Simian immunodeficiency virus (SIV) molecular epidemiology in non-human primates from West Africa

It is now scientifically proved that the human immunodeficiency viruses, HIV-1
and HIV-2, are the results of cross-species transmissions of the simian
immunodeficiency viruses (SIV) that naturally infect non-human primates in sub-
Saharan Africa. SIVsmm from sooty mangabeys (Cercocebus atys atys) is recognised
as the progenitor of HIV-2, whereas SIVcpz from chimpanzees (Pan troglodytes
troglodytes) and SIVgor from gorillas (Gorilla gorilla gorilla) in West-central Africa are
the ancestors of HIV-1, the virus responsible for the AIDS (Acquired ImmunoDeficiency
Syndrome) pandemic having already infected more than 60 million people.
Only non-human primates (NHPs) species from Africa are infected with SIVs.
Serological evidence of SIV positivity has been shown for at least 40 of the 69 primate
species found in Africa and this has been confirmed by DNA sequence analysis in 32
species.
Generally, SIVs do not induce an AIDS-like syndrome in their natural hosts,
suggesting that they have been associated and evolved with their hosts over an
extended period of time. However, if SIV crosses the species barrier, it may become
pathogenic to the new host. The ancestors of HIV-1 and HIV-2 have crossed the
species barrier to humans on multiple occasions, most likely through the contact with
infected blood and tissues from primates hunted for bushmeat.
Bushmeat hunting has been a longstanding practice throughout sub-Saharan
Africa, but the trade has increased in the last decades. Commercial logging has led to
the construction of roads into remote forest areas and hunters are now making use of
this newly developed infrastructure to penetrate previously inaccessible forests and
capture and transport bushmeat to major city markets. Moreover, villages around
logging concessions have become more densely populated; this has also increased the
trade and consumption around these areas.
The socio-economic and environmental changes occurring combined with the growing
genetic diversity and SIV prevalence among non-human primate populations, suggest
that today, more than previously, the human population is exposed to SIVs. Bushmeat
hunting is not limited to chimpanzees, gorillas or sooty mangabeys: the majority of
NHPs is represented by many Cercopithecus and Colobus species for example. It is
therefore important to continue the search and the characterisation of new SIVs and to
determine the prevalence of infection in the NHP, in order to better evaluate which of
these SIVs represent a health threat for the human population.
The main goal of this thesis were
(i) to determine SIV infection and investigate its prevalence among
different social groups of monkeys living in Taï National Park,
Côte d’Ivoire, knowing that these NHPs are heavily hunted
around this area
(ii) to determine SIV infection and prevalence and to characterise at
a molecular level the SIV possibly infecting the red colobus
species found in Abuko Nature Reserve, the Gambia. Two
different subspecies of red colobus are found in the Gambia and
in Côte d’Ivoire: this represented an opportunity to investigate
whether different subspecies may harbour genetically different
viruses and therefore to better understand the impact of
geographical barriers on the evolution of SIV
(iii) to compare the molecular structure of SIVs infecting red and olive
colobus, two sister species in the Colobinae subfamily
(iv) to determine if the chimpanzee subspecies found in West Africa
is infected with a virus similar to that of the monkey species it
preys upon, knowing that, to date, only the subspecies from
West-central and East Africa have been found to be infected with
SIV.
The majority of the results presented in this thesis have been obtained by
analysing data collected with non-invasive methods. SIV infection has been determined
in NHPs by detecting antibodies or by isolating viral sequences from freshly dropped
faecal samples collected in the forests of Côte d’Ivoire and The Gambia. In order to be
able to discriminate the faecal samples collected and, consequently, to reliably
determine the prevalence of infection in a monkey group, the host has been genotyped
by analysing the DNA extracted from the epithelial cells debris released from the
intestine. Host genotyping, antibody detection and isolation of viral RNA from faecal
samples have become possible thanks to the improvement of conservation methods
and DNA and RNA extraction techniques.
Wild-living non-human primate populations often live in inaccessible areas and
tend to be wary of the presence of observers or display cryptic behaviour; the difficulty in
sampling increases when the target species are arboreal primates exploiting the higher
layers of the forest canopy. To mitigate these problems, we selected two field sites
(Abuko Nature Reserve, The Gambia and Taï National Park, Côte d’Ivoire) where the
primate populations were at least partly habituated by the presence of human observers
and where behavioural-ecology studies have been conducted for more than 10 years.
In fact, SIV is transmitted mainly sexually, but possibly also vertically (from the
mother to the offspring) and through biting or infection of open wounds. It is therefore
important to consider factors such as mating system, patterns of dispersal, group size,
average number of adult males in a group, polyspecific associations, etc. as parameters
conducive to the transmission of the virus within or across groups and species.
