15 results on '"Harbolick, Elizabeth A."'
Search Results
2. Targeted deep sequencing of HIV-1 using the IonTorrentPGM platform
- Author
-
Kijak, Gustavo H., Sanders-Buell, Eric, Harbolick, Elizabeth A., Pham, Phuc, Chenine, Agnes L., Eller, Leigh Anne, Rono, Kathleen, Robb, Merlin L., Michael, Nelson L., Kim, Jerome H., and Tovanabutra, Sodsai
- Published
- 2014
- Full Text
- View/download PDF
3. T-cell mediated immunity after AZD1222 vaccination: A polyfunctional spike-specific Th1 response with a diverse TCR repertoire
- Author
-
Swanson, Phillip A., Padilla, Marcelino, Hoyland, Wesley, McGlinchey, Kelly, Fields, Paul A., Bibi, Sagida, Faust, Saul N., McDermott, Adrian B., Lambe, Teresa, Pollard, Andrew J., Durham, Nicholas M., Kelly, Elizabeth J., Adlou, Syed, Aley, Parvinder K., Angus, Brian, Anslow, Rachel, Baker, Philip, Bansal, Himanshu, Beveridge, Amy, Bridges-Webb, Alice, Ching, Steven, Cicconi, Paola, Clutterbuck, Elizabeth A., Collins, Andrea M., Darton, Thomas C., Demissie, Tesfaye, Dinesh, Tanya, Douglas, Alexander D., Duncan, Christopher J. A., Ewer, Katie J., Felle, Sally, Finn, Adam, Folegatti, Pedro M., Fuskova, Michelle, Gilbert, Sarah C., Goodman, Anna, Green, Christopher A., Harbolick, Elizabeth, Hart, Thomas C., Hayes, Susana, Hill, Adrian V. S., Jenkin, Daniel, Jepson, Brett M., Kasanyinga, Mwila, Kerridge, Simon, Libri, Vincenzo, Lillie, Patrick J., McGregor, Alastair C., Minassian, Angela M., Mujadidi, Yama F., Pilataxi, Fernanda, Plested, Emma, Provstgaard-Morys, Samuel, Ramasamy, Maheshi, Robinson, Hannah, Sanders, Katherine, Smith, Andrew, Snape, Matthew D., Song, Rinn, Sutherland, Rebecca K., Thomson, Emma C., Toshner, Mark, Turner, David P. J., Voysey, Merryn, and Williams, Christopher J.
- Subjects
COVID-19 Vaccines ,SARS-CoV-2 ,Immunogenicity ,T cell ,Vaccination ,T-cell receptor ,Receptors, Antigen, T-Cell ,COVID-19 ,Biology ,Peripheral blood mononuclear cell ,Article ,T cell mediated immunity ,medicine.anatomical_structure ,ChAdOx1 nCoV-19 ,Spike Glycoprotein, Coronavirus ,Immunology ,medicine ,Humans ,Receptor ,CD8 - Abstract
AZD1222 (ChAdOx1 nCoV-19), a replication-deficient simian adenovirus-vectored vaccine, has demonstrated safety, efficacy, and immunogenicity against coronavirus disease 2019 (COVID-19) in clinical trials and real-world studies. We characterized CD4+ and CD8+ T-cell responses induced by AZD1222 vaccination in peripheral blood mononuclear cells (PBMCs) from 280 unique vaccine recipients aged 18–85 years who enrolled in the phase 2/3 COV002 trial. Total spike-specific CD4+ T cell helper type 1 (Th1) and CD8+ T-cell responses were significantly increased in AZD1222-vaccinated adults of all ages following two doses of AZD1222. CD4+ Th2 responses following AZD1222 vaccination were not detected. Furthermore, AZD1222-specific Th1 and CD8+ T cells both displayed a high degree of polyfunctionality in all adult age groups. T-cell receptor (TCR) β sequences from vaccinated participants mapped against TCR sequences known to react to SARS-CoV-2 revealed substantial breadth and depth across the SARS-CoV-2 spike protein for the AZD1222-induced CD4+ and CD8+ T-cell responses. Overall, AZD1222 vaccination induced a robust, polyfunctional Th1-dominated T-cell response, with broad CD4+ and CD8+ T-cell coverage across the SARS-CoV-2 spike protein.One Sentence SummaryPolyfunctional CD4+ and CD8+ T-cell responses are elicited against the SARS-CoV-2 spike protein following vaccination with AZD1222
