Publications

2017

Zhang W, Morshed MM, Noyan K, Russom A, Sönnerborg A, Neogi U (2017) Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy. Sci Rep. 7(1):666. [PMID: 28386076]

Aralaguppe SG, Winner D, Singh K, Sarafianos SG, Quiñones-Mateu ME, Sönnerborg A, Neogi U(2017) Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa. J Med Virol . 89(1):106-111[PMID: 27328744].

Brännström J, Sönnerborg A, Svedhem V, Neogi U, Marrone G. (2017) A high rate of HIV-1 acquisition post immigration among migrants in Sweden determined by a CD4 T-cell decline trajectory model. HIV Med. Apr 26. doi: 10.1111/hiv.12509. [Epub ahead of print] [PMID:28444865]

Vesterbacka J, Rivera J, Noyan K, Parera M, Neogi U, Calle M, Paredes R, Sönnerborg A, Noguera-Julian M, Nowak P (2017) Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers. Sci Rep (Accepted)

Svärd J, Mugusi S, Mloka D, Neogi U, Meini G, Mugusi F, Incardona F, Zazzi M, Sönnerborg A (2017) Drug resistance testing through remote genotyping and predicted treatment options in Human Immunodeficiency Virus type 1 infected Tanzanian subjects failing first or second line antiretroviral therapy. PloS One (Accepted)

2016

Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U(2016) Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden. Lancet HIV 3(4):e166-74 [http://dx.doi.org/10.1016/S2352-3018(16)00023-0. [PMID: 27036992]

Aralaguppe SG, Siddik AB, Manickam A, Ambikan AT, Kumar MM, Fernandes SJ, Amogne W, Bangaruswamy DK, Hanna LE, Sonnerborg A, Neogi U (2016) Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus. J Virol Methods 236:98-104 [PMID: 27448822]

Gregson J, Tang M, Ndembi N, Hamers RL Rhee S, Marconi VC, Diero L, Brooks K, Theys K, Rinke de Wit TF, Arruda M, Garcia F, Monge S, Günthard HF, Hoffmann CJ, Kanki PJ, Kumarasamy N, Kerschberger B, Mor O, Charpentier C, Todesco E, Rokx C, Gras L, Halvas EK, Sunpath H, Di Carlo D, Antinori A, Andreoni M, Latini A, Mussini C, Aghokeng A, Sonnerborg A, Neogi U, Fessel WJ, Agolory S, Yang C, Blanco JL, Juma JM, Smit E, Schmidt D, Watera C, Asio J, Kirungi W, Tostevin A, El-Hay T,  Clumeck N, Goedhals D, van Vuuren C, Bester A,  Sabin C, Mukui I, Santoro MM, Perno CF, Hunt G, Morris L, Camacho R, de Oliveira T, Pillay D, Schulter  E, Murakami-Ogasawara A, Reyes-Terán G, Romero K, Avila-Rios S, Sirivichayakul S, Ruxrungtham K, Mekprasan S, Dunn D, Kaleebu P, Raizes E, Kantor R, Shafer RW, Gupta RK (2016) Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study. Lancet Infect Dis 16(5):565-575 [PMID: 26831472].

Gupta S, Palchaudhuri R, Neogi U, Srinivasa H, Ashorn P, De Costa A, Källander C, Shet (2016) Can HIV reverse transcriptase activity assay be a low cost alternative for viral load monitoring in resource-limited settings? BMJ Open, 6:e008795. doi:10.1136/bmjopen-2015- 008795 [PMID: 26817634]

Amogne W, Bontell I, Grossmann S, Aderaye G,  Lindquist L,  Sönnerborg A, Neogi U (2016) Phylogenetic analysis of Ethiopian HIV-1 subtype C near full-length genomes reveals high intra-subtype diversity and a strong geographical cluster. AIDS Res Hum Retroviruses 32(5):471-474.  [PMID: 26881451]

Neogi U, Engelbrecht S, Claassen M, Jacobs G, van Zyl G, Preiser W, Sönnerborg A. (2016) Mutational heterogeneity in p6 Gag late assembly (L) domains in HIV-1 subtype C viruses from South Africa. AIDS Res Hum Retroviruses 32(1):80-4 [PMID: 26413747]

Neogi U, Häggblom A, Singh K, Rogers L, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos S, Sonnerborg A (2016) Factors influencing the efficacy of rilpivirine on HIV-1 subtype C in low- and middle-income countries. J Antimicrob Chemother, 71(2):367-71. [PMID: 26518047]

2015

Nowak P*, Trøseid M*, Avershina E, Barqasho B, Neogi U, Holm K, Hov J, Noyan K, Vesterbacka J, Svärd J, Rudi MK, Sönnerborg (2015) Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS 29(18):2409-18. [PMID: 26355675]