In total, more than 300 faecal samples from two groups of western red colobus
(Piliocolobus badius badius), from two groups of black-and-white colobus (Colobus
polykomos polykomos), from three groups of olive colobus (Procolobus verus), from
three groups of Diana monkeys (Cercopithecus diana), from one group of Campbell’s
monkeys (Cercopithecus campbelli), from one group of lesser-spot nosed monkeys
(Cercopithecus petaurista) and from a group of greater spot-nosed monkeys
(Cercopithecus nictitans) were collected near the western border of the Taï Forest, in
Côte d’Ivoire, between March and July 2004.
To discriminate the faecal samples collected, 16 microsatellite loci were screened
in these seven monkey species using cross-specific human markers. Microsatellites are
di-tri-tetra-nucleotide tandem repeats, which length’s variability is transmitted by
Mendelian inheritance and can therefore be used in combination for individual
discrimination. Between 25% to 37% of the primers used were informative and
successfully and reliably amplified faecal extracted DNA from all species (Chapter 5).
Colobus and Cercopithecus samples were first tested for the presence of HIV
cross-reactive antibodies using an immunoblotting assay and were found to be all
negative or ‘non interpretable’.
Subsequently, Reverse Transcriptase-Polymerase Chain Reactions (RT-PCRs) using
universal as well as species-specific primers that target the gag, pol and env regions of
the SIV genome were performed: only the western red colobus tested positive for SIV
infection.
Among the inferred 53 adult individuals belonging to two neighbouring habituated
groups, 14 tested SIVwrc (western red colobus) positive with a prevalence of 26%.
Phylogenetic analysis of pol and env sequences revealed a low degree of viral genetic
diversity in each group. The viral sequences obtained were generally clustering together
according to their respective social group of origin. Conversely, the degree of viral
genetic diversity between the two groups was higher.
Behavioural and demographic data collected previously from these communities
indicate that western red colobus monkeys live in promiscuous multi-male societies,
where females leave their natal group as sub-adults and where extra-group copulations
or male immigration have been rarely observed. Phylogenetic data reflect these
behavioural characteristics (Chapter 6).
The negative SIV results obtained for the other investigated species may reflect
their social structure and mating system, but possibly also the difficulty of group
monitoring, faecal sample collection coverage in the field as well as the long term
conservation of viral RNA in the field and the sensitivity and specificity of SIV serological
and molecular detection tools respectively (Chapter 9).
In parallel, sixteen faecal samples from sixteen individuals and two tissue
samples from two carcasses of Temminck’s red colobus monkeys (Piliocolobus badius
temminckii) collected from the forest floor, between January and February 2005, in the
Abuko Nature Reserve were analysed. None of the 16 faecal samples from Temminck’s
red colobus analysed by RT-PCR were positive. However, SIV infection was identified in
one of the tissue samples, and phylogenetic analyses of partial pol and env sequences
showed that this SIVwrc-Pbt virus strain is closely related to SIVwrc-Pbb strains from
P.b.badius in the Taï Forest, suggesting that geographically separated subspecies can
be infected by closely related viruses. Molecular characterization and phylogenetic
analysis of a SIVwrc-Pbt and two SIVwrc-Pbb full-length genomes, subsequently
sequenced (Chapter 8), confirmed that SIVwrc-Pbt and SIVwrc-Pbb belong to a
species-specific SIV lineage, although distantly related to the SIVlho lineage comprising
SIVs from mandrills (Mandrillus sphinx), l’Hoest (Cercopithecus lhoesti) and sun-tailed
monkeys (Cercopithecus solatus) (Chapters 7 and 8).
More recently, we characterised the full-length genome of the SIV infecting the
olive colobus (SIVolc), by analysing a blood sample collected during a previous study
also conducted in Taï National Park. Olive and western red colobus are sister taxon and
results showed that SIVwrc and SIVolc form distinct lineages, but are closely related
across their entire genome (Chapter 8).
These results confirmed the complex evolutionary history of primate lentiviruses,
which has been driven by host-virus co-speciation, cross-species transmission and
recombination events over an extended period of time. Genomic characterization of
additional SIVs viruses from other Colobines is needed to better understand the
ancestral phylogenetic relationship to SIVs from the l’Hoest lineage and whether
recombination occurred between ancestors of these viruses.
Finally, 5 blood and tissue samples collected from 5 chimpanzee carcasses
during a previous study conducted in Taï National Park, were analysed for SIV infection
in this study. To date, no SIV has been isolated from this subspecies of chimpanzee
(Pan troglodytes verus) found in West Africa. It is known that the chimpanzee hunts
small monkeys and that SIVcpz, the precursor of HIV-1, isolated from the west-central
chimpanzee subspecies (Pan troglodytes troglodytes), is a mosaic virus resulting from
the recombination of viruses from different species of monkeys the chimpanzee preys
upon. Following this line of reasoning, we tested universal as well as species-specific
markers amplifying SIV infecting western red colobus, the favourite prey of chimpanzees
from the Taï Forest. Serological tests conducted on these 5 samples showed a weak
seropositivity in three of them. These results could not be confirmed by PCR. Whether
this chimpanzee subspecies is not infected with SIV or whether it harbours a highly
divergent virus not detected yet by the current molecular tools available remains to be
determined (Chapter 10).