Adam A. Capoferri
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View article: In vivo detection of antisense HIV-1 transcripts in untreated and ART-treated individuals
In vivo detection of antisense HIV-1 transcripts in untreated and ART-treated individuals Open
Natural antisense transcripts (AST) are expressed in eukaryotes, prokaryotes, and viruses and can possess regulatory functions at the transcriptional and/or post-transcriptional levels. In vitro studies have shown that HIV-1 AST promote vi…
View article: Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy
Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy Open
HIV-1 proviral landscapes were investigated using near-full-length HIV single-genome sequencing on blood samples from five children with vertically acquired infection and on ART for ~7–9 years. Proviral structures were compared to publishe…
View article: Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy
Differential HIV-1 Proviral Defects in Children vs. Adults on Antiretroviral Therapy Open
HIV-1 proviral landscapes were investigated using near full-length HIV single-genome sequencing on blood samples from 5 children with vertically acquired infection and on ART for ∼7-9 years. Proviral structures were compared to published d…
View article: Association between HIV-1 Nef-mediated MHC-I downregulation and the maintenance of the replication-competent latent viral reservoir in individuals with virally suppressed HIV-1 in Uganda: an exploratory cohort study
Association between HIV-1 Nef-mediated MHC-I downregulation and the maintenance of the replication-competent latent viral reservoir in individuals with virally suppressed HIV-1 in Uganda: an exploratory cohort study Open
Canadian Institutes of Health Research, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, and the REACH Martin Delaney Collaboratory.
View article: Divergent populations of HIV-infected naive and memory CD4+ T cell clones in children on antiretroviral therapy
Divergent populations of HIV-infected naive and memory CD4+ T cell clones in children on antiretroviral therapy Open
BACKGROUNDNaive cells comprise 90% of the CD4+ T cell population in neonates and exhibit distinct age-specific capacities for proliferation and activation. We hypothesized that HIV-infected naive CD4+ T cell populations in children on long…
View article: <i>In vivo</i>detection of HIV-1 antisense transcripts in untreated and ART-treated individuals
<i>In vivo</i>detection of HIV-1 antisense transcripts in untreated and ART-treated individuals Open
Natural antisense transcripts are expressed in eukaryotes, prokaryotes, and viruses and can possess regulatory functions at the transcriptional and/or post-transcriptional levels. In vitro studies have shown that HIV-1 antisense transcript…
View article: HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA
HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA Open
In the absence of antiretroviral therapy (ART), a subset of individuals, termed HIV controllers, have levels of plasma viremia that are orders of magnitude lower than non-controllers (NC) who are at higher risk for HIV disease progression.…
View article: HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA
HIV-1 control in vivo is related to the number but not the fraction of infected cells with viral unspliced RNA Open
In the absence of antiretroviral therapy (ART), a subset of individuals, termed HIV controllers, have levels of plasma viremia that are orders of magnitude lower than non-controllers who are at higher risk for HIV disease progression. In a…
View article: Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen
Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen Open
View article: HIV Expression in Infected T Cell Clones
HIV Expression in Infected T Cell Clones Open
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among…
View article: HIV Expression in Infected T Cell Clones
HIV Expression in Infected T Cell Clones Open
The principal barrier to an HIV-1 cure is the persistence of infected cells harboring replication-competent proviruses despite antiretroviral therapy (ART). HIV-1 transcriptional suppression, referred to as viral latency, is foremost among…
View article: Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen
Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen Open
The principal barrier to an HIV cure is the presence of a latent viral reservoir (LVR) made up primarily of latently infected resting CD4+ (rCD4) T-cells. Studies in the United States have shown that the LVR decays slowly (half-life=3.8 ye…
View article: PP 7.7 – 00055 Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to a Dolutegravir-based antiretroviral regiment
PP 7.7 – 00055 Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to a Dolutegravir-based antiretroviral regiment Open
View article: A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States
A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States Open
COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologi…
View article: 2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline
2020 SARS-CoV-2 diversification in the United States: Establishing a pre-vaccination baseline Open
In 2020, SARS-CoV-2 spread across the United States (U.S.) in three phases distinguished by peaks in the numbers of infections and shifting geographical distribution. We investigated the viral genetic diversity in each phase using sequence…
View article: Low genetic diversity may be an Achilles heel of SARS-CoV-2
Low genetic diversity may be an Achilles heel of SARS-CoV-2 Open
STEM PhDs increasingly contribute to commercial science, such as patenting. We analyze faculty's role in training STEM PhD students as new inventors on patents at leading research universities, emphasizing the drivers of gender differences…
View article: Haemopoietic cell transplantation in patients living with HIV
Haemopoietic cell transplantation in patients living with HIV Open
View article: Allogeneic bone marrow transplantation with post-transplant cyclophosphamide for patients with HIV and haematological malignancies: a feasibility study
Allogeneic bone marrow transplantation with post-transplant cyclophosphamide for patients with HIV and haematological malignancies: a feasibility study Open
View article: Reduced HIV-1 latent reservoir outgrowth and distinct immune correlates among women in Rakai, Uganda
Reduced HIV-1 latent reservoir outgrowth and distinct immune correlates among women in Rakai, Uganda Open
HIV-1 infection remains incurable owing to the persistence of a viral reservoir that harbors integrated provirus within host cellular DNA. Increasing evidence links sex-based differences in HIV-1 immune responses and pathogenesis; however,…
View article: Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial)
Impact of Myc in HIV-associated non-Hodgkin lymphomas treated with EPOCH and outcomes with vorinostat (AMC-075 trial) Open
EPOCH (etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin) is a preferred regimen for HIV-non-Hodgkin lymphomas (HIV-NHLs), which are frequently Epstein-Barr virus (EBV) positive or human herpesvirus type-8 (HHV-8) posit…
View article: Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda
Recombination Analysis of Near Full-Length HIV-1 Sequences and the Identification of a Potential New Circulating Recombinant Form from Rakai, Uganda Open
The Phylogenetics And Networks for Generalized HIV Epidemics in Africa (PANGEA-HIV) consortium has been vital in the generation and examination of near full-length HIV-1 sequences generated from Sub-Saharan Africa. In this study, we examin…
View article: Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors
Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors Open
Understanding HIV-1 persistence despite antiretroviral therapy (ART) is of paramount importance. Both single-genome sequencing (SGS) and integration site analysis (ISA) provide useful information regarding the structure of persistent HIV D…
View article: HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus
HIV Infected T Cells Can Proliferate in vivo Without Inducing Expression of the Integrated Provirus Open
These findings show that the vast majority of HIV-1 proviruses within expanded T cell clones, including intact proviruses, may be transcriptionally silent at any given time, implying that infected T cells may be able to be activated to pro…
View article: A15 Archived ART resistance in the latent reservoir of virally suppressed Ugandans
A15 Archived ART resistance in the latent reservoir of virally suppressed Ugandans Open
The increased access of antiretroviral therapy (ART) has drastically improved the health of infected individuals. However, increased levels of ART resistance globally threaten ART effectiveness. Resistance monitoring is currently limited t…
View article: Antiretroviral Adherence, Elevated Viral Load, and Drug Resistance Mutations in Human Immunodeficiency Virus–infected Women Initiating Treatment in Pregnancy: A Nested Case-control Study
Antiretroviral Adherence, Elevated Viral Load, and Drug Resistance Mutations in Human Immunodeficiency Virus–infected Women Initiating Treatment in Pregnancy: A Nested Case-control Study Open
Background Elevated viral load (VL) early after antiretroviral therapy (ART) initiation appears frequently in pregnant and postpartum women living with human immunodeficiency virus; however the relative contributions of pre-ART drug resist…
View article: Comparison of Immune Responses to Different Versions of VLP Associated Stabilized RSV Pre-Fusion F Protein
Comparison of Immune Responses to Different Versions of VLP Associated Stabilized RSV Pre-Fusion F Protein Open
Efforts to develop a vaccine for respiratory syncytial virus (RSV) have primarily focused on the RSV fusion protein. The pre-fusion conformation of this protein induces the most potent neutralizing antibodies and is the focus of recent eff…
View article: A quantitative approach for measuring the reservoir of latent HIV-1 proviruses
A quantitative approach for measuring the reservoir of latent HIV-1 proviruses Open
View article: Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays
Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays Open
Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long…
View article: Cross-reactive microbial peptides can modulate HIV-specific CD8+ T cell responses
Cross-reactive microbial peptides can modulate HIV-specific CD8+ T cell responses Open
Heterologous immunity is an important aspect of the adaptive immune response. We hypothesized that this process could modulate the HIV-1-specific CD8+ T cell response, which has been shown to play an important role in HIV-1 immunity and co…
View article: Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4+ T Cells Permissive for Latent HIV-1 Infection
Transcriptional Reprogramming during Effector-to-Memory Transition Renders CD4+ T Cells Permissive for Latent HIV-1 Infection Open