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Yang W, Wang H, Li Z, Zhang L, Liu J, Kirchhoff F, Huan C, Zhang W. RPLP1 restricts HIV-1 transcription by disrupting C/EBPβ binding to the LTR. Nat Commun 2024; 15:5290. [PMID: 38906865 PMCID: PMC11192919 DOI: 10.1038/s41467-024-49622-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 06/12/2024] [Indexed: 06/23/2024] Open
Abstract
Long-term non-progressors (LTNPs) of HIV-1 infection may provide important insights into mechanisms involved in viral control and pathogenesis. Here, our results suggest that the ribosomal protein lateral stalk subunit P1 (RPLP1) is expressed at higher levels in LTNPs compared to regular progressors (RPs). Functionally, RPLP1 inhibits transcription of clade B HIV-1 strains by occupying the C/EBPβ binding sites in the viral long terminal repeat (LTR). This interaction requires the α-helixes 2 and 4 domains of RPLP1 and is evaded by HIV-1 group M subtype C and group N, O and P strains that do not require C/EBPβ for transcription. We further demonstrate that HIV-1-induced translocation of RPLP1 from the cytoplasm to the nucleus is essential for antiviral activity. Finally, knock-down of RPLP1 promotes reactivation of latent HIV-1 proviruses. Thus, RPLP1 may play a role in the maintenance of HIV-1 latency and resistance to RPLP1 restriction may contribute to the effective spread of clade C HIV-1 strains.
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Affiliation(s)
- Weijing Yang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Hong Wang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Zhaolong Li
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
| | - Lihua Zhang
- State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Jianhui Liu
- State Key Laboratory of Medical Proteomics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, China
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany
| | - Chen Huan
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China.
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
| | - Wenyan Zhang
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China.
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.
- Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China.
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Prakash S, Aasarey R, Priyatma, Sharma M, Khan S, Medha. The development, evaluation, performance, and validation of micro-PCR and extractor for the quantification of HIV-1 &-2 RNA. Sci Rep 2024; 14:8700. [PMID: 38622191 PMCID: PMC11018814 DOI: 10.1038/s41598-024-56164-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 03/02/2024] [Indexed: 04/17/2024] Open
Abstract
HIV infection has been a global public health threat and overall reported ~ 40 million deaths. Acquired immunodeficiency syndrome (AIDS) is attributed to the retroviruses (HIV-1/2), disseminated through various body fluids. The temporal progression of AIDS is in context to the rate of HIV-1 infection, which is twice as protracted in HIV-2 transmission. Q-PCR is the only available method that requires a well-developed lab infrastructure and trained personnel. Micro-PCR, a portable Q-PCR device, was developed by Bigtec Labs, Bangalore, India. It is simple, accurate, fast, and operationalised in remote places where diagnostic services are inaccessible in developing countries. This novel micro-PCR determines HIV-1 and HIV-2 viral load using a TruePrep™ extractor device for RNA isolation. Five ml blood samples were collected at the blood collection centre at AIIMS, New Delhi, India. Samples were screened for serology, and a comparison of HIV-1/2 RNA was done between qPCR and micro-PCR in the samples. The micro-PCR assay of HIV-RNA has compared well with those from real-time PCR (r = 0.99, i < 0.002). Micro-PCR has good inter and intra-assay reproducibility over a wide dynamic range (1.0 × 102-1.0 × 108 IU/ml). The linear dynamic range was 102-108 IU/ml. The clinical and analytical specificity of the assay was comparable, i.e., 100%. Intra-assay and inter-assay coefficients of variation ranged from 1.17% to 3.15% and from 0.02% to 0.46%, respectively. Moreover, due to the robust, simple, and empirical method, the Probit analysis has also been done for qPCR LODs to avoid uncertainties in target recoveries. The micro-PCR is reliable, accurate, and reproducible for early detection of HIV-1 and HIV-2 viral loads simultaneously. Thus, it can easily be used in the field and in remote places where quantification of both HIV-1/2 is not reachable.
