{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T12:00:17Z","timestamp":1791892817633,"version":"4.3.4"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Virol J"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The Sydney blood bank cohort (SBBC) of long-term survivors consists of multiple individuals infected with attenuated, <jats:italic>nef<\/jats:italic>-deleted variants of human immunodeficiency virus type 1 (HIV-1) acquired from a single source. Long-term prospective studies have demonstrated that the SBBC now comprises slow progressors (SP) as well as long-term nonprogressors (LTNP). Convergent evolution of <jats:italic>nef<\/jats:italic> sequences in SBBC SP and LTNP indicates the <jats:italic>in vivo<\/jats:italic> pathogenicity of HIV-1 in SBBC members is dictated by factors other than <jats:italic>nef<\/jats:italic>. To better understand mechanisms underlying the pathogenicity of <jats:italic>nef<\/jats:italic>-deleted HIV-1, we examined the phenotype and <jats:italic>env<\/jats:italic> sequence diversity of sequentially isolated viruses (n = 2) from 3 SBBC members.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The viruses characterized here were isolated from two SP spanning a three or six year period during progressive HIV-1 infection (subjects D36 and C98, respectively) and from a LTNP spanning a two year period during asymptomatic, nonprogressive infection (subject C18). Both isolates from D36 were R5X4 phenotype and, compared to control HIV-1 strains, replicated to low levels in peripheral blood mononuclear cells (PBMC). In contrast, both isolates from C98 and C18 were CCR5-restricted. Both viruses isolated from C98 replicated to barely detectable levels in PBMC, whereas both viruses isolated from C18 replicated to low levels, similar to those isolated from D36. Analysis of <jats:italic>env<\/jats:italic> by V1V2 and V3 heteroduplex tracking assay, V1V2 length polymorphisms, sequencing and phylogenetic analysis showed distinct intra- and inter-patient <jats:italic>env<\/jats:italic> evolution.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Independent evolution of <jats:italic>env<\/jats:italic> despite convergent evolution of <jats:italic>nef<\/jats:italic> may contribute to the <jats:italic>in vivo<\/jats:italic> pathogenicity of <jats:italic>nef<\/jats:italic>-deleted HIV-1 in SBBC members, which may not necessarily be associated with changes in replication capacity or viral coreceptor specificity.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1743-422x-4-75","type":"journal-article","created":{"date-parts":[[2007,7,17]],"date-time":"2007-07-17T06:14:44Z","timestamp":1184652884000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Phenotype and envelope gene diversity of nef-deleted HIV-1 isolated from long-term survivors infected from a single source"],"prefix":"10.1186","volume":"4","author":[{"given":"Lachlan","family":"Gray","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa J","family":"Churchill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasminka","family":"Sterjovski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristie","family":"Witlox","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer C","family":"Learmont","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John S","family":"Sullivan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven L","family":"Wesselingh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dana","family":"Gabuzda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony L","family":"Cunningham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dale A","family":"McPhee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul R","family":"Gorry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2007,7,16]]},"reference":[{"issue":"5238","key":"288_CR1","doi-asserted-by":"publisher","first-page":"988","DOI":"10.1126\/science.270.5238.988","volume":"270","author":"NJ Deacon","year":"1995","unstructured":"Deacon NJ, Tsykin A, Solomon A, Smith K, Ludford-Menting M, Hooker DJ, McPhee DA, Greenway AL, Ellett A, Chatfield C, et al.: Genomic structure of an attenuated quasi species of HIV-1 from a blood transfusion donor and recipients. Science 1995,270(5238):988-991. 10.1126\/science.270.5238.988","journal-title":"Science"},{"issue":"8824","key":"288_CR2","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1016\/0140-6736(92)93281-Q","volume":"340","author":"J Learmont","year":"1992","unstructured":"Learmont J, Tindall B, Evans L, Cunningham A, Cunningham P, Wells J, Penny R, Kaldor J, Cooper DA: Long-term symptomless HIV-1 infection in recipients of blood products from a single donor. Lancet 1992,340(8824):863-867. 10.1016\/0140-6736(92)93281-Q","journal-title":"Lancet"},{"issue":"22","key":"288_CR3","doi-asserted-by":"publisher","first-page":"1715","DOI":"10.1056\/NEJM199906033402203","volume":"340","author":"JC Learmont","year":"1999","unstructured":"Learmont JC, Geczy AF, Mills J, Ashton LJ, Raynes-Greenow CH, Garsia RJ, Dyer WB, McIntyre L, Oelrichs RB, Rhodes DI, Deacon NJ, Sullivan JS: Immunologic and virologic status after 14 to 18 years of infection with an attenuated strain of HIV-1. A report from the Sydney Blood Bank Cohort. N Engl J Med 1999,340(22):1715-1722. 10.1056\/NEJM199906033402203","journal-title":"N Engl J Med"},{"issue":"2","key":"288_CR4","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1128\/JVI.80.2.1047-1052.2006","volume":"80","author":"MJ Churchill","year":"2006","unstructured":"Churchill MJ, Rhodes DI, Learmont JC, Sullivan JS, Wesselingh SL, Cooke IR, Deacon NJ, Gorry PR: Longitudinal analysis of human immunodeficiency virus type 1 nef\/long terminal repeat sequences in a cohort of long-term survivors infected from a single source. J Virol 2006,80(2):1047-1052. 10.1128\/JVI.80.2.1047-1052.2006","journal-title":"J Virol"},{"issue":"1","key":"288_CR5","doi-asserted-by":"publisher","first-page":"53","DOI":"10.2174\/1570162052772951","volume":"3","author":"PR Gorry","year":"2005","unstructured":"Gorry PR, Churchill M, Crowe SM, Cunningham AL, Gabuzda D: Pathogenesis of macrophage tropic HIV. Curr HIV Res 2005,3(1):53-60. 10.2174\/1570162052772951","journal-title":"Curr HIV Res"},{"key":"288_CR6","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1146\/annurev.immunol.17.1.657","volume":"17","author":"EA Berger","year":"1999","unstructured":"Berger EA, Murphy PM, Farber JM: Chemokine receptors as HIV-1 coreceptors: roles in viral entry, tropism, and disease. Annu Rev Immunol 1999, 17: 657-700. 10.1146\/annurev.immunol.17.1.657","journal-title":"Annu Rev Immunol"},{"issue":"21","key":"288_CR7","doi-asserted-by":"publisher","first-page":"2677","DOI":"10.1101\/gad.833300","volume":"14","author":"RW Doms","year":"2000","unstructured":"Doms RW, Trono D: The plasma membrane as a combat zone in the HIV battlefield. Genes Dev 2000,14(21):2677-2688. 10.1101\/gad.833300","journal-title":"Genes Dev"},{"issue":"5270","key":"288_CR8","doi-asserted-by":"publisher","first-page":"1955","DOI":"10.1126\/science.272.5270.1955","volume":"272","author":"G Alkhatib","year":"1996","unstructured":"Alkhatib G, Combadiere C, Broder CC, Feng Y, Kennedy PE, Murphy PM, Berger EA: CC CKR5: a RANTES, MIP-1alpha, MIP-1beta receptor as a fusion cofactor for macrophage-tropic HIV-1. Science 1996,272(5270):1955-1958. 10.1126\/science.272.5270.1955","journal-title":"Science"},{"issue":"7","key":"288_CR9","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1016\/S0092-8674(00)81313-6","volume":"85","author":"H Choe","year":"1996","unstructured":"Choe H, Farzan M, Sun Y, Sullivan N, Rollins B, Ponath PD, Wu L, Mackay CR, LaRosa G, Newman W, Gerard N, Gerard C, Sodroski J: The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 1996,85(7):1135-1148. 10.1016\/S0092-8674(00)81313-6","journal-title":"Cell"},{"issue":"6584","key":"288_CR10","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/381661a0","volume":"381","author":"H Deng","year":"1996","unstructured":"Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR: Identification of a major co-receptor for primary isolates of HIV-1. Nature 1996,381(6584):661-666. 10.1038\/381661a0","journal-title":"Nature"},{"issue":"7","key":"288_CR11","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1016\/S0092-8674(00)81314-8","volume":"85","author":"BJ Doranz","year":"1996","unstructured":"Doranz BJ, Rucker J, Yi Y, Smyth RJ, Samson M, Peiper SC, Parmentier M, Collman RG, Doms RW: A dual-tropic primary HIV-1 isolate that uses fusin and the beta-chemokine receptors CKR-5, CKR-3, and CKR-2b as fusion cofactors. Cell 1996,85(7):1149-1158. 10.1016\/S0092-8674(00)81314-8","journal-title":"Cell"},{"issue":"6584","key":"288_CR12","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1038\/381667a0","volume":"381","author":"T Dragic","year":"1996","unstructured":"Dragic T, Litwin V, Allaway GP, Martin SR, Huang Y, Nagashima KA, Cayanan C, Maddon PJ, Koup RA, Moore JP, Paxton WA: HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5. Nature 1996,381(6584):667-673. 10.1038\/381667a0","journal-title":"Nature"},{"issue":"5263","key":"288_CR13","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1126\/science.272.5263.872","volume":"272","author":"Y Feng","year":"1996","unstructured":"Feng Y, Broder CC, Kennedy PE, Berger EA: HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science 1996,272(5263):872-877. 10.1126\/science.272.5263.872","journal-title":"Science"},{"issue":"10","key":"288_CR14","doi-asserted-by":"crossref","first-page":"7478","DOI":"10.1128\/jvi.71.10.7478-7487.1997","volume":"71","author":"A Bjorndal","year":"1997","unstructured":"Bjorndal A, Deng H, Jansson M, Fiore JR, Colognesi C, Karlsson A, Albert J, Scarlatti G, Littman DR, Fenyo EM: Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype. Journal of Virology 1997,71(10):7478-7487.","journal-title":"Journal of Virology"},{"issue":"4","key":"288_CR15","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1084\/jem.185.4.621","volume":"185","author":"RI Connor","year":"1997","unstructured":"Connor RI, Sheridan KE, Ceradini D, Choe S, Landau NR: Change in coreceptor use coreceptor use correlates with disease progression in HIV-1--infected individuals. Journal of Experimental Medicine 1997,185(4):621-628. 10.1084\/jem.185.4.621","journal-title":"Journal of Experimental Medicine"},{"issue":"6","key":"288_CR16","first-page":"325","volume":"2","author":"M Jansson","year":"1999","unstructured":"Jansson M, Backstrom E, Bjorndal A, Holmberg V, Rossi P, Fenyo EM, Popovic M, Albert J, Wigzell H: Coreceptor usage and RANTES sensitivity of non-syncytium-inducing HIV-1 isolates obtained from patients with AIDS. J Hum Virol 1999,2(6):325-338.","journal-title":"J Hum Virol"},{"issue":"4","key":"288_CR17","doi-asserted-by":"publisher","first-page":"1106","DOI":"10.1086\/314987","volume":"180","author":"AM de Roda Husman","year":"1999","unstructured":"de Roda Husman AM, van Rij RP, Blaak H, Broersen S, Schuitemaker H: Adaptation to promiscuous usage of chemokine receptors is not a prerequisite for human immunodeficiency virus type 1 disease progression. J Infect Dis 1999,180(4):1106-1115. 10.1086\/314987","journal-title":"J Infect Dis"},{"issue":"6","key":"288_CR18","doi-asserted-by":"crossref","first-page":"4284","DOI":"10.1128\/jvi.71.6.4284-4295.1997","volume":"71","author":"SL Liu","year":"1997","unstructured":"Liu SL, Schacker T, Musey L, Shriner D, McElrath MJ, Corey L, Mullins JI: Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses. J Virol 1997,71(6):4284-4295.","journal-title":"J Virol"},{"issue":"1","key":"288_CR19","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1128\/jvi.71.1.663-677.1997","volume":"71","author":"S Ganeshan","year":"1997","unstructured":"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(1):663-677.","journal-title":"J Virol"},{"issue":"10","key":"288_CR20","doi-asserted-by":"crossref","first-page":"7498","DOI":"10.1128\/jvi.71.10.7498-7508.1997","volume":"71","author":"EL Delwart","year":"1997","unstructured":"Delwart EL, Pan H, Sheppard HW, Wolpert D, Neumann AU, Korber B, Mullins JI: Slower evolution of human immunodeficiency virus type 1 quasispecies during progression to AIDS. J Virol 1997,71(10):7498-7508.","journal-title":"J Virol"},{"issue":"10","key":"288_CR21","doi-asserted-by":"crossref","first-page":"6672","DOI":"10.1128\/jvi.68.10.6672-6683.1994","volume":"68","author":"EL Delwart","year":"1994","unstructured":"Delwart EL, Sheppard HW, Walker BD, Goudsmit J, Mullins JI: Human immunodeficiency virus type 1 evolution in vivo tracked by DNA heteroduplex mobility assays. J Virol 1994,68(10):6672-6683.","journal-title":"J Virol"},{"issue":"11","key":"288_CR22","doi-asserted-by":"crossref","first-page":"6911","DOI":"10.1128\/jvi.69.11.6911-6916.1995","volume":"69","author":"VV Lukashov","year":"1995","unstructured":"Lukashov VV, Kuiken CL, Goudsmit J: Intrahost human immunodeficiency virus type 1 evolution is related to length of the immunocompetent period. J Virol 1995,69(11):6911-6916.","journal-title":"J Virol"},{"issue":"7","key":"288_CR23","doi-asserted-by":"crossref","first-page":"4871","DOI":"10.1128\/jvi.71.7.4871-4881.1997","volume":"71","author":"T Shioda","year":"1997","unstructured":"Shioda T, Oka S, Xin X, Liu H, Harukuni R, Kurotani A, Fukushima M, Hasan MK, Shiino T, Takebe Y, Iwamoto A, Nagai Y: In vivo sequence variability of human immunodeficiency virus type 1 envelope gp120: association of V2 extension with slow disease progression. J Virol 1997,71(7):4871-4881.","journal-title":"J Virol"},{"issue":"24","key":"288_CR24","doi-asserted-by":"publisher","first-page":"9938","DOI":"10.1073\/pnas.87.24.9938","volume":"87","author":"TF Wolfs","year":"1990","unstructured":"Wolfs TF, de Jong JJ, Van den Berg H, Tijnagel JM, Krone WJ, Goudsmit J: Evolution of sequences encoding the principal neutralization epitope of human immunodeficiency virus 1 is host dependent, rapid, and continuous. Proc Natl Acad Sci U S A 1990,87(24):9938-9942. 10.1073\/pnas.87.24.9938","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5261","key":"288_CR25","doi-asserted-by":"publisher","first-page":"537","DOI":"10.1126\/science.272.5261.537","volume":"272","author":"SM Wolinsky","year":"1996","unstructured":"Wolinsky SM, Korber BT, Neumann AU, Daniels M, Kunstman KJ, Whetsell AJ, Furtado MR, Cao Y, Ho DD, Safrit JT: Adaptive evolution of human immunodeficiency virus-type 1 during the natural course of infection. Science 1996,272(5261):537-542. 10.1126\/science.272.5261.537","journal-title":"Science"},{"issue":"4","key":"288_CR26","first-page":"344","volume":"2","author":"M Goodenow","year":"1989","unstructured":"Goodenow M, Huet T, Saurin W, Kwok S, Sninsky J, Wain-Hobson S: HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J Acquir Immune Defic Syndr 1989,2(4):344-352.","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"21","key":"288_CR27","doi-asserted-by":"publisher","first-page":"12568","DOI":"10.1073\/pnas.95.21.12568","volume":"95","author":"RB Markham","year":"1998","unstructured":"Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A, Margolick J, Vlahov D, Quinn T, Farzadegan H, Yu XF: Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A 1998,95(21):12568-12573. 10.1073\/pnas.95.21.12568","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"21","key":"288_CR28","doi-asserted-by":"publisher","first-page":"10247","DOI":"10.1073\/pnas.89.21.10247","volume":"89","author":"T McNearney","year":"1992","unstructured":"McNearney T, Hornickova Z, Markham R, Birdwell A, Arens M, Saah A, Ratner L: Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease. Proc Natl Acad Sci U S A 1992,89(21):10247-10251. 10.1073\/pnas.89.21.10247","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"12","key":"288_CR29","doi-asserted-by":"crossref","first-page":"10489","DOI":"10.1128\/JVI.73.12.10489-10502.1999","volume":"73","author":"R Shankarappa","year":"1999","unstructured":"Shankarappa R, Margolick JB, Gange SJ, Rodrigo AG, Upchurch D, Farzadegan H, Gupta P, Rinaldo CR, Learn GH, He X, Huang XL, Mullins JI: Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J Virol 1999,73(12):10489-10502.","journal-title":"J Virol"},{"issue":"4","key":"288_CR30","doi-asserted-by":"publisher","first-page":"1637","DOI":"10.1128\/JVI.80.4.1637-1644.2006","volume":"80","author":"JT Herbeck","year":"2006","unstructured":"Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI: Human Immunodeficiency Virus Type 1 env Evolves toward Ancestral States upon Transmission to a New Host. J Virol 2006,80(4):1637-1644. 10.1128\/JVI.80.4.1637-1644.2006","journal-title":"J Virol"},{"issue":"12","key":"288_CR31","doi-asserted-by":"crossref","first-page":"9741","DOI":"10.1128\/JVI.73.12.9741-9755.1999","volume":"73","author":"S Li","year":"1999","unstructured":"Li S, Juarez J, Alali M, Dwyer D, Collman R, Cunningham A, Naif HM: Persistent CCR5 utilization and enhanced macrophage tropism by primary blood human immunodeficiency virus type 1 isolates from advanced stages of disease and comparison to tissue-derived isolates. Journal of Virology 1999,73(12):9741-9755.","journal-title":"Journal of Virology"},{"issue":"12","key":"288_CR32","doi-asserted-by":"publisher","first-page":"2181","DOI":"10.1086\/425585","volume":"190","author":"M Churchill","year":"2004","unstructured":"Churchill M, Sterjovski J, Gray L, Cowley D, Chatfield C, Learmont J, Sullivan JS, Crowe SM, Mills J, Brew BJ, Wesselingh SL, McPhee DA, Gorry PR: Longitudinal analysis of nef\/long terminal repeat-deleted HIV-1 in blood and cerebrospinal fluid of a long-term survivor who developed HIV-associated dementia. J Infect Dis 2004,190(12):2181-2186. 10.1086\/425585","journal-title":"J Infect Dis"},{"issue":"14","key":"288_CR33","doi-asserted-by":"publisher","first-page":"6966","DOI":"10.1128\/JVI.76.14.6966-6973.2002","volume":"76","author":"A Jekle","year":"2002","unstructured":"Jekle A, Schramm B, Jayakumar P, Trautner V, Schols D, De Clercq E, Mills J, Crowe SM, Goldsmith MA: Coreceptor phenotype of natural human immunodeficiency virus with nef deleted evolves in vivo, leading to increased virulence. J Virol 2002,76(14):6966-6973. 10.1128\/JVI.76.14.6966-6973.2002","journal-title":"J Virol"},{"issue":"12","key":"288_CR34","doi-asserted-by":"publisher","first-page":"6823","DOI":"10.1128\/JVI.77.12.6823-6835.2003","volume":"77","author":"L Alexander","year":"2003","unstructured":"Alexander L, Illyinskii PO, Lang SM, Means RE, Lifson J, Mansfield K, Desrosiers RC: Determinants of increased replicative capacity of serially passaged simian immunodeficiency virus with nef deleted in rhesus monkeys. J Virol 2003,77(12):6823-6835. 10.1128\/JVI.77.12.6823-6835.2003","journal-title":"J Virol"},{"issue":"8","key":"288_CR35","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1097\/01.aids.0000168984.05209.f1","volume":"19","author":"SM Crowe","year":"2005","unstructured":"Crowe SM, Ho DD, Marriott D, Brew B, Gorry PR, Sullivan JS, Learmont J, Mills J: In vivo replication kinetics of a nef-deleted strain of HIV-1. Aids 2005,19(8):842-843. 10.1097\/01.aids.0000168984.05209.f1","journal-title":"Aids"},{"issue":"21","key":"288_CR36","doi-asserted-by":"publisher","first-page":"10073","DOI":"10.1128\/JVI.75.21.10073-10089.2001","volume":"75","author":"PR Gorry","year":"2001","unstructured":"Gorry PR, Bristol G, Zack JA, Ritola K, Swanstrom R, Birch CJ, Bell JE, Bannert N, Crawford K, Wang H, Schols D, De Clercq E, Kunstman K, Wolinsky SM, Gabuzda D: Macrophage Tropism of Human Immunodeficiency Virus Type 1 Isolates from Brain and Lymphoid Tissues Predicts Neurotropism Independent of Coreceptor Specificity. J Virol 2001,75(21):10073-10089. 