rebecca P. Payne et al.

is associated with effective control of HIV infection, and lack of a broad

Gag-specific CTL response with ineffective control.

1.3.2. CTL responses targeting HIV Gag

There are three main reasons why CTL targeting of Gag might be partic-
ularly important in immune control of HIV infection (Fig. 1.1A and B).
Gag (‘group-specific antigen’) is so-called because of the conservation of
the amino acid sequence of the Gag protein between members of the
lentiviridae, which include HIV and SIV. Gag, in fact, is comprised of
several proteins, the largest of which is the capsid protein (p24 Gag),
which forms the central conal core of the virus and which contains two
copies of viral RNA and the viral enzymes such as reverse transcriptase.
p24 Gag is particularly conserved—that is, there is very little amino acid
sequence variation in this protein from one HIV-infected individual to
another, whereas for many of the other HIV proteins, in particular Enve-
lope and the Accessory and Regulatory proteins (Tat, Rev, Nef, Vif, Vpr
and Vpu), there is much inter-individual viral sequence variability. The
lack of sequence variability observed in p24 Gag, despite the vast poten-
tial for variation generated by the error-prone reverse transcriptase,
implies strong purifying selection driving conservation of amino acid
sequence in this protein.
The implication drawn from the lack of sequence variability in
p24 Gag is that amino acid sequence changes within this region are not
well tolerated by the virus. Accumulating evidence supports this hypoth-
esis, demonstrating that CTL escape mutations selected in Gag result
in significant fitness costs to the virus (Brumme et al., 2008). This
has been demonstrated in particular in relation to the HLA-B*57- and
HLA-B*5801-restricted epitope TSTLQEQIGW (Gag 240-249, TW10), the
HLA-B*57-restricted epitope, KAFSPEVIPMF (Gag 161-171, KF11) and
the HLA-B*27-restricted epitope, KRWIILGLNK (Gag 262-271, KK10)
(Crawford et al., 2007; Martinez-Picado et al., 2006; Schneidewind et al.,
2007). Similarly, escape mutations within the SIV Gag epitopes restricted
by Mamu-A*01, Mamu-90120-5 and Mane-A*10 have also been shown to
reduce viral replicative capacity significantly (Fernandez et al., 2005, 2007;
Friedrich et al., 2004; Kawada et al., 2006; Kobayashi et al., 2005; Matano
et al., 2004; Mothe et al., 2003; O’Connor et al., 2003; Tsukamoto et al., 2008).
The second reason why Gag may be an important CTL target for
effective immune control of HIV is that Gag is highly immunogenic.
More CTL responses are directed against Gag than any other HIV
protein (Kiepiela et al., 2007). The immunogenicity of Gag is likely to
relate to its abundance in virus-infected cells (Briggs et al., 2004), and to
the findings from studies in the SIV model that have shown early
presentation of epitopes from Gag and Pol proteins on the surface of
 HIV and HLA 7

A CTL responses CTL responses CTL responses

Magnitude of CTL responses

Magnitude of CTL responses

Magnitude of CTL responses

800 800 800

600 600 600

400 400 400

200 200 200

0 0 0
Gag Non-Gag Gag Non-Gag Gag Non-Gag
specific specific specific specific specific specific

107
Log virions per ml plasma

106
105
104
103
102
101
100
0 1 2 30 40 50 60 70 80 90 100
Time after infection (months)

B
CTL responses CTL responses
Magnitude of CTL responses
Magnitude of CTL responses

800 800

600 600

400 400

200 200

0 0
Gag Non-Gag Gag Non-Gag
specific specific specific specific

107
Log virions per ml plasma

106
105
104
103
102
101
100
0 1 2 30 40 50 60 70 80 90 100
Time after infection (months)

FIGURE 1.1 Schematic representation of cytotoxic T-lymphocyte (CTL) immune

control in HIV infection. (A) Subject with a predominately Gag-specific CTL response.
Gag-specific CTL (black circles) are temporally associated with a reduction in viral load
in acute infection and low viral set point. Selection of viral escape mutations
by Gag-specific CTL (grey circles) results in continued immune control due to the cost
of mutations to viral fitness. Selection of multiple Gag-specific mutations, including
8 Rebecca P. Payne et al.

