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Custer B, Altan E, Montalvo L, Coyne A, Grebe E, Deng X, Stone M, Delwart E, Bakkour S, Hailu B, Reik R, Kessler D, Stramer SL, Busch MP. HIV Subtypes and Drug-resistance-associated Mutations in US Blood Donors, 2015-2020. Open Forum Infect Dis 2024; 11:ofae343. [PMID: 38994445 PMCID: PMC11237352 DOI: 10.1093/ofid/ofae343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Background Monitoring genotypes of HIV infections in blood donors may provide insights into infection trends in the general population. Methods HIV RNA was extracted from plasma samples of blood donors confirmed as HIV positive by blood screening nucleic acid and antibody tests. HIV genome target regions were amplified using nested real time-polymerase chain reaction followed by next-generation sequencing. Sequences were compared to those in the Los Alamos National Laboratory (LANL) database. Sequences were also assessed for drug resistance mutations (DRM) using the Stanford HIV DRM Database. Results From available HIV-positive donations collected between 1 September 2015 and 31 December 2020, 563 of 743 (75.8%) were successfully sequenced; 4 were subtype A, 543 subtype B, 5 subtype C, 1 subtype G, 5 circulating recombinant forms (CRF), and 2 were subtype B and D recombinants. Overall, no significant differences between blood donor and available LANL genotypes were found, and the genotypes of newly acquired versus prevalent HIV infections in donors were similar. The proportion of non-B subtypes and CRF remained a small fraction, with no other subtype or CRF representing more than 1% of the total. DRM were identified in 122 (21.6%) samples with protease inhibitor, nucleoside reverse transcriptase inhibitor and non-nucleoside reverse transcriptase inhibitor DRMs identified in 4.9%, 4.6% and 14.0% of samples, respectively. Conclusions HIV genetic diversity and DRM in blood donors appear representative of circulating HIV infections in the US general population and may provide more information on infection diversity than sequences reported to LANL, particularly for recently transmitted infections.
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Affiliation(s)
- Brian Custer
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Eda Altan
- Vitalant Research Institute, San Francisco, California, USA
| | | | - Alison Coyne
- Vitalant Research Institute, San Francisco, California, USA
| | - Eduard Grebe
- Vitalant Research Institute, San Francisco, California, USA
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Mars Stone
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sonia Bakkour
- Global Medical Affairs Donor Screening, Grifols Diagnostic Solutions, Emeryville, California, USA
| | - Benyam Hailu
- Division of Blood Diseases and Resources, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Rita Reik
- Scientific, Medical, Technical and Research, OneBlood, St. Petersburg, Florida, USA
| | - Debra Kessler
- Medical Programs and Services, New York Blood Center, New York, New York, USA
| | | | - Michael P Busch
- Vitalant Research Institute, San Francisco, California, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
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Viral agents (2nd section). Transfusion 2024; 64 Suppl 1:S19-S207. [PMID: 38394038 DOI: 10.1111/trf.17630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 02/25/2024]
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3
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Delwart E, Slikas E, Stramer SL, Kamel H, Kessler D, Krysztof D, Tobler LH, Carrick DM, Steele W, Todd D, Wright DJ, Kleinman SH, Busch MP. Genetic diversity of recently acquired and prevalent HIV, hepatitis B virus, and hepatitis C virus infections in US blood donors. J Infect Dis 2012; 205:875-85. [PMID: 22293432 DOI: 10.1093/infdis/jir862] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genetic variations of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV) can affect diagnostic assays and therapeutic interventions. Recent changes in prevalence of subtypes/genotypes and drug/immune-escape variants were characterized by comparing recently infected vs more remotely infected blood donors. METHODS Infected donors were identified among approximately 34 million US blood donations, 2006-2009; incident infections were defined as having no or low antiviral antibody titers. Viral genomes were partially sequenced. RESULTS Of 321 HIV strains (50% incident), 2.5% were non-B HIV subtypes. Protease and reverse transcriptase (RT) inhibitor resistance mutations were found in 2% and 11% of infected donors, respectively. Subtypes in 278 HCV strains (31% incident) yielded 1a>1b>3a>2b>2a>4a>6d, 6e: higher frequencies of 3a in incident cases vs higher frequencies of 1b in prevalent cases were found (P = .04). Twenty subgenotypes among 193 HBV strains (26% incident) yielded higher frequencies of A2 in incident cases and higher frequencies of A1, B2, and B4 in prevalent cases (P = .007). No HBV drug resistance mutations were detected. Six percent of incident vs 26% of prevalent HBV contained antibody neutralization escape mutations (P = .01). CONCLUSIONS Viral genetic variant distribution in blood donors was similar to that seen in high-risk US populations. Blood-borne viruses detected through large-scale routine screening of blood donors can complement molecular surveillance studies of highly exposed populations.