Grossmann S, Nowak P, Neogi U. (2015) Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management. J Int AIDS Soc. 2015 Jun 25;18(1):20035. doi: 10.7448/IAS.18.1.20035. [PMID: 26115688]

Shet A, Neogi U, Kumarasamy N, DeCosta A, Shastri S, Rewari BB. (2015) Virological efficacy with first-line antiretroviral treatment in India: predictors of viral failure and evidence of viral resuppression. Trop Med Int Health. 20(11):1462-1472. [PMID: 26146863]

Gupta S, Neogi U, Srinivasa H, Shet A. (2015) Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences. Intervirology. 2015 Jan 7;58 (1):1-5. [PMID: 25573618]

2014

Ekici H, Rao SD, Sönnerborg A, Ramprasad VL, Gupta R, Neogi U (2014) Cost-efficient HIV-1 drug resistance surveillance using multiplexed high throughput amplicon sequencing: Implications for use in low and middle income countries. J Antimicrob Chemother, 69(12):3349-55. [PMID:25085657]

Neogi U, Rao SD, Bontell I, Verheyen J, Rao VR, Gore SC, Soni N, Shet A, Schülter E, Ekstrand ML, Wondwossen A, Kaiser R, Madhusudhan MS, Prasad VR, Sonnerborg A (2014) Novel tetra-peptide insertion in Gag p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients. AIDS; 28(15): 2319-22. [PMID: 25102091]

Neogi U*, Häggblom A*, Santacatterina M, Bratt G , Gisslén M, Albert J, Sonnerborg A (2014) Temporal trends in the Swedish HIV-1 epidemic: Increase in non-B subtypes and recombinant forms over three decades. PLoS One, 9(6):e99390. doi: 10.1371/journal.pone.0099390. [*Equal contribution] [PMID: 24922326]

Neogi U, Gupta S, Palchaudhuri R, Rao SD, Shastri S, Diwan V, Laishram RS, De Costa A, Shet A (2014) Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitors resistance mutations in therapy naive HIV-1 infected individuals in India. Antivir Ther, 19(8): 813-818. [PMID: 24699043]

Hanna LE*, Neogi U*, Ranga U, Swaminathan S, Prasad VR. (2014) Phylogenetic characterization of six full-length HIV-1 subtype C molecular clones from three patients: Identification of rare subtype C strains containing two NF-κB motifs in the long terminal repeat. AIDS Res Hum Retroviruses. 30(6): 586-591. [PMID:24387762] [*Equal contribution]

Shet A, De Costa A, Kumarasamy N, Rodrigues R, Rewari BB, Ashorn P, Eriksson B, Diwan V; HIVIND Study Team (D’souza G, Neogi U, Arumugam K, Krishnamurthy S, Antony J, Gupta S, Kuttiatt V, Poongulali S, Beulah EF, Balaji K, Iqbal S, Saravanan S,Ezhilarasi C, Naik V, Srinivasa M, Rajendra K, Shastri S, Dodderi S, Källander C).(2014) Effect of mobile telephone reminders on treatment outcome in HIV: evidence from a randomised controlled trial in India. BMJ 24;349:g5978. doi: 10.1136/bmj.g5978. [PMID:25742320]

Rao VR, Neogi U, Eugenin E, Prasad VR (2014) The gp120 protein is a second determinant of increased neurovirulence of Southern African HIV-1C isolates compared to Indian HIV-1C isolates. PLoS One, 2014 Sep 4;9(9):e107074. doi: 10.1371/journal.pone.0107074. [PMID: 25188269]

Chaudhuri RP, Neogi U, Rao SD, Shet A. (2014) Genetic factors associated with slow progression of HIV among perinatally-infected Indian children. Indian Pediatr. 2014 Oct 8;51(10):801-803. [With Editorial Commentary] PMID: 25362010]

2013

Neogi U, Palchaudhuri R, Bommana S, Shet A. (2013) Genetic architecture of HIV type 1 Nef and Tat from HLA-B57-typed long-term survivors in an Indian cohort of perinatally HIV-infected children. AIDS Res Hum Retroviruses. 29(12):1613-6. [PMID: 24020900]

*Neogi U, Shet A, Sahoo PN , Bontell I, Ekstrand ML, Banerjea AC, Sönnerborg A. (2013) Human APOBEC3G-mediated hypermutation is associated with antiretroviral therapy failure in HIV-1 subtype C- infected individuals. J Int AIDS Soc 16:18472. doi: 10.7448/IAS.16.1.18472. [PMID: 23443042]

*Neogi U, Heylen E, Shet A, Chandy S, Shamsunder R, Sönnerborg A, Ekstrand ML. (2013) Long-term efficacy of first line antiretroviral therapy in Indian HIV-1 infected patients: A longitudinal cohort study. PLoS ONE 8(1): e55421. doi:10.1371/journal.pone.0055421.[PMID:23383185]

Gupta S, Neogi U, Srinivasa H, Banerjea AC, Shet A.(2013) HIV-1 co-receptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades. J Acquir Immune Defic Syndr. 65(4):397-404 [PMID:24189148]

Rao VR, Neogi U, Talboom JS, Padilla L, Rahman M, Fritz-French C, Gonzalez-Ramirez S, Verma A, Wood C, Ruprecht RM, Ranga U, Azim T, Joska J, Eugenin E, Shet A, Bimonte-Nelson H, Tyor WR, Prasad VR (2013) Clade C HIV-1 isolates circulating in Southern Africa exhibit a greater frequency of dicysteine motif-containing Tat variants than those in Southeast Asia and cause increased neurovirulence. Retrovirology 10:61. doi: 10.1186/1742-4690-10-61. [Highly Accessed] [PMID: 23758766]

Gupta S, Neogi U, Srinivasa H, Shet A. (2013) High concordance of genotypic co-receptor prediction in plasma-viral RNA and pro-viral DNA of HIV-1 subtype C virus: implications in use of whole-blood DNA in resource-limited settings. J Antimicrob Chemother 68(9):2003-2006.. [PMID: 23633683].

Shet A, Neogi U, Sahoo PN, De Costa A. (2013) Effectiveness of first-line antiretroviral therapy and acquired drug resistance among HIV-1-infected children in India. Pediatr Infect Dis J  32: e227–e229] [PMID: 23249907].

2011

Neogi U, Shet A, Shamsundar R, Ekstrand ML. (2011) Selection of non-nucleoside reverse transcriptase inhibitor-associated mutations in HIV-1 subtype C: evidence of etravirine cross-resistance. AIDS 25:1123–1126. [PMID:21505320].

Neogi U, Sahoo PN, Kumar R, De Costa A, Shet A (2011) Characterizations of HIV-1 subtype C protease gene: selection of L63P mutation in protease inhibitor-naive Indian patients. AIDS Res Hum Retroviruses 27(11):1249-53. [PMID:21453185].

2010

De Costa A, Shet A, Kumarasamy N, Ashorn P, Eriksson B, Bogg L, Diwan VK, and the HIVIND STUDY Team (Rodrigues R, Neogi U, Källander C, et al.) (2010) Design of a randomized trial to evaluate the influence of mobile phone reminders on adherence to first line antiretroviral treatment in South India – the HIVIND study protocol. BMC Med Res Methodol. Mar 26;10(1):25. [PMID:20346136].

Neogi U, Prarthana BS, Gupta S, D’souza G, De Costa A, Kuttiatt VS, Arumugam K, Shet A (2010) Naturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naïve individuals in Bangalore, India. AIDS Res Hum Retroviruses 26(10): 1097-1101. [PMID:20836706]

Neogi U, Prarthana BS, D’Souza G, De Costa A, Kuttiatt VS, Ranga U, Shet A (2010) Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India. AIDS Res. Ther. 7:24 (21 July 2010) doi:10.1186/1742-6405-7-24. [PMID:20646329]

Neogi U, Sharma Y, Sood V, Wanchu A, Banerjea AC. (2010) Diversity of HIV-1 Long Terminal Repeat (LTR) Sequences following Mother-to-Child Transmission in North India. AIDS Res Hum Retroviruses 26(12): 1299-1305. [PMID: 20929348].

Sharma Y, Neogi U, Sood V, Banerjee S, Samrat S, Wanchu A, Singh S, Banerjea AC (2010) Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India. AIDS Res. Ther. 7:28.[PMID:20682034]

2009

Neogi U, Sood V, Chowdhury A, Das S, Ramachandran VG, Sreedhar VK, Wanchu A, Ghosh N, Banerjea AC (2009) 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: doi:10.1186/1742-6405-6-28. [PMID:19954551]

Bano AS*, Sood V*, Neogi U*, Goel N, Kuttiat VS, Wanchu A, Banerjea AC (2009) Genetic and functional characterization of HIV-1 VprC variants from North India: Presence of unique recombinants with mosaic genomes from B, C and D subtypes within the ORF of Vpr. Gen. Virol. ; 90: 2768 – 2776.[PMID:19605589] [*Equal Contributions]

2008

Neogi U*, Sood V*, Sood V, Goel N, Wanchu A, Banerjea AC (2008). Novel HIV-1 Long Terminal Repeat (LTR) sequences of Subtype B and mosaic inter subtype B/C Recombinants in North India. Virol. 153 (10): 1961-1966. [PMID: 18818865]. [*Equal Contributions]