Kineti s, T-Lympho ytes De line and
Immunosenes en e
by
Joseph Ssebuliba
Thesis presented in ful lment of the a ademi requirements
for the degree of Master of S ien e at the
University of Stellenbos h
Supervisor: Prof John Hargrove
Co-supervisors: Dr Ra hid Ouifki & Dr Farai Nyabadza
I, the undersigned, hereby de larethat the work ontained inthis thesis ismy own
originalworkand has not previously,in itsentirety or inpart, been submitted atany
University for adegree.
--- ---
-Joseph Ssebuliba Date
Copyright © 2009 Stellenbos h University
The severity of the numerous fa tors that in uen e the rate of HIV-1 disease progression
leadstoalterationsintheobserved lini alpi tureofHIV-1infe tedindividuals. Ageofthe
humanimmune systematinfe tionisone ofsu hfa tors, whoseimpa tonHIV-1's
patho-genesis has not been previously well evaluatedmathemati ally. The time of emergen e of
HIV-1 asso iated opportunisti diseases alsovaries a ording to the patient's immune
re-generative apa ity,whi hispartlydependentonage. Theprin ipleobje tiveofthisthesis
proje t is to a ount for the puzzling qualitative and quantitative features of age-related
immunede ien y with respe t toHIV-1 infe tion. The study isbasedonamathemati al
model onsisting of a system of ordinary dierentialequations des ribing the
immunolog-i al hanges in the on entration of the CD4
+
and CD8
+
T ells, ma rophages, stem- ell
reservoirand freely ir ulating virions in the blood. We review the biologi alme hanisms
ofHIV, theimmunesystem,T- ellaging,andprovideadetailedanalysisofthe basi
HIV-1 model. We assess the dynami s of HIV-1 infe tion with respe t to immunosenes en e
and de line of CD4
+
T lympho ytes. We also investigate the kineti hara terisation of
a de reasing haematopoieti stem- ell reservoir whi h ontinuously supplies the immune
system with HIV-1 spe i CD4
+
T ells. We address the rapid exhaustion of the T- ell
reservoirand the a elerated ageing of the immune system as a onsequen e of HIV-1
in-fe tion. We ndthatageatHIV-1infe tionisasigni antpredi torofapatient'slifespan.
Themodeltoosuggests thatelderlyindividualsprogresstoAIDSmu hfaster anddiemore
qui kly ompared to younger individuals. The model is extended by in orporating
anti-retroviraltherapy. Tuber ulosis as anexample of opportunisti diseases is alsointegrated
intothe model. Resultsindi atethat anearly,orlate treatmentinitiationfailstoin rease
the populationdensity ofthe haematopoieti stem- ellreservoir,thoughitstrengthensthe
Verkeiefaktore beinvloed dieprogressie vandiekliniese situasie van'n MIV geinfekteerde
individu. Die ouderdom van die immuunstelsel is een van die faktore, waarvan die
im-pak nog nie deur middel van wiskundige modelle geevalueer is nie. Die tyd interval tot
dieverskyning vanopportunistiese siektes word onder andere bepaal deur die hernuwings
kapasiteit van die immuunstelsel, en dié is gedeeltelik afhanklik van die patient en die
immuunstelsel se ouderdom. Hierdie verhandeling ondersoek die kwantitatieve en
kwal-itatiewe aspekte van ouderdom verwante immuniteits gebrekke, in die konteks van MIV
infeksie. Die studie is gebasseer op 'n wiskundige model van gewone dierensiaal
verge-lyking watdieimmunologiese verandering in diekonsentrasie vanCD4
+
en CD8
+
Tselle,
makrofage, stam sel poel and vry sirkulerende virus in die bloed. Ons doen verslag oor
biologiese meganismes van MIV, die immuunstelsel, T sel veroudering, en bied 'n
gede-tailleerde analise van die basiese MIV model aan. Hoermee ondersoek die dinamika van
MIV infeksie met betrekking tot immuniteit en die afname van CD4
+
limfosiete. Ons
ondersoek ook die kinetiese karakterisering van 'n dalende stam sell vormings poel. Ons
ondersoek die hoë koers waarteen die T-sel poel uitgeput word as gevolg van 'n
veroud-erende immuunstelsel tydens MIV infeksie. Ons vind dat die ouderdom vanMIV infeksie
'n beduidende indikator is van 'n pasient se prognose. Die model wys daarop dat ouer
pasientevinniger 'nverworwe immuniteitsgebreksindroomontwikkel. Diemodelword
uit-gebrei deur anti-retrovirale behandeling in te sluit. Tuberkulose, 'n belangrike verbeeld
van 'n opportunistiese siekte, word ook ingesluit. Resultate wys daarop dat behandeling
niedaarin slaag om diepopulasiedigtheid vandie stem sel vormings poel teverhoog nie,
I thank Prof. John Hargrove, Dr. Ra hid Ouifki, Dr. Farai Nyabadza and Mr. Carel
Diederik Pretorius for many fruitful dis ussions, and for their areful readingand editing
of this thesis proje t. Thanks are due to the entire sta of the South Afri an Centre
for Epidemiologi al Modelling and Analysis for their endless support of my stay at the
Centre. IamgreatlyindebtedtoallmyfellowSACEMAstudents,notonlyfortheir many
helpful dis ussions, but also for the ontinuous spirit of togetherness they have exer ised
allthrough the ourse.
This work was supported by funds from the Afri an Institute for Mathemati al S ien es
(AIMS), and from the South Afri an Centre for Epidemiologi alModelling and Analysis
Abstra t i
1 Introdu tion 1
1.1 Ba kground: Infe tious diseases . . . 1
1.1.1 Sexually transmitted diseases . . . 3
1.2 Proje t motivation . . . 4
1.2.1 Proje t des ription . . . 6
1.3 Thesisstru ture . . . 7
2 Basi Virology and Cellular Immune Response to HIV 8 2.1 Introdu tion . . . 8
2.1.1 The HIVBiology . . . 9
2.1.2 The lini al behaviourof HIV-1 infe tion . . . 11
2.2 Immunologi al on epts . . . 13
2.2.1 Intera tion between HIV infe tion and the immune system . . . 14
2.2.2 Impa t of HIV-1 infe tion onMa rophages and T- ells . . . 15
2.4 Parallels between Immune senes en e and HIV-1 pathogenesis . . . 18
2.5 Fa tors ontributingto alterations inan agingimmune system . . . 20
2.5.1 Bone marrow . . . 20 2.5.2 B ellprogenitors . . . 21 2.5.3 Thymi atrophy . . . 22 2.6 Summary . . . 23 3 Literature Review 24 3.1 Introdu tion . . . 24
3.2 HIVinfe tion models . . . 25
3.3 HIV-TB o-infe tionmodels . . . 28
3.4 HIV-Immunosenes en e models . . . 29
3.5 Summary . . . 30
4 Mathemati al Modelling 31 4.1 Introdu tion . . . 31
4.2 Basi Mathemati al Con epts . . . 33
4.3 A simpleinfe ted ellmodelforviral kineti s. . . 36
4.3.1 Model analysis . . . 37
4.3.1.1 Reprodu tionnumber of the model . . . 38
4.3.1.2 Globalstability for the virus-free equilibrium . . . 41
4.3.2 Numeri alresults . . . 42
4.4.1 Model analysis . . . 46
4.4.1.1 Model's reprodu tionratio . . . 47
4.4.2 Numeri alresults and Dis ussion . . . 49
4.5 Summary . . . 51
5 HIV-1 Immune System Modelling 52 5.1 Model development . . . 52
5.1.1 Model des ription . . . 54
5.1.2 Disease free model . . . 58
5.2 Dis ussion of results . . . 61
5.2.1 Variationof age at infe tionwith HIV-1 . . . 69
5.3 Summary . . . 72
6 Extension of the HIV-1 Model to In orporate TB and Antiretroviral Therapy 73 6.1 Introdu tion . . . 73
6.2 Model onstru tion . . . 74
6.2.1 Modelling the emergen e of M. tuber ulosis . . . 75
6.2.2 In orporatingaCombinedAntiretroviralTherapeuti Strategiesinto the Co-infe ted model . . . 76
6.3 Numeri alsolutions . . . 77
6.3.1 Ee ts of M. tuber ulosis onHIV-1 repli ation . . . 78
6.3.4 Impa t of treatmentinterruption on HIV-1 and M. tuber ulosis . . 85
6.4 Summary . . . 87
7 Con lusions and Re ommendations 88
2.1 Diagrammati representation of an HIV-1 virionstru ture. . . 9
2.2 The ourse of HIV-1 infe tionovertime. . . 12
2.3 S hemati illustration of how the ourse of HIV-1 infe tion hypotheti ally
relatesto human ageing. . . 19
4.1 Basi modelforviral dynami s. . . 36
4.2 Impa t of
R
0
onthe dynami albehaviourof the simpleHIV model. . . 44 4.3 Bifur ation diagramsshowing the behaviour of CTL's response inthe HIVbasi model . . . 50
5.1 State-Task Network for the HIV-1 immune system dynami s model. . . 58
5.2 Systemi exhaustion of ellularimmune apa ity . . . 61
5.3 HIVrepli ationkineti s withrespe t tothedownregulationof thestem- ell