infected cells (Sacha et al., 2007a,b). This latter observation represents the
third important reason why Gag may be a critical target for effective
immune CTL responses. Presentation of HIV epitopes from the Regu-
latory and Accessory proteins and from Envelope proteins appear to
occur after de novo synthesis of progeny virions, some 12 h following
infection of the target cell. However, Gag and Pol proteins are suffi-
ciently abundant to be processed and presented directly from the incom-
ing virions in as little as 2 h post-infection. The advantage of early Gag
epitope presentation is that CTL recognition and targeting of infected
cells may occur early enough to prevent the production and release of
progeny virus and hence prevent HIV dissemination. Additionally, once
Nef has been synthesised, MHC class I expression on the cell surface is
down-regulated and the subsequent decreased presentation of HIV-epi-
topes on the cell surface reduces CTL killing (Collins et al., 1998). How-
ever, although Gag and Pol are both presented early, there is nonetheless
a substantially greater abundance of Gag within the infected cell (20-fold
higher Gag vs Pol) (Shehu-Xhilaga et al., 2001), on the cell surface pre-
sented by HLA molecules (20-fold higher, Gag vs Pol) (Tsomides et al.,
1994), and in HIV particles (1,000–1,500 molecules present in mature HIV
particle) (Briggs et al., 2004). In conclusion, protective CTL responses in
HIV infection are linked to HLA-B expression and to the ability of
particular HLA-B molecules to present multiple Gag epitopes. HIV
protein sequence conservation, T-cell immunogenicity and early presen-
tation are likely to be the crucial factors explaining the effectiveness of
Gag-specific CTL responses.

1.4. IMMUNE ESCAPE—VIRAL ESCAPE

MUTATIONS FROM CTL
1.4.1. Impact of HIV escape mutations within a host
Although the concept of CTL escape was first described in 1991 (Phillips
et al., 1991), the consequences of such mutations on disease progression
have remained unclear. There is only one clear-cut example of an

compensatory mutations that restore viral fitness followed by the appearance of

non-Gag-specific CTL (open boxes), is associated with loss of immune control and
progression to AIDS (black bar). (B) Subject with a predominately non-Gag-specific CTL
response. Non-Gag-specific CTL (open boxes) are temporally associated with a reduc-
tion in viral load in acute infection and high viral load set point. Selection of viral escape
mutations by non-Gag-specific CTL (grey boxes) has no effect on viral load or viral
fitness. Loss of immune control and progression to AIDS typically occurs earlier than
in subjects who target multiple Gag-specific CTL (black bar).
 HIV and HLA 9

HIV-specific CTL escape mutation precipitating disease progression—the

R264K escape mutation in the HLA-B*27-restricted Gag epitope
KRWIILGLNK (KK10, Gag 263-272) (Feeney et al., 2004; Goulder et al.,
2001). Indeed, the majority of CTL escape mutations do not significantly
affect viraemia (Kiepiela et al., 2007; Matthews et al., 2008). However, a
recent study of more than 700 HIV-infected South African study subjects
showed that the greater the number of escape mutations in Gag associated
with each HLA-B allele, the better the immune control linked to that
HLA-B allele (Matthews et al., 2008). These data support the notion that
CTL are effective against HIV either by rapid recognition and killing of
virus-infected cells, or by driving escape mutations that partially cripple
the virus. For the reasons described previously (see Section 1.3.2), Gag is
the HIV protein most likely to enable CTL to deliver effective hits to the
virus via either of these means.

1.4.2. Impact of HIV escape mutations transmitted

to a new host
The transmission of viral escape mutations that were selected in response
to the donor’s HLA alleles might be anticipated to have two particular
consequences for the newly infected recipient. For recipients HLA-
matched with the donor, the transmission of viruses encoding escape
mutations in epitopes commonly presented by the matched HLA allele
might be disadvantageous, since those epitopes would be unavailable to
the recipient. For recipients HLA-mismatched with the donor, the trans-
mission of viruses encoding escape variants does not affect epitope pre-
sentation by the recipient, but might be advantageous due to reduce viral
replicative capacity. (Fig. 1.2).