10.1128\/JVI.75.21.10073-10089.2001","journal-title":"J Virol"},{"issue":"1","key":"288_CR37","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/nm0198-072","volume":"4","author":"GA Donzella","year":"1998","unstructured":"Donzella GA, Schols D, Lin SW, Este JA, Nagashima KA, Maddon PJ, Allaway GP, Sakmar TP, Henson G, De Clercq E, Moore JP: AMD3100, a small molecule inhibitor of HIV-1 entry via the CXCR4 co-receptor. Nat Med 1998,4(1):72-77. 10.1038\/nm0198-072","journal-title":"Nat Med"},{"issue":"8","key":"288_CR38","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1084\/jem.186.8.1383","volume":"186","author":"D Schols","year":"1997","unstructured":"Schols D, Struyf S, Van Damme J, Este JA, Henson G, De Clercq E: Inhibition of T-tropic HIV strains by selective antagonization of the chemokine receptor CXCR4. J Exp Med 1997,186(8):1383-1388. 10.1084\/jem.186.8.1383","journal-title":"J Exp Med"},{"issue":"10","key":"288_CR39","doi-asserted-by":"publisher","first-page":"5698","DOI":"10.1073\/pnas.96.10.5698","volume":"96","author":"M Baba","year":"1999","unstructured":"Baba M, Nishimura O, Kanzaki N, Okamoto M, Sawada H, Iizawa Y, Shiraishi M, Aramaki Y, Okonogi K, Ogawa Y, Meguro K, Fujino M: A small-molecule, nonpeptide CCR5 antagonist with highly potent and selective anti-HIV-1 activity. Procedings of the National Academy of Sciences USA 1999,96(10):5698-5703. 10.1073\/pnas.96.10.5698","journal-title":"Procedings of the National Academy of Sciences USA"},{"issue":"3","key":"288_CR40","doi-asserted-by":"publisher","first-page":"1480","DOI":"10.1128\/JVI.79.3.1480-1486.2005","volume":"79","author":"Y Yi","year":"2005","unstructured":"Yi Y, Shaheen F, Collman RG: Preferential use of CXCR4 by R5X4 human immunodeficiency virus type 1 isolates for infection of primary lymphocytes. J Virol 2005,79(3):1480-1486. 10.1128\/JVI.79.3.1480-1486.2005","journal-title":"J Virol"},{"issue":"7","key":"288_CR41","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1172\/JCI10565","volume":"106","author":"L Zhang","year":"2000","unstructured":"Zhang L, Chung C, Hu BS, He T, Guo Y, Kim AJ, Skulsky E, Jin X, Hurley A, Ramratnam B, Markowitz M, Ho DD: Genetic characterization of rebounding HIV-1 after cessation of highly active antiretroviral therapy. J Clin Invest 2000,106(7):839-845.","journal-title":"J Clin Invest"},{"issue":"3","key":"288_CR42","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1097\/00002030-200002180-00002","volume":"14","author":"B Wang","year":"2000","unstructured":"Wang B, Spira TJ, Owen S, Lal RB, Saksena NK: HIV-1 strains from a cohort of American subjects reveal the presence of a V2 region extension unique to slow progressors and non-progressors. Aids 2000,14(3):213-223. 10.1097\/00002030-200002180-00002","journal-title":"Aids"},{"issue":"24","key":"288_CR43","doi-asserted-by":"publisher","first-page":"13376","DOI":"10.1128\/JVI.77.24.13376-13388.2003","volume":"77","author":"MA Jensen","year":"2003","unstructured":"Jensen MA, Li FS, van 't Wout AB, Nickle DC, Shriner D, He HX, McLaughlin S, Shankarappa R, Margolick JB, Mullins JI: Improved coreceptor usage prediction and genotypic monitoring of R5-to-X4 transition by motif analysis of human immunodeficiency virus type 1 env V3 loop sequences. J Virol 2003,77(24):13376-13388. 10.1128\/JVI.77.24.13376-13388.2003","journal-title":"J Virol"},{"issue":"1","key":"288_CR44","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1006\/viro.1997.8821","volume":"239","author":"L Milich","year":"1997","unstructured":"Milich L, Margolin BH, Swanstrom R: Patterns of amino acid variability in NSI-like and SI-like V3 sequences and a linked change in the CD4-binding domain of the HIV-1 Env protein. Virology 1997,239(1):108-118. 10.1006\/viro.1997.8821","journal-title":"Virology"},{"issue":"18","key":"288_CR45","doi-asserted-by":"publisher","first-page":"2937","DOI":"10.1097\/00002030-200012220-00016","volume":"14","author":"DR Briggs","year":"2000","unstructured":"Briggs DR, Tuttle DL, Sleasman JW, Goodenow MM: Envelope V3 amino acid sequence predicts HIV-1 phenotype (co-receptor usage and tropism for macrophages). Aids 2000,14(18):2937-2939. 