reservoir . . . 62
5.4 Model simulationsfor the ourseof HIV-1 infe tion. . . 64
5.5 Numeri alsimulationsfor the ourse ofHIV-1 infe tionininfe tedCD4
+
T
ells, ma rophages,and the ytotoxi Tlympho ytes. . . 65
5.6 Phase spa e diagramsforthe intera tion between immunesystem ells and
5.7 Age-dependent hara teristi exhausitibility of anindividual's
immunologi- alsystem with respe t to the time of HIV-1 infe tion. . . 70
5.8 Relationshipbetween the patient'ssurvival time and age atinfe tion. . . . 71
6.1 Pathogenesisof anHIV-1 asso iatedopportunisti infe tion(M. tuber ulosis). 79
6.2 Impa t of emerging tuber ulosisonthe progressionkineti s of HIV-1. . . . 80
6.3 Comparisonof the immune system intera tion with one, and two infe tious
pathogens. . . 82
6.4 Ee t of ontinuous highly a tive antiretroviral therapy at three dierent
initiations enarios. . . 84
6.5 Impa t of early and late anti-retroviral therapy on the downregulation of
the haematopoieti stem- ellreservoir. . . 85
6.6 Ee t of dis ontinuing highly a tive antiretroviral therapy for hroni ally
5.1 Mathemati alelaborationsfor the State-Task Network. . . 59
5.2 Numeri al values onsidered for the initial populations of the dependent
state variables . . . 60
5.3 Parametervalues onsideredinmodellingthehaematopoieti stem ell
reser-voir. . . 61
5.4 List of all the onstants and parameter values used in the numeri al
simu-lationof the HIV-1 immune system model. . . 67
5.5 Data generation using the disease free model (5.9), and the HIV-1 model
equations(5.15.8). . . 71
6.1 List of all the parameter values used in modelling the emergen e of an
Introdu tion
1.1 Ba kground: Infe tious diseases
The major reason as to why developed or industrialised ountries have be ome so
pro-du tive and su essful with their e onomy today is that their population (man power)
remains healthy and free from infe tious diseases. This responsibility is arried out by
skilled personnel known as epidemiologists in ea h ountry's health se tor. The inputs
and ollaborations of epidemiologists with other s ientists in the medi al eld has led to
the awareness of disastrous infe tiousdiseases, their modes of transmission,and the likely
ontrolorpreventionstrategies. Additionally,fa tsregardingthein iden e andprevalen e
levels, andthe statisti alinformationaboutmorbidityandmortalityrates,allofwhi hare
required by lini ians and physi ians to pave ontrol methodologieswould not have been
availablewithout the eorts of epidemiologists[16℄.
An infe tious diseaseis an illness ausedby a diseaseagent that an be transmitted from
one organism to another. Infe tious diseases have had a very big impa t on the human
populationthroughouthistory,andthishasplayedasigni antroleinshapingthe onquest
of the New World. Diseases an be ategorised into several forms but they are generally
hara terised by the weakening of the infe ted organism, the degree of whi h depends on
the organism's resistan e toinfe tion and virulen e of the disease agent ausing it. There
Mi roparasites: These ausepathogeni diseasessu h asEbolahemorrhagi fever,
malaria, and Lyme disease. Mi roparasites that ontribute to the emergen e of the
diseaseslistedareviruses,parasiti protozoans,andba terialpathogensrespe tively.
Ma roparasites: These are generally largerand havelonger generation timesthan
mi roparasites. Examples of ma roparasites in lude atworms (Platyhelminthes),
roundworms (Nematoda) and arthropods. Ma roparasites ause parasiti diseases
su h ass histosomiasis, aused by aquati trematodes.
Infe tious diseases have two major modes of transmission, that is; Dire t physi al
on-ta t between hosts, where the disease is transmitted from an infe ted host to the an
uninfe ted host. Diseases involved in this mode of transmission are sexually transmitted
diseases and u. The se ond mode is indire t transmission where an intermediate host
is required to omplete the spreading y le of the disease. In this mode of transmission,
ve tors (intermediate host) transfer the disease fromone host tothe other. For example,
mosquitoestransmitmalaria,dengue,andtheWestNileVirus;ti kstransmitLymedisease
and spotted fevers; and the Kissingbug transmitsChagasdisease.
An organismsus eptible to an infe tion is referred to as a host. Hosts are lassi ed into
three distin t groups. First, a host an be a member of the same spe ies, for example,
a quiring u from a friend. Se ond, hosts an as well be of dierent spe ies. The best
examples in this ategory are zoonoti diseases whi h are aused by bites and s rat hes
resulting from the intera tion between human beings and animals. Some theories laim
that the HIV(HumanImmunode ien y Virus) originbelongstothis group,that is: man
a quired HIV-1 through as rat hfrom anSIV (SimianImmunode ien y Virus) infe ted
wild himpanzee(Pantroglodytestroglodytes)[57,82℄,andHIV-2fromtheSootyMangabey
(Cer o ebus atys), an old green world monkey of Guinea-Bissau, Garbon, and Cameroon
[127℄. Therefore, abundan e of the animal reservoirs islikely toin rease the human
expo-sure rate be ause of anin reased availability of infe ted hosts from whi h ve tors su h as
mosquitoesmay take abloodmeal. Lastly, some of the parasiti diseases su h as
1.1.1 Sexually transmitted diseases
Sexually transmitted diseases or infe tions (STDs), are infe tions that an be transferred
from one individual to another through sexual onta ts. The rate at whi h they spread
is determined by the patterns of an infe ted individual's sexual en ounters within a
sus- eptible population. The e ology of endemi , epidemi and emergent infe tious diseases
espe iallysexuallytransmitteddiseases isatopi of lo aland globalimportan ewith
on-siderables ienti , so ietal, ethi aland poli yaspe ts [17℄. Despite the fa t that sexually
transmitted diseases should have been the easiest to avoid and ontrol, they remain the
most ommonand among the most serious diseases inour so iety today.
The use of strong antibioti s and the implementation of the ABC (Abstinen e, Being
faithful, and Condom use) approa h towards the ght against some of the STDs has not
been veryee tivedue tothe fa tthathigh resistantstrainsof pathogens,and newsexual
attitudesandpra ti eshaveemerged. Va inesthathavebeensoee tiveinthe ontrolof
otherseriousdiseasesseemtobeofaninsigni antimpa tonthesediseases. Forexample,
viral diseasessu h as AIDS have resisted allthe attempts put forward toeliminate them,
yetthe same attempts have been su essfulin the eradi ation of other viraldiseases.
It is also worth noting that the omparison of disease progression rates between HIV-1
transmissionriskgroupshasyielded ontradi ting ndings. Anearlystudyfound a
signi - antlyfasterprogressionrateamongsthomosexualsthanheterosexuals[113℄. Nevertheless,
more re ent studies analysing mu h larger ohorts have reported no dieren e in disease
progression rates following adjustments for age and ex lusion of Kaposi's sar oma as an
AIDS de ning illness[11, 128℄. Throughthe use of Mathemati almodels,the dynami sof
sexuallytransmitteddiseases anbestudiedwithanaimofdis overing thelikelyout ome
of anepidemi ortohelp managethem by various ontrolstrategies.
In sexually transmitted diseases, having a deepened understanding of the intera tion
be-tween physi al and psy hoso ial fa tors in disease progression is important to maximise
the holisti are for the patients. For the ase of HIV-1 infe tion, a number of studies
have demonstrated signi ant relationships between poorer lini al out omes and la k of
satisfa tion with so ial support, stressful life events, depression and denial based opying
adheren etotherapyanddepression,singlenessandhomelessness[6,119℄. Patient
manage-mentshouldin lude onsiderationofthepsy hoso ial ontextandaimtoprovideassistan e
in problemati areas su h assub-Saharan Afri a.