1.4.2.1. Horizontal transmission

In an analysis of 114 adult transmission pairs in Zambia, there is evidence
of both of these effects operating. The viral load of the newly infected
recipients was negatively correlated with the number of HLA-B-asso-
ciated, Gag-specific escape mutations transmitted (Goepfert et al., 2008).
This association was strongest when the recipients were infected with
virus that did not carry mutations in epitopes presented by their own
HLA alleles. Thus, Gag-specific mutations are not only of clinical benefit
to the individual donor but also to an HLA-mismatched recipient upon
transmission, in all likelihood due to the fitness cost of the transmitted
escape mutations. A complementary study in South Africa showed that,
despite reversion of transmitted Gag-specific escape variants in HLA-
mismatched recipients, a significantly lower viral load and higher CD4
count was observed at 12 months post-infection in these recipients, than
compared to HLA-mismatched recipients who became infected with the
 B
Acute phase Gag-specific CTL

CTL Wildtype-specific
CTL in HLA-
No lysis matched recipient
cant recongnise
escape variant
Escape variant
Transmission of CTL HIV with
escape variant to reduced High virion
replicative Infected production
HLA-matched recipient capacity
+
CD4 T cell during acute
phase

Log virions per ml plasma

A 107
Acute phase Gag-specific CTL 106
Chronic phase CTL 105
CTL 104
CTL
CTL 103
Lysis
Wildtype- 102
specific-CTL 101
no longer
effective Lysis 100
0 1 2 3 4 5 6 7 8 9 10 11 12
HIV Infected CD4+ T Infected CD4 T
+
Time after infection (months)
cell cell
Escape
Log virions per ml plasma

variant
107 production

106 Reduced C Acute phase CTL

replicative
105
capacity
104 CTL CTL in HLA-
103 mismatched
Lysis recipient can
102 recognise escpae
101 variant virus
Escape variant
100 HIV with
0 1 2 30 40 50 60 70 80 90 100 reduced Low virion
replicative
Time after infection (months) capacity
Infected production
CD4+ T cell during acute
phase

Log virions per ml plasma

107
106
Transmission of CTL 105
escape variant to 104
HLA-mismatched 103
recipient 102
101
100
0 1 2 3 4 5 6 7 8 9 10 11 12
Time after infection (months)
 HIV and HLA 11

wild-type virus (Chopera et al., 2008). Since there is a link between viral
load during primary infection and viral load set-point (Kelley et al., 2007),
it is likely that escape mutations that incur a fitness cost to the virus will be
of long-term benefit to an HLA-mismatched recipient, despite subsequent
reversion, by reducing viraemia during acute infection. While these stud-
ies have highlighted the potential clinical benefit of transmission of viruses
with HLA-selected escape mutations, it is important to emphasise that
only Gag-specific escape mutations mediated this effect. Indeed transmis-
sion of HLA class I-associated Nef escape mutations had no impact on the
viral load of recipients (Goepfert et al., 2008).

1.4.2.2. Vertical transmission

Mother-to-child transmission (MTCT) represents a special case where
donor and recipient share at least half of their HLA alleles. MTCT
involves infection of children who are HLA matched with their transmit-
ter mother through at least one of the two HLA-B class I molecules
expressed in the mother; in some cases, both HLA-B alleles are shared,
especially where the HLA-B alleles concerned are highly prevalent in the
population. Indeed, it is possible that one factor contributing to the more
rapid progression to HIV disease observed in infected children compared
to adults is the likelihood that the transmitted virus, adapted to the
mother’s HLA alleles, is also pre-adapted to at least some of the child’s
HLA alleles. A small study of HLA-B*27-positive infants supports this
hypothesis. This showed that HLA-B*27-positive infants, whose mothers

FIGURE 1.2 Schematic representation of cytotoxic T-lymphocyte (CTL) immune

control upon transmission of Gag-specific CTL escape variants to human leukocyte
antigen (HLA)-matched and HLA-mismatched recipients. (A) Subject A expresses an HLA
allele, which confers a protective phenotype in human immunodeficiency virus
(HIV) infection. Gag-specific CTL (red CTL) help elicit a reduction in viraemia during
acute infection and establish a low viral set-point through early presentation and
recognition of infected cells. Selection of Gag-specific escape mutations (blue dots)
leads to a loss of recognition by the Gag-specific CTL but results in a fitness cost to the
virus. CTL responses arise during the chronic phase of infection (blue CTL). (B) Trans-
mission of virus with Gag-specific escape mutations (blue dots) to an HLA-matched
recipient that shares the protective HLA allele. Gag-specific CTL in HLA-matched
recipient (red CTL) are unable to recognise viral variant resulting in a higher virion
production during acute infection and consequently a higher viral set-point than
expected for subjects expressing the protective HLA allele. (C) Transmission of virus with
Gag-specific escape mutations to an HLA-mismatched recipient with no protective HLA
alleles. Acute-phase CTL in HLA-mismatched recipient (green CTL) can recognise viral
variant (blue dots). Combined effect of CTL activity and reduced replicative capacity of
transmitted virus results in a lower viral load set-point than expected for subjects expres-
sing non-protective HLA alleles.
12 Rebecca P. Payne et al.