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Affiliation(s)
- Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.
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4
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Seroconverting blood donors as a resource for characterising and optimising recent infection testing algorithms for incidence estimation. PLoS One 2011; 6:e20027. [PMID: 21694760 PMCID: PMC3111407 DOI: 10.1371/journal.pone.0020027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/09/2011] [Indexed: 11/25/2022] Open
Abstract
Introduction Biomarker-based cross-sectional incidence estimation requires a Recent Infection Testing Algorithm (RITA) with an adequately large mean recency duration, to achieve reasonable survey counts, and a low false-recent rate, to minimise exposure to further bias and imprecision. Estimating these characteristics requires specimens from individuals with well-known seroconversion dates or confirmed long-standing infection. Specimens with well-known seroconversion dates are typically rare and precious, presenting a bottleneck in the development of RITAs. Methods The mean recency duration and a ‘false-recent rate’ are estimated from data on seroconverting blood donors. Within an idealised model for the dynamics of false-recent results, blood donor specimens were used to characterise RITAs by a new method that maximises the likelihood of cohort-level recency classifications, rather than modelling individual sojourn times in recency. Results For a range of assumptions about the false-recent results (0% to 20% of biomarker response curves failing to reach the threshold distinguishing test-recent and test-non-recent infection), the mean recency duration of the Vironostika-LS ranged from 154 (95% CI: 96–231) to 274 (95% CI: 234–313) days in the South African donor population (n = 282), and from 145 (95% CI: 67–226) to 252 (95% CI: 194–308) days in the American donor population (n = 106). The significance of gender and clade on performance was rejected (p−value = 10%), and utility in incidence estimation appeared comparable to that of a BED-like RITA. Assessment of the Vitros-LS (n = 108) suggested potentially high false-recent rates. Discussion The new method facilitates RITA characterisation using widely available specimens that were previously overlooked, at the cost of possible artefacts. While accuracy and precision are insufficient to provide estimates suitable for incidence surveillance, a low-cost approach for preliminary assessments of new RITAs has been demonstrated. The Vironostika-LS and Vitros-LS warrant further analysis to provide greater precision of estimates.
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Brennan CA, Yamaguchi J, Devare SG, Foster GA, Stramer SL. Expanded evaluation of blood donors in the United States for human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains: 2005 through 2007. Transfusion 2011; 50:2707-12. [PMID: 20576010 DOI: 10.1111/j.1537-2995.2010.02767.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND In a previous study of 66 human immunodeficiency virus (HIV)-infected US blood donors from 1999 to 2005, HIV-1 non-B and antiretroviral drug-resistant strains accounted for 4.7 and 6.5% of HIV infections, respectively. This study was expanded to include an additional 11 recently acquired infections and 197 established infections collected from January 2005 through December 2007. STUDY DESIGN AND METHODS HIV-infected donors were detected using FDA-licensed assays. Drug resistance profiles for protease and reverse transcriptase (RT) genes were determined using a genotyping system (ViroSeq, Celera Diagnostics); genetic subtype was determined by phylogenetic analysis of these sequences. RESULTS Drug resistance profiles were obtained for 203 of 208 specimens; 9.9% had mutations that confer drug resistance. Ten showed resistance to a single drug class: nine to nonnucleoside RT inhibitors (NNRTIs) and one to nucleoside RT inhibitors (NRTIs). Eight showed two drug class resistance: five NRTI plus NNRTI, two NRTI plus protease inhibitor (PI), and one NNRTI plus PI. Two showed three drug class resistance. Non-B strains were identified in 2.5% of donors and consisted of subtypes A1 and D, CRF02_AG, CRF43-02G, and URF_BF. CONCLUSIONS Data from this and the previous study show that antiretroviral drug-resistant HIV-1 is present in 9.1% of HIV-infected donors from 1999 through 2007; 9.3% of established infections and 6.9% of recent infections. Diverse HIV-1 non-B strains presently account for 3.0% of HIV infections in US donors.
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Analytical and clinical performance evaluation of the cobas TaqScreen MPX Test for use on the cobas s 201 system. J Virol Methods 2010; 165:246-53. [DOI: 10.1016/j.jviromet.2010.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 02/01/2010] [Accepted: 02/03/2010] [Indexed: 11/18/2022]
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Fishman SL, Branch AD. The quasispecies nature and biological implications of the hepatitis C virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2009; 9:1158-67. [PMID: 19666142 PMCID: PMC2790008 DOI: 10.1016/j.meegid.2009.07.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/24/2009] [Accepted: 07/31/2009] [Indexed: 12/18/2022]
Abstract
Many RNA viruses exist as a cloud of closely related sequence variants called a quasispecies, rather than as a population of identical clones. In this article, we explain the quasispecies nature of RNA viral genomes, and briefly review the principles of quasispecies dynamics and the differences with classical population genetics. We then discuss the current methods for quasispecies analysis and conclude with the biological implications of this phenomenon, focusing on the hepatitis C virus.