1.2 Proje t motivation
TheHIVpandemi isavery omplex ompositionofdistin tepidemi swithinandbetween
ountries and regions of the world, thus be oming the indubitable de nition for
publi -health atastropheofthe urrentgeneration. A ordingtothe2007AIDSepidemi update
report published by the Joint United Nations Programme on HIV/AIDS (UNAIDS) in
onjun tionwithWorldHealthOrganisation(WHO),anestimated33.2(30.636.1)million
people livewith HIV-1worldwide. Everyday, over6800persons be omeinfe tedwith HIV
and over5700 persons diefromAIDS, mostly due toinadequate a ess toHIVprevention
and treatmentservi es [159℄,in reased levelsof poverty as wellas the dismantling of HIV
ontrol programmes. Sub-Saharan Afri a urrently remains the most seriously ae ted
region with AIDS as the leading ause of death. The estimated number of deaths due
to AIDS in 2007 was 2.1 (1.92.4) million people worldwide of whi h 76% o urred in
sub-Saharan Afri a[153℄.
Inthe absen eof massivelyexpanded prevention, treatmentand areeorts, itisexpe ted
that the worldwide AIDS death toll will ontinue to rise. This means that the mena e
HIV/AIDS poses on our so ieties will be felt most strongly during the foreseeable future,
espe ially in developing ountries. The so ial and e onomi onsequen es AIDS has had
on our so iety are already widely felt, not only in the health se tor but also in
edu a-tion, industry, agri ulture, transport, human resour es and the e onomy in general [17℄.
A ording to the United Nations, HIV/AIDS is the biggest threat to the development of
the Afri an e onomy sin e this disease is ommonin young tea hers, health-workers, ivil
servants,and young professionals.
To make matters worse, a tive My oba terium tuber ulosis, the ba teriathat auses TB,
whi his the se ond leading ause of death in sub-SaharanAfri a, is ommonlydiagnosed
opportunisti infe tions worsens the status of HIV infe ted individuals. These infe tions
play a signi ant role in a eleratingand amplifyingthe progression of HIV toAIDS. TB
isranked asthe rst worldwideHIVrelated ompli ation[112℄. Thismeans thatHIV
pos-itiveindividualshavehigher han esof developing a tiveTB. Further more,HIV infe ted
individuals are prone to rea tivation of latent TB be ause the CD4
+
T lympho ytes, the
ells that keep latent TB in he k, are exa tly the ells that are rendered dysfun tionalin
HIV positive patients. This implies that a further in rease in TB rates an be expe ted
in areas with a high prevalen e of HIV infe tion, onsidering that the rate of progressing
from latent to a tive disease in these individuals is 500 times higher than those without
HIV [85℄.
Ingeneral,the two diseases(HIVand TB)are not mutuallyex lusivethough theytend to
exa erbate theseverity ofea hother. Between 1985and 1992, theTB in iden einUnited
States in reased due tonumberof fa tors, but approximately 64% of these ases were
at-tributabletoHIV-1infe tion[154℄. ThroughvariousTB ontroleorts, agradualde rease
inTB ase rateswasa hieved sin e1993. However, in1999, ontrarytoUnited states,the
worldwide TB ases in reased to8.4 million, thus making a 5% in rease from 1998 [159℄.
HIV-1 asso iated in rease in TB in iden e is likely the result of the immunosuppression
aused by HIV-1. Re ent eviden e asserts that a tive TB may have adverse ee ts on
HIV-1 disease by in reasing both systemi ally [8, 147℄, and at the sites of infe tion [148℄.
These TB mediated ee ts may in turn result into in reased systemi heterogeneity and
viral tness.
Various drugs and interventions have been developed and more are being produ ed in an
attempt to bring down the alarming levels of mortality and morbidity aused by AIDS.
Despite the positive impa ts (in reased longevity among people living with AIDS) these
drugs have had on the disease, most of the lini al trials for va ines have been based
on subtype B (found in developed ountries su h as Europe, the Ameri as, Japan and
Australia) and not on subtype C whi h is the most prevalent in the hardest hit
develop-ing ountries like those in sub-Saharan Afri a [100℄. There are on erns that the drugs
developed in a parti ular region may not yield the same ee t in another region due to
the fa t that dierent regions of the world possess dierent HIV-1 subtypes. For equal
lini iansandpharma istsonhowHIV
+
populationsindeveloping ountries would obtain
the same exa t treatment re overy as those individualsin the developed nations.
Bra ed with these fa ts, I feel motivated to work for the wellbeing of sub-Saharan Afri a
andtheworldatlarge,throughresear hthatendeavourstoreversetheHIVpandemi . Itis
againstthisba kgroundthatwedevelopmathemati almodelsand omputersimulationsto
help lini ians,medi al pra titionersand pharma ists to understandsome of the
ounter-intuitive fa tsabout HIV-1 dynami sin spa e and time.
1.2.1 Proje t des ription
The prin iple purpose of this resear h proje t is to onstru t mathemati al models that
an elu idate various important aspe ts about the dynami s of HIV-1 infe tion (that is;
intera tion of target ells, virions, ma rophages, ytotoxi T lympho ytes and infe ted
ells) in relation to immune senes en e. Two mathemati al models were formulated to
help usin a hieving the obje tives of the resear h.
⋆
Inthe rstmodel,weanalysetheT- ellsde lineinabsen eandpresen eofHIV infe -tion respe tively, and then assess the impa tof anassumed existen eof asteadilyde reasing nite immunologi alT- ell reservoir whi h is ontinuously supplying the
immune system with HIV-1 spe i T- ells meant toredu e viralrepli ation.
⋆
The se ond model is a re ap of the rst model, but with an introdu tion of My o-baterium tuber ulosisas anopportunisti infe tion. Combinationtherapy (proteaseinhibitorandreversetrans riptaseinhibitor)isalsoin orporatedintothismodelwith
an aim of identifying the appropriate time to initiate treatment, so as to maximise
the patient's survivalperiod.
Sin e viral evolution is entral to a number of lini ally and epidemiologi ally relevant
questions, and is the subje t of mu h ongoingresear h, a deeper understanding of all the
phenomenademonstrated inthe twomodels listedaboveisessentialforoptimaltreatment
planning. As a onsequen e, they will ontribute dire tions in per eiving the dangers
approximatingthetimeintervalrequiredtore-de netheregimenwhenevertheee tiveness
tothe previousones islost.
1.3 Thesis stru ture
Chapter 2 isfor the reader's average per eption of the phenomena of disease progression.
It starts with a des ription of the biologi al, immunologi al, and virologi al me hanisms
involved inthe kineti intera tionof thehumanimmunesystem ells withHIV-1infe tion.
ThevariousHIVtreatmentstrategiesarealsopresented. Furthermore,theee ts ofaging
on the fun tioning of the immune system, and the resulting hanges in the pathogenesis
of HIV-1 are dis ussed. Chapter 3 is an overview of mathemati al models for the human
immune system, in luding laboratory and experimental results whi h have attempted to
elu idate the repli ation kineti s of HIV-1 infe tion, its asso iated ellular immune
re-sponses, and anti-retroviraltreatment. Additionally, modellingof opportunisti infe tions
is brie y reviewed in terms of oinfe tion models. The last se tion of this hapter is a
summary of the HIV-Immunosenes en e model, whi h,a ording to our literature sear h,
pioneered the modellingofanaging immunesystem. Chapter 4outlinessome ofthe basi
mathemati al on epts usedin the numeri alandsimulationanalysisof the models
devel-oped inthis thesis. The simpleHIV-1 infe tedmodelispresented tofamiliarisethe reader
with the most signi ant immune system, and pathogen parameters that are ru ial in
the monitoring of HIV's repli ation patterns. A detailedmathemati al analysis is arried
out, and simulationsare run, both inpresen e and absen e of immune responsiveness. In
Chapter 5, the basi HIV-1 model dis ussed in Chapter 4 is extended by in orporating
age in terms of a nite haematopoieti stem- ell reservoir. Simulations and dis ussions of
the several disease phases that the modeldisplays are ta kled. The survivalperiodof the
patients is determined, and the relationship with their respe tive ages of HIV infe tion
are presented. Chapter 6 is an extension of the model onstru ted in Chapter 5. HIV-1
anti-retroviral treatment, and tuber ulosisare introdu edinto the model. Numeri al
sim-ulations are performed to examine the model's exhibitedbehaviour. Se ondarily, we vary
the simultaneous administration of RTIs and PIs, to enable us assess the impa t of early
and late treatment onthe depletion rate of the nite stem- ellreservoir. Chapter 7 forms
Basi Virology and Cellular Immune
Response to HIV
2.1 Introdu tion
There are several on i ting theories that have attempted to explain the origin of AIDS
and HIV sin e its rst emergen e in the early 1980s. Despite the ountless number of
arguments s ientists have had regarding these theories (su h as AIDS being an out ome
of a biologi alwarfare experimentation that went wrong [1,76℄), the most likely
explana-tion investigated supports the theory of zoonoti transmission from non-human primate
lentiviruses tohumanbeings [51, 57, 62℄. This transmission was through a idental
expo-sures of humans to monkey blood [83℄, keeping them as pets and hunting them for food
[103℄.