10.1097\/00002030-200012220-00016","journal-title":"Aids"},{"issue":"21","key":"288_CR46","doi-asserted-by":"publisher","first-page":"13250","DOI":"10.1128\/JVI.79.21.13250-13261.2005","volume":"79","author":"G Ghaffari","year":"2005","unstructured":"Ghaffari G, Tuttle DL, Briggs D, Burkhardt BR, Bhatt D, Andiman WA, Sleasman JW, Goodenow MM: Complex Determinants in Human Immunodeficiency Virus Type 1 Envelope gp120 Mediate CXCR4-Dependent Infection of Macrophages. J Virol 2005,79(21):13250-13261. 10.1128\/JVI.79.21.13250-13261.2005","journal-title":"J Virol"},{"key":"288_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.2174\/1874285800701010001","volume":"1","author":"PR Gorry","year":"2007","unstructured":"Gorry PR, McPhee DA, Wesselingh SL, Churchill MJ: Macrophage tropism and cytopathicity of HIV-1 variants isolated sequentially from a long-term survivor infected with nef-deleted virus. The Open Microbiology Journal 2007, 1: 1-7.","journal-title":"The Open Microbiology Journal"},{"issue":"12","key":"288_CR48","doi-asserted-by":"publisher","first-page":"6277","DOI":"10.1128\/JVI.76.12.6277-6292.2002","volume":"76","author":"PR Gorry","year":"2002","unstructured":"Gorry PR, Taylor J, Holm GH, Mehle A, Morgan T, Cayabyab M, Farzan M, Wang H, Bell JE, Kunstman K, Moore JP, Wolinsky SM, Gabuzda D: Increased CCR5 affinity and reduced CCR5\/CD4 dependence of a neurovirulent primary human immunodeficiency virus type 1 isolate. Journal of Virology 2002,76(12):6277-6292. 10.1128\/JVI.76.12.6277-6292.2002","journal-title":"Journal of Virology"},{"issue":"7","key":"288_CR49","doi-asserted-by":"publisher","first-page":"3435","DOI":"10.1128\/JVI.75.7.3435-3443.2001","volume":"75","author":"P Kolchinsky","year":"2001","unstructured":"Kolchinsky P, Kiprilov E, Bartley P, Rubinstein R, Sodroski J: Loss of a single N-linked glycan allows CD4-independent human immunodeficiency virus type 1 infection by altering the position of the gp120 V1\/V2 variable loops. J Virol 2001,75(7):3435-3443. 10.1128\/JVI.75.7.3435-3443.2001","journal-title":"J Virol"},{"issue":"5","key":"288_CR50","doi-asserted-by":"publisher","first-page":"2041","DOI":"10.1128\/JVI.75.5.2041-2050.2001","volume":"75","author":"P Kolchinsky","year":"2001","unstructured":"Kolchinsky P, Kiprilov E, Sodroski J: Increased neutralization sensitivity of CD4-independent human immunodeficiency virus variants. J Virol 2001,75(5):2041-2050. 10.1128\/JVI.75.5.2041-2050.2001","journal-title":"J Virol"},{"issue":"6686","key":"288_CR51","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1038\/31514","volume":"393","author":"R Wyatt","year":"1998","unstructured":"Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, Hendrickson WA, Sodroski JG: The antigenic structure of the HIV gp120 envelope glycoprotein. Nature 1998,393(6686):705-711. 10.1038\/31514","journal-title":"Nature"},{"issue":"8","key":"288_CR52","doi-asserted-by":"crossref","first-page":"4557","DOI":"10.1128\/jvi.67.8.4557-4565.1993","volume":"67","author":"R Wyatt","year":"1993","unstructured":"Wyatt R, Sullivan N, Thali M, Repke H, Ho D, Robinson J, Posner M, Sodroski J: Functional and immunologic characterization of human immunodeficiency virus type 1 envelope glycoproteins containing deletions of the major variable regions. J Virol 1993,67(8):4557-4565.","journal-title":"J Virol"},{"issue":"4","key":"288_CR53","doi-asserted-by":"publisher","first-page":"377","DOI":"10.3109\/13550289809114536","volume":"4","author":"P Gorry","year":"1998","unstructured":"Gorry P, Purcell D, Howard J, McPhee D: Restricted HIV-1 infection of human astrocytes: potential role of nef in the regulation of virus replication. Journal of Neurovirology 1998,4(4):377-386.","journal-title":"Journal of Neurovirology"},{"key":"288_CR54","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1016\/j.virol.2005.04.034","volume":"337","author":"L Gray","year":"2005","unstructured":"Gray L, Sterjovski J, Churchill M, Ellery P, Nasr N, Lewin SR, Crowe SM, Wesselingh S, Cunningham AL, Gorry PR: Uncoupling coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from macrophage tropism reveals biological properties of CCR5-restricted HIV-1 isolates from patients with acquired immunodeficiency syndrome. Virology 2005, 337: 384-398. 10.1016\/j.virol.2005.04.034","journal-title":"Virology"},{"issue":"9320","key":"288_CR55","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.1016\/S0140-6736(02)08681-6","volume":"359","author":"PR Gorry","year":"2002","unstructured":"Gorry PR, Zhang C, Wu S, Kunstman K, Trachtenberg E, Phair J, Wolinsky S, Gabuzda D: Persistence of dual-tropic HIV-1 in an individual homozygous for the CCR5 Delta 32 allele. Lancet 2002,359(9320):1832-1834. 10.1016\/S0140-6736(02)08681-6","journal-title":"Lancet"},{"issue":"11","key":"288_CR56","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1089\/08892220260139530","volume":"18","author":"AM Klevytska","year":"2002","unstructured":"Klevytska AM, Mracna MR, Guay L, Becker-Pergola G, Furtado M, Zhang L, Jackson JB, Eshleman SH: Analysis of length variation in the V1-V2 region of env in nonsubtype B HIV type 1 from Uganda. AIDS Res Hum Retroviruses 2002,18(11):791-796. 10.1089\/08892220260139530","journal-title":"AIDS Res Hum Retroviruses"},{"issue":"5666","key":"288_CR57","doi-asserted-by":"publisher","first-page":"2019","DOI":"10.1126\/science.1093137","volume":"303","author":"CA Derdeyn","year":"2004","unstructured":"Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, Denham SA, Heil ML, Kasolo F, Musonda R, Hahn BH, Shaw GM, Korber BT, Allen S, Hunter E: Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 2004,303(5666):2019-2022. 10.1126\/science.1093137","journal-title":"Science"},{"issue":"3","key":"288_CR58","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1128\/jvi.70.3.1651-1667.1996","volume":"70","author":"F Gao","year":"1996","unstructured":"Gao F, Morrison SG, Robertson DL, Thornton CL, Craig S, Karlsson G, Sodroski J, Morgado M, Galvao-Castro B, von Briesen H, et al.: Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization. J Virol 1996,70(3):1651-1667.","journal-title":"J Virol"},{"issue":"6617","key":"288_CR59","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1038\/385645a0","volume":"385","author":"J He","year":"1997","unstructured":"He J, Chen Y, Farzan M, Choe H, Ohagen A, Gartner S, Busciglio J, Yang X, Hofmann W, Newman W, Mackay CR, Sodroski J, Gabuzda D: CCR3 and CCR5 are co-receptors for HIV-1 infection of microglia. Nature 1997,385(6617):645-649. 10.1038\/385645a0","journal-title":"Nature"},{"issue":"22","key":"288_CR60","doi-asserted-by":"publisher","first-page":"12336","DOI":"10.1128\/JVI.77.22.12336-12345.2003","volume":"77","author":"A Ohagen","year":"2003","unstructured":"Ohagen A, Devitt A, Kunstman KJ, Gorry PR, Rose PP, Korber B, Taylor J, Levy R, Murphy RL, Wolinsky SM, Gabuzda D: Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS. Journal of Virology 2003,77(22):12336-12345. 10.1128\/JVI.77.22.12336-12345.2003","journal-title":"Journal of Virology"}],"container-title":["Virology Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1743-422X-4-75.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T07:34:51Z","timestamp":1630481691000},"score":1,"resource":{"primary":{"URL":"https:\/\/virologyj.biomedcentral.com\/articles\/10.1186\/1743-422X-4-75"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,7,16]]},"references-count":60,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["288"],"URL":"https:\/\/doi.org\/10.1186\/1743-422x-4-75","relation":{},"ISSN":["1743-422X"],"issn-type":[{"value":"1743-422X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,7,16]]},"assertion":[{"value":"6 July 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"75"}}