HIV 4

Phylogeny
Phylogenies are used to determine the taxonomic relationship among
pathogens and explain evolutionary mechanisms that produced these
genetic structures (Holmes, 1998). Based upon phylogenetic taxonomy,
HIV is a member of the lentivirus subfamily of retroviruses that
produces chronic infection in the host and gradually damages the
host’s immune system (De Cock et al., 1993; Hu et al., 1996; Grez
et al., 1994; Beer et al., 1999; Hahn, 2000). Three major types of
lentiviruses have been characterized in primates: Simian immunodeficiency
viruses (SIVs); HIV-1, the predominant type in the world;
and HIV-2, primarily found inWest Africa and India (De Cock et al.,
1993; Grez et al., 1994; Beer et al., 1999).
HIV and other infectious diseases conform to the clonal model
where genomes are not easily reshuffled by recombination and mutation.
In the clonal model there is nonrandom association of alleles
(linkage dis-equilibrium) allowing the identification of relationships
among pathogens (Levin et al., 1999). Based on phylogenetic relationships,
HIV-1 viral strains can be divided into three major groups: ‘M’,
‘N’ and ‘O’ (Louwagie et al., 1993; Sharp et al., 1994; Leitner et al.,
1997; Simon et al., 1998; Gao et al., 1999).The predominantMgroup
consists of 11 separate subtypes or ‘clades’ denoted ‘A’ through ‘K’
(Los Alamos National Laboratory, 1998). Multiple strains are found
in many countries but in the United States the majority of isolates
have been subtype B. The occasional presence of HIV-2 and HIV-1
subtypes other than B suggest multiple HIV introductions to North
America because the genomes of the strains are different (Delwart
et al., 1993; Hu et al., 1996). Subtypes found in Africa belong to four
clades (A–D). Subtype C is found mainly along the south and east
coast of Africa (and the west coast of India: Delwart et al., 1993; Stine,
2000). E, B andCare found in Southeast Asia (Louwagie et al., 1993) –
one, subtype E, almost exclusively infects heterosexuals in Thailand
while genotype B and E are found in intravenous drug users (Moore
and Anderson, 1994; Kunanusont et al., 1995).
Nucleic acid sequencing of the N group reveals this appears to be
restricted to Cameroon (Simon et al., 1998).HIV-1 variants outside the
Mand N groups have been provisionally categorized as group O (De
Leys et al., 1990; Gurtler et al., 1994).Within groupO, strains may differ
as much from each other as the variants within groupMsubtypes
differ from each other (Sharp et al., 1994). Group O is also primarily
found in Cameroon (De Leys et al., 1990; Gurtler et al., 1994) but it accounts
for less than 10% of HIV infections there (Gurtler et al., 1994).

It must be recognized that the subtypes identified for HIV are provisional
and reflect those isolates that have been collected and characterised
(Hu et al., 1996) –other subtypes may be identified in the
future.
Phylogenies are thought primarily to be the product of natural
selection operating on genetic diversity. Branches of these phylogenies
are sometimes associated with biological properties such as virulence,
mode of transmission, susceptibility/resistance and tropism
(Holmes, 1998). As such, evolutionary mechanisms such as natural
selection, as discussed earlier in this section, drive these properties.
The following sections of this chapter examine the association between
genetic diversity and these biological properties.
Susceptibility and resistance
A genetic basis for human variation in susceptibility to infectious
diseases has been shown in twin, pedigree, adoptee and candidate
gene studies. These studies show the inheritance of specific genes
and their association with infectious diseases. For instance, there
is a strong genetic association of susceptibility with common variants
of malaria, tuberculosis (Huebner, 1996), Helicobacter pylori infection
(Malaty et al., 1994), hepatitis B (Lin et al., 1989), leprosy
(Chakravari and Vogel, 1973), and HIV infection (see Table 2.1).
Susceptibility or protection can occur in a number of ways. For
example, IL-10 is a cell cytokine that inhibits T cell cytokine secretion
and macrophage growth (Fiorentino et al., 1989, 1991). IL-10 may
limit the number of activated macrophages accessible for HIV-1
replication thereby limiting its duplication. On the other hand, another
genetic polymorphism at that site, IL-10-5’A, is linked to an
accelerated progression to AIDS (Winkler et al., 1998). This indicates
that variants at this IL site can inhibit or promote HIV/AIDS
disease.
Some exposed-uninfected individuals harbour identical mutations
on both chromosomal copies of CC-chemokine receptor 5 (CCR-5:
Hill and Littman, 1996; Samson et al., 1996). A frame shift mutation,
32-base-pair deletion, generates a non-functional receptor that
does not allow membrane fusion or infection by macrophage- and