The zoonoti transmission resulted into two strains of HIV, that is; HIV-1 whi h is the
mostprevalentand overing5560%ofalltheworld'sHIV-1infe tions[81,146℄,andHIV-2
whi hisless ommonandknowntohaveaverylongin ubationperiodfrominitialinfe tion
to illness as ompared toHIV-1. Investigations arried out on the nu leotide sequen e of
HIV-2 and SIV showed a very lose relationship between HIV-2 and SIV
sm
than it is to
HIV-1 [34℄. Due to the existen e of other fa tors, an er, hemotherapy, orti osteroids,
and alkylating agents, that are apable of produ ing AIDS-related symptoms and signs
2.1.1 The HIV Biology
The Human Immunode ien y Virus(HIV) is a lentivirus belongingto a family of
retro-viruses, that are etiologi al agents responsible for the slow and progressive impairment
of the host's immune system, thus leading to a long period of hroni infe tion. HIV
results into a quired immunode ien y syndrome (AIDS), a ondition distinguished by
life-threatening opportunisti infe tions. A number of the HIV positive individualsin the
AIDS developmentalstage diedue totheseopportunisti infe tionsormalignan ieslinked
tothe gradualand ontinuous weakening of the immuneresponse [96℄.
FIG. 2.1. Diagrammati representation of an HIV-1 virion stru ture aspresented in [17 ℄. The
virion'ssurfa eismadeupofenvelope gly oproteinsgp120andgp41. Theviralreverse
trans rip-tase,theviral genome,theintegraseand various hostproteinsare allen apsidated.
Retroviruses have a slightly homogeneous stru ture whi h omprises three genes (that is;
gag, pol, and env)that en ode the stru turalproteins and enzymesused inthe HIV
repli- ation y le [46℄. Although the fun tion of ea h gene is poorly understood, the gag gene
odesforthe manufa tureofthe dense ylindri al oreproteinsandtheviralnu leo apsid.
[46, 160℄.
TheHIVvirionstru tureisroughlyspheri alhavingaradiusofabout 60nanometres[93℄.
Ithasanexternalviralenvelopethat ontainsseveralspikes. Ea hspikeis omposedoffour
mole ulesofgly oproteinsgp120andgp41allofwhi hareinsertedinthemembrane( gure
2.1). HIV virion binding and its subsequent aspid fusing, in luding its geneti material
is enhan ed by the surfa e gly oprotein omplex [2, 29℄. Another layer of matrix protein
(p17) bordering the aspid, lies underneath the viral envelope. The p17 matrix protein
lo alises the assembling virion to its ell membrane, transports the provirus integration
omplex a rossthe nu learenvelope,an hors gp41 onto the surfa e of the virusand helps
inviralpenetration [104℄. The apsidhas ahollow,trun ated oneshapeand is omposed
of anotherprotein, p24 whi h onsists the geneti materialof the HIVvirus [152℄.
Withinthehost ell,thedire tionofgeneti informationisreversedbyre trovirusessu has
HIV,resultingintoproteinprodu tion. Proteinsynthesisintheregulargeneexpressionisa
onsequen eoftheDNAbeing opiedintoRNA,andtheRNAbeingtranslatedintospe i
proteins. The reverse trans riptase enzyme opies the viralRNA into DNA[138℄. As the
reversetrans riptase(RT)movesalongtheRNAinthe ytoplasm,a omplementarystrand
of DNA is produ ed. When the rst DNA strand is a omplished, the RT immediately
startstobuildthe se ondstrandwith thehelp ofthe rstone asatemplate[25, 144,160℄.
The infe tion of the ell then be omespermanent afterthe penetration of the nu leus by
the doublestranded HIVDNA whi hsti ks intothe host DNAand hanges toaprovirus.
The provirus may then enter a lengthy quies ent period,during whi h itsgenes are never
expressed unless the host ell's trans ription ma hinery makes the RNA opies [33, 64℄.
After the a tivation of the ell's RNA polymerase II, by the geneti swit hes at the ends
of the provirus' long terminal repeats, trans ription begins [25, 172℄. After the ell is
ompletelyinfe ted by HIV, trans riptionfollows intwo phases.
The rst phase takesaperiodof about 24hours. During this phase, when the DNA
provirus manufa tures omplementary opies of RNA strands, the ellular enzymes
partition some of the strands into segments, and they are later spli ed into lengths
of RNA appropriate for protein synthesis. The regulatory proteins required for the
messenger RNA [55℄. When the RNAstrands attaina lengthof approximately2000
nu leotides, they shiftfrom the nu leus tothe ytoplasm.
In the se ond phase, new viral strands su h as genome RNA or stru tural genes,
emergefromunspli edRNAtrans riptsandenterthe ytoplasmaftertheirmovement
fromthe nu leus. It isduring this phasethat the produ tionof othertwonew RNA
ategoriestakespla e. The rst ategoryis thelong-unspli edstrands of nearly9749
bases onsisting of the genome RNA, and the se ond ategory is the medium-length
orsinglyspli ed trans ripts of roughly4500 bases, virion assembly,whi hen odes
thestru ture ofHIVanditsproteinenzymes. Thenew matureHIVvirions(viruses)
whi h move out of the ell are produ ed after the en losure of the HIV's stru tural
and enzymati proteins withinthe viralprotein ore [55, 65℄.
2.1.2 The lini al behaviour of HIV-1 infe tion
Theprogression patternofHIV-1 infe tionslightlyvariesamong individualsdependingon
the dieren es in their lini al symptoms, CD4
+
ell ount, viral load and time taken to
enter the AIDS stage. Nevertheless, three majorphases approved by WHOin 2005 de ne
the diseaseprogression ourseofHIV-1 infe tedindividuals,andthese stagesaremeantto
deepen the lini ians'knowledge and understanding of prognosti determinants whi h are
fundamental in guiding the patients' management and treatment strategies espe ially for
those patients inpoorlyfa ilitated environmentalsetups likethe ones ommonly found in
sub-Saharan Afri a. Figure 2.2 summarises the lassi ation system of the three phases
whi hin ludethe A ute stage,the Asymptomati stage, and the AIDS stage respe tively.
A ute (primary) phase: This phase is hara terised by rapid viral repli ation
in the range of
10
3
10
5
virions mm−
3
of blood [138℄. This happens with or without
lini alsymptomsimmediatelyaftertheindividual'sexposuretoHIV[44℄. Symptoms
linked to this stage are mild u-like illness with fever and mus le a hes that last
for a few weeks, and it takes a period of 618 weeks (window period) for the HIV
FIG.2.2. The ourseofHIV-1infe tionovertimeaspresentedinSimonetal [138℄. (Top): shows
the dynami hanges in plasma viraemia. During primary infe tion, the evolution of HIV viral
loadishighandthe riskoftransmissionishighestinthe rstweekswhentheviraemiapeaks are
at their maximum. (Bottom): It illustrates the dynami hanges of theCD4
+
Tlympho ytes
ompartments. Inthe rst weeksof infe tion, there isa fallinthe CD4
+
ount (green line),and
anabsen eofHIV-1spe i antibodies(orangeline). Theviralloaddropsduetothedevelopment
of ytotoxi CD8
+
T lympho ytes (blue line), and the viral set point is rea hed during hroni
infe tion. GALT=gut-asso iated lymphoid tissues.
the viralload to about one to two orders of magnitude, thus resulting into a CD4
+
T- ellsrebound from1200 ells ml
−
3
(normal bloodvalue) toaround800 ells ml
−
3
.
This de line is also asso iated with the target elllimitation-that is, the virus runs
out of ells to infe t [122, 140, 161℄.
