Ayehunie S, Johansson B, Sonnerborg A, Salminen M, Zewdie DW, Fehniger T, Britton S, Strannegard O. New subtype of HIV-1 in Ethiopia. Lancet. 1990;336(8720):942.
Article
CAS
PubMed
Google Scholar
Salminen MO, Johansson B, Sonnerborg A, Ayehunie S, Gotte D, Leinikki P, Burke DS, McCutchan FE. Full-length sequence of an ethiopian human immunodeficiency virus type 1 (HIV-1) isolate of genetic subtype C. AIDS Res Hum Retrovir. 1996;12(14):1329–39.
Article
CAS
PubMed
Google Scholar
Bjorndal A, Sonnerborg A, Tscherning C, Albert J, Fenyo EM. Phenotypic characteristics of human immunodeficiency virus type 1 subtype C isolates of Ethiopian AIDS patients. AIDS Res Hum Retrovir. 1999;15(7):647–53.
Article
CAS
PubMed
Google Scholar
Lengauer T, Sander O, Sierra S, Thielen A, Kaiser R. Bioinformatics prediction of HIV coreceptor usage. Nat Biotechnol. 2007;25(12):1407–10.
Article
CAS
PubMed
Google Scholar
Crous S, Shrestha RK, Travers SA. Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C viruses. BMC Infect Dis. 2012;12:203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vandekerckhove LP, Wensing AM, Kaiser R, Brun-Vezinet F, Clotet B, De Luca A, Dressler S, Garcia F, Geretti AM, Klimkait T, et al. European guidelines on the clinical management of HIV-1 tropism testing. Lancet Infect Dis. 2011;11(5):394–407.
Article
CAS
PubMed
Google Scholar
Gupta S, Neogi U, Srinivasa H, Shet A. Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences. Intervirology. 2015;58(1):1–5.
Article
CAS
PubMed
Google Scholar
Abbate I, Vlassi C, Rozera G, Bruselles A, Bartolini B, Giombini E, Corpolongo A, D’Offizi G, Narciso P, Desideri A, et al. Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection. AIDS. 2011;25(5):611–7.
Article
PubMed
Google Scholar
Cilliers T, Nhlapo J, Coetzer M, Orlovic D, Ketas T, Olson WC, Moore JP, Trkola A, Morris L. The CCR5 and CXCR4 coreceptors are both used by human immunodeficiency virus type 1 primary isolates from subtype C. J Virol. 2003;77(7):4449–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neogi U, Sood V, Chowdhury A, Das S, Ramachandran VG, Sreedhar VK, Wanchu A, Ghosh N, Banerjea AC. Genetic analysis of HIV-1 Circulating Recombinant Form 02_AG, B and C subtype-specific envelope sequences from Northern India and their predicted co-receptor usage. AIDS Res Ther. 2009;6:28.
Article
PubMed
PubMed Central
Google Scholar
Neogi U, Prarthana SB, D’Souza G, Decosta A, Kuttiatt VS, Ranga U, Shet A. Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India. AIDS Res Ther. 2010;7:24.
Article
PubMed
PubMed Central
Google Scholar
Ataher Q, Portsmouth S, Napolitano LA, Eng S, Greenacre A, Kambugu A, Wood R, Badal-Faesen S, Tressler R. The epidemiology and clinical correlates of HIV-1 co-receptor tropism in non-subtype B infections from India, Uganda and South Africa. J Int AIDS Soc. 2012;15(1):2.
Article
PubMed
PubMed Central
Google Scholar
Green TN, Archary M, Gordon ML, Padayachi N, Lie Y, Anton ED, Reeves JD, Grobler A, Bobat R, Coovadia H, et al. Drug resistance and coreceptor usage in HIV type 1 subtype C-infected children initiating or failing highly active antiretroviral therapy in South Africa. AIDS Res Hum Retrovir. 2012;28(4):324–32.
Article
CAS
PubMed
PubMed Central
Google Scholar
Connell BJ, Michler K, Capovilla A, Venter WD, Stevens WS, Papathanasopoulos MA. Emergence of X4 usage among HIV-1 subtype C: evidence for an evolving epidemic in South Africa. AIDS. 2008;22(7):896–9.
Article
PubMed
Google Scholar
Neogi U, Sahoo PN, Arumugam K, Sonnerborg A, De Costa A, Shet A. Higher prevalence of predicted X4-tropic strains in perinatally infected older children with HIV-1 subtype C in India. J Acquir Immune Defic Syndr. 2012;59(4):347–53.
Article
PubMed
Google Scholar
Ketseoglou I, Lukhwareni A, Steegen K, Carmona S, Stevens WS, Papathanasopoulos MA. Viral tropism and antiretroviral drug resistance in HIV-1 subtype C-infected patients failing highly active antiretroviral therapy in Johannesburg, South Africa. AIDS Res Hum Retrovir. 2014;30(3):289–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sollerkvist LP, Gaseitsiwe S, Mine M, Sebetso G, Mphoyakgosi T, Diphoko T, Essex M, Ehrnst A. Increased CXCR4 use of HIV-1 subtype C identified by population sequencing in patients failing antiretroviral treatment compared with treatment-naive patients in Botswana. AIDS Res Hum Retrovir. 2014;30(5):436–45.
Article
CAS
PubMed
Google Scholar
Abebe A, Kuiken CL, Goudsmit J, Valk M, Messele T, Sahlu T, Yeneneh H, Fontanet A, De Wolf F, Rinke De Wit TF. HIV type 1 subtype C in Addis Ababa, Ethiopia. AIDS Res Hum Retrovir. 1997;13(12):1071–5.
Article
CAS
PubMed
Google Scholar
Abebe A, Pollakis G, Fontanet AL, Fisseha B, Tegbaru B, Kliphuis A, Tesfaye G, Negassa H, Cornelissen M, Goudsmit J, et al. Identification of a genetic subcluster of HIV type 1 subtype C (C’) widespread in Ethiopia. AIDS Res Hum Retrovir. 2000;16(17):1909–14.
Article
CAS
PubMed
Google Scholar
Hussein M, Abebe A, Pollakis G, Brouwer M, Petros B, Fontanet AL, Rinke de Wit TF. HIV-1 subtype C in commerical sex workers in Addis Ababa, Ethiopia. J Acquir Immune Defic Syndr. 2000;23(2):120–7.
Article
CAS
PubMed
Google Scholar
Kassu A, Fujino M, Matsuda M, Nishizawa M, Ota F, Sugiura W. Molecular epidemiology of HIV type 1 in treatment-naive patients in north Ethiopia. AIDS Res Hum Retrovir. 2007;23(4):564–8.
Article
CAS
PubMed
Google Scholar
Mulu A, Maier M, Liebert UG. Deworming of intestinal helminths reduces HIV-1 subtype C viremia in chronically co-infected individuals. Int J Infect Dis. 2013;17(10):e897–901.
Article
PubMed
Google Scholar
Delwart EL, Herring B, Rodrigo AG, Mullins JI. Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay. PCR Methods Appl. 1995;4(5):S202–16.
Article
CAS
PubMed
Google Scholar
Siepel AC, Halpern AL, Macken C, Korber BT. A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retrovir. 1995;11(11):1413–6.
Article
CAS
PubMed
Google Scholar
Gene Cutter Sequence Alignment and Protein Extraction. HIV database, https://www.hiv.lanl.gov/content/sequence/GENE_CUTTER/cutter.html. Accessed 20 Mar 2016.
Sing T, Low AJ, Beerenwinkel N, Sander O, Cheung PK, Domingues FS, Buch J, Daumer M, Kaiser R, Lengauer T, et al. Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther. 2007;12(7):1097–106.
CAS
PubMed
Google Scholar
Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gomez-Lopez A, Camacho RJ, de Oliveira T, Vandamme AM. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol. 2013;19:337–48.
Article
CAS
PubMed
Google Scholar
RIP Recombinant Identification Program. http://www.hiv.lanl.gov/content/sequence/RIP/RIP.html. Accessed 24 Mar 2016.
Struck D, Lawyer G, Ternes AM, Schmit JC, Bercoff DP. COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res. 2014;42(18):e144.
Article
PubMed
PubMed Central
Google Scholar
Neogi U, Rao SD, Bontell I, Verheyen J, Rao VR, Gore SC, Soni N, Shet A, Schulter E, Ekstrand ML, et al. Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients. AIDS. 2014;28(15):2319–22.
Article
CAS
PubMed
PubMed Central
Google Scholar
Johansson B, Sherefa K, Sonnerborg A. Multiple enhancer motifs in HIV type 1 strains from Ethiopia. AIDS Res Hum Retrovir. 1995;11(6):761–4.
Article
CAS
PubMed
Google Scholar
Prosperi MC, Bracciale L, Fabbiani M, Di Giambenedetto S, Razzolini F, Meini G, Colafigli M, Marzocchetti A, Cauda R, Zazzi M, et al. Comparative determination of HIV-1 co-receptor tropism by Enhanced Sensitivity Trofile, gp120 V3-loop RNA and DNA genotyping. Retrovirology. 2010;7:56.
Article
PubMed
PubMed Central
Google Scholar
Shioda T, Levy JA, Cheng-Mayer C. Small amino acid changes in the V3 hypervariable region of gp120 can affect the T-cell-line and macrophage tropism of human immunodeficiency virus type 1. Proc Natl Acad Sci U S A. 1992;89(20):9434–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
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):13376–88.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cashin K, Gray LR, Harvey KL, Perez-Bercoff D, Lee GQ, Sterjovski J, Roche M, Demarest JF, Drummond F, Harrigan PR, et al. Reliable genotypic tropism tests for the major HIV-1 subtypes. Sci Rep. 2015;5:8543.
Article
CAS
PubMed
PubMed Central
Google Scholar
Seclen E, Soriano V, Gonzalez MM, Gomez S, Thielen A, Poveda E. High concordance between the position-specific scoring matrix and geno2pheno algorithms for genotypic interpretation of HIV-1 tropism: V3 length as the major cause of disagreement. J Clin Microbiol. 2011;49(9):3380–2.
Article
PubMed
PubMed Central
Google Scholar
Abebe A, Demissie D, Goudsmit J, Brouwer M, Kuiken CL, Pollakis G, Schuitemaker H, Fontanet AL, Rinke de Wit TF. HIV-1 subtype C syncytium- and non-syncytium-inducing phenotypes and coreceptor usage among Ethiopian patients with AIDS. AIDS. 1999;13(11):1305–11.
Article
CAS
PubMed
Google Scholar
Santoro MM, Armenia D, Fabeni L, Santoro M, Gori C, Forbici F, Svicher V, Bertoli A, Dori L, Surdo M, et al. The lowest X4 Geno2Pheno false-positive rate is associated with greater CD4 depletion in HIV-1 infected patients. Clin Microbiol Infect. 2012;18(8):E289–98.
Article
CAS
PubMed
Google Scholar
Weiser B, Philpott S, Klimkait T, Burger H, Kitchen C, Burgisser P, Gorgievski M, Perrin L, Piffaretti JC, Ledergerber B, et al. HIV-1 coreceptor usage and CXCR4-specific viral load predict clinical disease progression during combination antiretroviral therapy. AIDS. 2008;22(4):469–79.
Article
PubMed
Google Scholar
Brumme ZL, Dong WW, Yip B, Wynhoven B, Hoffman NG, Swanstrom R, Jensen MA, Mullins JI, Hogg RS, Montaner JS, et al. Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS. 2004;18(4):F1–9.
Article
CAS
PubMed
Google Scholar
Waters L, Mandalia S, Randell P, Wildfire A, Gazzard B, Moyle G. The impact of HIV tropism on decreases in CD4 cell count, clinical progression, and subsequent response to a first antiretroviral therapy regimen. Clin Infect Dis. 2008;46(10):1617–23.
Article
PubMed
Google Scholar
Seclen E, Soriano V, Gonzalez MM, Martin-Carbonero L, Gellermann H, Distel M, Kadus W, Poveda E. Impact of baseline HIV-1 tropism on viral response and CD4 cell count gains in HIV-infected patients receiving first-line antiretroviral therapy. J Infect Dis. 2011;204(1):139–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Daumer M, Kaiser R, Klein R, Lengauer T, Thiele B, Thielen A. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis. BMC Med Inform Decis Mak. 2011;11:30.
Article
PubMed
PubMed Central
Google Scholar
Armenia D, Soulie C, Di Carlo D, Fabeni L, Gori C, Forbici F, Svicher V, Bertoli A, Sarmati L, Giuliani M, et al. A very low geno2pheno false positive rate is associated with poor viro-immunological response in drug-naive patients starting a first-line HAART. PLoS One. 2014;9(8):e105853.
Article
PubMed
PubMed Central
Google Scholar
Rozera G, Abbate I, Giombini E, Castagna A, De Luca A, Ceccherini-Silberstein F, Cozzi Lepri A, Cassola G, Torti C, d’Arminio Monforte A, et al. Evolution of HIV-1 tropism at quasispecies level after 5 years of combination antiretroviral therapy in patients always suppressed or experiencing episodes of virological failure. J Antimicrob Chemother. 2014;69(11):3085–94.
Article
CAS
PubMed
Google Scholar
Hunt PWHW, Coakley E, Petropoulos C, Bates M, Hoh R, Deeks SG, Martin JN. Longitudinal evaluation of viral co-receptor tropism switches among HIV-infected patients with drugresistant viremia. In: Conference on Retroviruses and Opportunistic Infections (CROI). 2007.
Google Scholar
Gupta S, Neogi U, Srinivasa H, Banerjea AC, Shet A. HIV-1 coreceptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades. J Acquir Immune Defic Syndr. 2014;65(4):397–404.
Article
PubMed
Google Scholar