SIV Viral Variation; Implications for Vaccines and Transmission PART 1 Viral diversity at mucosal transmission -determine if vaginal SIV inoculation of rhesus macaques recapitulates HIV-1 variant transmission PART 2 Viral diversity in vaccine setting -Characterize the replication levels and anatomic distribution of vaccine (SHIV 89.6) and challenge (SIVmac239) virus in monkeys prior to and after challenge. -Characterize evolution of SIV env population complexity of SIV DNA in PBMC of SHIV immunized and control animals

1. SIV Viral Variation; Implications
for Vaccines and Transmission
Mars Stone, Ph.D.
California National Primate Research Center
University of California, Davis

2. PART 1 Viral diversity at mucosal transmission
-determine if vaginal SIV inoculation of rhesus macaques
recapitulates HIV-1 variant transmission
PART 2 Viral diversity in vaccine setting
-Characterize the replication levels and anatomic distribution
of vaccine (SHIV 89.6) and challenge (SIVmac239) virus in
monkeys prior to and after challenge.
-Characterize evolution of SIV env population complexity of
SIV DNA in PBMC of SHIV immunized and control animals.

3. Error in Reverse Transcription
leads to Viral Population Complexity
Reverse transcriptase
synthesizes viral DNA from
viral RNA
Error rate of 1.7x105
nucleotide incorporations
Host RNA polymerase II
transcribes the proviral DNA
into RNA which will be packed
into virions.
Mutation can occur during one
or all of these replication steps
~1 error per replication
cycle

4. RNA viruses exist as a quasispecies
Raul Andino, PLoS Pathog. 2010
Every round of replication mutations are
generated, constantly introducing variation as
population expands.

6. Important findings:
Studied 5 seroconverters, 2 linked transmission partners
•Homogeneous HIV env populations within newly infected
patients
•No common signature sequence among transmitted
variants
•Transmitted sequence represented only minor variant in
complex population of chronically infected transmitting
partner
They conclude that the transmitted virus
should be the target of vaccines

7. 3 proposed models of transmission bottleneck
1. Limited variability
from transmitter
3. Selective
amplification
2. Selective
transmission
Homogeneous
Systemic
infection

8. Single Genome Amplification
Methods were developed to generate and sequence
amplicons derived from a single template,
avoiding artifacts common to basic cloning and
sequencing approach

9. Single Genome Amplification
• Proportional representation of variants
• Excludes PCR induced misincorporation error
• Eliminates PCR-mediated recombination

10. Why env?
• Env is primary determinant of cellular tropism and
selective transmission would likely involve
selection among env variants
• Is the most variable gene in the HIV quasispecies

11. Is the SIVenv variant population
transmitted by vaginal inoculation
• Homogeneous?
• Heterogeneous?

12. SIVmac251
stock
intravaginal
inoculation
7 animals
Plasma collected from earliest vRNA+
45 SGAs >20 SGAs / animal
Variant Transfer in Mucosal Infection
Test this observation in a controlled experiment using SGA techniques
Ma ZM, Stone M et al J Virol. 2009

13. Variant transmission is not related to
inoculum dose
Stone, Keele et al JVI 2010

14. Purpose:
1. Determine the number and identity of SIVmac251 env
variants in stock
2. Determine the number and identity of SIVmac251 env
variants transmitted by vaginal inoculation
3. Determine if signature sequence is selected for by
vaginal inoculation

15. SIVmac251 Stock
Stone, Keele et al JVI 2010

16. Single transmission event
Fig 2A

17. Multiple Transmission Events
Fig 3

18. Composite NJ
tree of
SIVmac251
stock and
transmitted
variants
-No two low diversity
lineages were identical
-each lineage distributed
throughout the tree

19. Composite
Highlighter plot of
SIVmac251variants
and recipient variants
One 251 variant
transmitted
unchanged to 3
different animals!