also expressed HLA-B*27 and who had transmitted the escape mutation
in the critical KK10 Gag epitope, progressed relatively rapidly. In con-
trast, an HLA-B*27-positive child whose mother did not express HLA-
B*27, and who therefore transmitted a virus encoding the unmutated
KK10 epitope, was able to target CTL to the KK10 epitope and thereby
attain successful immune control (Feeney et al., 2004; Goulder et al., 2001).
However, the sharing of HLA alleles between donor and recipient
may only be relevant if key HLA-B alleles associated with control of
HIV are involved.

1.5. HIV EVOLUTION AND IMMUNE SELECTION

1.5.1. Origin and evolution of HIV

HIV-1 emerged in humans after transmission of non-pathogenic SIV from
chimpanzees (Pan troglodytes) in central Africa, with three separate trans-
mission events suggested by the phylogenetic division of HIV-1 into
groups M, N and O interspersed between SIV lineages (Wain et al.,
2007). The origins of M-group viruses—the most prevalent, and the
most diverse, of the three groups—can be traced to a common ancestral
sequence calculated to have arisen in the early 1930s (Korber et al., 2000).
The continued genetic diversification of HIV-1 is attributable to the
combined influence of selectively neutral genetic drift (Shriner et al.,
2004), and positive selection pressure imposed on the virus—for example,
by host immune responses (Leslie et al., 2004, 2005; McMichael and
Klenerman, 2002; Moore et al., 2002, Wain et al., 2007) or by ART (Lemey
et al., 2005; Little et al., 2008). Here we focus on two dominant, and inter-
related, evolutionary forces with a strong impact on HIV phylogeny;
descent from a common ancestral sequence—termed ‘founder effect’
(Bhattacharya et al., 2007)—and immunological pressure imposed by
HLA-selection (Matthews et al., 2008; Moore et al., 2002; O’Brien et al.,
2001; Rousseau et al., 2008).
M-group viruses are phylogenetically sub-divided into clades, genetic
sub-groups that are defined by sequence differences at the nucleotide
level. There are several strands of evidence to suggest that these clades
arose from founder strains in Africa rather than diverging subsequently
as a consequence of immunological selection pressure in different human
populations (Peeters and Sharp 2000; Vidal et al., 2000). First, the star-
burst appearance of the M-group phylogenetic tree suggests near simul-
taneous evolution of viral sub-types from SIV transmission events
(Rambaut et al., 2001). Second, analysis of envelope sequences from
HIV-1 strains circulating in central Africa reflects the enormous genetic
diversity of HIV in this region, encompassing sequences from all M-group
 HIV and HLA 13

clades (Nkengasong et al., 1994; Rambaut et al., 2001; Vidal et al., 2000).
Additionally, study of phylogeny and geographic routes of dissemination
of the different clades suggests direct transmission events from African
founder viruses (Gilbert et al., 2007; McCutchan et al., 1996; Thomson et al.,
2007; Vidal et al., 2000). The presence of distinct viral sub-clades in
different geographical locations—for example, the characteristic cluster-
ing of C-clade Indian viruses—is also suggestive of descent from a single
common ancestor (Gaschen et al., 2002). Likewise, viruses circulating in
Thailand form a distinct sub-cluster within E-clade, as well as bearing
similarities to strains that have been identified in central Africa
(McCutchan et al., 1996).

