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About me

I obtained my doctoral degree from Department of Medicine Huddinge, Karolinska Institutet (KI) in 2013. Following my two year postdoc  I joined the  Department of Laboratory Medicine as Assistant Professor in 2015, where my research focuses  on multi-omics system biology approach to understand the disease control mechanism in a group of HIV-1 positive individuals who control viral replication without any therapy called Elite Controller.


March 2014- May 2015

Post-Doctoral Fellow, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden 

June 2013-March 2014

Post-Doctoral Reserach Scientist, St. John's Research Institute, Bangalore, India

2009 – 2013

Ph.D. in Medical Sciences, Karolinska Institutet, Stockholm, Sweden 

Thesis title: Translational genomics of HIV-1 subtype C in India: Molecular phylogeny and drug resistance


M.Sc Microbiology, Bangalore University Bangalore, India                                                        

Research description

The aim my research team is through translational research integrating multi-omics techniques and clinical data to understand the disease control mechanism in a group of HIV-1 positive individuals, who control viral replication and restrained progression to immunodeficiency, without any antiretroviral therapy for a longer duration of time (Elite controllers). 

In a systemic approach, we apply the molecular data-first approach (using genomics, transcriptomics, proteomics, and metabolomics) classifies persistent genetic variants or expression patterns to reduce host influenced heterogeneity followed by the phenotypic profiling, virological and immunological characterizations of the disease control mechanisms. This understanding of the unique gene expression and immunological characteristics of EC will predict a frame of reference for what may be required in clinical intervention strategies to induce immune control of HIV-1 and the future development of functional HIV-cure.

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Teaching portfolio

Teaching assignments under the Biomedical Laboratory Science program

Academic honours, awards and prizes




Jonas Söderquist’s Stipendium for Experimental Virology and Immunology Research-2016 for research in development of high-throughput techniques to quantify HIV-1 latent reservoir.


AIDS International Training and Research Program (AITRP) fellowship, sponsored by National Institute of Health (NIH), US for training at Albert Einstein College of Medical Science, NY.


1.1. Ongoing 

01/2018-12/2021 Swedish Research Council (Startup grant- 2017-01330)

A multi-omics system biology approach to identify disease control mechanisms in HIV-1 positive Elite Controllers and the importance for HIV-cure

Role: Principal Investigator

11/2017-10/2021 Karolinska Institutet Doctoral Student Funding (KID2016-0022)

Characterization of HIV-1 persistence and dynamics in the latent viral reservoir

Role: Co-Investigator

11/2016-10/2018 Harald and Greta Jeansson Foundation (JS2016-0185)

Mechanisms of HIV-1 persistence and latency: Implications for a cure

Role: Principal Investigator

01/2017-12/2019 Stockholm County Council, ALF-Project Funding Medicine (Ref#20160074)

Clinical and translational studies of virus-host interactions for optimization of HIV treatment and possible cure of HIV

Role: Co-Investigator

07/2016-06/2020  US National Institute of Health (R01 GM118012-01)

Reverse transcriptase multi-class drug resistance and rilpivirine susceptibility in diverse HIV-1 Subtypes

Role: Site-PI

03/2016-02/2020 Karolinska Institutet Doctoral Student Funding (KID2015-154)

High throughput system biology approach to identify resistance mechanisms against protease inhibitors in South African HIV-1C

Role: Principal Investigator

01/2016-07/2017  Swedish Physicians Against AIDS Foundation (Fob2015-009)

Viral genome wide association study to understand the mechanism of protease inhibitor failure

Role: Principal Investigator

01/2016-12/2018 Swedish Research Council  (2015-05914) 

Development of a molecular surveillance phylogeographic tool to track HIV transmission networks in Bangladesh

Role: Co-Investigator

06/2015-05/2019 Karolinska Institutet Doctoral Student Funding (KID2014-114)

Role of viral evolution for HIV-1 subtype C fitness, host-reactivity and therapeutic response

