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Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality.

Skar H, Gutenkunst RN, Wilbe Ramsay K, Alaeus A, Albert J, Leitner T.

PLoS One. 2011;6(8):e21747. doi: 10.1371/journal.pone.0021747. Epub 2011 Aug 2.


Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease.

Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM.

J Virol. 1997 Jan;71(1):663-77.


Lack of temporal structure in the short term HIV-1 evolution within asymptomatic naïve patients.

Bello G, Casado C, García S, Rodríguez C, del Romero J, Carvajal-Rodriguez A, Posada D, López-Galíndez C.

Virology. 2007 Jun 5;362(2):294-303. Epub 2007 Jan 31.


Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection.

Shriner D, Shankarappa R, Jensen MA, Nickle DC, Mittler JE, Margolick JB, Mullins JI.

Genetics. 2004 Mar;166(3):1155-64.


The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin.

Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz PN, Girard M, Shaw GM, Hahn BH, Sharp PM.

J Virol. 1996 Oct;70(10):7013-29.


Evolution of subtype C HIV-1 Env in a slowly progressing Zambian infant.

Zhang H, Hoffmann F, He J, He X, Kankasa C, Ruprecht R, West JT, Orti G, Wood C.

Retrovirology. 2005 Nov 7;2:67.


RT-SHIV subpopulation dynamics in infected macaques during anti-HIV therapy.

Shao W, Kearney M, Maldarelli F, Mellors JW, Stephens RM, Lifson JD, KewalRamani VN, Ambrose Z, Coffin JM, Palmer SE.

Retrovirology. 2009 Nov 4;6:101. doi: 10.1186/1742-4690-6-101.


Genetic analyses reveal structured HIV-1 populations in serially sampled T lymphocytes of patients receiving HAART.

Potter SJ, Lemey P, Dyer WB, Sullivan JS, Chew CB, Vandamme AM, Dwyer DE, Saksena NK.

Virology. 2006 Apr 25;348(1):35-46. Epub 2006 Feb 7.


Phylogenetic reconstruction of a known HIV-1 CRF04_cpx transmission network using maximum likelihood and Bayesian methods.

Paraskevis D, Magiorkinis E, Magiorkinis G, Kiosses VG, Lemey P, Vandamme AM, Rambaut A, Hatzakis A.

J Mol Evol. 2004 Nov;59(5):709-17.


Human immunodeficiency virus type 1 genetic evolution in patients with prolonged suppression of plasma viremia.

Martínez MA, Cabana M, Ibáñez A, Clotet B, Arnó A, Ruiz L.

Virology. 1999 Apr 10;256(2):180-7.


Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression.

Williamson S.

Mol Biol Evol. 2003 Aug;20(8):1318-25. Epub 2003 May 30.


Intra-host evolutionary rates in HIV-1C env and gag during primary infection.

Novitsky V, Wang R, Rossenkhan R, Moyo S, Essex M.

Infect Genet Evol. 2013 Oct;19:361-8. doi: 10.1016/j.meegid.2013.02.023. Epub 2013 Mar 20.


Host-specific modulation of the selective constraints driving human immunodeficiency virus type 1 env gene evolution.

Bagnarelli P, Mazzola F, Menzo S, Montroni M, Butini L, Clementi M.

J Virol. 1999 May;73(5):3764-77.


Long-term intrapatient viral evolution during HIV-2 infection.

MacNeil A, Sankale JL, Meloni ST, Sarr AD, Mboup S, Kanki P.

J Infect Dis. 2007 Mar 1;195(5):726-33. Epub 2007 Jan 18.


Intercompartmental recombination of HIV-1 contributes to env intrahost diversity and modulates viral tropism and sensitivity to entry inhibitors.

Brown RJ, Peters PJ, Caron C, Gonzalez-Perez MP, Stones L, Ankghuambom C, Pondei K, McClure CP, Alemnji G, Taylor S, Sharp PM, Clapham PR, Ball JK.

J Virol. 2011 Jun;85(12):6024-37. doi: 10.1128/JVI.00131-11. Epub 2011 Apr 6.


Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster.

Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM.

Mol Phylogenet Evol. 2014 Jun;75:126-37. doi: 10.1016/j.ympev.2014.02.022. Epub 2014 Feb 28.

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