20. Variant transmission is not related to
inoculum dose
Stone, Keele et al JVI 2010
Low dose
high dose

21. Number of founder variants in blood of
infected animals
Variant Transmission
29459
25948
25479
27337
29271
31523
30991
0
2
4
6
8
animal number
numberofvariants

22. 3 proposed models of transmission bottleneck
1. Limited variability
from transmitter
3. Selective
amplification
2. Selective
transmission
Systemic
infection
Complex inoculum!
Homogeneous
Systemic
infection
No common
signature sequence

23. Model of Mucosal Infection (B. Keele)

24. Model of Early Diversification (B. Keele)

25. Conclusions 1:
-Rhesus macaque/SIV model of HIV-1 vaginal transmission
recapitulates human infection.
•Relatively few genetic variants establish systemic infection
even when exposed to complex inoculum
•A specific viral variant was not consistently transmitted by
i.vag. Inoculations

26. PART 1 Viral diversity at mucosal transmission
-Recapitulate HIV-1 variant transmission in rhesus macaque
model of vaginal SIV infection.
-Explore possible host factors affecting variant transmission
PART 2 Viral diversity in vaccine setting
-Characterize the replication levels and distribution of
vaccine (SHIV 89.6) and challenge (SIVmac239) virus in
monkeys prior to and after challenge.
-Characterize the population complexity of SIV in PBMC
vDNA of SHIV immunized and control animals over time.

27. PART 2 Viral diversity in vaccine setting
• HIV is primarily transmitted mucosally, and a vaccine to prevent mucosal
transmission is the best opportunity to stop the AIDS pandemic
• Live attenuated vaccines have demonstrated the best protection from
pathogenic vaginal SIV challenge
• Live attenuated vaccines are not likely to be used due to safety concerns, but
they do provide a good model to understand the nature of immune protection.
• In unprotected animals it is important to know if there are specific anatomic
sites that are resistant to vaccine-induced immune control of challenge virus
replication.

28. Immunization with
nonpathogenic
SHIV89.6
IV
pathogenic
SIVmac239
IVAG
6-12 month immunization period 6 month follow up period
Nx
Live-attenuated SHIV89.6 /
IVAG SIVmac239 challenge
system

30. gag
1303-1381
SIVenv
7298-7389 (C3)
Primer Binding Sites for RT-PCR Viral
Detection and Differentiation
HIVenv
6955-7053

31. Intravaginal SIVmac239 challenge outcome in
SHIV89.6 vaccinated female macaques
Prior SHIV89.6 infection “protects” 60% of rhesus monkeys from
vaginal challenge with SIVmac239
Abel et al. J Virol, 2003

32. Goals:
AIM 1
• Characterize the replication levels and distribution of vaccine (SHIV
89.6) and challenge (SIVmac239) virus in monkeys prior to and after
challenge.
AIM 2
• Determine relationship between SIV population diversity and viral
replication in control animals and animals that eventually fail vaccine
protection

33. Vaccine or Challenge virus?
In other attenuated lentivirus vaccine models it is unclear if “vaccine
failure” is due to replication of the vaccine virus, the challenge virus,
or both
Display Settings: Abstract
We found 1 article by title matching your search:
J Gen Virol. 2008 Sep;89(Pt 9):2240-51.
Resistance to superinfection by a vigorously replicating,
uncloned stock of simian immunodeficiency virus (SIVmac251)
stimulates replication of a live attenuated virus vaccine
(SIVmacC8).
Berry N, Stebbings R, Ferguson D, Ham C, Alden J, Brown S, Jenkins A, Lines J, Duffy L, Davis L, Elsley W, Page M, Hull R,
Stott J, Almond N.
Division of Retrovirology, National Institute for Biological Standards and Control, Blanche Lane, Sou th Mimms, Potters Bar,
Hertfordshire EN6 3QG, UK. rberry@nibsc.ac.uk
Abstract
Vaccination with live attenuated simian immunodeficiency virus (SIVmacC8) confers potent, reproducibl e protection against
homologous wild-type virus challenge (SIVmacJ5). The ability of SIVmacC8 to confer resistance to supe rinfection with an
uncloned ex vivo derivative of SIVmac251 (SIVmac32H/L28) was investigated. In naïve, Mauritian-derive d cynomolgus
macaques (Macaca fascicularis), SIVmac32H/L28 replicated to high peak titres (>10(8) SIV RNA copies ml(-1)), persisted at
high levels and induced distinctive pathology in lymphoid tissues. In cynomolgus macaques vaccinated with SIVmacC8, no
evidence of detectable superinfection was observed in 3/8 vaccinates following challenge 3 or 20 week s later with
SIVmac32H/L28. Analyses after SIVmac32H/L28 challenge revealed a significant reduction in viral RNA (P<0.001) and DNA
levels between 20 week vaccinates and challenge controls. Amongst 3 week vaccinates, less potent prot ection was
observed. However, analysis of env from breakthrough virus indicated >99% sequence similarity with th e vaccine virus.
Highly sensitive PCR assays that distinguish vaccine and challenge virus stocks demonstrated restimul ation of replication of
the vaccine virus SIVmacC8 in the face of potent protection against a vigorous, homologous challenge virus. Vaccine-induced
antiviral neutralizing antibodies and anti-Nef CD8+ cytotoxic T cell responses did not correlate with the outcome of the
challenge. Defining the mechanism of vaccine protection will need to account for the ef fective control of a genetically closely
related challenge virus whilst remaining unable to suppress replication of the pre-existing vaccine v irus. The role of innate
and intrinsic anti-retroviral immunity in the protection conferred by live attenuated SIV vaccines wa rrants careful study.
PMID: 18753233 [PubMed - indexed for MEDLINE] Free Article
PubMed
U.S. National Library of Medicine
National Institutes of Health
Search: Resistance[Title] AND superinfection[Title] AND vigor ously[Title] AND replicating[Title] AND uncloned[Title]
AND stock[Title] AND simian[Title] AND immunodeficiency[Title]
Publication Types, MeSH Terms, Substances, Grant Support
LinkOut - more resources
References
1 The Recurrent Miscarriage Immunotherapy Trialists Group.
Worldwide collaborative observational analysis on allogenic
leucocyte immunotherapy for recurrent spontaneous abortion.
Am J Reprod Immunol 1994; 32: 55-72.
2 Coulam CB. Immunologic tests in the evaluation of reproductive
disorders: a critical review. Am J Obstet Gynecol 1992; 167: 1844-51.
3 Bulmer JN, Morrison L, Longfellow M, Riston A, Pace D. Granulated
lymphocytes in human endometrium: histochemical and
immunohistochemical studies. Hum Reprod 1991; 6: 791-98.
4 King A, Loke YW. Human trophoblast and JEG choriocarcinoma cells
are sensitive to lysis by IL-2 stimulated decidual NK cells. Cell Immunol
1990; 129: 435-48.
5 Tartof D, Curran JJ, Yang SL, Livingston C. NK cell activity and skin
test antigen stimulation of NK like CMC in vitro are decreased to
different degrees in pregnancy and sarcoidosis. Clin Exp Immunol 1984;
57: 502-10.
6 Higuchi K, Aoki K, Kimbara T, Hosoi N, Yamamoto T, Okada H.
Suppression of natural killer cell activity by monocytes following
immunotherapy for recurrent spontaneous aborters.
Am J Reprod Immunol 1995; 33: 221-27.
7 Clark DA, Chaouat G, Mogil R, Wegmann TG. Prevention of
spontaneous abortion in DBA/2-mated CBA/J mice by GM-CSF
involves CD8+ T cell-dependent suppression of natural effector cell
cytotoxicity against trophoblast target cells. Cell Immunol 1994; 154:
143-52.
8 Toder V, Nebel L, Elrad H, Blank M, Durnada A, Gleicher N. Studies
of natural killer cells in pregnancy II: the immunoregulatory effect of
pregnancy substances. J Clin Lab Immunol 1984; 14: 129-33.
9 Makida R, Minami M, Takamizawa M, Juji T, Fujii T, Mizuno M.
Natural killer cell activity and immunotherapy for recurrent
spontaneous abortion. Lancet 1991; 338: 579-80.
Department of Obstetrics and Gynaecology, Nagoya City University
Medical School, Nagoya, Japan (K Aoki MD, S Kajiura MD,
Y Matsumoto MD, M Ogasawara MD, S Okada MD,
Prof Y Yagami MD); and Center for Human Reproduction and
Foundation for Reproductive Medicine, Chicago, Illinois, USA
(Prof N Gleicher MD)
Correspondence to: Dr Koji Aoki
Protection by attenuated simian
immunodeficiency virus in macaques
against challenge with virus-infected cells
A vaccine against AIDS will probably have to protect
against challenge both by viable virus-infected cells and by
cell-free virus. Eight cynomolgus macaques infected with
attenuated simian immunodeficiency virus (SIV) were
challenged (four each) with cell-free and cell-associated
SIV. All were protected, whereas eight controls were all
Two molecular clones of SIV, called J5 and C8, have
been isolated. They are identical in sequence, except for
seven differences located in the nef gene or the 3’ long-
terminal-repeat. One of these differences is a 12 basepair
deletion, in C8, where the nef gene overlaps the U3 region
of the repeat.3 We have found by PCR and the persistence
of anti-SIV antibodies that J5 and C8 viruses can infect
cynomolgus macaques chronically. However, the C8 virus
expresses an attenuated phenotype in vivo. 2 weeks after
infection, virus is readily reisolated from the blood of C8-
infected or J5-infected animals, but the proportion of
infected lymphocytes is 10-100 times lower in the former.
By 8-12 weeks, reisolation of C8 virus becomes sporadic
and mean antibody titres are 10-fold lower in C8-infected
than in J5-infected macaques. None of the C8-infected
protect
and by
ed with
) were
sociated
were all
at live-
SIV in
require
enuated
potent
by less
e AIDS
virus-
s. The
iciency
In this
mbinant
munity
cloned
chronic
d clone
logous
Using
whether
tection
ction is
ee virus
terminal-repeat. basepair
deletion, in C8, where the nef gene overlaps the U3 region
of the repeat.3 We have found by PCR and the persistence
of anti-SIV antibodies that J5 and C8 viruses can infect
cynomolgus macaques chronically. However, the C8 virus
expresses an attenuated phenotype in vivo. 2 weeks after
infection, virus is readily reisolated from the blood of C8-
infected or J5-infected animals, but the proportion of
infected lymphocytes is 10-100 times lower in the former.
By 8-12 weeks, reisolation of C8 virus becomes sporadic
and mean antibody titres are 10-fold lower in C8-infected
than in J5-infected macaques. None of the C8-infected
animals has developed AIDS-like disease even after 2
years (ref 3 and our data).
Four purpose-bred macaques (L103-L106) were
injected intravenously with 104 median tissue-culture
infective doses (TCIDso) of a titrated stock (from the 9/90
pool) of C8 grown in the human T-cell line C8166.3 All
macaques became infected. Although virus was rarely
isolated by co-cultivation of C8166 cells with 107
peripheral blood mononuclear cells after 8 weeks, proviral
DNA was repeatedly detected by PCR. Antibodies to
recombinant SIV p27 and gpl40 reached a plateau by 12
weeks and persisted (mean loglo ELISA 2-8 [SD 01] and
2-9 [0’3], respectively). Neutralising antibodies against J5
reached titres between loglo 1-8 and 2-7 (mean 2-1 [0-4]).
At 39 weeks after infection with C8, these macaques and
four control animals were challenged with 10 median
infective doses (MID50) of J5M, a cell-free stock of J5
virus, prepared in peripheral blood mononuclear cells
from macaques.3 The course of infection was assessed by
virus recovery and a diagnostic PCR in which a region of
nef is amplified and the two clones J5 and C8 can be
distinguished.4 Virus was recovered from all controls after
challenge but not from the animals that had been
preinfected with C8 (table). After challenge, the nef PCR
identified proviral sequences derived from J5 in all
controls. By contrast, no such sequences were detected in
the blood of macaques previously infected with C8.
Furthermore, no anamnestic antibody responses to SIV
envelope were detected by ELISA with recombinant SIV
gpl40 (Repligen)’ in macaques infected with C8 (table).
The Lancet
Display Settings: Abstract
Arch Virol. 2002 Jun;147(6):1091-104.
Characterization of simian and human immunodeficiency
chimeric viruses re-isolated from vaccinated macaque monkeys
after challenge infection.
Kwofie TB, Miura T, Ibuki K, Enose Y, Suzuki H, Ui M, Kuwata T, Hayami M.
Laboratory of Viral Pathogenesis, Research Center for AIDS, Institute for V irus Research, Kyoto University, Japan.
Abstract
Monkeys that have been vaccinated with nef-deleted SHIVs were either fully or partially protected aga inst challenge with
acute pathogenic SHIV-89.6 P. Viruses isolated from these vaccinated monkeys were all found to be the 89.6 P challenge
virus using PCR amplification and restriction enzyme analysis of the env region of the viruses. Analy sis of the 3'-end of the
env region and 5'-half of the nef region using a heteroduplex mobility assay revealed that the parent al 89.6 P and
re-isolated viruses from unvaccinated 89.6 P-infected monkeys had quite an abundant and similar heter ogeneous
quasispecies population. In contrast, the viruses isolated from the vaccinated monkeys had dif ferent and fewer
quasispecies indicating a selective immune pressure in the vaccinated monkeys. The in vitro replicati on of the viruses
isolated from the vaccinated monkeys in human and macaque peripheral blood mononucular cells (PBMCs) as well as in
established cell lines such as M8166 and HSC-F cells, were slow and delayed when compared to the pare ntal 89.6 P and
re-isolated viruses from unvaccinated 89.6 P-infected monkeys. Further comparison revealed that in HS C-F cells the
viruses from vaccinated monkeys again showed delayed and weak CD4(+) cell down-modulation as well as having little or
no effect on cell growth or cell viability on HSC-F cells and monkey PBMC. Thus we noticed that these re-isolated 89.6 P
viruses from the vaccinated monkeys had changed or had been selected for low pathogenic viruses in th e monkeys. This
suggests that though the vaccination did not completely prevent the replication of the challenge viru s in the monkeys it did
contain the challenge virus by suppressing the pathogenic variants. This further enhances the prospec ts of this nef-deleted
SHIV as the bases for effective anti-HIV vaccine candidates.
PubMed
U.S. National Library of Medicine
National Institutes of Health

34. Experimental Design: Acute infection
3 days 7 days 14 days
vaccination
SHIV89.6
IV
pathogenic
SIVmac239
IVAG6 months
Nx time points for
21 SIV controls
Nx time points for
30 SHIV-vaccinated animals

35. Stone et al, Virology 2009
Fig. 1
Fig. 1
Challenge outcome
Plasma vRNA
7 days PC 14 days PC

36. Stone et al, Virology 2009
Fig. 1
Fig. 1
Challenge outcome
Plasma vRNA
7 days PC 14 days PC

37. Which virus is where?
Digging deeper
11 Tissues
-cervix
-vagina (3)
-Obturator LN
-Inguinal LN
-Iliac LN
-Axillary LN
-Spleen
-Mesenteric LN
-Colon
3 Targets
SIVgag
SIVenv
HIVenv

38. 32357
32365
25907
29372
26817
30886
30851
30616
30811
30831
31298
32664
26820
26833
27076
28415
31631
27373
31371
27130
28843
31475
25988
32330
26960
28850
30906
30933
32427
32578
1
2
3
4
5
6
7
8
9
0d 7d 14d3d
Log10HIVenvRNACopies/mgTissueRNA
Inguinal LN
cervix
vagina 1
vagina 2
vagina 3
Obturator LN
Iliac LN
Axillary LN
Spleen
Mesenteric LN
colon
HIVenv vRNA levels in tissues
SHIV immunized animals

39. 28167
28257
29599
29612
29683
30678
27768
28953
28726
26715
28752
30322
28629
28827
28366
30946
31391
32604
26984
28630
29967
1
2
3
4
5
6
7
8
9
7d 14d3d
Log10SIVenvRNACopies/mgTissueRNA
32357
32365
25907
29372
26817
30886
30851
30616
30811
30831
31298
32664
26820
26833
27076
28415
31631
27373
31371
27130
28843
31475
25988
32330
26960
28850
30906
30933
32427
32578
1
2
3
4
5
6
7
8
9
0d 7d 14d3d
Log10SIVenvRNACopies/mgTissueRNA
cervix
vagina 1
vagina 2
vagina 3
Obturator LN
Inguinal LN
Iliac LN
Axillary LN
Spleen
Mesenteric LN
colon
SIVenv vRNA levels in tissues
SHIV immunized animals
SIV control animals

40. Nx time point for
5 SHIV-immunized animals,
CD8 depleted animals
anti-CD8
(cM T807;
50mg/kg)
Experimental Design: Acute infection
3 days 7 days 14 days
vaccination
SHIV89.6
IV
pathogenic
SIVmac239
IVAG6 months
Nx time points for
21 SIV controls
Nx time points for
30 SHIV-vaccinated animals
Genescà et al J Virology
What role do CD8+ play in vRNA levels and distribution?

41. CD8+ Depleted
Plasma vRNA levels
after vaginal
SIV challenge
SIVgag
SIVenv
Stone et al, Virology 2009
7 days PC 14 days PC

42. SIV replication in tissues 14 days post SIV challenge

43. Conclusions 2:
• Pathogenic challenge virus SIVmac239 is responsible for Vaccine
failure
– Although vaccine virus persists in some tissues, it is not responsible for vaccine failure in
this model.
– No anatomic sites the immune system can’t reach to control SIV replication
• In vaccinated animals that control virus replication, dissemination of
SIV beyond the genital lymph nodes is limited
• CD8+ depletion abrogates protective effect of SHIV immunization
– There is increased SIV replication in CD8- SHIV vaccinated animals in the female genital
tract consistent with an increase in target cells

44. Goals:
AIM 1
• Characterize the replication levels and distribution of vaccine (SHIV
89.6) and challenge (SIVmac239) virus in monkeys prior to and after
challenge.
AIM 2
• Determine relationship between SIV population diversity and viral
replication in control animals and animals that eventually fail vaccine
protection

45. IVAG SIVmac239 challenge outcome in
SHIV89.6 vaccinated female macaques
Apply SGA methods to determine if increase in population
diversity precedes increase in viral replication in animals that
eventually fail vaccine protection

46. Unvaccinated Controls
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9
Weeks Post-Challenge
25537
27578
25301
28433
PlasmaViralLoad(vRNACopies/ml)
Late Vaccine Failure
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9
Weeks Post-Challenge
30474
31411
31416
31413
24767
PlasmaViralLoad(vRNACopies/ml)
Figure 1
SHIV89.6 Vaccinated
SIVmac239 challenged
Rhesus macaques

47. Why env?
• Env has appropriate properties of molecular
biology and immunology for serving as a marker
of genetic diversity
– Tolerates variability without change in biological
properties
– There is no vaccine – induced immune pressure acting
on env in immunized animals, vaccine and challenge
virus are heterologous.

48. SIVmac239 stock

49. Early/late diversity in SIV infected animals
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000

50. Early/late diversity in SIV infected animals
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000

51. Early/late diversity in SHIV vaccinated
SIV infected animals
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000

52. Early/late diversity in SHIV vaccinated
SIV infected animals

53. 27578 30474
239
w
9
Uncoupling
of
replication
and
diversity0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000
27578 control
Weeks Post-Challenge
PlasmaViralLoad(vRNAcopies/ml)
Diversity
0 5 10 15 20 25 30 35
0
1
2
3
4
5
6
7
8
9 0.985
0.990
0.995
1.000
31416
Weeks Post-Challenge
PlasmaViralLoad(vRNAcopies/ml)
Diversity
239
w9
 Viral load,
but purifying
selection keeps
diversity 
 Viral load,
but lack of
competition for
target cells allows
diversity 

54. Early SIVenv diversity
Vx
control
0.0
0.5
1.0
1.5
Diversity
Vx
control
0.0
0.5
1.0
1.5 Early SIVenv Divergence
Divergence
Late SIVenv diversity
Vx
control
0.0
0.5
1.0
1.5
Diversity
Late SIVenv Divergence
Vx
control
0.0
0.5
1.0
1.5
Divergence
p=0.048
SIVenv genetic diversity and divergence in
vaccinated and control rhesus macaques
A.
B.

55. Model of Mucosal Infection (B. Keele)

56. Model of Early Diversification (B. Keele)

57. Model of Mucosal Infection with Pre-existing
Immune selection pressures (modified from B. Keele)
R0=1
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8
CD8

58. Conclusions 3:
– Although plasma vRNA not detected by our assays, some replication must
be occurring to provide substrate that allows generation of breakthrough
variants
– Competition between parental and mutant variants for target cells leads to
purifying selection that accounts for relatively low levels of diversity in
animals with high viral replication
– Conversely, lack of competition between parental and mutant variants for
target cells in animals with low replication levels allows diversity to
accumulate
Regardless of levels of replication, diversity increases over time in all animals
...so a vaccine must block transmission and prevent establishment of systemic
infection after which the viral quasispecies becomes a complex moving target.

59. Thanks to:
Chris Miller
Mike McChesney
Meritxell Genesca
Zhong-Min Ma
Linda Fritts
Vero deSilva
Joe Dutra
Ding Lu
Tracy Rourke
Lili Guo
Primate Services Unit
NIH/NCI
Brandon Keele
UAB
George Shaw
Beatrice Hahn
University of Nottingham
Liz Bailes
University of California-Davis