Asymptomati phase: This phase is sometimes referred toas the Chroni or the
Laten y stage. It is distinguished by very low viral repli ation interspersed with
periods of in reases in the viral load and by a very slow but onstant de reasing
numbers of the CD4
+
ells ount[22, 54℄. Despite the fa tthat HIVpatients inthis
stagela kserioussymptoms,theHIV-1repli ation y leremainsdynami throughout
the disease. A singlevirionhas avery shorthalf-lifein thatit takesonly30minutes
of virions produ ed in a hroni ally infe ted individual an rea h more than
10
10
parti lesperday [124, 126, 137℄. Longitudinalstudies of HIV-1 infe ted individuals
have shown that this laten y phase lasts for a period of about 10 years [54, 114℄
before the development of AIDS. However, other studies have indi ated that the
durability of this stage may vary signi antly depending on whether the region of
the HIV patient is industrialised or underdeveloped [111℄. The variability of this
hroni period and the pre ise me hanisms by whi h HIV overwhelms the immune
system remain shallowly understood.
AIDS and death phase: This is the last stage signalised by a progressive and
ontinuous pathogeni pro ess involving a slow and steady de line of the CD4
+
T
ell-mediatedimmunity [22, 53, 114℄, neoplasms, and an emergen eof opportunisti
mi robes[5, 53, 157℄. The initialmost ommonsymptomsand diseases ofthis stage
in ludea moderateand unexplained weightlossof more than 10%,skin rashes,
My- oba terium tuber ulosis, oral ul erations and repeated respiratory tra t infe tions
like bron hitis, pharyngitis and sinusitis [41, 56, 68℄. The CD4
+
T ell ount in the
blood redu es to less than 200 ml
−
3
[66, 72℄, and the patient an averagely survive
9.2 months [111℄ if treatment interventions are not arried out. A ording to the
urrent treatment strategies, an AIDS diagnosed patient has a lifespan of atleast 5
years [131℄.
2.2 Immunologi al on epts
The immune system is the major body's natural defen e or guard that ghts all types
of organisms against atta king the host, and destroys mutant and an erous ells within
the body. It is partitioned into the innate (natural) immune response, and the adaptive
(a quired)immuneresponse. Theinnateimmuneresponsepioneerstheinitial ghtagainst
the harmful intruding pathogens. Be ause of the rapid response demonstrated, when the
samepathogenattempts toinvadethebodylater,it ertainlyes apestheinnate'simmune
surveillan e,whi hisa onsequen eofitsmemorisationinability. Itsduetothis
memorisa-tionfailurethat theadaptiveimmuneresponse omesintoa tion. Itin orporates the ells
dete t and establisha strongly ee tivedefen e against allthe re-atta kingpathogens.
The human immunesystem has two typesof lympho ytes known asthe B and the T ells
whose fun tionis todete tforeign substan es (non-self). The B ells retaliatetoantigens
by produ ing and se reting antibodies [117℄. The T ells have three main subgroups.
The rst is the ytotoxi or T killer ells whose fun tion is to destroy all the virus
infe ted ells, and to or hestrate immune re overy from the viral infe tion. The se ond is
the suppressor T ells whose responsibility is tomoderate the immune system afterthe
learan eofanantigen. ThehelperT ellsor CD4 +
ellssometimesalsoknownastheT4
ells onstitutethe lastsubgroup. They a t asindi atorstothe immunesystem aboutthe
presen e of foreign substan es, and alert other ells inthe system to assail the infe tions.
Generally,these CD4
+
T ells do not kill ells, but rather oordinate the a tivities of the
B ells and T ells in resistingand ontrolling infe tion[144℄.
The T ell's surfa e is omposed of spe ialised re eptors used for identi ation of body
invading antigens. Re eptors expressed by T ells bind with antigens on the infe tious
parti le and destroy them. The killer T ells and the helper T ells possess the CD8
and CD4 re eptors respe tively. It's the ombination of these ells that modulates the
body'simmune response towards foreign antigens[144℄
2.2.1 Intera tion between HIV infe tion and the immune system
The duration and out ome of HIV-1's life y le entirely depends on the target ell type
and ell a tivation [36℄. During the initial stages of infe tion, HIV-1 gains a ess to the
ellswithout ausingimmediatelethaldamages. However, theentrypro essmaystimulate
intra ellular signal as ades, thus leading to viral repli ation [13, 31℄. The major targets
of HIV-1 are CD4
+
Tlympho ytes and CD4
+
ells of ma rophagelineage [42℄
The gradual loss of CD4
+
T ells results from numerous pro esses su h as;
a tivation-indu ed elldeathorapoptosisprodu edby T4 ell'sdefe ts emerging fromHIVinfe tion
[117℄, syn ytia formation, wherethe immune fun tion is lostas a onsequen e of massing
healthyT ellsaroundasingleHIVinfe tedT4 ell[75,139℄,anddire tmembrane
pro ess starts with the pla ement of the virus onto the surfa e of the ells. The infe ted
ells are then tra ked down and destroyed by the killer ells.
Nonetheless, some of the HIV infe ted ells evade the host immunity. This happens when
additionalvirulen eee tslikethe downregulationofMHC lass1mole ulesfromthe
sur-fa eoftheinfe ted ellsimpedesre ognitionbythe ytotoxi Tlympho ytes[37,38℄. This
elusion te hnique renders severe sele tion pressures for HIV viral diversi aion. Through
HIV'sinfe tion pro edureof ells andtissues, many variantswith spe i elltropismsare
generated, thusleadingto the deteriorationof the immuneresponse and weakening of the
sele tionpressures [19, 21℄.
2.2.2 Impa t of HIV-1 infe tion on Ma rophages and T- ells
During the pathogenesis of HIV-1 infe tion, the viral tropism experien es temporal
vari-ations. The viral strains of approximately 50% of the HIV infe ted individuals evolves
within a period of 45 years [105, 145℄. Due to these temporal alterations, the virus'
po-tentialtoinfe tma rophagesissometimeslost, althoughthispropertyisoftenlysustained,
making the virus dual tropi [39℄. HIV viruses that are nonsyn ytium-indu ing
(in a-pable of forming syn ytia on T- ell lines) and able to infe t ma rophages are known as
ma rophage tropi (M-tropi ),whereasthose thatare syn yntium-indu ingand apable
of infe ting the T- ell lines are alled T-tropi . The T- ell line adapted viruses are
those that develop on the transformed elllines through ontinualpassage[47, 136℄.
Despitethesu ien yofCD4re eptorsinbindingHIV-1totheT4lympho ytemembrane,
thepenetrationofthevirusintothe target ellsismediatedby ore eptors. Therearevery
many ore eptors althoughHIV-1 mostly relies on the CXCR4 and CCR5 ore eptors for
its repli ation. Viral strains are lassi ed depending on the type of ore eptor they use.
ThosethatutilisetheCXCR4 ore eptorarereferredtoastheX4viralstrains[14,32,45℄,
and they are distinguished by a high level of T- ell learan e and an expression of the
syn ytium-indu ing (SI) phenotype. The CCR5 ore eptor is utilised by the R5 viral
strain whi h is dierentiated by a slow disease progression and a relative ytopathi ity
[41℄. HIV positive individuals possessing a dual tropi property utilise a ombination of
the SI phenotype.
As a result of the hara teristi dieren es between the X4 and R5 viral strains, the
variations in the repli ation kineti s of HIV-1 have been dire tly linked to the swit hing
of ore eptor usage from CCR5 tropism to CXCR4 tropism [26, 52℄. This phenotypi
swit hingisasso iatedwiththeinitialimmunologi aland lini alsignsofthelatentdisease
progression phase [43, 91℄. Compelling eviden e has demonstrated that the X4 strain
repli ation kineti s is very fast ompared to that of the R5 strain [164, 166℄. This is one
of the underlying me hanisms that attempts to learly explain the dieren es in HIV-1's
progression pattern.
The limitation of the overall viral repli ation kineti s is partly handled by the CD8
+
T lympho ytes (killer ells) through the use of both lyti and non-lyti CD8 responses.
The CTLs release HIV suppressive fa tors su h as beta- hemokines that are a tive on
mono ytesandlympho ytes,granulysinandperforinproteinswhi hindu ethe ell'sdeath
bypun turingitsmembrane[24℄. Thedestru tionofthese ellstakespla eafterthebinding
of HIV-1 spe i CD8
+
T ells tothe MHC-peptide omplex. After the a tivation of the
CD8
+
T ells, the lonal expansion phase follows, leading to more produ tion of HIV-1
spe i CD8
+
T ells that promptly wipesout the unexhausted virallyinfe ted ells.