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Affiliation(s)
- Shyam Prakash
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India.
| | - Ram Aasarey
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India
| | - Priyatma
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India
| | - Meenakshi Sharma
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India
| | - Shahid Khan
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India
| | - Medha
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Room No 11, 2nd Floor, Ansari Nagar, New Delhi, 110029, India
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Zhang X, Chen J. HIV Reservoir: How to Measure It? Curr HIV/AIDS Rep 2023; 20:29-41. [PMID: 37004676 DOI: 10.1007/s11904-023-00653-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2023] [Indexed: 04/04/2023]
Abstract
PURPOSEOF REVIEW In the current quest for a complete cure for HIV/AIDS, the persistence of a long-lived reservoir of cells carrying replication-competent proviruses is the major challenge. Here, we describe the main elements and characteristics of several widely used assays of HIV latent reservoir detection. RECENT FINDINGS To date, researchers have developed several different HIV latent reservoir detection assays. Among them, the in vitro quantitative viral outgrowth assay (QVOA) has been the gold standard for assessing latent HIV-1 viral load. The intact proviral DNA assay (IPDA) based on PCR also demonstrated the predominance of defective viruses. However, these assays all have some drawbacks and may still be inadequate in detecting the presence of ultralow levels of latent virus in many patients who were initially thought to have been cured, but eventually showed viral rebound. An accurate and precise measurement of the HIV reservoir is therefore needed to evaluate curative strategies, aimed to functional cure or sterilizing cure.
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Affiliation(s)
- Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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Kim J, Behzadi ES, Nehring M, Carver S, Cowan SR, Conry MK, Rawlinson JE, VandeWoude S, Miller CA. Combination Antiretroviral Therapy and Immunophenotype of Feline Immunodeficiency Virus. Viruses 2023; 15:822. [PMID: 37112803 PMCID: PMC10146003 DOI: 10.3390/v15040822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Feline Immunodeficiency Virus (FIV) causes progressive immune dysfunction in cats similar to human immunodeficiency virus (HIV) in humans. Although combination antiretroviral therapy (cART) is effective against HIV, there is no definitive therapy to improve clinical outcomes in cats with FIV. This study therefore evaluated pharmacokinetics and clinical outcomes of cART (2.5 mg/kg Dolutegravir; 20 mg/kg Tenofovir; 40 mg/kg Emtricitabine) in FIV-infected domestic cats. Specific pathogen free cats were experimentally infected with FIV and administered either cART or placebo treatments (n = 6 each) for 18 weeks, while n = 6 naïve uninfected cats served as controls. Blood, saliva, and fine needle aspirates from mandibular lymph nodes were collected to quantify viral and proviral loads via digital droplet PCR and to assess lymphocyte immunophenotypes by flow cytometry. cART improved blood dyscrasias in FIV-infected cats, which normalized by week 16, while placebo cats remained neutropenic, although no significant difference in viremia was observed in the blood or saliva. cART-treated cats exhibited a Th2 immunophenotype with increasing proportions of CD4+CCR4+ cells compared to placebo cats, and cART restored Th17 cells compared to placebo-treated cats. Of the cART drugs, dolutegravir was the most stable and long-lasting. These findings provide a critical insight into novel cART formulations in FIV-infected cats and highlight their role as a potential animal model to evaluate the impact of cART on lentiviral infection and immune dysregulation.
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Affiliation(s)
- Jeffrey Kim
- Comparative Medicine Research Unit, School of Medicine, University of Louisville, Louisville, KY 40292, USA
| | - Elisa S. Behzadi
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mary Nehring
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Shannon R. Cowan
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Megan K. Conry
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Jennifer E. Rawlinson
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Craig A. Miller
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA
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Chen TY, Yang HW, Lin DS, Huang ZD, Chang L. HIV fragments detected in Kaposi sarcoma tumor cells in HIV-infected patients. Medicine (Baltimore) 2022; 101:e31310. [PMID: 36316837 PMCID: PMC9622637 DOI: 10.1097/md.0000000000031310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Kaposi sarcoma (KS) is a malignant vascular neoplasm caused by KS-associated herpesvirus (KSHV) infection. HIV plays a major role in KS pathogenesis. KS in HIV usually produces more malignant features than classic KS. Despite the close KS-HIV relationship, no study has reported the existence of HIV in KS tissue. We used ddPCR to detect HIV and KSHV in HIV+ KS samples and classic KS control. We verified KS cell types through immunohistochemistry and applied hypersensitive in situ hybridization (ISH) to detect HIV and KSHV in tumor cells. Furthermore, we co-stained samples with ISH and immunohistochemistry to identify HIV and KSHV in specific cell types. Regarding pathological stages, the KS were nodular (58.3%), plaque (33.3%), and patch (8.3%) tumors. Moreover, ddPCR revealed HIV in 58.3% of the KS samples. ISH revealed positive Pol/Gag mRNA signals in CD34 + tumor cells from HIV + patients (95.8%). HIV signals were absent in macrophages and other inflammatory cells. Most HIV + KS cells showed scattered reactive particles of HIV and KSHV. We demonstrated that HIV could infect CD34 + tumor cells and coexist with KSHV in KS, constituting a novel finding. We hypothesized that the direct KSHV-HIV interaction at the cellular level contributes to KS oncogenesis.