- Published
- 2021
4. Factors influencing estimates of HIV-1 infection timing using BEAST.
- Author
-
Dearlove, Bethany, Tovanabutra, Sodsai, Owen, Christopher L., Lewitus, Eric, Li, Yifan, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, Anne-Marie, Kijak, Gustavo, Miller, Shana, Poltavee, Kultida, Lee, Jenica, Bonar, Lydia, Harbolick, Elizabeth, Ahani, Bahar, Pham, Phuc, Kibuuka, Hannah, Maganga, Lucas, Nitayaphan, Sorachai, and Sawe, Fred K.
- Subjects
HIV ,MOLECULAR clock ,GENES ,BAYESIAN analysis ,TIME management ,INFECTION - Abstract
While large datasets of HIV-1 sequences are increasingly being generated, many studies rely on a single gene or fragment of the genome and few comparative studies across genes have been done. We performed genome-based and gene-specific Bayesian phylogenetic analyses to investigate how certain factors impact estimates of the infection dates in an acute HIV-1 infection cohort, RV217. In this cohort, HIV-1 diagnosis corresponded to the first RNA positive test and occurred a median of four days after the last negative test, allowing us to compare timing estimates using BEAST to a narrow window of infection. We analyzed HIV-1 sequences sampled one week, one month and six months after HIV-1 diagnosis in 39 individuals. We found that shared diversity and temporal signal was limited in acute infection, and insufficient to allow timing inferences in the shortest HIV-1 genes, thus dated phylogenies were primarily analyzed for env, gag, pol and near full-length genomes. There was no one best fitting model across participants and genes, though relaxed molecular clocks (73% of best fitting models) and the Bayesian skyline (49%) tended to be favored. For infections with single founders, the infection date was estimated to be around one week pre-diagnosis for env (IQR: 3–9 days) and gag (IQR: 5–9 days), whilst the genome placed it at a median of 10 days (IQR: 4–19). Multiply-founded infections proved problematic to date. Our ability to compare timing inferences to precise estimates of HIV-1 infection (within a week) highlights that molecular dating methods can be applied to within-host datasets from early infection. Nonetheless, our results also suggest caution when using uniform clock and population models or short genes with limited information content. Author summary: Molecular dating using phylogenetics allows us to estimate the date of an infection from time-stamped within-host sequences alone. There are large datasets of HIV-1 sequences, but genome and gene analyses are not often performed in parallel and rarely with the possibility to compare results against a known narrow window of infection. We showed that all but the longest genes are near-clonal in acute infection, with little information for dating purposes. For infections with single founders, we estimated the eclipse phase—the time between HIV-1 exposure and the first positive diagnostic test—to last between one and two weeks using env, gag, pol and near full-length genomes. This approach could be used to narrow the date of suspected infection in ongoing clinical trials for the prevention of HIV-1 infection. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
5. Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand.
- Author
-
Rolland, Morgane, Tovanabutra, Sodsai, Dearlove, Bethany, Li, Yifan, Owen, Christopher L., Lewitus, Eric, Sanders-Buell, Eric, Bose, Meera, O'Sullivan, AnneMarie, Rossenkhan, Raabya, Labuschagne, Jan Phillipus Lourens, Edlefsen, Paul T., Reeves, Daniel B., Kijak, Gustavo, Miller, Shana, Poltavee, Kultida, Lee, Jenica, Bonar, Lydia, Harbolick, Elizabeth, and Ahani, Bahar
- Subjects
HAMMING distance ,PEAK load ,PATHOLOGY ,ADULTS ,VIRAL load ,ECLIPSES - Abstract
Most HIV-1 infected individuals do not know their infection dates. Precise infection timing is crucial information for studies that document transmission networks or drug levels at infection. To improve infection timing, we used the prospective RV217 cohort where the window when plasma viremia becomes detectable is narrow: the last negative visit occurred a median of four days before the first detectable HIV-1 viremia with an RNA test, referred below as diagnosis. We sequenced 1,280 HIV-1 genomes from 39 participants at a median of 4, 32 and 170 days post-diagnosis. HIV-1 infections were dated by using sequence-based methods and a viral load regression method. Bayesian coalescent and viral load regression estimated that infections occurred a median of 6 days prior to diagnosis (IQR: 9–3 and 11–4 days prior, respectively). Poisson-Fitter, which analyzes the distribution of hamming distances among sequences, estimated a median of 7 days prior to diagnosis (IQR: 15–4 days) based on sequences sampled 4 days post-diagnosis, but it did not yield plausible results using sequences sampled at 32 days. Fourteen participants reported a high-risk exposure event at a median of 8 days prior to diagnosis (IQR: 12 to 6 days prior). These different methods concurred that HIV-1 infection occurred about a week before detectable viremia, corresponding to 20 days (IQR: 34–15 days) before peak viral load. Together, our methods comparison helps define a framework for future dating studies in early HIV-1 infection. Author summary: HIV-1 infected individuals rarely know when they became infected but knowing when an infection occurred provides critical information regarding HIV-1 pathogenesis and epidemiology. Using a unique cohort in which infection was known to have occurred in a narrow interval, we investigated methods to estimate the timing of infections. Several methods suggested that HIV-1 infection typically occurs a median of one week before the infection can be detected by HIV-1 RNA testing. Going forward, we provide a strategy that can be used to elucidate the origin of an acute/early infection. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
6. Correction: Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
- Author
-
Kijak, Gustavo H., primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurence, additional, Eller, Michael A., additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth A., additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O’Sullivan, Anne Marie, additional, Billings, Erik, additional, Merbah, Melanie, additional, Costanzo, Margaret C., additional, Warren, Joanna A., additional, Slike, Bonnie, additional, Li, Hui, additional, Peachman, Kristina K., additional, Fischer, Will, additional, Gao, Feng, additional, Cicala, Claudia, additional, Arthos, James, additional, Eller, Leigh A., additional, O’Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rao, Mangala, additional, Marovich, Mary A., additional, Krebs, Shelly J., additional, Rolland, Morgane, additional, Korber, Bette T., additional, Shaw, George M., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, and Kim, Jerome H., additional
- Published
- 2017
- Full Text
- View/download PDF
7. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
- Author
-
Kijak, Gustavo H., primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurence, additional, Eller, Michael A., additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth A., additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O’Sullivan, Anne Marie, additional, Billings, Erik, additional, Merbah, Melanie, additional, Costanzo, Margaret C., additional, Warren, Joanna A., additional, Slike, Bonnie, additional, Li, Hui, additional, Peachman, Kristina K., additional, Fischer, Will, additional, Gao, Feng, additional, Cicala, Claudia, additional, Arthos, James, additional, Eller, Leigh A., additional, O’Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rao, Mangala, additional, Marovich, Mary A., additional, Krebs, Shelly J., additional, Rolland, Morgane, additional, Korber, Bette T., additional, Shaw, George M., additional, Michael, Nelson L., additional, Robb, Merlin L., additional, Tovanabutra, Sodsai, additional, and Kim, Jerome H., additional
- Published
- 2017
- Full Text
- View/download PDF
8. Cryptic Multiple HIV-1 Infection Revealed by Early, Frequent, and Deep Sampling during Acute Infection
- Author
-
Kijak, Gustavo Hernan, primary, Sanders-Buell, Eric, additional, Chenine, Agnes-Laurance, additional, Eller, Michael, additional, Goonetilleke, Nilu, additional, Thomas, Rasmi, additional, Leviyang, Sivan, additional, Harbolick, Elizabeth, additional, Bose, Meera, additional, Pham, Phuc, additional, Oropeza, Celina, additional, Poltavee, Kultida, additional, O'Sullivan, Anne Marie, additional, Merbah, Melanie, additional, Costanzo, Margaret, additional, Li, Hui, additional, Fischer, Will, additional, Gao, Feng, additional, Eller, Leigh Anne, additional, O'Connell, Robert J., additional, Sinei, Samuel, additional, Maganga, Lucas, additional, Kibuuka, Hannah, additional, Nitayaphan, Sorachai, additional, Rolland, Morgane, additional, Korber, Bette, additional, McCutchan, Francine, additional, Shaw, George, additional, Michael, Nelson, additional, Robb, Merlin, additional, Tovanabutra, Sodsai, additional, and Kim, Jerome, additional
- Published
- 2014
- Full Text
- View/download PDF
9. No Selection for Env with Shorter Variable Loops in Acute HIV-1 Infection
- Author
-
Rolland, Morgane, primary, Tovanabutra, Sodsai, additional, Sanders-Buell, Eric, additional, Bose, Meera, additional, Sullivan, Anne Marie O, additional, Howell, Shana, additional, Poltavee, Kultida, additional, Lee, Jenica, additional, Ibitamuno, Grace, additional, Muhammad, Sevan, additional, Ahani, Bahar, additional, Lepore, Steven, additional, Harbolick, Elizabeth, additional, Oropeza, Celina, additional, Patterson, Joey, additional, Bates, Adam, additional, Lazzaro, Michelle, additional, Kijak, Gustavo, additional, Dommaraju, Kalpana, additional, Herr, Christopher, additional, Eller, Leigh Anne, additional, Nitayaphan, Sorachai, additional, Rono, Kathleen, additional, Maganga, Lucas, additional, Sekiziyivu, Arthur, additional, Michael, Nelson, additional, Kim, Jerome, additional, and Robb, Merlin, additional
- Published
- 2014
- Full Text
- View/download PDF
10. Nautilus: A Bioinformatics Package for the Analysis of HIV Type 1 Targeted Deep Sequencing Data
- Author
-
Kijak, Gustavo H., primary, Pham, Phuc, additional, Sanders-Buell, Eric, additional, Harbolick, Elizabeth A., additional, Eller, Leigh Anne, additional, Robb, Merlin L., additional, Michael, Nelson L., additional, Kim, Jerome H., additional, and Tovanabutra, Sodsai, additional
- Published
- 2013
- Full Text
- View/download PDF
11. Complete Genome Sequence of Prepandemic Vibrio parahaemolyticus BB22OP
- Author
-
Jensen, Roderick V., primary, DePasquale, Saylem M., additional, Harbolick, Elizabeth A., additional, Hong, Tian, additional, Kernell, Alison L., additional, Kruchko, David H., additional, Modise, Thero, additional, Smith, Cimarron E., additional, McCarter, Linda L., additional, and Stevens, Ann M., additional
- Published
- 2013
- Full Text
- View/download PDF
12. Deep Sequencing Reveals Central Nervous System Compartmentalization in Multiple Transmitted/Founder Virus Acute HIV-1 Infection.
- Author
-
Tovanabutra, Sodsai, Sirijatuphat, Rujipas, Pham, Phuc T., Bonar, Lydia, Harbolick, Elizabeth A., Bose, Meera, Song, Hongshuo, Chang, David, Oropeza, Celina, O'Sullivan, Anne Marie, Balinang, Joyce, Kroon, Eugene, Colby, Donn J., Sacdalan, Carlo, Hellmuth, Joanna, Chan, Phillip, Prueksakaew, Peeriya, Pinyakorn, Suteeraporn, Jagodzinski, Linda L., and Sutthichom, Duanghathai
- Subjects
CENTRAL nervous system ,CENTRAL nervous system physiology ,CEREBROSPINAL fluid ,CEREBROSPINAL fluid examination ,INFECTION - Abstract
HIV-1 disseminates to a broad range of tissue compartments during acute HIV-1 infection (AHI). The central nervous system (CNS) can serve as an early and persistent site of viral replication, which poses a potential challenge for HIV-1 remission strategies that target the HIV reservoir. CNS compartmentalization is a key feature of HIV-1 neuropathogenesis. Thus far, the timing of how early CNS compartmentalization develops after infection is unknown. We examined whether HIV-1 transmitted/founder (T/F) viruses differ between CNS and blood during AHI using single-genome sequencing of envelope gene and further examined subregions in pol and env using next-generation sequencing in paired plasma and cerebrospinal fluid (CSF) from 18 individuals. Different proportions of mostly minor variants were found in six of the eight multiple T/F-infected individuals, indicating enrichment of some variants in CSF that may lead to significant compartmentalization in the later stages of infection. This study provides evidence for the first time that HIV-1 compartmentalization in the CNS can occur within days of HIV-1 exposure in multiple T/F infections. Further understanding of factors that determine enrichment of T/F variants in the CNS, as well as potential long-term implications of these findings for persistence of HIV-1 reservoirs and neurological impairment in HIV, is needed. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
13. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
- Author
-
O’Connell, Robert J., Michael, Nelson L., Oropeza, Celina, Arthos, James, Bose, Meera, Nitayaphan, Sorachai, Slike, Bonnie, Thomas, Rasmi, Chenine, Agnes-Laurence, Tovanabutra, Sodsai, Marovich, Mary A., O’Sullivan, Anne Marie, Rolland, Morgane, Maganga, Lucas, Merbah, Melanie, Warren, Joanna A., Shaw, George M., Billings, Erik, Goonetilleke, Nilu, Cicala, Claudia, Eller, Michael A., Poltavee, Kultida, Kibuuka, Hannah, Pham, Phuc, Kim, Jerome H., Sanders-Buell, Eric, Korber, Bette T., Fischer, Will, Li, Hui, Peachman, Kristina K., Leviyang, Sivan, Sinei, Samuel, Harbolick, Elizabeth A., Eller, Leigh A., Krebs, Shelly J., Gao, Feng, Costanzo, Margaret C., Rao, Mangala, Robb, Merlin L., and Kijak, Gustavo H.
- Subjects
3. Good health - Abstract
In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.
14. Cryptic Multiple HIV-1 Infection Revealed by Early, Frequent, and Deep Sampling during Acute Infection.
- Author
-
Sanders-Buell, Eric, Chenine, Agnes-Laurance, Eller, Michael, Goonetilleke, Nilu, Thomas, Rasmi, Leviyang, Sivan, Harbolick, Elizabeth, Bose, Meera, Pham, Phuc, Oropeza, Celina, Poltavee, Kultida, O'Sullivan, Anne Marie, Merbah, Melanie, Costanzo, Margaret, Li, Hui, Fischer, Will, Gao, Feng, Eller, Leigh Anne, O'Connell, Robert J., and Sinei, Samuel
- Abstract
An abstract of the article "Cryptic Multiple HIV-1 Infection Revealed by Early, Frequent, and Deep Sampling during Acute Infection" by Gustavo Hernan Kijak, Eric Sanders-Buell, Agnes-Laurance Chenine and colleagues is presented.
- Published
- 2014
- Full Text
- View/download PDF
15. No Selection for Env with Shorter Variable Loops in Acute HIV-1 Infection.
- Author
-
Tovanabutra, Sodsai, Sanders-Buell, Eric, Bose, Meera, Sullivan, Anne Marie O, Howell, Shana, Poltavee, Kultida, Lee, Jenica, Ibitamuno, Grace, Muhammad, Sevan, Ahani, Bahar, Lepore, Steven, Harbolick, Elizabeth, Oropeza, Celina, Patterson, Joey, Bates, Adam, Lazzaro, Michelle, Kijak, Gustavo, Dommaraju, Kalpana, Herr, Christopher, and Eller, Leigh Anne
- Abstract
An abstract of the article "No Selection for Env with Shorter Variable Loops in Acute HIV-1 Infection" by Morgane Rolland, Sodsai Tovanabutra, Eric Sanders-Buell and colleagues is presented.
- Published
- 2014
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.