A ombinationof hemi alme hanismsthatis;beta- hemokineslikeMIP-1
α
(Ma rophage In ammatoryProtein1α
),MIP-1β
and RANTES (Regulated uponA tivationNormal T- ellExpressedandSe reted),stronglyredu ethe repli ationrate ofHIV-1[35℄, andduringtheviralpenetrationphase,this ombinationpreventstheprimarynonsyn ytium-indu ing
(NSI) HIV-1 strains from infe ting CD4
+
T ells. Be ause of the insensitivity of SI viral
strains tobeta- hemokines, some CD4
+
T-helper ells from HIV-1 exposed-uninfe ted
in-dividuals be ome infe ted. However, it is still not learly explored if the progression of
HIV-1 infe tion an be held ba k by the se retion of high levels of beta- hemokines[35℄.
2.3 Drugs and treatment strategies for HIV/AIDS
At the moment, the available HIV/AIDS drugs annot eradi ate HIV-1 infe tion nor
to undete table levels, thus in reasing the CD4 ount of the infe ted individual. These
drugs have signi antly improved the general health status and quality of life for the
patients resultingintothe minimisationofallHIV-related morbidity and mortality
world-wide [116, 170℄. Presently, highly a tive antiretroviral therapy (HAART) is the most
remarkable therapeuti approa h that has kept the HIV-1 repli ation pattern in he k,
hen e putting forward the hope that HIV-1 infe tion an be transformed intoa treatable
hroni disease [74, 109, 116℄. HAART is omprised of a on urrent administrationof at
least three antiretroviral drugs. The patient's simultaneous onsumptionof three or more
anti-HIV drugs vastly redu es the developmentalrate of drug-resistant HIV mutants.
All anti-HIV drugs are ategorised into two major lasses of potent antiretroviral agents.
The rst lassisthenu leoside-analoguereversetrans riptaseinhibitor,andthese ondone
is either a protease inhibitor or a non-nu leoside reverse trans riptase inhibitor. Reverse
trans riptase inhibitors inhibit the HIV reverse trans riptase enzyme from trans ribing
the viral RNA into DNA, whereas the protease inhibitors inhibitsthe a tivity of the HIV
protease enzyme by preventing it from leaving the Gag polyprotein into proteins and
enzymes that make up a fun tionalHIV virion. The extension of the viral DNAmole ule
isput toahalt by in orporatingnu leosideanalogues intoit. Thisisa hieved throughthe
mimi kingof the stru ture of the host ell's DNAbuildingblo ks.
The urrent HIV-1 infe tion treatment re ommended is for patients having CD4 ounts
below 350 ells mm
−
3
of blood or a viral load of more than
3.0 × 10
4
opies ml
−
1
[23℄,
althoughadvi e variesslightlyamongthedierentnationalguidelines. However, theexa t
time toinitiateHIV-1treatment stillremainsa topi of ontroversial debate. A su essful
antiretroviral treatment is hara terised by an in rease in CD4 ounts and a long-lasting
viralsuppressiontoapproximatelylessthan50 opiesml
−
1
. Be ausethereisnoHIV/AIDS
ure, the use of HAART automati ally be omes an endless ontinuous pro ess. This not
onlymakesitextremelyexpensiveand toodi ultforthepatientstoabidebyits omplex
regimens, but has also generated drug toxi ity that has lead to serious side ee ts
(med-i ation intoleran e) that in lude; elevation of holesterol and trigly eride on entration,
poor redistribution of body fat, insulin resistan e, mito hondrial dysfun tion in several
tissues, and an in rease in ardiovas ularrisks and birth defe ts [7, 130, 158℄. Therefore,
patients dis ontinue HAART and experien e a rapid viral rebound and loss of CD4
+
the restoration of HIV-spe i immune responses [118℄. Despite the outlinedside ee ts,
the major reasons to why a big number of HIV positive individuals do not bene t from
HAARTare non-adheren e and non-persisten e with antiretroviral therapy.
Stru tured treatment interruptions (adrug holiday that enablespatientstohalt anti-HIV
treatmenttemporarily)havebeenusedasakeystrategyinaddressinglife-long omplian e
toHAART. This approa h was optedfor due tothe fa t that the host's immune response
an onlykeep thevirusin he k ifexposedtoaverymodestlevelofviralrepli ation.
The-oreti alSTI-asso iated bene tsare; lowmedi ation osts, redu ed drugtoxi ity,improved
quality of life, and in reased adheren e todrug regimens(psy hologi al bene t). Despite
the bene ts, the re ent early losure of the SMART trial was based on an in rement in
the mortalityand morbidity levelsinthe treatment interruption group[50℄. Nevertheless,
SMART's losure did not ne essarily implythat all STIs are unsafe. A number of
inves-tigators have strongly suggested that other STI types may be as ee tive as ontinuous
treatmentin ertain ir umstan es, thoughtheir ndings are not yet on lusive.
2.4 Parallels between Immune senes en e and HIV-1
pathogenesis
The reasons justifying the failure of the immune system to ontrol HIV-1 infe tion, and
theresulting lini alimmunode ien yremainun lear. Despitevigorousimmuneresponses
su h as arobust and perhaps a fun tionalHIV-spe i ytotoxi T-lympho yte response,
HIV-1persistsinitshost. Theintriguings enarioisthattheimmunologi alfeaturesofthe
elderly people withoutHIV infe tion show a lotof similaritiesto thoseobserved inHIV-1
infe ted individuals[8℄.
Variousstudiessofar arriedouthavede nedprogressivealterationsoftheimmunesystem
to be asso iated with in reased mortality in the very elderly. Many of these hanges are
due to hroni T ellstimulationbypersistentantigen, parti ularlyfromCytomegalovirus
(CMV). The ompositionof T ellsubsets, their fun tionalintegrityand representation in
the repertoire are all markedly in uen ed by age and CMV. Therefore, the in reased
sus- eptibilityoftheelderlytoinfe tiousdiseasesisduetothe ontributionofanage-asso iated
The omplex pro esses of aging hinder many of the physiologi al fun tions, in ludingthe
development and maintenan e of the peripheral immune system [107℄. It is strongly
be-lievedthattheme hanismsunderlyingtheseage-relateddefe tsattenuatesthehost'sability
tomountastrongandee tiveimmuneresponse. Advan esin ellularandmole ular
phe-notyping have re ently enabled resear hers to more learly explain the me hanisms that
underlieimmunosenes en e in relationtoaging. Forexample, resear h has already shown
thatthe CD4
+
/CD8
+
ratio,andIL-4 produ tionboth de rease withageinhuman
periph-eral blood lympho ytes [3, 27℄, and that the natural killer (NK) a tivity also de reases
with age, as observed inmi e, and internallymphoid tissue [4℄.
FIG. 2.3. S hemati illustration of how the ourse of HIV-1 infe tion hypotheti ally relates to
humanageing. (a): CD8
+
ytotoxi Tlympho ytesarerapidlyprodu edduringtheinitial phase
ofHIV-1infe tion, thus leadingtoasubstantial de lineintheviralload, althoughthevirusisnot
ompletely wipedout due to HIV immune-es ape strategies [9℄. (b): Throughout thelifespanof
anHIV-1uninfe ted individual, the typi al maintenan e oftheimmune responsiveness toseveral
hallengesgraduallyexhauststheimmuneresour es. Italsoshowsan `ideal'virusthatrepresents
imaginary infe tions (in uenza-like) whi h do not dire tlydamage the immune system but they
areeliminated bythe CTL response.
The thymusis a entrallymphoidorganthat atersfor produ tionofnaïve T ells, whose
vitalrole istomediatebetween ellularand humoralimmunity. Oneofthemostly thought
ontributingfa torstolossofimmunefun tionwithin reasingageisChroni involutionof
the thymusgland. It has re ently been demonstrated that thymi atrophy is mediated by
in the de line of thymi and peripheral immune fun tion with ageing. We on lude with
the lini al impli ations of age-asso iated immunosenes en e to va ine development for
tumoursand infe tiousdiseases. Athoroughunderstanding ofthe omplexme hanismsby
whi h aging attenuates immune fun tion will enable resear hers to develop new therapies
and va ines spe i ally aimed at over oming these defe ts in immunologi alfun tion in
the aged.
2.5 Fa tors ontributing to alterations in an aging
im-mune system
The peripheralimmune system develops fromhaematopoieti stem ells that originate in
the bone marrow. Lymphoidprogenitors (in ludingTand B ells)leavethe bone marrow
and move to spe ialised peripheral sites, that is; thymus, spleen and lymph nodes, where
they further mature and dierentiate. When aforeign invaderis dete ted, innateimmune
ellsrespondbydestroyinginfe ted ells(NK ells)andreleasing ytokinesand hemokines
tore ruit additional ells to ght the infe tionand alter host tissues, apro ess ommonly
referred toas `in ammation'.