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Affiliation(s)
- Tung-Ying Chen
- Department of Pathology, MacKay Memorial Hospital, Taipei, Taiwan
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Horng-Woei Yang
- Department of Medical Research, MacKay Memorial Hospital, New Taipei City, Taiwan
| | - Dar-Shong Lin
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, New Taipei City, Taiwan
- Department of Pediatric, MacKay Memorial Hospital, Taipei, Taiwan
- Division of Genetics, MacKay Children’s Hospital, Taipei, Taiwan
| | - Zo-Darr Huang
- Department of Medical Research, MacKay Memorial Hospital, New Taipei City, Taiwan
| | - Lung Chang
- Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
- Department of Medical Research, MacKay Memorial Hospital, New Taipei City, Taiwan
- Department of Pediatric, MacKay Memorial Hospital, Taipei, Taiwan
- Division of Infectious Disease, MacKay Children’s Hospital, Taipei, Taiwan
- *Correspondence: Lung Chang, Division of Infectious Diseases, MacKay Children’s Hospital, No. 92, Sec. 2, Zhongshan N. Rd., 10449 Taipei, Taiwan (e-mail: )
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Kong J, Li W, Hu J, Zhao S, Yue T, Li Z, Xia Y. The Safety of Cold-Chain Food in Post-COVID-19 Pandemic: Precaution and Quarantine. Foods 2022; 11:foods11111540. [PMID: 35681292 PMCID: PMC9180738 DOI: 10.3390/foods11111540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/20/2022] [Indexed: 02/04/2023] Open
Abstract
Since the outbreak of coronavirus disease-19 (COVID-19), cold-chain food contamination caused by the pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has attracted huge concern. Cold-chain foods provide a congenial environment for SARS-CoV-2 survival, which presents a potential risk for public health. Strengthening the SARS-CoV-2 supervision of cold-chain foods has become the top priority in many countries. Methodologically, the potential safety risks and precaution measures of SARS-CoV-2 contamination on cold-chain food are analyzed. To ensure the safety of cold-chain foods, the advances in SARS-CoV-2 detection strategies are summarized based on technical principles and target biomarkers. In particular, the techniques suitable for SARS-CoV-2 detection in a cold-chain environment are discussed. Although many quarantine techniques are available, the field-based quarantine technique on cold-chain food with characteristics of real-time, sensitive, specific, portable, and large-scale application is urgently needed.
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Affiliation(s)
- Jia Kong
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Wenxin Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Jinyao Hu
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Shixuan Zhao
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Zhonghong Li
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Laboratory of Quality & Safety Risk Assessment for Agro-Products, Ministry of Agriculture, Xianyang 712100, China
| | - Yinqiang Xia
- College of Food Science and Engineering, Northwest A&F University, Xianyang 712100, China; (J.K.); (W.L.); (J.H.); (S.Z.); (T.Y.); (Z.L.)
- Correspondence: ; Tel.: +86-151-2222-5493
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De Brun ML, Cosme B, Petersen M, Alvarez I, Folgueras-Flatschart A, Flatschart R, Panei CJ, Puentes R. Development of a droplet digital PCR assay for quantification of the proviral load of bovine leukemia virus. J Vet Diagn Invest 2022; 34:439-447. [PMID: 35369822 PMCID: PMC9254064 DOI: 10.1177/10406387221085581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Droplet digital PCR (ddPCR) is a highly sensitive tool developed for the detection and quantification of short-sequence variants—a tool that offers unparalleled precision enabling measurement of smaller-fold changes. We describe here the use of ddPCR for the detection of Bovine leukemia virus (BLV) DNA provirus. Serum samples and whole blood from experimentally infected sheep and naturally infected cattle were analyzed through ddPCR to detect the BLV gp51 gene, and then compared with serologic and molecular tests. The ddPCR assay was significantly more accurate and sensitive than AGID, ELISA, nested PCR, and quantitative PCR. The limit of detection of ddPCR was 3.3 copies/µL, detecting positive experimentally infected sheep beginning at 6 d post-infection. The ddPCR methodology offers a promising tool for evaluating the BLV proviral load, particularly for the detection of low viral loads.
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Affiliation(s)
- María L. De Brun
- Instituto de Patobiología, Unidad de Microbiología, Facultad de Veterinaria–Universidad de la República, Montevideo, Uruguay
| | - Bruno Cosme
- Instituto Nacional de Metrología, Calidad y Tecnología (Inmetro), Rio de Janeiro, Brazil
| | - Marcos Petersen
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas (IVIT), Buenos Aires, Argentina
| | - Irene Alvarez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas (IVIT), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Roberto Flatschart
- Instituto Nacional de Metrología, Calidad y Tecnología (Inmetro), Rio de Janeiro, Brazil
| | - Carlos Javier Panei
- Laboratorio de Virología, Facultad de Ciencias Veterinarias, Universidad Nacional de la Plata (FCV-UNLP), La Plata, Argentina
| | - Rodrigo Puentes
- Instituto de Patobiología, Unidad de Microbiología, Facultad de Veterinaria–Universidad de la República, Montevideo, Uruguay
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External quality assessment of HIV-1 DNA quantification assays used in the clinical setting in Italy. Sci Rep 2022; 12:3291. [PMID: 35228581 PMCID: PMC8885833 DOI: 10.1038/s41598-022-07196-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/14/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractTotal cell-associated HIV-1 DNA is a surrogate marker of the HIV-1 reservoir, however, certified systems for its quantification are not available. The Italian HIV DNA Network was launched to validate HIV-1 DNA quantification methods in use at University and Hospital labs. A quality control panel including HIV-1 DNA standards, reconstructed blood samples (RBSs) and DNA from different HIV-1 subtypes was blindly tested by 12 participating labs by quantitative real-time PCR (n = 6), droplet digital PCR (n = 3) or both (n = 3). The median 95% hit rate was 4.6 (3.7–5.5) copies per test and linearity in the tested range was excellent (R2 = 1.000 [1.000–1.000]). The median values obtained across labs were 3,370 (2,287–4,245), 445 (299–498), 59 (40–81) and 7 (6–11) HIV-1 DNA copies, for the 3,584, 448, 56 and 7-copy standards, respectively. With RBSs, measured values were within twofold with respect to the median in two thirds of cases. HIV-1 subtypes were missed (CRF01_AE by 3 labs) or underestimated by > 1 log (subtypes A, C, D, F by one lab; CRF01_AE by one lab; CRF02_AG by one lab). The overall performance was excellent with HIV-1 DNA standards, however detection of different HIV-1 subtypes must be improved.
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Abstract
Recently the Tat/rev Induced Limiting Dilution Assay, or TILDA, has been proposed as a possible alternative method to quantify the HIV-1 reservoir. TILDA estimates the frequency of latently infected cells by probing, in a limiting dilution format, the presence or inducibility of tat and rev multiply spliced HIV-1 RNA. In doing so, TILDA reduces overestimation of reservoir size compared to HIV-1 DNA measurements because multiply spliced HIV-1 RNA is less likely to be transcribed from dysfunctional genomes with replication defects. TILDA is easy to perform, requires a very low input number of cells and has a fast turnaround time, making it ideal for use in clinical settings. Here we describe the execution of TILDA with particular emphasis on cell preparation and the limiting dilution scheme.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland.
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Lau CY, Adan MA, Maldarelli F. Why the HIV Reservoir Never Runs Dry: Clonal Expansion and the Characteristics of HIV-Infected Cells Challenge Strategies to Cure and Control HIV Infection. Viruses 2021; 13:2512. [PMID: 34960781 PMCID: PMC8708047 DOI: 10.3390/v13122512] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/27/2021] [Indexed: 12/13/2022] Open
Abstract
Antiretroviral therapy (ART) effectively reduces cycles of viral replication but does not target proviral populations in cells that persist for prolonged periods and that can undergo clonal expansion. Consequently, chronic human immunodeficiency virus (HIV) infection is sustained during ART by a reservoir of long-lived latently infected cells and their progeny. This proviral landscape undergoes change over time on ART. One of the forces driving change in the landscape is the clonal expansion of infected CD4 T cells, which presents a key obstacle to HIV eradication. Potential mechanisms of clonal expansion include general immune activation, antigenic stimulation, homeostatic proliferation, and provirus-driven clonal expansion, each of which likely contributes in varying, and largely unmeasured, amounts to maintaining the reservoir. The role of clinical events, such as infections or neoplasms, in driving these mechanisms remains uncertain, but characterizing these forces may shed light on approaches to effectively eradicate HIV. A limited number of individuals have been cured of HIV infection in the setting of bone marrow transplant; information from these and other studies may identify the means to eradicate or control the virus without ART. In this review, we describe the mechanisms of HIV-1 persistence and clonal expansion, along with the attempts to modify these factors as part of reservoir reduction and cure strategies.
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Affiliation(s)
- Chuen-Yen Lau
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
| | - Matthew A. Adan
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
- Vagelos College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Bethesda, MD 20892, USA; (C.-Y.L.); (M.A.A.)
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Assessing sensitivity and reproducibility of RT-ddPCR and RT-qPCR for the quantification of SARS-CoV-2 in wastewater. J Virol Methods 2021; 297:114230. [PMID: 34252511 PMCID: PMC8267102 DOI: 10.1016/j.jviromet.2021.114230] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/29/2022]
Abstract
Throughout the COVID-19 global pandemic there has been significant interest and investment in using Wastewater-Based Epidemiology (WBE) for surveillance of viral pathogen presence and infections at the community level. There has been a push for widescale implementation of standardized protocols to quantify viral loads in a range of wastewater systems. To address concerns regarding sensitivity, limits of quantification, and large-scale reproducibility, a comparison of two similar workflows using RT-qPCR and RT-ddPCR was conducted. Sixty raw wastewater influent samples were acquired from nine distinct wastewater treatment plants (WWTP’s) served by the Hampton Roads Sanitation District (HRSD, Virginia Beach, Virginia) over a 6-month period beginning March 9th, 2020. Common reagents, controls, master mixes and nucleic acid extracts were shared between two individual processing groups based out of HRSD and the UNC Chapel Hill Institute of Marine Sciences (IMS, Morehead City, North Carolina). Samples were analyzed in parallel using One-Step RT-qPCR and One-Step RT-ddPCR with Nucleocapsid Protein 2 (N2) specific primers and probe. Influent SARS-CoV-2 N2 concentrations steadily increased over time spanning a range from non-detectable to 2.13E + 05 copies/L. Systematic dilution of the extracts indicated that inhibitory components in the wastewater matrices did not significantly impede the detection of a positive N2 signal for either workflow. The RT-ddPCR workflow had a greater analytical sensitivity with a lower Limit of Detection (LOD) at 0.066 copies/μl of template compared to RT-qPCR with a calculated LOD of 12.0 copies/μL of template. Interlaboratory comparisons using non-parametric correlation analysis demonstrated that there was a strong, significant, positive correlation between split extracts when employing RT-ddPCR for analysis with a ρ value of 0.86.
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12
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Lungu C, Banga R, Gruters RA, Procopio FA. Inducible HIV-1 Reservoir Quantification: Clinical Relevance, Applications and Advancements of TILDA. Front Microbiol 2021; 12:686690. [PMID: 34211450 PMCID: PMC8239294 DOI: 10.3389/fmicb.2021.686690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/21/2021] [Indexed: 01/07/2023] Open
Abstract
The presence of a stable HIV-1 reservoir persisting over time despite effective antiretroviral suppression therapy precludes a cure for HIV-1. Characterizing and quantifying this residual reservoir is considered an essential prerequisite to develop and validate curative strategies. However, a sensitive, reproducible, cost-effective, and easily executable test is still needed. The quantitative viral outgrowth assay is considered the gold standard approach to quantify the reservoir in HIV-1-infected patients on suppressive ART, but it has several limitations. An alternative method to quantify the viral reservoir following the reactivation of latent HIV-1 provirus detects multiply-spliced tat/rev RNA (msRNA) molecules by real-time PCR [tat/rev induced limiting dilution assay (TILDA)]. This article provides a perspective overview of the clinical relevance, various applications, recent advancements of TILDA, and how the assay has contributed to our understanding of the HIV-1 reservoir.
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Affiliation(s)
- Cynthia Lungu
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Riddhima Banga
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Rob A. Gruters
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francesco A. Procopio
- Department of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland,*Correspondence: Francesco A. Procopio,
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13
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Anderson EM, Simonetti FR, Gorelick RJ, Hill S, Gouzoulis MA, Bell J, Rehm C, Pérez L, Boritz E, Wu X, Wells D, Hughes SH, Rao V, Coffin JM, Kearney MF, Maldarelli F. Dynamic Shifts in the HIV Proviral Landscape During Long Term Combination Antiretroviral Therapy: Implications for Persistence and Control of HIV Infections. Viruses 2020; 12:v12020136. [PMID: 31991737 PMCID: PMC7077288 DOI: 10.3390/v12020136] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/13/2020] [Accepted: 01/16/2020] [Indexed: 12/19/2022] Open
Abstract
Combination antiretroviral therapy (cART) controls but does not eradicate HIV infection; HIV persistence is the principal obstacle to curing infections. The proportion of defective proviruses increases during cART, but the dynamics of this process are not well understood, and a quantitative analysis of how the proviral landscape is reshaped after cART is initiated is critical to understanding how HIV persists. Here, we studied longitudinal samples from HIV infected individuals undergoing long term cART using multiplexed Droplet Digital PCR (ddPCR) approaches to quantify the proportion of deleted proviruses in lymphocytes. In most individuals undergoing cART, HIV proviruses that contain gag are lost more quickly than those that lack gag. Increases in the fraction of gag-deleted proviruses occurred only after 1–2 years of therapy, suggesting that the immune system, and/or toxicity of viral re-activation helps to gradually shape the proviral landscape. After 10–15 years on therapy, there were as many as 3.5–5 times more proviruses in which gag was deleted or highly defective than those containing intact gag. We developed a provirus-specific ddPCR approach to quantify individual clones. Investigation of a clone of cells containing a deleted HIV provirus integrated in the HORMAD2 gene revealed that the cells underwent a massive expansion shortly after cART was initiated until the clone, which was primarily in effector memory cells, dominated the population of proviruses for over 6 years. The expansion of this HIV-infected clone had substantial effects on the overall proviral population.
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Affiliation(s)
- Elizabeth M. Anderson
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - Francesco R. Simonetti
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Robert J. Gorelick
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Shawn Hill
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Monica A. Gouzoulis
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Jennifer Bell
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (R.J.G.); (J.B.)
| | - Catherine Rehm
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20814, USA;
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Eli Boritz
- Virus Persistence and Dynamics Section, VRC, NIAID, NIH, Bethesda, MD 20814, USA; (L.P.); (E.B.)
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Daria Wells
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; (X.W.); (D.W.)
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC 20064, USA;
| | - John M. Coffin
- Department of Biology, Tufts University, Boston, MA 02155, USA;
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA; (E.M.A.); (F.R.S.); (S.H.); (M.A.G.); (S.H.H.); (M.F.K.)
