List of works - Ujjwal Neogi

A high rate of HIV-1 acquisition post immigration among migrants in Sweden determined by a CD4 T-cell decline trajectory model

scientific article published on 26 April 2017

A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2

scientific article published on 01 January 2022

A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort

scientific article published on 01 July 2019

Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine

scientific article published on 21 December 2020

Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa

scientific article published on 16 March 2018

Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes

article

Author Correction: Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and availability of integrase inhibitors in Cape Town, South Africa

scientific article published on 16 April 2018

Can HIV reverse transcriptase activity assay be a low-cost alternative for viral load monitoring in resource-limited settings?

scientific article published on 27 January 2016

Characterization of HIV type 1 subtype C protease gene: selection of L63P mutation in protease inhibitor-naive Indian patients

scientific article published on 9 May 2011

Characterization of Inducible Transcription and Translation-Competent HIV-1 Using the RNAscope ISH Technology at a Single-Cell Resolution

article

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.

scientific article published on 08 June 2013

Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India

scientific article

Community prevalence of methicillin and vancomycin resistant Staphylococcus aureus in and around Bangalore, southern India

scientific article published on 01 May 2011

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

scientific article published on 31 July 2014

Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative (HESN) Women

scientific article published on 27 October 2021

Diversity of HIV type 1 long terminal repeat (LTR) sequences following mother-to-child transmission in North India

scientific article published on 7 October 2010

Dried blood spot HIV-1 RNA quantification: a useful tool for viral load monitoring among HIV-infected individuals in India

scientific article published on December 2012

Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa

scientific article published on 20 March 2020

Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors

scientific article

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.

scientific article

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells

scientific article published on 21 July 2020

Effect of therapy switch on time to second-line antiretroviral treatment failure in HIV-infected patients

scientific article published on 20 July 2017

Effectiveness of first-line antiretroviral therapy and acquired drug resistance among HIV-1-infected children in India

scientific article

Emergence of HIV-1 drug resistance in antiretroviral therapy experienced perinatally infected children in South India

scientific article published on 4 May 2012

Emergence of unique recombinant forms (URFs) in Indian HIV-1 epidemic: data from nationwide clinical cohort between 2007 and 2011.

scientific article

Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes

scientific article published on 12 December 2017

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries

scientific article

GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds

scientific article published on 20 June 2019

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

scientific article published on 03 December 2009

Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India

scientific article

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.

scientific article published on 15 July 2009

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.

scientific article published on 5 October 2013

Genetic architecture of HIV-1 genes circulating in north India & their functional implications

scientific article

Genetic characterization of HIV type 1 Tat exon 1 from a southern Indian clinical cohort: identification of unique epidemiological signature residues

scientific article

Genetic factors associated with slow progression of HIV among perinatally-infected Indian children

scientific article published on October 2014

Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection

scientific article published on 10 May 2022

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.

scientific article published on June 2009

Gut microbiota diversity predicts immune status in HIV-1 infection.

scientific article published on 9 September 2015

HIV elite control is associated with reduced TRAILshort expression

scientific article published on 01 September 2019

HIV-1 Subtype C with PYxE Insertion Has Enhanced Binding of Gag-p6 to Host Cell Protein ALIX and Increased Replication Fitness

scientific article published on 17 April 2019

HIV-1 coreceptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades

scientific article published on April 2014

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

scientific article published on 30 April 2013

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

scientific article

High viremia in HIV-1 subtype C infection and spread of the epidemic

scientific article published on 10 June 2013

Higher prevalence of predicted X4-tropic strains in perinatally infected older children with HIV-1 subtype C in India

scientific article

Human APOBEC3G-mediated hypermutation is associated with antiretroviral therapy failure in HIV-1 subtype C-infected individuals

scientific article published on 25 February 2013

Immune Checkpoints as the Immune System Regulators and Potential Biomarkers in HIV-1 Infection

article

In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

scientific article published on 17 February 2020

Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa.

scientific article

Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitor resistance mutations in therapy-naive HIV-1-infected individuals in India.

scientific article published on 4 April 2014

Long-term efficacy of first line antiretroviral therapy in Indian HIV-1 infected patients: a longitudinal cohort study

scientific article

MDR1 gene polymorphisms and HIV therapeutic response in South Indian population

article

MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors

scientific article published on 30 August 2019

Microfluidic centrifugation assisted precipitation based DNA quantification

scientific article published on 01 April 2019

Minor viral population with drug-resistant mutation and risk of persistent low-level viremia or 'blips' in HIV-1 subtype C.