1.5.2. HLA footprints and HIV evolution

Distribution of HLA class I alleles is geographically diverse, with differ-
ent human populations having marked differences in phenotypic fre-
quency of HLA alleles (Goulder and Watkins, 2008). Phylogenetic
clustering of HIV taxa in different geographical areas may therefore also
relate to the common selection of particular ‘HLA footprints’ that arise in
response to prevalent alleles in the human population. Perhaps the best-
studied example is the strong selection pressure imposed by HLA-B*57
(Leslie et al., 2004; Martinez-Picado et al., 2006). HLA-B*5703 is the most
common sub-type of HLA-B*57 in sub-Saharan Africa, and this allele is
associated both with the most effective control of HIV and also with the
greatest number of escape mutations in Gag (Crawford et al., 2007;
Matthews et al., 2008; Fig. 1.3). As a consequence of this shared external
selection pressure, even genetically disparate viruses exposed to the same
HLA selection pressure may acquire enough shared polymorphisms to
result in some degree of phylogenetic clustering (Matthews et al., personal
communication). In this way, HLA selects for sequence similarities,
potentially driving convergent evolution in populations where the select-
ing alleles are common. Sites in Gag, Pol and Nef at which there are
differences in amino acid consensus sequence between clades in fact

p24 Gag
A ISPRTLNAW KAFSPEVIPMF H TSTLQEQIAW

ISW9, 145−155 KF11, 162−172 TW10, 240−249

FIGURE 1.3 Schematic View of p24 Gag. Positions of HLA-B*57-restricted epitopes

ISW9, KF11 and TW10 are shown in grey boxes. Mutation sites selected by HLA-B*5703
are shown by black arrows. White boxes denote positions of a processing mutation
(A146X) and a compensatory mutation (H219Q).
14 Rebecca P. Payne et al.

correspond closely to those sites of HLA-mediated selection pressure

(Matthews et al., personal communication), suggesting that although
HIV-1 clades arose as a consequence of founder effect, HLA-selection
may be a determinant of on-going viral evolution.
A key question is whether the impact of this HLA-driven evolution of
HIV results in an adaptation of HIV to the key HLA alleles, such as B*57,
B*27 and B*51, currently central to immune control of HIV. A study of
viral sequences and HLA types of more than 2,500 HIV-infected indivi-
duals from eight diverse human populations has examined whether the
frequency of escape mutations in critical epitopes is accumulating in
populations where the prevalence of the restricting HLA allele is high
(Goulder et al., in press). Overall, the prevalence of polymorphisms in
well-defined epitopes correlates strongly with the phenotypic frequency
of the selecting allele in the study population. For example, the prevalence
of escape mutations at position 8 in the HLA-B*51 restricted epitope TI8
(TAFTIPSI, RT 128-135) is proportional to the phenotypic frequency of
HLA-B*51 in the population. In Japan, where HLA-B*51 is highly preva-
lent, the TI8 escape mutation is present in two-thirds of the population.
Similarly, Gag mutations associated with HLA-B*57 (Fig. 1.3), and asso-
ciated with HLA-B*27 are strongly correlated with the prevalence of these
alleles in the different populations studied. These studies suggest that,
over time, the accumulation of escape mutations in these epitopes may
lead to the establishment of a new consensus, replacing original popula-
tion wild-type. As described previously in this review (see Section 1.4), it
seems likely that the well-established associations between certain HLA
alleles and control of HIV are shifting. While the consequences of these
changes at this early stage of the HIV epidemic are uncertain, it is clear
that the particular HIV-specific CTL responses that are currently effective
in immune control of HIV may not be effective in the future. The antigen
targets for the best of the immune responses may be constantly changing
in sequence, but in turn, this creates new opportunities for the immune
system, both for previously sub-dominant responses to become domi-
nant, and for new responses to be induced.

1.6. SUMMARY

Successful immune control of HIV is the exception, but is well-described

and achievable. Induction of these effective immune responses is the aim
of a CTL-based HIV vaccine. HLA class I molecules and CTL play a
central role in suppression of HIV, in particular certain HLA-B molecules
such as HLA-B*57 and HLA-B*27. CTL responses targeting the HIV Gag
protein are consistently associated with low viral set-point, and therefore
with slow progression to AIDS. Gag-specific CTL may recognise
 HIV and HLA 15

HIV-infected cells early in the viral life cycle and therefore typically kill
virus-infected cells well before new virions are released. Mutations aris-
ing in non-Gag virus proteins that result in loss of CTL recognition of
HIV-infected cells are rapidly selected and typically do not affect viral
load or viral replicative capacity. Mutations arising in Gag may allow
escape, but usually also incur a cost to viral replicative capacity, especially
if arising in the highly conserved capsid protein p24 Gag. Accumulation
of escape mutations in populations where the selecting HLA molecules
are highly prevalent indicates the dynamic and shifting nature of the
co-evolutionary struggle between HIV and human populations.

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