Table 2.1. Host genes and susceptibility to HIV/AIDS
Disease Chromosome/system References
HIV/AIDS HLA-B*35 & Cw*04 Carrington et al., 1999
HLA-A29 & B22 MacDonald et al., 2000
IL10–5’A Winkler et al., 1998
HLA-B*5701 Migueles et al., 2000
HLA- B14 and C8 MacDonald et al., 2000
HLA-A2 MacDonald et al., 2000
HLA-DR1 class II MacDonald et al., 2000
CCR-5 Samson et al., 1996
Hill and Littman, 1996
CCR-2 Smith et al., 1997a; 1997b
Anzala et al., 1998
AIDS-related
non-Hodgkin’s
B cell lymphoma CCR-5 Rabkin et al., 1999
dual-tropic HIV-1 strains (Liu et al., 1996; Samson et al., 1996). The
individual is thereby protected because the protein product is not expressed
on the surface of the cell (Liu et al., 1996; Zimmerman et al.,
1997). Therefore, the virus does not have a receptor to attach to and
enter the cell.
The prevalence of heterozygotes for the CC-chemokine receptor
was lower in anHIV-infected sample compared to the uninfected population
(Hill and Littman, 1996; Samson et al., 1996). Heterozygous
individuals for the normal CCR5+ allele and the CCR5- 32 mutant
allele are not protected against HIV-1 infection although they
progress to AIDS more slowly –about two to four years on average
after HIV-1 seroconversion, relative to CCR5+/+ (homozygote) individuals
(Michael et al., 1997; Zimmerman et al., 1997). This indicates
that CCR5- 32 heterozygotes exhibit reduced viral loads in
vivo and impaired HIV-1 replication in vitro (Vlahov et al., 1991; de
Roda Husman et al., 1997; Bratt et al., 1998). The CCR5- 32/+
genotype also protects against AIDS-related non-Hodgkin’s B cell
lymphoma (Rabkin et al., 1999). So there is a possible partial protection
from infection among individuals with a single copy of the
mutant allele. However, both research groups showed that thoseheterozygous for the CCR5 mutation were susceptible to viral infection
although at reduced levels (Hill and Littman, 1996; Samson et
al., 1996).
The CCR2 gene is within 10 kilobases of CCR5 and the two genes
are in strong linkage dis-equilibrium (Smith et al., 1997a). Seroconverters
(those who test positive for HIV after exposure) with CCR2-64I,
a variant of CCR2, have significantly lower viral loads 9–12 months
after seroconversion (Kostrikis et al., 1998). Like the heterozygote,
CCR5- 32/+, individuals with two copies of CCR2-64I progress
to AIDS more slowly –tw o to four years later than progression observed
among individualswho are homozygous for the normal allele –
although they are still susceptible to infection (Smith et al., 1997a;
Anzala et al., 1998; Kostrikis et al., 1998).
There are statistically significant associations between HLA (the
histocompatibility system) class I homozygotes (HLA-A, HLA-B,
HLA-C: at one or more loci) and accelerated progression to AIDS.
Each locus of HLA Class I loci contribute independently to the association
with AIDS and the effect is greater in individuals homozygous
for two or three loci. Heterozygosity for HLA showed a graded protective
effect with greater protection with HLA-A, -B, and -C with
the least protection against disease progression to AIDS and death.
Heterozygotes at all loci showed the slowest progression (Carrington
et al., 1999). Also, heterozygous advantage suggests that those heterozygous
at the HLA loci present a greater variety of genetic variants
than homozygotes loci, resulting in a more effective immune reaction
to a greater variety of HIV pathogens (Doherty and Zinkernagel,
1975; Zinkernagel, 1996).
In a study of rapid progressors (i.e. those who develop AIDS in
the first two to three years following initial infection) and long-term
non-progressors (i.e. those who remain healthy for 15 or more years) a
variety of alleles were associated with both susceptibility and protection
(Hendel et al., 1999). For instance, HLA-A29 and B22were significantly
associated with rapid progression, B14 and C8 were strongly
associated with protection while B27, B57 and C14 were less strongly
associated with protection (MacDonald et al., 2000). Although HLA
class II associations are less evident in studies of HIV/AIDS (Hill,
2001), HLA-A2 was associated with resistance to disease progression