scientific article published in November 2014

Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

scientific article

Multiple NF-κB sites in HIV-1 subtype C long terminal repeat confer superior magnitude of transcription and thereby the enhanced viral predominance

scientific article

Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus

scientific article published on 19 July 2016

Mutational Heterogeneity in p6 Gag Late Assembly (L) Domains in HIV-1 Subtype C Viruses from South Africa

scientific article published on 28 September 2015

Mutations in Long Terminal Repeats κB Transcription Factor Binding Sites in Plasma Virus Among South African People Living with HIV-1

scientific article published on 04 April 2019

Naturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naive individuals in Bangalore, India

scientific article published on 13 September 2010

Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India

scientific article published on 26 September 2008

Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients.

scientific article

Nucleoside-Modified mRNA Vaccines Protect IFNAR-/- Mice against Crimean-Congo Hemorrhagic Fever Virus Infection

scientific article published on 24 November 2021

P20-05. Emergence of HIV-1 circulatory recombinant forms (CRFs) and unique recombinant forms (URFs) in North India: functional and pathogenic implications

article

Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease

scientific article published in 2024

Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences

scientific article published on 7 January 2015

Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals

scientific article published on 13 April 2022

Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa

scientific article

Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster

scientific article published on 16 February 2016

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

scientific article

Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy

scientific article published on 30 September 2019

Plasma soluble factor following two decades prolonged suppressive antiretroviral therapy in HIV-1-positive males: A cross-sectional study.

scientific article published in February 2018

Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing

scientific article published on 15 May 2018

Proceedings of the Frontiers of Retrovirology Conference 2016.

scientific article published on 26 September 2016

Publisher Correction: In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

scientific article published on 10 August 2020

Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy

scientific article

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden

scientific article

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers

scientific article

Selection of nonnucleoside reverse transcriptase inhibitor-associated mutations in HIV-1 subtype C: evidence of etravirine cross-resistance

scientific article published on May 2011

Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes

article

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

scientific article

Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy

scientific article published on 27 August 2019

Temporal trends in the Swedish HIV-1 epidemic: increase in non-B subtypes and recombinant forms over three decades

scientific article

The expanding HIV-1 epidemic aggravates therapeutics and vaccine development programs in India

scientific article

The gp120 protein is a second determinant of decreased neurovirulence of Indian HIV-1C isolates compared to southern African HIV-1C isolates

scientific article

The microbial metabolite trimethylamine-N-oxide in association with inflammation and microbial dysregulation in three HIV cohorts at various disease stages

scientific article published on 01 July 2018

Trans cohort metabolic reprogramming towards glutaminolysis in long-term successfully treated HIV-infection

scientific article published on 11 January 2022

Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.

scientific article published on 12 December 2017

Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells

scientific article published on 18 May 2021

Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses

scientific article

Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses

scientific article published on 23 October 2020

Virological efficacy with first-line antiretroviral treatment in India: predictors of viral failure and evidence of viral resuppression

scientific article published on 3 July 2015

Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden

scientific article

List of works by Ujjwal Neogi

A high rate of HIV-1 acquisition post immigration among migrants in Sweden determined by a CD4 T-cell decline trajectory model

A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2

A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort

Altered Gut Microbiome under Antiretroviral Therapy: Impact of Efavirenz and Zidovudine

Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and available of integrase inhibitors in Cape Town, South Africa

Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes

Author Correction: Analyses of HIV-1 integrase sequences prior to South African national HIV-treatment program and availability of integrase inhibitors in Cape Town, South Africa

Can HIV reverse transcriptase activity assay be a low-cost alternative for viral load monitoring in resource-limited settings?

Characterization of HIV type 1 subtype C protease gene: selection of L63P mutation in protease inhibitor-naive Indian patients

Characterization of Inducible Transcription and Translation-Competent HIV-1 Using the RNAscope ISH Technology at a Single-Cell Resolution

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.

Co-receptor tropism prediction among 1045 Indian HIV-1 subtype C sequences: Therapeutic implications for India

Community prevalence of methicillin and vancomycin resistant Staphylococcus aureus in and around Bangalore, southern India

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative (HESN) Women

Diversity of HIV type 1 long terminal repeat (LTR) sequences following mother-to-child transmission in North India

Dried blood spot HIV-1 RNA quantification: a useful tool for viral load monitoring among HIV-infected individuals in India

Drug Resistance Mutations Against Protease, Reverse Transcriptase and Integrase Inhibitors in People Living With HIV-1 Receiving Boosted Protease Inhibitors in South Africa

Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors

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.