Thisinnateimmuneresponse anfurtherprogresstoanadaptive(antigen-spe i )immune
response with the re ruitment of ee tor T and B lympho ytes. After ingestion of the
invading pathogen,the hostimmuneresponse wanesand returnstoaquies entstate, thus
over ominginadvertentdamages. Thislatterpro essispartiallymediatedbyaspe ialised
subsetofT ells knownasregulatoryT ells. T ellsare onsideredtobehighlyvulnerable
tothe ee ts ofaging. Althoughseveral fa tors havebeenlinked tothe deteriorationinT
ell fun tion with age, it appears that hroni age-indu ed thymi atrophy and resultant
de reased output of naïve T ells is the most important fa tor [70℄. An overview of the
ee ts of aging onthe immune fun tionin lude;
2.5.1 Bone marrow
(non-into fun tional immune ells (haematopoieti lineages). A essory ells (megakaryo ytes,
osteoblasts, osteo lasts, adipo ytes, hondro ytes, myoblastsand broblasts)makeup the
stromalmatrix of thebonemarrow ompartment. Thesea essory ells nurture and drive
stem ellprodu tion. Resear hhasdemonstrated thatthehaematopoieti ompartmentof
the bonemarrowde reases within reasing ageand isrepla edby fatty adiposetissue[40℄,
thus suggesting avery earlymorphologi alimpa t of ageing onimmune system ontogeny.
The bone marrow produ es and responds to a number of ytokines and hormones.
Dis-turban es in this ytokine milieu may partly be responsible for the age-indu ed hanges
in bone marrowmorphologyand haematopoieti stem elloutput. For example, systemi
growth hormone signi antly de reases with age and this loss is linked to in reased
adi-posity and de reased ellularity of the aged bone marrow [94℄. Current studies impli ate
age-indu eddysregulationof ytokineandhormonenetworkswiththislossinbonemarrow
stem elloutput a ross the lifespan.
Despite a general age-indu ed de rease in ellularity of the bone marrow, resear h has
proved that there is surprisingly an in rease in the number of bone marrow-resident
ma rophages with age, althoughthese aged ma rophageshave a mildpotentialto se rete
tumour ne rosis fa tor, akey in ammatory ytokine [156℄. Tsuboi et al have shown that
ageingdampensthese retionofIL-7bybonemarrowstromal ells[150℄. IL-7isanessential
survival ytokine for developing lympho ytes. In a nut shell, aging substantially
ompro-mises the omposition of bone marrow stroma and its ability to nurture haematopoieti
pre ursors.
2.5.2 B ell progenitors
A deterioration in numbers of ommon lymphoid progenitors and a redu tion in their
orrespondingproliferationratesinvivohasbeendire tlylinkedtoage-indu edalterations
[108℄. Originally, reports suggested that there wasno de line in pro-B ell ounts despite
agingoftheimmunesystem[143℄. Butlater,Johnsonand olleagues[79℄,showedthatwhile
the frequen yof pro-B ells redu edwith age,the absolutenumberremained onstant,yet
bone marrow ellularity in reased. Other studies have reported a de rease in pro-B ells
in onsistent ways of de ning the pro-B ell with rapidly evolving te hni al advan es in
identifyingthese ells and uores en e a tivated ellsorting.
Conversely, pre-B ell ounts de linemarkedly with age, probablydue to ablo k between
thepro-andpre-B elldevelopmentalstages[79,135℄. A ordingtomurinestudies,redu ed
responsivenessofdevelopingB ellstoIL-7de reasesthere ombinationofimmunoglobulin
genes [108℄, and de reased expressions of surrogate light hain
λ5
[150℄, have all been observed inaged mi e. These fa tors play a key role in the pro-to pre-B ellblo k. Moreproof has showed that aged bone marrowstromal ells are in apable of supporting B ell
expansionprobablybe auseofanattenuatedIL-7produ tion[28℄. Despitethedis repan y
over the pre ise site of blo k in B ell development, it is lear that there is a general
age-indu ed de linein B ell lymphopoiesis that is initiatedatthe stem ell level in the bone
marrow.
2.5.3 Thymi atrophy
The new T ells output falls signi antly and the thymus involutes as an individual ages
[141℄. Steinmanetal investigationsshowedthatthymi fun tionslowlystartsdeteriorating
fromyearoneoflife[142℄. Theobservationofthehumanthymus,thetruethymi epithelial
spa e (TES), and the non-epithelial non-thymopoieti perivas ularspa e [141, 142℄, were
fundamental to the urrent understanding of thymi atrophy. The shift in the ratio of
true TEStoperivas ularspa e isa onsequen e ofthe expansionof theperivas ularspa e
(adipo ytes, peripheral lympho ytes,stroma)with age. Bythe timeanindividualrea hes
70 years of age, the TES will have shrunk to less than 10% of the total thymus tissue.
ExtrapolationofSteinman'sdatasuggestedthatthethymus utsothegenerationofnew
T ells at approximately105 years of age, and its omplete losswould o ur at an age of
approximately 120 years [60℄.
Thymi atrophy an be monitored through the use of various te hniques. The te hnique
that was used to monitor signal joint T ell re eptor ex ision ir les produ ed in mi e
[132℄, waslater adapted by Sempowskiet al [133℄, whose ndingsindi ated a redu tionof
thymopoiesis atthe mole ularlevel inhealthy thymustissue throughoutnormalageing in
T ells inin reasinglyaging humans.
Althoughthethymopoieti areaofthehumanthymusde reaseswithage,thethymopoieti
potentialper ell was found to remain onstant for a period of roughly 50years [48, 133℄.
Therefore, a ombinationof thymopoieti potential out omes in the aged thymus tissues
guarantees hopethenormalthymi fun tionintheelderly ouldberes onstitutedthrough
future therapeuti regeneration of the true thymi epitheliumspa e.
2.6 Summary
This hapter provided an overview of the key underlying biologi al and immunologi al
on epts that the reader ought to understand inorder to have a lear follow-up of the
interdis iplinary approa hused inthe onstru tion of the models in Chapters 4,5, and 6.
All the models to be studied in this proje t are a translation of the on epts presented
here,intomathemati alformalismsofnon-linearsystemsofordinarydierentialequations,
whosesolutionsarenumeri allydeterminedusing omputersoftwares. Analyti alsolutions
are not trivial due to non-linearities and the omplex intera tions involved during ell
Literature Review
3.1 Introdu tion
Thedynami sofbothinfe tiousandnon-infe tiousdiseases anbewellelu idatedthrough
the formulationof linear and nonlinear mathemati almodels. Immunologists, statistians,
mathemati iansand lini ianshave worked together for the last 20 years with a ommon
obje tive of gaining deeper insights into the kineti s of HIV. This a hievement was a
onsequen e of the onstru tion of mathemati al models that des ribed the intera tion
between HIVand the immunesystem, and the resultingperturbations dueto initiationof
highlya tive antiretroviral therapy.
Mathemati almodellingisde ned asasimpli editerativepro ess representing the
under-lying omplexbiologi alme hanismsof anepidemi outbreakatboth ellularand
popula-tion levels. Althoughmathemati almodels an not independently ta kleall the questions
on erning HIV's pathogenesis, some of the disease's mysteries have been satisfa torily
answered. Nevertheless, tting these models toeither HIV-1 lini alor experimentaldata
would earn them more redibility, thus be oming undoubtedly reliable. These models
would further be used in parameter estimation, hypothesis development and predi tions
from lini al datato assist inthe making of reasonable poli yde isionsthat ae t human
populations.
InthisChapter, wereview someofthe resear hstudiesthathavebeena omplishedinthe
phasesofprogression,andthetherapeuti ee tsofantiretroviraldrugsonitspathogenesis.
We on entrate this review on the intera tion of CD4
+
T- ells, ma rophages, CD8
+
T
lympho ytes and the virus, sin e they are the key ompartmental populations onsidered
in the formulation of the HIV model presented in hapter 5. Besides, the multiple ell
types, and re eptor-ligand intera tions, whi hregulate the makeup of the host's immune
system,aretoomanyforasinglemodelto apturealltheirrespe tivefun tionsinpresen e
ofaviralpathogen. Itisthereforethemodeller'sobligationtospe i allysele tthe riti al
subset of the various virologi al and immunologi al fa tors to be studied, depending on
the level(systemi ormi ro) he prefers to arry out hisdemonstration.
3.2 HIV infe tion models
There are several issues that have been en ountered sin e the modellingof HIV was
initi-ated. Some of these issues ontradi t HIV's lini al and immunologi alexperiments, and
literature,whereas othersthattendto,ora uratelyagreewiththe experimentsare
some-times onsidered unbelievable espe ially if they la k data validation. The issues we are
going to present in this se tion stri tly relate to immune ell populations mentioned in
se tion 3.1.
The mathemati almodels thathavebeenproposedtoexamine thedynami alintera tions
between the viralinfe tionand the CD8
+
Tlympho ytes[168℄ haveyielded on i ting
re-sultsduetothe omplexitiesinvolvedinattemptingtoa ountfortheee tsofresistan e,
and the intera tions among the pres ribed antiretroviral drugs. This further onstituted
ontroversial debates on itsrelevan e in ontrolling HIVprogression pattern sin e no
or-relation seemed to exist between the two. Despite the disagreements, the model authors
of [18, 163℄, agreed that a ontinuous HIV-1 spe i ytotoxi T lympho yte response is
needed to sustain the repli ation kineti s of the virus at low levels during the
asymp-tomati stage of disease's pathogenesis. These ndingswere veri ed using lini al data in
[80℄, whereit was observed that HIV-1 spe i CD8
+
T lympho ytea tivity in reased in
patients who experien ed viral rebounds, either as a spike during ongoing suppression or
as a onsequen e of alterations in the drug regimens. The CD8 memory ells guarding
of the CTL immune response [165, 169℄. No on lusions have been rea hed on whether
CD4
+
T helper ells, orantigens sustain the ontinuan e of CD8memory ells. However,
Dominik,et al. [162, 169℄ who investigated this phenomena proposed that a ollaboration
between these me hanisms isne essary forviral ontrol, and this would bedetermined by
the disease's repli ation stage.
Before ommen ement of the CTL a tivity, the CD4
+
T helper ells are ompromised by
thealarminglevelsofthevirus. Asaresult,the highantigenlevelsbe omethekeyplayers
of the antigen-dependent immune response. A ording to [162, 169℄, when the ell
medi-ated response minimallysuppresses the viralload towards the end of the a ute phase,the
restoration of the CD4
+
T ell pool starts, and the antigen level falls. They laimedthat
thisisthestagewheretheCD4-dependentresponse beginstoeliminatethevirionparti les
tomu hlowerlevels.
Sin ethe CD8 memory ells have alifespan longerthanthat of theCD8
+
T lympho ytes,
then theirdierentiationintoCTL ee tors an lead tothe omplete replenishment ofthe
CD8 memory ells. The model Wodarz, et al. [163℄ studied showed that the diminishing
rate of the CD8
+
T lympho ytes (CTL exhaustion) was driven by a fast repli ationrate
andthe viralpathogen'sabilitytoinfe thealthyCD4
+
T ells. In general,they on luded
that:
A high viral repli ation rate ontributes to a faster de line in the CD4
+
T ells
populationdensity, and
the dierentiation rate of CD8 memory ells into short lived CD8
+
T lympho ytes
in reased as the viralload steadily shot up.
Initially when mathemati al models had just been introdu ed into the assessment of the
dynami s of the virus and the CD4
+
T lympho yte populations, the modellers assumed
that inadequate viral repli ations were responsible for the observed stability of the HIV
parti les and the CD4
+
T ells, during the lini al laten y of HIV infe tion. However,
when Ho, et al., [73℄, and Perelson,et al.,[124℄ tted data of 20HIV positive patients on
antiretroviraltherapy, ontotheirrespe tivestudy mathemati almodels. From the results,
they proved and on luded that thetheory of ahighlyfastand ontinuousturnover ofthe
virus and the infe ted CD4
+
Kim and Perelson [84℄ further investigated why the HIV positive patient's immune
sys-tem failed to ompletely eliminate the virus during HAART, despite the fa t that HIV's
ability to spread within the body was overly suppressed. In this study, they onsidered
an additional physiologi al pro ess of latently infe ted ells by assuming that they
expe-rien e bystander proliferationwithout shifting intoa tive viralprodu tion, and thattheir
a tivationratediminishedwith prolongedtime onantiretroviraltreatment. Their ndings
were too dramati as they showed that the onstant a tivation of the latently infe ted
ellswould generate morevirusparti lesdespitetheuse ofsu iently highdruge a ies.
Their on lusion was that the viral ontinuan e observed in HIV patients on suppressive
HAART is a onsequen e of several intrinsi physiologi al parameters, whi h are mainly
in uen ed by the persistent a tivation of the latent CD4
+
T ell population. This
moti-vates the in orporation of the latently infe ted CD4
+
T lympho yte ompartment in the
HIV model onstru tedin Chapter 5.
Staord and olleagues,[140℄used the basi HIV-1 model(4.11),toanalyse its parameter
variations by tting it to lini al data of nine patients, and dis overed that they ould
a ount for the alterations inthe shooting and fallingof viral load levelsobserved among
the patients. The demonstrationalsoindi ated that the viral load inmost of the patients
dropped beyond the limits that the simplest HIV-1 model (4.11), ould predi t. When
they in orporatedanimmune response fun tionintothe model, itwasable to apture low
viral set points. Nonetheless, Staord's experiment was unable to learly elu idate how
the ontributions of dierentpro esses in viralload de rease may bedistinguished.
Kirs hnerand Webb [88℄built amathemati almodelwhi hhad ma rophagesand
thymo- ytes as part of the ell ompartments in orporated into it. They studied the dynami s
of these two ell populations, and the obtained results re e ted a failure of these ells in
a ounting for the dramati in rease in the viral load be ause their ombined produ tion
was extremely smaller than CD4
+
T ells. However, their ndings were in parallel with
[87℄, sin e the authors argued that ma rophages and thymo ytes are profoundly relevant
inviralprodu tion. Otherresear h studies[67℄ have suggestedthat the generationof HIV
parti lesand the high viralload seenduring the AIDS stage mightbedriven by other ell
typesotherthan the CD4
+
Tlympho ytes. A ording to murineand animalstudies,[77℄,
our motivation toin ludema rophages inthe modelsystem (5.15.8).
3.3 HIV-TB o-infe tion models
In 1998, Denise Kirs hner [85℄, pioneered the rst attempt in analysing the impa t, the
introdu tionof anopportunisti infe tionsu h asMy oba terium tuber ulosis,would have
onthedynami intera tionofHIV-1andthe immunesystem. Thisstudywas on entrated
onthe hypothesis that the presen e ofboth HIVand M. tuber ulosis inthe host's system
worsens HIV's lini al pi ture, and that the progression rate of M. tuber ulosis to a tive
diseaserapidly in reases. Thestudy was ondu ted usingamathemati almodelthat
on-sisted of four systems of ordinary dierential equationswhi hdes ribed the hara teristi
hanges in CD4
+
T lympho ytes,
T (t)
; Ma rophages,M(t)
; Freely ir ulating virion par-ti les,V (t)
; and M. tuber ulosis,T
b
(t)
.The intera tion of the two pathogens with the immune system were keenly examined,
and the results obtained revealed that the on entration of the CD4
+
T elldensity in a
host-virussystem islowerthan the on entrationinthe HIV-TB oinfe tedsystem.
Addi-tionally,thevariationintheviralloadlevelswastoospe ta ularinthattheoneseeninthe
oinfe tedpatientswasextremelyhigh omparedtoasingle-pathogeninfe tedindividuals.
Afterallthe observations, they on ludedthat sin ethe viralload andthe quantity ofthe
CD4
+
T ellsare thekeydeterminantsofthepatient'ssurvivaltime,thenthepatientwith
both pathogens is expe ted to progress to full blown AIDS in a shorter period ompared
toa patient whoseimmune system is ompromisedwith one pathogen, and that anHIV
+
patient who gets infe ted with M. tuber ulosis has very high han esof developing a tive
tuber ulosis, thus in reasingthe ba terialload whi h further impairsthe immunesystem.
Lastly, Kirs hner [85℄ investigated immune re onstitution in a oinfe ted individuals by
in orporating M. tuber ulosis treatment into the model. She dis overed that the CD4
+
T ell population re overed plausibly within a short period of time, whi h implied that
the treatment of M. tuber ulosis had a signi ant impa t on the repli ation kineti s of
HIV. Fromthe M. tuber ulosis therapeuti ndings, Kirs hner suggestedthat drugswhi h
suppress ba terialgrowth were better than the ones used to enhan e ba terialdeath, and