- Correspondence: ; Tel.: +01-301-846-5611
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14
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Patro SC, Brandt LD, Bale MJ, Halvas EK, Joseph KW, Shao W, Wu X, Guo S, Murrell B, Wiegand A, Spindler J, Raley C, Hautman C, Sobolewski M, Fennessey CM, Hu WS, Luke B, Hasson JM, Niyongabo A, Capoferri AA, Keele BF, Milush J, Hoh R, Deeks SG, Maldarelli F, Hughes SH, Coffin JM, Rausch JW, Mellors JW, Kearney MF. Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors. Proc Natl Acad Sci U S A 2019; 116:25891-25899. [PMID: 31776247 PMCID: PMC6925994 DOI: 10.1073/pnas.1910334116] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
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 DNA populations; however, until recently, there was no way to link integration sites to their cognate proviral sequences. Here, we used multiple-displacement amplification (MDA) of cellular DNA diluted to a proviral endpoint to obtain full-length proviral sequences and their corresponding sites of integration. We applied this method to lymph node and peripheral blood mononuclear cells from 5 ART-treated donors to determine whether groups of identical subgenomic sequences in the 2 compartments are the result of clonal expansion of infected cells or a viral genetic bottleneck. We found that identical proviral sequences can result from both cellular expansion and viral genetic bottlenecks occurring prior to ART initiation and following ART failure. We identified an expanded T cell clone carrying an intact provirus that matched a variant previously detected by viral outgrowth assays and expanded clones with wild-type and drug-resistant defective proviruses. We also found 2 clones from 1 donor that carried identical proviruses except for nonoverlapping deletions, from which we could infer the sequence of the intact parental virus. Thus, MDA-SGS can be used for "viral reconstruction" to better understand intrapatient HIV-1 evolution and to determine the clonality and structure of proviruses within expanded clones, including those with drug-resistant mutations. Importantly, we demonstrate that identical sequences observed by standard SGS are not always sufficient to establish proviral clonality.
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Affiliation(s)
- Sean C Patro
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702;
| | - Leah D Brandt
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Michael J Bale
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Kevin W Joseph
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Shuang Guo
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, 171 65 Stockholm, Sweden
| | - Ann Wiegand
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Castle Raley
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Christopher Hautman
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | | | - Christine M Fennessey
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Wei-Shau Hu
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Brian Luke
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jenna M Hasson
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Aurelie Niyongabo
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Adam A Capoferri
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jeff Milush
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94143
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA 02111;
| | - Jason W Rausch
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - John W Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
| | - Mary F Kearney
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702
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15
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McManus WR, Bale MJ, Spindler J, Wiegand A, Musick A, Patro SC, Sobolewski MD, Musick VK, Anderson EM, Cyktor JC, Halvas EK, Shao W, Wells D, Wu X, Keele BF, Milush JM, Hoh R, Mellors JW, Hughes SH, Deeks SG, Coffin JM, Kearney MF. HIV-1 in lymph nodes is maintained by cellular proliferation during antiretroviral therapy. J Clin Invest 2019; 129:4629-4642. [PMID: 31361603 PMCID: PMC6819093 DOI: 10.1172/jci126714] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 07/23/2019] [Indexed: 12/19/2022] Open
Abstract
To investigate the possibility that HIV-1 replication in lymph nodes sustains the reservoir during ART, we looked for evidence of viral replication in 5 donors after up to 13 years of viral suppression. We characterized proviral populations in lymph nodes and peripheral blood before and during ART, evaluated the levels of viral RNA expression in single lymph node and blood cells, and characterized the proviral integration sites in paired lymph node and blood samples. Proviruses with identical sequences, identical integration sites, and similar levels of RNA expression were found in lymph nodes and blood samples collected during ART, and no single sequence with significant divergence from the pretherapy population was present in either blood or lymph nodes. These findings show that all detectable persistent HIV-1 infection is consistent with maintenance in lymph nodes by clonal proliferation of cells infected before ART and not by ongoing viral replication during ART.
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Affiliation(s)
- William R. McManus
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Michael J. Bale
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jonathan Spindler
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ann Wiegand
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Andrew Musick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Sean C. Patro
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | | | - Victoria K. Musick
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Elizabeth M. Anderson
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Joshua C. Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Wei Shao
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daria Wells
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Brandon F. Keele
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | - Rebecca Hoh
- Department of Medicine, UCSF, San Francisco, California, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Steven G. Deeks
- Department of Medicine, UCSF, San Francisco, California, USA
| | - John M. Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
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