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells

Effect of therapy switch on time to second-line antiretroviral treatment failure in HIV-infected patients

Effectiveness of first-line antiretroviral therapy and acquired drug resistance among HIV-1-infected children in India

Emergence of HIV-1 drug resistance in antiretroviral therapy experienced perinatally infected children in South India

Emergence of unique recombinant forms (URFs) in Indian HIV-1 epidemic: data from nationwide clinical cohort between 2007 and 2011.

Ex-vivo antiretroviral potency of newer integrase strand transfer inhibitors cabotegravir and bictegravir in HIV type 1 non-B subtypes

Factors influencing the efficacy of rilpivirine in HIV-1 subtype C in low- and middle-income countries

GS-CA Compounds: First-In-Class HIV-1 Capsid Inhibitors Covering Multiple Grounds

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

Genetic and functional analysis of HIV-1 Rev Responsive Element (RRE) sequences from North-India

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.

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.

Genetic architecture of HIV-1 genes circulating in north India & their functional implications

Genetic characterization of HIV type 1 Tat exon 1 from a southern Indian clinical cohort: identification of unique epidemiological signature residues

Genetic factors associated with slow progression of HIV among perinatally-infected Indian children

Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection

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.

Gut microbiota diversity predicts immune status in HIV-1 infection.

HIV elite control is associated with reduced TRAILshort expression

HIV-1 Subtype C with PYxE Insertion Has Enhanced Binding of Gag-p6 to Host Cell Protein ALIX and Increased Replication Fitness

HIV-1 coreceptor tropism in India: increasing proportion of X4-tropism in subtype C strains over two decades

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

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

High viremia in HIV-1 subtype C infection and spread of the epidemic

Higher prevalence of predicted X4-tropic strains in perinatally infected older children with HIV-1 subtype C in India

Human APOBEC3G-mediated hypermutation is associated with antiretroviral therapy failure in HIV-1 subtype C-infected individuals

Immune Checkpoints as the Immune System Regulators and Potential Biomarkers in HIV-1 Infection

In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

Increased replication capacity following evolution of PYxE insertion in Gag-p6 is associated with enhanced virulence in HIV-1 subtype C from East Africa.

Limited evolution but increasing trends of primary non-nucleoside reverse transcriptase inhibitor resistance mutations in therapy-naive HIV-1-infected individuals in India.

Long-term efficacy of first line antiretroviral therapy in Indian HIV-1 infected patients: a longitudinal cohort study

MDR1 gene polymorphisms and HIV therapeutic response in South Indian population

MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors

Microfluidic centrifugation assisted precipitation based DNA quantification

Minor viral population with drug-resistant mutation and risk of persistent low-level viremia or 'blips' in HIV-1 subtype C.

Molecular epidemiology of HIV-1 subtypes in India: origin and evolutionary history of the predominant subtype C.

Multiple NF-κB sites in HIV-1 subtype C long terminal repeat confer superior magnitude of transcription and thereby the enhanced viral predominance

Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus

Mutational Heterogeneity in p6 Gag Late Assembly (L) Domains in HIV-1 Subtype C Viruses from South Africa

Mutations in Long Terminal Repeats κB Transcription Factor Binding Sites in Plasma Virus Among South African People Living with HIV-1

Naturally occurring polymorphisms and primary drug resistance profile among antiretroviral-naive individuals in Bangalore, India

Novel HIV-1 long terminal repeat (LTR) sequences of subtype B and mosaic intersubtype B/C recombinants in North India

Novel tetra-peptide insertion in Gag-p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients.

Nucleoside-Modified mRNA Vaccines Protect IFNAR<sup>-/-</sup> Mice against Crimean-Congo Hemorrhagic Fever Virus Infection

P20-05. Emergence of HIV-1 circulatory recombinant forms (CRFs) and unique recombinant forms (URFs) in North India: functional and pathogenic implications

Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease

Performance of genotypic tools for prediction of tropism in HIV-1 subtype C V3 loop sequences

Peripheral blood CD4<sup>+</sup>CCR6<sup>+</sup> compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals

Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa

Phylogenetic Analysis of Ethiopian HIV-1 Subtype C Near Full-Length Genomes Reveals High Intrasubtype Diversity and a Strong Geographical Cluster

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

Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy

Plasma soluble factor following two decades prolonged suppressive antiretroviral therapy in HIV-1-positive males: A cross-sectional study.

Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing

Proceedings of the Frontiers of Retrovirology Conference 2016.

Publisher Correction: In vitro replicative fitness of early Transmitted founder HIV-1 variants and sensitivity to Interferon alpha

Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers