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Russell ML, Fish CS, Drescher S, Cassidy NAJ, Chanana P, Benki-Nugent S, Slyker J, Mbori-Ngacha D, Bosire R, Richardson B, Wamalwa D, Maleche-Obimbo E, Overbaugh J, John-Stewart G, Matsen FA, Lehman DA. Using viral sequence diversity to estimate time of HIV infection in infants. PLoS Pathog 2023; 19:e1011861. [PMID: 38117834 PMCID: PMC10732395 DOI: 10.1371/journal.ppat.1011861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 12/22/2023] Open
Abstract
Age at HIV acquisition may influence viral pathogenesis in infants, and yet infection timing (i.e. date of infection) is not always known. Adult studies have estimated infection timing using rates of HIV RNA diversification, however, it is unknown whether adult-trained models can provide accurate predictions when used for infants due to possible differences in viral dynamics. While rates of viral diversification have been well defined for adults, there are limited data characterizing these dynamics for infants. Here, we performed Illumina sequencing of gag and pol using longitudinal plasma samples from 22 Kenyan infants with well-characterized infection timing. We used these data to characterize viral diversity changes over time by designing an infant-trained Bayesian hierarchical regression model that predicts time since infection using viral diversity. We show that diversity accumulates with time for most infants (median rate within pol = 0.00079 diversity/month), and diversity accumulates much faster than in adults (compare previously-reported adult rate within pol = 0.00024 diversity/month [1]). We find that the infant rate of viral diversification varies by individual, gene region, and relative timing of infection, but not by set-point viral load or rate of CD4+ T cell decline. We compare the predictive performance of this infant-trained Bayesian hierarchical regression model with simple linear regression models trained using the same infant data, as well as existing adult-trained models [1]. Using an independent dataset from an additional 15 infants with frequent HIV testing to define infection timing, we demonstrate that infant-trained models more accurately estimate time since infection than existing adult-trained models. This work will be useful for timing HIV acquisition for infants with unknown infection timing and for refining our understanding of how viral diversity accumulates in infants, both of which may have broad implications for the future development of infant-specific therapeutic and preventive interventions.
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Affiliation(s)
- Magdalena L. Russell
- Computational Biology Program, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
| | - Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Sara Drescher
- University of Washington Medical Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Noah A. J. Cassidy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Pritha Chanana
- Bioinformatics Shared Resource, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Sarah Benki-Nugent
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Dorothy Mbori-Ngacha
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Rose Bosire
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Barbra Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Center, Seattle, Washington, United States of America
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | | | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutch Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Dara A. Lehman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
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2
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Yucha R, Litchford ML, Fish CS, Yaffe ZA, Richardson BA, Maleche-Obimbo E, John-Stewart G, Wamalwa D, Overbaugh J, Lehman DA. Higher HIV-1 Env gp120-Specific Antibody-Dependent Cellular Cytotoxicity (ADCC) Activity Is Associated with Lower Levels of Defective HIV-1 Provirus. Viruses 2023; 15:2055. [PMID: 37896832 PMCID: PMC10611199 DOI: 10.3390/v15102055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/03/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
A cure for HIV-1 (HIV) remains unrealized due to a reservoir of latently infected cells that persist during antiretroviral therapy (ART), with reservoir size associated with adverse health outcomes and inversely with time to viral rebound upon ART cessation. Once established during ART, the HIV reservoir decays minimally over time; thus, understanding factors that impact the size of the HIV reservoir near its establishment is key to improving the health of people living with HIV and for the development of novel cure strategies. Yet, to date, few correlates of HIV reservoir size have been identified, particularly in pediatric populations. Here, we employed a cross-subtype intact proviral DNA assay (CS-IPDA) to quantify HIV provirus between one- and two-years post-ART initiation in a cohort of Kenyan children (n = 72), which had a median of 99 intact (range: 0-2469), 1340 defective (range: 172-3.84 × 104), and 1729 total (range: 178-5.11 × 104) HIV proviral copies per one million T cells. Additionally, pre-ART plasma was tested for HIV Env-specific antibody-dependent cellular cytotoxicity (ADCC) activity. We found that pre-ART gp120-specific ADCC activity inversely correlated with defective provirus levels (n = 68, r = -0.285, p = 0.0214) but not the intact reservoir (n = 68, r = -0.0321, p-value = 0.800). Pre-ART gp41-specific ADCC did not significantly correlate with either proviral population (n = 68; intact: r = -0.0512, p-value = 0.686; defective: r = -0.109, p-value = 0.389). This suggests specific host immune factors prior to ART initiation can impact proviruses that persist during ART.
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Affiliation(s)
- Ryan Yucha
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Morgan L. Litchford
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zak A. Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | | | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi P.O. Box 30197, Kenya
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Dara A. Lehman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
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3
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Neary J, Fish CS, Cassidy NAJ, Wamalwa D, Langat A, Ngugi E, Benki-Nugent S, Moraa H, Richardson BA, Njuguna I, Slyker JA, Lehman DA, John-Stewart G. Predictors of intact HIV DNA levels among children in Kenya. AIDS 2023; 37:871-876. [PMID: 36723512 PMCID: PMC10079608 DOI: 10.1097/qad.0000000000003499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
OBJECTIVE We determined predictors of both intact (estimate of replication-competent) and total (intact and defective) HIV DNA in the reservoir among children with HIV. DESIGN HIV DNA in the reservoir was quantified longitudinally in children who initiated antiretroviral therapy (ART) at less than 1 year of age using a novel cross-subtype intact proviral DNA assay that measures both intact and total proviruses. Quantitative PCR was used to measure pre-ART cytomegalovirus (CMV) viral load. Linear mixed effects models were used to determine predictors of intact and total HIV DNA levels (log 10 copies/million). RESULTS Among 65 children, median age at ART initiation was 5 months and median follow-up was 5.2 years; 86% of children had CMV viremia pre-ART. Lower pre-ART CD4 + percentage [adjusted relative risk (aRR): 0.87, 95% confidence intervals (95% CI): 0.79-0.97; P = 0.009] and higher HIV RNA (aRR: 1.21, 95% CI: 1.06-1.39; P = 0.004) predicted higher levels of total HIV DNA during ART. Pre-ART CD4 + percentage (aRR: 0.76, 95% CI: 0.65-0.89; P < 0.001), CMV viral load (aRR: 1.16, 95% CI: 1.01-1.34; P = 0.041), and first-line protease inhibitor-based regimens compared with nonnucleoside reverse transcriptase-based regimens (aRR: 1.36, 95% CI: 1.04-1.77; P = 0.025) predicted higher levels of intact HIV DNA. CONCLUSION Pre-ART immunosuppression, first-line ART regimen, and CMV viral load may influence establishment and sustainment of intact HIV DNA in the reservoir.
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Affiliation(s)
- Jillian Neary
- Department of Epidemiology, University of Washington
| | | | | | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Agnes Langat
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Evelyn Ngugi
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | | | - Hellen Moraa
- Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Barbra A Richardson
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Irene Njuguna
- Department of Global Health
- Kenyatta National Hospital, Nairobi, Kenya
| | - Jennifer A Slyker
- Department of Epidemiology, University of Washington
- Department of Global Health
| | - Dara A Lehman
- Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Global Health
| | - Grace John-Stewart
- Department of Epidemiology, University of Washington
- Department of Global Health
- Department of Medicine
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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Begnel ER, Chohan BH, Ojee E, Adhiambo J, Owiti P, Ogweno V, Holland LA, Fish CS, Richardson BA, Khan AK, Maqsood R, Lim ES, Sadarangani M, Lehman DA, Slyker J, Kinuthia J, Wamalwa D, Gantt S. HIV and SARS-CoV-2 infection in postpartum Kenyan women and their infants. PLoS One 2023; 18:e0278675. [PMID: 36649247 PMCID: PMC9844875 DOI: 10.1371/journal.pone.0278675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND HIV may increase SARS-CoV-2 infection risk and COVID-19 severity generally, but data are limited about its impact on postpartum women and their infants. As such, we characterized SARS-CoV-2 infection among mother-infant pairs in Nairobi, Kenya. METHODS We conducted a nested study of 62 HIV-uninfected and 64 healthy women living with HIV, as well as their HIV-exposed uninfected (N = 61) and HIV-unexposed (N = 64) infants, participating in a prospective cohort. SARS-CoV-2 serology was performed on plasma collected between May 1, 2020-February 1, 2022 to determine the incidence, risk factors, and symptoms of infection. SARS-CoV-2 RNA PCR and sequencing was also performed on available stool samples from seropositive participants. RESULTS SARS-CoV-2 seropositivity was found in 66% of the 126 mothers and in 44% of the 125 infants. There was no significant association between SARS-CoV-2 infection and maternal HIV (Hazard Ratio [HR] = 0.810, 95% CI: 0.517-1.27) or infant HIV exposure (HR = 1.47, 95% CI: 0.859-2.53). Maternal SARS-CoV-2 was associated with a two-fold increased risk of infant infection (HR = 2.31, 95% CI: 1.08-4.94). Few participants (13% mothers, 33% infants) had symptoms; no participant experienced severe COVID-19 or death. Seroreversion occurred in about half of mothers and infants. SARS-CoV-2 sequences obtained from stool were related to contemporaneously circulating variants. CONCLUSIONS These data indicate that postpartum Kenyan women and their infants were at high risk for SARS-CoV-2 infection and that antibody responses waned over an average of 8-10 months. However, most cases were asymptomatic and healthy women living with HIV did not have a substantially increased risk of infection or severe COVID-19.
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Affiliation(s)
- Emily R. Begnel
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Bhavna H. Chohan
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Ednah Ojee
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Judith Adhiambo
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Prestone Owiti
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Vincent Ogweno
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Adam K. Khan
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dara A. Lehman
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Jennifer Slyker
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Dalton Wamalwa
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Centre de Recherche du CHU St-Justine, Montréal, Québec, Canada
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5
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Fish CS, Owiti P, Begnel ER, Itell HL, Ojee E, Adhiambo J, Ogweno V, Holland LA, Richardson BA, Khan AK, Maqsood R, Gantt S, Lim ES, Slyker J, Kinuthia J, Overbaugh J, Wamalwa D, Lehman DA, Chohan BH. Comparison of nucleocapsid and spike antibody ELISAs for determining SARS-CoV-2 seropositivity in Kenyan women and infants. J Med Virol 2023; 95:e28221. [PMID: 36251533 PMCID: PMC9839577 DOI: 10.1002/jmv.28221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/23/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023]
Abstract
A multitude of enzyme-linked immunosorbent assays (ELISAs) has been developed to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies since the coronavirus disease 2019 pandemic started in late 2019. Assessing the reliability of these assays in diverse global populations is critical. This study compares the use of the commercially available Platelia Total Ab Assay (Bio-Rad) nucleocapsid ELISA to the widely used Mount Sinai spike IgG ELISA in a Kenyan population seroprevalence study. Using longitudinal plasma specimens collected from a mother-infant cohort living in Nairobi, Kenya between May 2019 and December 2020, this study demonstrates that the two assays have a high qualitative agreement (92.7%) and strong correlation of antibody levels (R2 = 0.973) in repeated measures. Within this cohort, seroprevalence detected by either ELISA closely resembled previously published seroprevalence estimates for Kenya during the sampling period and no significant difference in the incidence of SARS-CoV-2 antibody detection by either assay was observed. Assay comparability was not affected by HIV exposure status. These data support the use of the Platelia SARS-CoV-2 Total Ab ELISA as a suitable high-throughput method for seroprevalence studies in Kenya.
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Affiliation(s)
- Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Prestone Owiti
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Emily R. Begnel
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Hannah L. Itell
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Molecular and Cellular Biology Graduate ProgramUniversity of Washington and Fred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Ednah Ojee
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Judith Adhiambo
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - Vincent Ogweno
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Barbra A. Richardson
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Adam K. Khan
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA
| | - Soren Gantt
- Département de Microbiologie, Infectiologie et Immunologie, Centre de Recherche du CHU St‐JustineUniversité de MontréalMontréalQuébecCanada
| | - Efrem S. Lim
- Center for Fundamental and Applied Microbiomics, Biodesign InstituteArizona State UniversityTempeArizonaUSA,School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Jennifer Slyker
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - John Kinuthia
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Department of Research and Programs, Kenyatta National HospitalNairobiKenya
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Division of Public Health SciencesFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Dalton Wamalwa
- Department of Paediatrics and Child HealthUniversity of NairobiNairobiKenya,Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Dara A. Lehman
- Division of Human Biology, Fred Hutchinson Cancer CenterSeattleWashingtonUSA,Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA
| | - Bhavna H. Chohan
- Department of Global Health, Hans Rosling CenterUniversity of WashingtonSeattleWashingtonUSA,Kenya Medical Research InstituteNairobiKenya
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6
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Fish CS, Cassidy NAJ, Levy CN, Hughes SM, Jerome KR, Overbaugh J, Hladik F, Lehman DA. Protocol for high-throughput reservoir quantification across global HIV subtypes using a cross-subtype intact proviral DNA assay. STAR Protoc 2022; 3:101681. [PMID: 36178789 PMCID: PMC9525950 DOI: 10.1016/j.xpro.2022.101681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/13/2022] [Accepted: 08/10/2022] [Indexed: 01/26/2023] Open
Abstract
The cross-subtype intact proviral DNA assay (CS-IPDA) is a high-throughput method to quantify HIV reservoir size in populations infected with any of the dominant global HIV-1 subtypes. Our protocol includes genomic DNA isolation optimized to minimize DNA shearing, a reference droplet digital PCR (ddPCR) assay to quantify T cells and assess DNA shearing, and a multiplex ddPCR targeting three distinct regions across the HIV genome to quantify intact proviruses as an estimate of replication-competent proviruses in the reservoir. For complete details on the use and execution of this protocol, please refer to Cassidy et al. (2022).
