Genetic variation in mother-child acute seroconverter pairs from Zambia

AIDS

Volumn 22, Issue 7, 2008, Pages 817-824

  Hoffmann, Federico G ^a   He, Xiang ^a,d   West, John T ^a,e   Lemey, Philippe ^b   Kankasa, Chipepo ^c   Wood, Charles ^a  

^a UNIVERSITY OF NEBRASKA   (United States)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF ZAMBIA   (Zambia)

^d CAIDS   (China)

^e UNIVERSITY OF OKLAHOMA HEALTH SCIENCES CENTER   (United States)

Author keywords

Acute infection; Genetic analysis; HIV; Mother to child transmission

Indexed keywords

VIRUS ENVELOPE PROTEIN;

ADULT; ARTICLE; CONTROLLED STUDY; FEMALE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOTYPE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INFANT; MAJOR CLINICAL STUDY; MALE; MOLECULAR EVOLUTION; MOTHER CHILD RELATION; PHYLOGENY; PRIORITY JOURNAL; SEROCONVERSION; VIRUS TRANSMISSION; ZAMBIA;

ADULT; BREAST FEEDING; DISEASE TRANSMISSION, VERTICAL; EVOLUTION, MOLECULAR; FEMALE; FOLLOW-UP STUDIES; GENES, ENV; HIV SEROPOSITIVITY; HIV-1; HUMANS; INFANT; MALE; PHYLOGENY; PREGNANCY; SEQUENCE ANALYSIS, PROTEIN; VARIATION (GENETICS); ZAMBIA;

EID: 42449134402     PISSN: 02699370     EISSN: None     Source Type: Journal    
DOI: 10.1097/QAD.0b013e3282f486af     Document Type: Article

References (33)

1. Kaufmann GR, Cunningham P, Kelleher AD, Zaunders J, Carr A, Vizzard J, et al. Patterns of viral dynamics during primary human immunodeficiency virus type 1 infection. The Sydney Primary HIV Infection Study Group. J Infect Dis 1998; 178:1812-1815.
2. Little SJ, McLean AR, Spina CA, Richman DD, Havlir DV. Viral dynamics of acute HIV-1 infection. J Exp Med 1999; 190:841-850.
3. Pilcher CD, Shugars DC, Fiscus SA, Miller WC, Menezes P, Giner J, et al. HIV in body fluids during primary HIV infection: implications for pathogenesis, treatment and public health. AIDS 2001; 15:837-845.
4. Pilcher CD, Eron JJ Jr, Galvin S, Gay C, Cohen MS. Acute HIV revisited: new opportunities for treatment and prevention. J Clin Invest 2004; 113:937-945.
5. Wawer MJ, Gray RH, Sewankambo NK, Serwadda D, Li X, Laeyendecker O, et al. Rates of HIV-1 transmission per coital act, by stage of HIV-1 infection, in Rakai, Uganda. J Infect Dis 2005; 191:1403-1409.
6. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, et al. Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004; 303:2019-2022.
7. Scarlatti G, Leitner T, Halapi E, Wahlberg J, Marchisio P, Clerici-Schoeller MA, et al. Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers. Proc Natl Acad Sci USA 1993; 90:1721-1725.
8. Wolinsky SM, Wike CM, Korber BT, Hutto C, Parks WP, Rosenblum LL, et al. Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science 1992; 255:1134-1137.
9. Zhang H, Hoffmann F, He J, He X, Kankasa C, West JT, et al. Characterization of HIV-1 subtype C envelope glycoproteins from perinatally infected children with different courses of disease. Retrovirology 2006; 3:73.
10. Verhofstede C, Demecheleer E, De Cabooter N, Gaillard P, Mwanyumba F, Claeys P, et al. Diversity of the human immunodeficiency virus type 1 (HIV-1) env sequence after vertical transmission in mother-child pairs infected with HIV-1 subtype A. J Virol 2003; 77:3050-3057.
11. Edwards CT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ. Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1. BMC Evol Biol 2006; 6:28.
12. Pasquier C, Cayrou C, Blancher A, Tourne-Petheil C, Berrebi A, Tricoire J, et al. Molecular evidence for mother-to-child transmission of multiple variants by analysis of RNA and DNA sequences of human immunodeficiency virus type 1. J Virol 1998; 72:8493-8501.
13. Lamers SL, Sleasman JW, She JX, Barrie KA, Pomeroy SM, Barrett DJ, Goodenow MM. Persistence of multiple maternal genotypes of human immunodeficiency virus type 1 in infants infected by vertical transmission. J Clin Invest 1994; 93:380-390.
14. Frost SD, Liu Y, Pond SL, Chappey C, Wrin T, Petropoulos CJ, et al. Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol 2005; 79:6523-6527.
15. Yun Z, Fredriksson E, Sonnerborg A. Quantification of human immunodeficiency virus type 1 proviral DNA by the TaqMan real-time PCR assay. J Clin Microbiol 2002; 40:3883-3884.
16. Brayfield BP, Kankasa C, West JT, Muyanga J, Bhat G, Klaskala W, et al. Distribution of Kaposi sarcoma-associated herpes-virus/human herpesvirus 8 in maternal saliva and breast milk in Zambia: implications for transmission. J Infect Dis 2004; 189:2260-2270.
17. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994; 22:4673-4680.
18. Kumar S, Tamura K, Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 2004; 5:150-163.
19. Jobb G, von Haeseler A, Strimmer K. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 2004; 4:18.
20. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19:1572-1574.
21. Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005; 22:1208-1222.
22. Pond SL, Frost SD, Grossman Z, Gravenor MB, Richman DD, Brown AJ. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol 2006; 2:e62.
23. Lemey P, Kosakovsky Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, et al. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol 2007; 3:e29.
24. Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002; 51:492-508.
25. Zhang H, Hoffmann F, He J, He X, Kankasa C, Ruprecht R, et al. Evolution of subtype C HIV-1 Env in a slowly progressing Zambian infant. Retrovirology 2005; 2:67.
26. Wu X, Parast AB, Richardson BA, Nduati R, John-Stewart G, Mbori-Ngacha D, et al. Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. J Virol 2006; 80:835-844.
27. Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999; 73:10489-10502.
28. Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM. Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease. J Virol 1997; 71:663-677.
29. Ross HA, Rodrigo AG. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J Virol 2002; 76:11715-11720.
30. Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol Biol Evol 2003; 20:1318-1325.
31. Salvatori F, Masiero S, Giaquinto C, Wade CM, Brown AJ, Chieco-Bianchi L, De Rossi A. Evolution of human immunodeficiency virus type 1 in perinatally infected infants with rapid and slow progression to disease. J Virol 1997; 71:4694-4706.
32. Huber M, Trkola A. Humoral immunity to HIV-1: neutralization and beyond. J Intern Med 2007; 262:5-25.
33. Ostrowski MA, Yu Q, Yue FY, Liu J, Jones B, Gu XX, et al. Why can't the immune system control HIV-1? Defining HIV-1-specific CD4+ T cell immunity in order to develop strategies to enhance viral immunity. Immunol Res 2006; 35:89-102.