and, another variant, HLA-DR1 class II, was associated with resistance
to HIV infection among African individuals (MacDonald et al.,
2000).
There is other evidence ofHLAassociation with the rate of advance
of HIV infection. For instance, HLA-B*5701 is found in the majority
(11 of 13) of long-term non-progressors with low viral loads. Only
10% of controls (HIV-negative ‘Caucasians’ from the US population)
had this variant (Migueles et al., 2000). In North American AIDS
patients, HLA-DRB1*1501 is associated with increased rate of onset
of disseminated Mycobacterium avium complex disease (an environmentderived
disease (i.e. fromwater, food, animals) that unlike tuberculosis
is systemic and not limited to the lungs: LeBlanc et al., 2000). In a
larger study, haplotypes (combinations of alleles from closely linked
loci) of the HLA such as HLA-B*35 and Cw*04 were associated with
increased rate of progression from HIV-positivity to AIDS disease.
Homozygotes for B*35-Cw*04 haplotype progress to AIDS faster
than heterozygotes and B*35-Cw*04 heterozygotes progress more
rapidly than those without this haplotype (Carrington et al., 1999). A
common mechanism seems to underlie these diseases (Hill, 2001).
Variation in secretion of RANTES and MIP-1β show an inverse
correlation between these chemokines and rate of disease progression.
CD4+ lymphocytes from exposed uninfected individuals secrete
more RANTES than those infected with HIV-1 (Paxton et al., 1998).
A promoter region of RANTES composed of –403A/−28G is associated
with significantly slower rates of CD4+ lymphocyte depletion
relative to other genes (Liu et al., 1996). There is more RANTES secretion
in individuals with −403A/−28G haplotype III than those
without this haplotype. This explains the gene association with slower
CD4+ T cell depletion and protection of this genetic variant against
progression to AIDS (McDermott et al., 2000).
Tumor necrosis factor-α (TNF-α) is a pro-inflammatory cytokine
(secreted by T cells that mediate immune interaction) implicated in
the pathogenesis of auto-immune and infectious diseases (Brennan
and Feldmann, 1996). TNF-α and lymphotoxin (TNF-β) induce HIV
replication through activation of the transcription factor NF-kB (Duh
et al., 1989; Matsuyama et al., 1991). Elevated levels of TNF-α have
been reported in AIDS patients (Brinkman et al., 1997).

Properties discussed here, i.e. susceptibility and resistance, are likely
to be the product of evolutionary forces with natural selection being
the driving force behind these polymorphisms. Acting on variation
from high mutation rates and recombinogenic effects, the pathogen
evolves. As a species, Homo sapiens is also changing at the genetic level
in response to these infectious agents. It is the interaction between genetic
diversity of the host and pathogen that determines susceptibility
or protection from HIV infection and the rate of progression to AIDS.