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Affiliation(s)
- Carolyn S Fish
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Noah A J Cassidy
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Claire N Levy
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA
| | - Sean M Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA
| | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 8109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Dara A Lehman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA.
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7
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Cassidy NA, Fish CS, Levy CN, Roychoudhury P, Reeves DB, Hughes SM, Schiffer JT, Benki-Nugent S, John-Stewart G, Wamalwa D, Jerome KR, Overbaugh J, Hladik F, Lehman DA. HIV reservoir quantification using cross-subtype multiplex ddPCR. iScience 2022; 25:103615. [PMID: 35106463 PMCID: PMC8786636 DOI: 10.1016/j.isci.2021.103615] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/15/2021] [Accepted: 12/09/2021] [Indexed: 11/23/2022] Open
Abstract
A major barrier to conducting HIV cure research in populations with the highest HIV burden is the lack of an accurate assay to quantify the replication-competent reservoir across the dominant global HIV-1 subtypes. Here, we modify a subtype B HIV-1 assay that quantifies both intact and defective proviral DNA, adapting it to accommodate cross-subtype HIV-1 sequence diversity. We show that the cross-subtype assay works on subtypes A, B, C, D, and CRF01_AE and can detect a single copy of intact provirus. In longitudinal blood samples from Kenyan infants infected with subtypes A and D, patterns of intact and total HIV DNA follow the decay of plasma viral load over time during antiretroviral therapy, with intact HIV DNA comprising 7% (range 1%-33%) of the total HIV DNA during HIV RNA suppression. This high-throughput cross-subtype reservoir assay will be useful in HIV cure research in Africa and Asia, where HIV prevalence is highest.
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Affiliation(s)
- Noah A.J. Cassidy
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Carolyn S. Fish
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire N. Levy
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Daniel B. Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sean M. Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Joshua T. Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Grace John-Stewart
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Dalton Wamalwa
- Department of Pediatrics and Child Health, University of Nairobi, Kenyatta National Hospital, Nairobi, Kenya
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Dara A. Lehman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
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Itell HL, Weight H, Fish CS, Logue JK, Franko N, Wolf CR, McCulloch DJ, Galloway J, Matsen FA, Chu HY, Overbaugh J. SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma. Microbiol Spectr 2021; 9:e0129821. [PMID: 34668728 PMCID: PMC8528110 DOI: 10.1128/spectrum.01298-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022] Open
Abstract
Wide-scale assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions, such as requiring venipuncture for collection and a cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by enzyme-linked immunosorbent assay (ELISA) and epitope profiles using phage display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays. IMPORTANCE Plasma and sera isolated from venous blood represent conventional sample types used for the evaluation of SARS-CoV-2 antibody responses after infection or vaccination. However, collection of these samples is invasive and requires trained personnel and equipment for immediate processing. Once collected, plasma and sera must be stored and shipped at cold temperatures. To define the risk of emerging SARS-CoV-2 variants and the longevity of immune responses to natural infection and vaccination, it will be necessary to measure various antibody features in populations around the world, including in resource-limited areas. A sampling method that is compatible with these settings and is suitable for a variety of SARS-CoV-2 antibody assays is therefore needed to continue to understand and curb the COVID-19 pandemic.
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Affiliation(s)
- Hannah L. Itell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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