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Affiliation(s)
- Sarah L Fishman
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
| | - Andrea D Branch
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
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8
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Brennan CA, Stramer SL, Holzmayer V, Yamaguchi J, Foster GA, Notari IV EP, Schochetman G, Devare SG. Identification of human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains in United States blood donors. Transfusion 2009; 49:125-33. [DOI: 10.1111/j.1537-2995.2008.01935.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Chan PA, Wakeman SE, Flanigan T, Cu-Uvin S, Kojic E, Kantor R. HIV-2 diagnosis and quantification in high-risk patients. AIDS Res Ther 2008; 5:18. [PMID: 18700986 PMCID: PMC2529329 DOI: 10.1186/1742-6405-5-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 08/14/2008] [Indexed: 11/16/2022] Open
Abstract
Current diagnostic assays for HIV-1 do not always test for the presence of HIV-2 in the United States. We present the case of a patient from Cape Verde, who was admitted to our hospital with rapidly deteriorating neurological function and multiple white matter lesions on MRI likely secondary to progressive multifocal leukoencephalopathy (PML). Initially, the patient had a positive EIA for HIV, but a negative HIV-1 Western Blot and no viral load detected on a branched-DNA assay. A repeat viral load by reverse transcriptase methodology (RT-DNA) detected 121,000 copies and an HIV-2 Western Blot was positive. The case highlights an extremely rare presentation of HIV-2 with severe neurological disease. We discuss the different tests available for the diagnosis and monitoring of HIV-2 in the United States.
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Epidemiology, Natural History and Treatment of HIV-2 Infections. GLOBAL HIV/AIDS MEDICINE 2008. [PMCID: PMC7151785 DOI: 10.1016/b978-1-4160-2882-6.50060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Tang N, Huang S, Salituro J, Mak WB, Cloherty G, Johanson J, Li YH, Schneider G, Robinson J, Hackett J, Swanson P, Abravaya K. A RealTime HIV-1 viral load assay for automated quantitation of HIV-1 RNA in genetically diverse group M subtypes A–H, group O and group N samples. J Virol Methods 2007; 146:236-45. [PMID: 17707519 DOI: 10.1016/j.jviromet.2007.07.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Revised: 07/03/2007] [Accepted: 07/09/2007] [Indexed: 12/31/2022]
Abstract
The Abbott RealTime HIV-1 assay is an automated test for monitoring HIV-1 viral load in plasma samples. The assay uses reverse transcription polymerase chain reaction (RT-PCR) technology with homogeneous real-time fluorescent detection. Automated sample preparation is performed on the m2000sp instrument where RNA is isolated using magnetic microparticle technology and dispensed to a PCR tray together with the amplification reagents. The PCR tray is then transferred to the Abbott m2000rt instrument for amplification and real-time detection. The assay utilizes two distinct sets of primers and probes for HIV-1 and for internal control (IC). The IC is processed along with each sample to control for sample recovery and inhibition. The HIV-1 primer and probe sequences are targeted to the integrase (IN) region of the polymerase (pol) gene. Due to the selection of a highly conserved target region and a novel, mismatch tolerant probe design, the assay can quantitate HIV-1 group M subtypes A-H, group O, and group N isolates. The assay provides high reproducibility and a wide dynamic range, allowing quantitation from 40 copies to 10 million copies of HIV-1 RNA per milliliter of plasma. HIV-1 RNA concentrations detected with 95% probability were 25copies/mL with 1.0mL of plasma, 39copies/mL with 0.6mL of plasma, 65copies/mL with 0.5mL of plasma, and 119copies/mL with 0.2mL of plasma.
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Affiliation(s)
- Ning Tang
- Abbott Molecular Inc., D-9ND, Bldg. DP1, 1300 E Touhy Avenue, Des Plaines, IL 60018-3315, USA
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12
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13
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Busch MP. Lessons and opportunities from epidemiologic and molecular investigations of infected blood donors. Transfusion 2006; 46:1663-6. [PMID: 17002621 DOI: 10.1111/j.1537-2995.2006.00987.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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14
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Busch MP. Transfusion-transmitted viral infections: building bridges to transfusion medicine to reduce risks and understand epidemiology and pathogenesis. Transfusion 2006; 46:1624-40. [PMID: 16965593 DOI: 10.1111/j.1537-2995.2006.00957.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Michael P Busch
- Blood Systems Research Institute, University of California at San Francisco, California 94118, USA.
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15
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Brennan CA, Bodelle P, Coffey R, Harris B, Holzmayer V, Luk KC, Swanson P, Yamaguchi J, Vallari A, Devare SG, Schochetman G, Hackett J. HIV global surveillance: foundation for retroviral discovery and assay development. J Med Virol 2006; 78 Suppl 1:S24-9. [PMID: 16622874 DOI: 10.1002/jmv.20603] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The high level of HIV genetic diversity has important implications for screening, diagnostic testing and patient monitoring. Continued diversification and global redistribution of HIV groups, subtypes and recombinants make it imperative that serological and molecular assays be designed and evaluated to ensure reliable performance on all HIV infections. Recognizing the importance of this issue, we initiated a comprehensive program to monitor global diversification of HIV, search for newly emerging variants, assemble large-volume panels of genetically and geographically diverse strains, and develop strategies to determine the impact of HIV diversity on assays used for detecting and monitoring HIV infection. Efforts to identify and characterize rare and emerging HIV strains have lead to the identification of HIV-1 group O, group N, and dual infections of groups M and O. A panel of plasma specimens was established that includes specimens collected from 12 countries in Africa, Asia, Europe, and South America; the panel comprises infections due to HIV-1 group M subtypes A, B, C, D, F, and G, as well as CRF01, CRF02, and unique recombinant forms, group N, and group O. Serological and molecular characterization of this unique panel has provided vital sequence data to support assay development and an invaluable source of well-defined specimens to evaluate and compare assay performance. The ability to address the challenge posed by ongoing evolution of HIV and the emergence of new variants requires continued surveillance of global HIV strain diversity, a sound scientific foundation for assay development, and suitable panels to evaluate and validate assay performance.
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Affiliation(s)
- Catherine A Brennan
- Abbott Diagnostics, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064-6015, USA
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16
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Delwart E, Kuhns MC, Busch MP. Surveillance of the genetic variation in incident HIV, HCV, and HBV infections in blood and plasma donors: implications for blood safety, diagnostics, treatment, and molecular epidemiology. J Med Virol 2006; 78 Suppl 1:S30-5. [PMID: 16622875 DOI: 10.1002/jmv.20604] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surveillance for molecular variants in blood donors is vital to assuring that blood screening and supplemental assays are sensitive to circulating strains of blood-borne viruses. Blood screening and diagnostic assays licensed in the United States are largely based on prototype viral strains. Documentation of divergent viral strains in the donor pool can lead to accelerated development and licensure of robust serologic and nucleic acid amplification (NAT) assays for donor screening and diagnostic applications. In addition, surveillance for viral variants among donors has implications for assessing the prevalence of drug and vaccine escape mutants and for detecting and monitoring rare variants that may be newly introduced or increasing in the United States donor population. Combined NAT and serologic screening, supplemented by novel serologic testing strategies, can be used to identify donors with incident infections, which are of particular interest with respect to blood safety and public health implications. A systematic program is proposed for the genetic characterization of viral genomes in donors with incident HIV, HCV, or HBV infections.
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Affiliation(s)
- Eric Delwart
- Blood Systems Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, California, USA.
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Karchava M, Pulver W, Smith L, Philpott S, Sullivan TJ, Wethers J, Parker MM. Prevalence of drug-resistance mutations and non-subtype B strains among HIV-infected infants from New York State. J Acquir Immune Defic Syndr 2006; 42:614-9. [PMID: 16868498 PMCID: PMC2925654 DOI: 10.1097/01.qai.0000225871.87456.e7] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Prevalence studies indicate that transmission of drug-resistant HIV has been rising in the adult population, but data from the perinatally infected pediatric population are limited. In this retrospective study, we sequenced the pol region of HIV from perinatally infected infants diagnosed in New York State in 2001-2002. Analyses of drug resistance, subtype diversity, and perinatal antiretroviral exposure were conducted, and the results were compared with those from a previous study of HIV-infected infants identified in 1998-1999. Eight of 42 infants (19.1%) had provirus carrying at least 1 drug-resistance mutation, an increase of 58% over the 1998-1999 results. Mutations conferring resistance to nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and protease inhibitors were detected in 7.1%, 11.9%, and 2.4% of specimens, respectively. Consistent with previous results, perinatal antiretroviral exposure was not associated with drug resistance (P = 0.70). Phylogenetic analysis indicated that 16.7% of infants were infected with a non-subtype B strain of HIV. It seems that drug-resistant and non-subtype B strains of HIV are becoming increasingly common in the perinatally infected population. Our results highlight the value of resistance testing for all HIV-infected infants upon diagnosis and the need to consider subtype diversity in diagnostic and treatment strategies.
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Affiliation(s)
- Marine Karchava
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Wendy Pulver
- Center for Community Health, New York State Department of Health, Albany, NY
| | - Lou Smith
- Center for Community Health, New York State Department of Health, Albany, NY
| | - Sean Philpott
- Wadsworth Center, New York State Department of Health, