-
1
-
-
0035967960
-
The Leeuwenhoek Lecture 2001. Animal origins of human infectious disease
-
Weiss RA (2001) The Leeuwenhoek Lecture 2001. Animal origins of human infectious disease. Philos Trans R Soc Lond B Biol Sci 356(1410):957-977.
-
(2001)
Philos Trans R Soc Lond B Biol Sci
, vol.356
, Issue.1410
, pp. 957-977
-
-
Weiss, R.A.1
-
3
-
-
0034732201
-
Viral load and heterosexual transmission of human immunodeficiency virus type 1
-
Quinn TC, et al.; Rakai Project Study Group (2000) Viral load and heterosexual transmission of human immunodeficiency virus type 1. N Engl J Med 342(13):921-929.
-
(2000)
N Engl J Med
, vol.342
, Issue.13
, pp. 921-929
-
-
Quinn, T.C.1
-
4
-
-
0030070991
-
Prognosis in HIV-1 infection predicted by the quantity of virus in plasma
-
Mellors JW, et al. (1996) Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272(5265):1167-1170.
-
(1996)
Science
, vol.272
, Issue.5265
, pp. 1167-1170
-
-
Mellors, J.W.1
-
5
-
-
36849064140
-
Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis
-
Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP (2007) Variation in HIV-1 set-point viral load: Epidemiological analysis and an evolutionary hypothesis. Proc Natl Acad Sci USA 104(44):17441-17446.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.44
, pp. 17441-17446
-
-
Fraser, C.1
Hollingsworth, T.D.2
Chapman, R.3
De Wolf, F.4
Hanage, W.P.5
-
6
-
-
84155168018
-
Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission
-
Herbeck JT, et al. (2012) Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS 26(2):193-205.
-
(2012)
AIDS
, vol.26
, Issue.2
, pp. 193-205
-
-
Herbeck, J.T.1
-
7
-
-
43549109265
-
Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients
-
Goepfert PA, et al. (2008) Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients. J Exp Med 205(5):1009-1017.
-
(2008)
J Exp Med
, vol.205
, Issue.5
, pp. 1009-1017
-
-
Goepfert, P.A.1
-
8
-
-
84870786421
-
Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis
-
Prince JL, et al. (2012) Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLoS Pathog 8(11):e1003041.
-
(2012)
PLoS Pathog
, vol.8
, Issue.11
, pp. e1003041
-
-
Prince, J.L.1
-
9
-
-
84866490075
-
HIV and HLA class I: An evolving relationship
-
Goulder PJR, Walker BD (2012) HIV and HLA class I: An evolving relationship. Immunity 37(3):426-440.
-
(2012)
Immunity
, vol.37
, Issue.3
, pp. 426-440
-
-
Goulder, P.J.R.1
Walker, B.D.2
-
10
-
-
33645240933
-
Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1
-
Martinez-Picado J, et al. (2006) Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J Virol 80(7):3617-3623.
-
(2006)
J Virol
, vol.80
, Issue.7
, pp. 3617-3623
-
-
Martinez-Picado, J.1
-
11
-
-
85047684409
-
Evolution of HLA-B∗5703 HIV-1 escape mutations in HLA-B∗5703-positive individuals and their transmission recipients
-
Crawford H, et al. (2009) Evolution of HLA-B∗5703 HIV-1 escape mutations in HLA-B∗5703-positive individuals and their transmission recipients. J Exp Med 206(4):909-921.
-
(2009)
J Exp Med
, vol.206
, Issue.4
, pp. 909-921
-
-
Crawford, H.1
-
12
-
-
84875527661
-
Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins
-
Boutwell CL, et al. (2013) Frequent and variable cytotoxic-T-lymphocyte escape-associated fitness costs in the human immunodeficiency virus type 1 subtype B Gag proteins. J Virol 87(7):3952-3965.
-
(2013)
J Virol
, vol.87
, Issue.7
, pp. 3952-3965
-
-
Boutwell, C.L.1
-
13
-
-
63949087100
-
Adaptation of HIV-1 to human leukocyte antigen class I
-
Kawashima Y, et al. (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458(7238):641-645.
-
(2009)
Nature
, vol.458
, Issue.7238
, pp. 641-645
-
-
Kawashima, Y.1
-
14
-
-
84873042035
-
Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in Japan
-
Nomura S, et al. (2013) Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in Japan. J Virol 87(3):1465-1476.
-
(2013)
J Virol
, vol.87
, Issue.3
, pp. 1465-1476
-
-
Nomura, S.1
-
15
-
-
77954059111
-
HIV-1 transmitting couples have similar viral load setpoints in Rakai, Uganda
-
Hollingsworth TD, et al. (2010) HIV-1 transmitting couples have similar viral load setpoints in Rakai, Uganda. PLoS Pathog 6(5):e1000876.
-
(2010)
PLoS Pathog
, vol.6
, Issue.5
, pp. e1000876
-
-
Hollingsworth, T.D.1
-
16
-
-
77950927522
-
HIV RNA level in early infection is predicted by viral load in the transmission source
-
Hecht FM, et al. (2010) HIV RNA level in early infection is predicted by viral load in the transmission source. AIDS 24(7):941-945.
-
(2010)
AIDS
, vol.24
, Issue.7
, pp. 941-945
-
-
Hecht, F.M.1
-
17
-
-
77957194223
-
Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: Associations with HLA type and clinical parameters
-
Wright JK, et al. (2010) Gag-protease-mediated replication capacity in HIV-1 subtype C chronic infection: Associations with HLA type and clinical parameters. J Virol 84(20):10820-10831.
-
(2010)
J Virol
, vol.84
, Issue.20
, pp. 10820-10831
-
-
Wright, J.K.1
-
18
-
-
58149398654
-
HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1
-
Miura T, et al. (2009) HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1. J Virol 83(1):140-149.
-
(2009)
J Virol
, vol.83
, Issue.1
, pp. 140-149
-
-
Miura, T.1
-
19
-
-
78049495989
-
Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection
-
Brockman MA, et al. (2010) Early selection in Gag by protective HLA alleles contributes to reduced HIV-1 replication capacity that may be largely compensated for in chronic infection. J Virol 84(22):11937-11949.
-
(2010)
J Virol
, vol.84
, Issue.22
, pp. 11937-11949
-
-
Brockman, M.A.1
-
20
-
-
79955533328
-
Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations
-
Huang KH, et al.; Bloemfontein-Oxford Collaborative Group (2011) Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS ONE 6(4):e19018.
-
(2011)
PLoS ONE
, vol.6
, Issue.4
, pp. e19018
-
-
Huang, K.H.1
-
21
-
-
84905491726
-
-
Available at Accessed July 1, 2014
-
World Health Organization (2014) Consolidated ARV guidelines 2013. Available at www.who.int/hiv/pub/guidelines/arv2013/art/statartadolescents-rationale/en/index.htm. Accessed July 1, 2014.
-
(2014)
Consolidated ARV Guidelines 2013
-
-
World Health Organization1
-
22
-
-
80051633217
-
Prevention of HIV-1 infection with early antiretroviral therapy
-
Cohen MS, et al.; HPTN 052 Study Team (2011) Prevention of HIV-1 infection with early antiretroviral therapy. N Engl J Med 365(6):493-505.
-
(2011)
N Engl J Med
, vol.365
, Issue.6
, pp. 493-505
-
-
Cohen, M.S.1
-
23
-
-
84904915806
-
Global update on HIV treatment 2013
-
Available at Accessed July 1, 2014
-
WHO Report in partnership with UNICEF and UNAIDS (2013) Global update on HIV treatment 2013. Available at apps.who.int/iris/bitstream/10665/85326/1/9789241505734-eng.pdf. Accessed July 1, 2014.
-
(2013)
WHO Report in Partnership with UNICEF and UNAIDS
-
-
-
24
-
-
84918525070
-
-
Available at Accessed July 1, 2014
-
AVERT (2014) HIV & AIDS in South Africa. Available at www.avert.org/hiv-aids-southafrica.htm. Accessed July 1, 2014.
-
(2014)
HIV & AIDS in South Africa
-
-
-
25
-
-
85067711777
-
-
Available at . Accessed July 1, 2014
-
The World Bank (2014) Data. Available at data.worldbank.org. Accessed July 1, 2014.
-
(2014)
-
-
The World Bank1
-
26
-
-
84861325273
-
Widespread impact of HLA restriction on immune control and escape pathways of HIV-1
-
Carlson JM, et al. (2012) Widespread impact of HLA restriction on immune control and escape pathways of HIV-1. J Virol 86(9):5230-5243.
-
(2012)
J Virol
, vol.86
, Issue.9
, pp. 5230-5243
-
-
Carlson, J.M.1
-
27
-
-
10644267588
-
Dominant influence of HLA-B in mediating the potential coevolution of HIV and HLA
-
Kiepiela P, et al. (2004) Dominant influence of HLA-B in mediating the potential coevolution of HIV and HLA. Nature 432(7018):769-775.
-
(2004)
Nature
, vol.432
, Issue.7018
, pp. 769-775
-
-
Kiepiela, P.1
-
28
-
-
77956827161
-
Additive contribution of HLA class I alleles in the immune control of HIV-1 infection
-
Leslie A, et al. (2010) Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. J Virol 84(19):9879-9888.
-
(2010)
J Virol
, vol.84
, Issue.19
, pp. 9879-9888
-
-
Leslie, A.1
-
29
-
-
48749103238
-
Impact of MHC class I diversity on immune control of immunodeficiency virus replication
-
Goulder PJR, Watkins DI (2008) Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol 8(8):619-630.
-
(2008)
Nat Rev Immunol
, vol.8
, Issue.8
, pp. 619-630
-
-
Goulder, P.J.R.1
Watkins, D.I.2
-
30
-
-
50149117938
-
Central role of reverting mutations in HLA associations with human immunodeficiency virus set point
-
Matthews PC, et al. (2008) Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J Virol 82(17):8548-8559.
-
(2008)
J Virol
, vol.82
, Issue.17
, pp. 8548-8559
-
-
Matthews, P.C.1
-
31
-
-
72849140105
-
Replicative capacity of human immunodeficiency virus type 1 transmitted from mother to child is associated with pediatric disease progression rate
-
Prado JG, et al. (2010) Replicative capacity of human immunodeficiency virus type 1 transmitted from mother to child is associated with pediatric disease progression rate. J Virol 84(1):492-502.
-
(2010)
J Virol
, vol.84
, Issue.1
, pp. 492-502
-
-
Prado, J.G.1
-
32
-
-
0344845200
-
Gradual adaptation of HIV to human host populations: Good or bad news?
-
Brander C, Walker BD (2003) Gradual adaptation of HIV to human host populations: Good or bad news? Nat Med 9(11):1359-1362.
-
(2003)
Nat Med
, vol.9
, Issue.11
, pp. 1359-1362
-
-
Brander, C.1
Walker, B.D.2
-
33
-
-
64049111619
-
Transmission and long-term stability of compensated CD8 escape mutations
-
Schneidewind A, et al. (2009) Transmission and long-term stability of compensated CD8 escape mutations. J Virol 83(8):3993-3997.
-
(2009)
J Virol
, vol.83
, Issue.8
, pp. 3993-3997
-
-
Schneidewind, A.1
-
34
-
-
34547138161
-
Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B∗5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection
-
Crawford H, et al. (2007) Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B∗5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J Virol 81(15):8346-8351.
-
(2007)
J Virol
, vol.81
, Issue.15
, pp. 8346-8351
-
-
Crawford, H.1
-
35
-
-
79251491677
-
Modelling the evolution and spread of HIV immune escape mutants
-
Fryer HR, et al.; SPARTAC Trial Investigators (2010) Modelling the evolution and spread of HIV immune escape mutants. PLoS Pathog 6(11):e1001196.
-
(2010)
PLoS Pathog
, vol.6
, Issue.11
, pp. e1001196
-
-
Fryer, H.R.1
-
36
-
-
80052396244
-
Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic
-
Schellens IM, et al. (2011) Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic. AIDS 25(14):1691-1700.
-
(2011)
AIDS
, vol.25
, Issue.14
, pp. 1691-1700
-
-
Schellens, I.M.1
-
37
-
-
84901335748
-
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic
-
Cotton LA, et al. (2014) Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet 10(4):e1004295.
-
(2014)
PLoS Genet
, vol.10
, Issue.4
, pp. e1004295
-
-
Cotton, L.A.1
-
38
-
-
79551672781
-
-
Available at Accessed July 1, 2014
-
UNAIDS (2013) Global Report: UNAIDS report on the global AIDS epidemic 2013. Available at www.unaids.org/en/media/unaids/contentassets/documents/epidemiology/2013/gr2013/UNAIDS-Global-Report-2013-en.pdf. Accessed July 1, 2014.
-
(2013)
Global Report: UNAIDS Report on the Global AIDS Epidemic 2013
-
-
UNAIDS1
-
39
-
-
84860725970
-
Access to antiretroviral treatment in South Africa, 2004-2011
-
Johnson LF (2012) Access to antiretroviral treatment in South Africa, 2004-2011. South Afr J HIV Med 13(1):22-26.
-
(2012)
South Afr J HIV Med
, vol.13
, Issue.1
, pp. 22-26
-
-
Johnson, L.F.1
-
40
-
-
20244368227
-
Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda
-
Wawer MJ, et al. (2005) Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda. J Infect Dis 191(9):1403-1409.
-
(2005)
J Infect Dis
, vol.191
, Issue.9
, pp. 1403-1409
-
-
Wawer, M.J.1
-
41
-
-
84859729459
-
Concurrent partnerships, acute infection and HIV epidemic dynamics among young adults in Zimbabwe
-
Goodreau SM, et al. (2012) Concurrent partnerships, acute infection and HIV epidemic dynamics among young adults in Zimbabwe. AIDS Behav 16(2):312-322.
-
(2012)
AIDS Behav
, vol.16
, Issue.2
, pp. 312-322
-
-
Goodreau, S.M.1
-
42
-
-
82755164385
-
Role of acute infection in HIV transmission - Authors' reply
-
Powers KA, et al. (2011) Role of acute infection in HIV transmission - Authors' reply. Lancet 378:1914.
-
(2011)
Lancet
, vol.378
, pp. 1914
-
-
Powers, K.A.1
-
43
-
-
0035857959
-
Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda
-
Gray RH, et al.; Rakai Project Team (2001) Probability of HIV-1 transmission per coital act in monogamous, heterosexual, HIV-1-discordant couples in Rakai, Uganda. Lancet 357(9263):1149-1153.
-
(2001)
Lancet
, vol.357
, Issue.9263
, pp. 1149-1153
-
-
Gray, R.H.1
-
44
-
-
33846101731
-
CD8+ T-cell responses to different HIV proteins have discordant associations with viral load
-
Kiepiela P, et al. (2007) CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat Med 13(1):46-53.
-
(2007)
Nat Med
, vol.13
, Issue.1
, pp. 46-53
-
-
Kiepiela, P.1
-
45
-
-
79956209349
-
HLA-A∗7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B∗5703
-
Matthews PC, et al. (2011) HLA-A∗7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B∗5703. J Immunol 186(10):5675-5686.
-
(2011)
J Immunol
, vol.186
, Issue.10
, pp. 5675-5686
-
-
Matthews, P.C.1
-
46
-
-
77953725982
-
Antiretroviral regimens in pregnancy and breast-feeding in Botswana
-
Shapiro RL, et al. (2010) Antiretroviral regimens in pregnancy and breast-feeding in Botswana. N Engl J Med 362(24):2282-2294.
-
(2010)
N Engl J Med
, vol.362
, Issue.24
, pp. 2282-2294
-
-
Shapiro, R.L.1
-
47
-
-
34247203565
-
Common and well-documented HLA alleles: Report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics
-
Cano P, et al. (2007) Common and well-documented HLA alleles: Report of the Ad-Hoc committee of the american society for histocompatiblity and immunogenetics. Hum Immunol 68(5):392-417.
-
(2007)
Hum Immunol
, vol.68
, Issue.5
, pp. 392-417
-
-
Cano, P.1
-
48
-
-
20244373940
-
Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA
-
Leslie A, et al. (2005) Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med 201(6):891-902.
-
(2005)
J Exp Med
, vol.201
, Issue.6
, pp. 891-902
-
-
Leslie, A.1
-
49
-
-
57149090493
-
Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag
-
Carlson JM, et al. (2008) Phylogenetic dependency networks: Inferring patterns of CTL escape and codon covariation in HIV-1 Gag. PLOS Comput Biol 4(11):e1000225.
-
(2008)
PLOS Comput Biol
, vol.4
, Issue.11
, pp. e1000225
-
-
Carlson, J.M.1
-
50
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100(16):9440-9445.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.16
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
52
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
-
Guindon S, et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol 59(3):307-321.
-
(2010)
Syst Biol
, vol.59
, Issue.3
, pp. 307-321
-
-
Guindon, S.1
-
53
-
-
15844406550
-
HyPhy: Hypothesis testing using phylogenies
-
Pond SL, Frost SD, Muse SV (2005) HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21:676-679.
-
(2005)
Bioinformatics
, vol.21
, pp. 676-679
-
-
Pond, S.L.1
Frost, S.D.2
Muse, S.V.3
-
54
-
-
77953156810
-
Solving differential equations in R: Package deSolve
-
Soetaert K, Petzoldt T, Setzer R (2010) Solving differential equations in R: Package deSolve. J Stat Softw 33(9):1-25.
-
(2010)
J Stat Softw
, vol.33
, Issue.9
, pp. 1-25
-
-
Soetaert, K.1
Petzoldt, T.2
Setzer, R.3
|