Role: Co-Investigator




A high rate of HIV-1 acquisition post immigration among migrants in Sweden determined by a CD4 T-cell decline trajectory model
Brännström J, Sönnerborg A, Svedhem V, Neogi U, Marrone G
HIV medicine 2017;18(9):677-684

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
Svärd J, Mugusi S, Mloka D, Neogi U, Meini G, Mugusi F, et al
PloS one 2017;12(6):e0178942-

Effect of therapy switch on time to second-line antiretroviral treatment failure in HIV-infected patients
Häggblom A, Santacatterina M, Neogi U, Gisslen M, Hejdeman B, Flamholc L, et al
PloS one 2017;12(7):e0180140-

Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa
Aralaguppe Sg, Winner D, Singh K, Sarafianos Sg, Quiñones-mateu Me, Sönnerborg A, et al
Journal of medical virology 2017;89(1):106-111

Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy
Zhang W, Morshed Mm, Noyan K, Russom A, Sönnerborg A, Neogi U
Scientific reports 2017;7(1):666-

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden
Neogi U, Siddik Ab, Kalaghatgi P, Gisslén M, Bratt G, Marrone G, et al
Scientific reports 2017;7(1):6371-

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers
Vesterbacka J, Rivera J, Noyan K, Parera M, Neogi U, Calle M, et al
Scientific reports 2017;7(1):6269-

Can HIV reverse transcriptase activity assay be a low-cost alternative for viral load monitoring in resource-limited settings?
Gupta S, Palchaudhuri R, Neogi U, Srinivasa H, Ashorn P, De Costa A, et al
BMJ open 2016;6(1):e008795-

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries
Neogi U, Häggblom A, Singh K, Rogers Lc, Rao Sd, Amogne W, et al
The Journal of antimicrobial chemotherapy 2016;71(2):367-71

Global epidemiology of drug resistance after failure of WHO recommended first-line regimens for adult HIV-1 infection: a multicentre retrospective cohort study
Tenores Study Grp, Gregson J, Tang M, Ndembi N, Hamers Rl, Rhee Sy, et al

Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus
Aralaguppe Sg, Siddik Ab, Manickam A, Ambikan At, Kumar Mm, Fernandes Sj, et al
Journal of virological methods 2016;236():98-104

Mutational Heterogeneity in p6 Gag Late Assembly (L) Domains in HIV-1 Subtype C Viruses from South Africa
Neogi U, Engelbrecht S, Claassen M, Jacobs Gb, Van Zyl G, Preiser W, et al
AIDS research and human retroviruses 2016;32(1):80-4

Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster
Amogne W, Bontell I, Grossmann S, Aderaye G, Lindquist L, Sönnerborg A, et al
AIDS research and human retroviruses 2016;32(5):471-4

Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden
Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U
The lancet. HIV 2016;3(4):e166-74

Gut microbiota diversity predicts immune status in HIV-1 infection
Nowak P, Troseid M, Avershina E, Barqasho B, Neogi U, Holm K, et al
AIDS (London, England) 2015;29(18):2409-18

Performance of Genotypic Tools for Prediction of Tropism in HIV-1 Subtype C V3 Loop Sequences
Gupta S, Neogi U, Srinivasa H, Shet A
INTERVIROLOGY 2015;58(1):1-5

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management
Grossmann S, Nowak P, Neogi U
Journal of the International AIDS Society 2015;18():20035-

Virological efficacy with first-line antiretroviral treatment in India: predictors of viral failure and evidence of viral resuppression
Shet A, Neogi U, Kumarasamy N, Decosta A, Shastri S, Rewari Bb

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries
Ekici H, Rao Sd, Sönnerborg A, Ramprasad Vl, Gupta R, Neogi U
The Journal of antimicrobial chemotherapy 2014;69(12):3349-55

Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors
Singh K, Flores Ja, Kirby Ka, Neogi U, Sonnerborg A, Hachiya A, et al
Viruses 2014;6(9):3535-62

Effect of mobile telephone reminders on treatment outcome in HIV: evidence from a randomised controlled trial in India
Shet A, De Costa A, Kumarasamy N, Rodrigues R, Rewari Bb, Ashorn P, et al
BMJ (Clinical research ed.) 2014;349():g5978-

Genetic Factors Associated with Slow Progression of HIV among Perinatally-Infected Indian Children
Chaudhuri Rp, Neogi U, Rao Sd, Shet A
INDIAN PEDIATRICS 2014;51(10):801-3

HIV-1 coreceptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades
Gupta S, Neogi U, Srinivasa H, Banerjea Ac, Shet A
Journal of acquired immune deficiency syndromes (1999) 2014;65(4):397-404

Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitor resistance mutations in therapy-naive HIV-1-infected individuals in India
Neogi U, Gupta S, Palchaudhuri R, Rao Sd, Shastri S, Diwan V, et al
Antiviral therapy 2014;19(8):813-8

Minor viral population with drug-resistant mutation and risk of persistent low-level viremia or 'blips' in HIV-1 subtype C
Neogi U, Sonnerborg A
AIDS (London, England) 2014;28(17):2635-6

Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients
Neogi U, Rao Sd, Bontell I, Verheyen J, Rao Vr, Gore Sc, et al
AIDS (London, England) 2014;28(15):2319-22

Phylogenetic Characterization of Six Full-Length HIV-1 Subtype C Molecular Clones from Three Patients: Identification of Rare Subtype C Strains Containing Two NF-kappa B Motifs in the Long Terminal Repeat
Hanna Le, Neogi U, Ranga U, Swaminathan S, Prasad Vr

Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades
Neogi U, Häggblom A, Santacatterina M, Bratt G, Gisslén M, Albert J, et al
PloS one 2014;9(6):e99390-

The gp120 protein is a second determinant of decreased neurovirulence of Indian HIV-1C isolates compared to southern African HIV-1C isolates
Rao Vr, Neogi U, Eugenin E, Prasad Vr
PloS one 2014;9(9):e107074-

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
Rao Vr, Neogi U, Talboom Js, Padilla L, Rahman M, Fritz-french C, et al
Retrovirology 2013;10():61-

Effectiveness of First-line Antiretroviral Therapy and Acquired Drug Resistance Among HIV-1-infected Children in India
Shet A, Neogi U, Sahoo Pn, De Costa A

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
Neogi U, Palchaudhuri R, Bommana S, Shet A

High concordance of genotypic coreceptor prediction in plasma-viral RNA and proviral DNA of HIV-1 subtype C: implications for use of whole blood DNA in resource-limited settings
Gupta S, Neogi U, Srinivasa H, Shet A

High Viremia in HIV-1 Subtype C Infection and Spread of the Epidemic
Neogi U, Palchaudhuri R, Shet A

Human APOBEC3G-mediated hypermutation is associated with antiretroviral therapy failure in HIV-1 subtype C-infected individuals
Neogi U, Shet A, Sahoo Pn, Bontell I, Ekstrand Ml, Banerjea Ac, et al
Journal of the International AIDS Society 2013;16():18472-

Long-term efficacy of first line antiretroviral therapy in Indian HIV-1 infected patients: a longitudinal cohort study
Neogi U, Heylen E, Shet A, Chandy S, Shamsunder R, Sönnerborg A, et al
PloS one 2013;8(1):e55421-

Dried blood spot HIV-1 RNA quantification: A useful tool for viral load monitoring among HIV-infected individuals in India
Neogi U, Gupta S, Rodridges R, Sahoo Pn, Rao Sd, Rewari Bb, et al

Emergence of unique recombinant forms (URFs) in Indian HIV-1 epidemic: data from nationwide clinical cohort between 2007 and 2011
Neogi U, Gupta S, Shet A, De Costa A, Laishram Rl, Wanchu A, et al

Genetic Characterization of HIV Type 1 Tat Exon 1 from a Southern Indian Clinical Cohort: Identification of Unique Epidemiological Signature Residues
Neogi U, Gupta S, Sahoo Pn, Shet A, Rao Sd, Ranga U, et al

Higher Prevalence of Predicted X4-Tropic Strains in Perinatally Infected Older Children With HIV-1 Subtype C in India
Neogi U, Sahoo Pn, Arumugam K, Sonnerborg A, De Costa A, Shet A

High viremia and low level of transmitted drug resistance in anti-retroviral therapy-naïve perinatally-infected children and adolescents with HIV-1 subtype C infection
Neogi U, Sahoo Pn, De Costa A, Shet A
BMC infectious diseases 2012;12():317-

Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C
Neogi U, Bontell I, Shet A, De Costa A, Gupta S, Diwan V, et al
PloS one 2012;7(6):e39819-

Characterization of HIV Type 1 Subtype C protease Gene: Selection of L63P Mutation in Protease Inhibitor-Naive Indian Patients
Neogi U, Sahoo Pn, Kumar R, De Costa A, Shet A

Genetic architecture of HIV-1 genes circulating in north India & their functional implications
Neogi U, Sood V, Ronsard L, Singh J, Lata S, Ramachandran Vg, et al

Selection of nonnucleoside reverse transcriptase inhibitor-associated mutations in HIV-1 subtype C: evidence of etravirine cross-resistance
Neogi U, Shet A, Shamsundar R, Ekstrand Ml
AIDS 2011;25(8):1123-6

Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India
Neogi U, Prarthana Sb, D'souza G, Decosta A, Kuttiatt Vs, Ranga U, et al

Diversity of HIV Type 1 Long Terminal Repeat (LTR) Sequences Following Mother-to-Child Transmission in North India
Neogi U, Sharma Y, Sood V, Wanchu A, Banerjea Ac

Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India
Sharma Y, Neogi U, Sood V, Banerjee S, Samrat S, Wanchu A, et al
AIDS research and therapy 2010;7():28-

Naturally Occurring Polymorphisms and Primary Drug Resistance Profile Among Antiretroviral-Naive Individuals in Bangalore, India
Neogi U, Prarthana Bs, Gupta S, D'souza G, De Costa A, Kuttiatt Vs, et al

Emergence of HIV-1 circulatory recombinant forms (CRFs) and unique recombinant forms (URFs) in North India: functional and pathogenic implications
Neogi U, Sood V, Bano As, Wanchu A, 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
Neogi U, Sood V, Chowdhury A, Das S, Ramachandran Vg, Sreedhar Vk, et al
AIDS research and therapy 2009;6():28-

Genetic and functional characterization of human immunodeficiency virus type 1 VprC variants from north India: presence of unique recombinants with mosaic genomes from B, C and D subtypes within the open reading frame of Vpr
Bano As, Sood V, Neogi U, Goel N, Kuttiat Vs, Wanchu A, et al

Global HIV-1 molecular epidemiology with special reference to genetic analysis of HIV-1 subtypes circulating in North India: functional and pathogenic implications of genetic variation
Neogi U, Sood V, Banerjee S, Ghosh N, Verma S, Samrat S, et al
Indian journal of experimental biology 2009;47(6):424-31

The expanding HIV-1 epidemic aggravates therapeutics and vaccine development programs in India
Neogi U
Bioinformation 2009;4(3):90-1

Host genes that affect progression of AIDS/HIV in India and novel gene therapeutic approaches against HIV
Sood V, Rathore A, Husain S, Khan S, Patra S, Shankar V, et al

Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India
Neogi U, Sood V, Goel N, Wanchu A, Banerjea Ac
ARCHIVES OF VIROLOGY 2008;153(10):1961-6

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