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Ujjwal Neogi

Assistant professor

Visiting address : Alfred Nobels Allé 8, Plan 7, Karolinska Universitetssjukhuset, Huddinge 141 86 Stockholm, Sweden
Postal address : Department of Laboratory Medicine (LABMED), H5, Division of Clinical Microbiology, F68, Karolinska Universitetssjukhuset, Huddinge 141 86 Stockholm, Sweden
Delivery address : F68, Karolinska Universitetssjukhuset, Huddinge 141 86 Stockholm, Sweden

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  drug resistance, molecular adaptation, pathogenic fitness, HIV-1 latency and latency reversal.


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 key aspect of my research is to understand the virus adaptation in the environment of host and antiretroviral those together influence the viral transmission, pathogenesis, disease progression, therapeutic response and cure.

Project Theme I: Mechanisms of drug resistance dynamics and efficacy of newly emerging long acting antiretroviral compounds in diverse HIV-1 subtypes

The prime research question in this program is to achieve the maximum efficacy of the newly emerging antiretroviral compounds (reverse transcriptase inhibitors, integrase inhibitor and protease inhibitor) understanding the viral suppression potentials, mechanisms of resistance and viral persistence across diverse subtypes. The consequent optimization of the use of these drugs could potentially lead to that they will become the drug-of-choice in globally including the low- and middle- income countries. The studies run as a part of large multi-disciplinary expert project in the field of molecular biology, virology, structural protein modelling and biochemistry, high throughput genomics, evolutionary dynamics and clinical science.

Project Theme II: Mechanisms of viral persistence in patients on suppressive antiretroviral therapy

The major research question in this program is to understand the mechanism of HIV persistence and phyloanatomical evolutionary dynamics in the HIV reservoir, the major barrier to cure of HIV-1 infection. We are developing high throughput techniques to measure the size of the latent reservoir in order to understand the HIV-1 dynamics and persistent replication in the reservoir that is of key importance for either a cure or long term HIV remission. Our research also focuses on understanding the mechanisms of the host gene regulations after the reversal of the HIV-1 latency using the latency reversal agents (LRAs).

Project Theme III: System biology approach to understand replicative fitness and pathogenic properties of the emerging new viral strains of HIV-1 in Sweden

The third area where we are working extensively is to understand in depth the molecular epidemiology and phylodynamics of HIV-1 subtypes in Sweden, India, Bangladesh and South Africa. The main aim is to understand intra- and inter-country the spread of the HIV-1 subtypes and newly emerging recombinant forms. Rather than smaller gene fragment, we are focusing more on HIV-1 near full-length genome (HIV-NFLG). We are also working to understand the differences in pathogenic fitness and therapy response using in vitro phenotypic assays.

Academic honors, awards and prizes


Doctoral Study

1.1. Main Supervisor

1.2. Co-supervisor

Master Thesis

  • Ms. Maike Sperk, Master in Molecular MedicineTübingen University, 03/2017-
  • Ms. Mira Akber, Master Thesis (30 Credits), Uppsala Graduate School in Biomedical Research (UGSBR), Uppsala University, 08/2016 - present 
  • Md. Monzur Morshed, Master Thesis (30 Credits), Cell and Molecular Biology Uppsala University, (04/2016-10/2016)
  • Mr. Abu Bakar Siddik, Master Thesis (60 Credits), Molecular Biotechnology, University of Skövde (06/2015- 08/2016).
  • Md Shanawazur Rahman, Master Thesis (15 Credits), Infectious Disease Control, Sodertorns Hogskola, Sweden (04/2016 – 08/2016)

Research Internship

  • Mr Philipp Kalus, Vrije Universiteit Brussel Bachelor’s Program Biomedical Science (02/2017-04/2017)



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                                  

2017-2021 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: Co-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

Amount: SEK 1,140, 000

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

1.2. Completed

01/2015-12/2016 Karolinska Institutet Research Foundation Grants (2014fobi41250)

Genome Wide Association Study in HIV-1: Molecular adaptation following therapy failure affecting viral fitness

(Special grant for Young Scientist)

Role: Principal Investigator

Amount: SEK 248,000

03/2015-02/2019 (Declined)  Wellcome Trust/ DBT India Alliance Early Career Fellowship (IA/E/13/1/501245)

A multi-approach translational research for better therapeutic management: Viral genomic adaptation in HIV-1 subtype C affecting viral fitness following drug resistance

Role: Principal Investigator

10/2010-06/2013     European Commission

Erasmus Mundus External Co-operation Window 13 (India) fellowship

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

Role: Principal Investigator

01/2011-06/2012 Swedish Physicians against AIDS Research Foundation (FOa2011-0014)

Human APOBEC mediated hypermutations induced drug resistance

Role: Main Applicant




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

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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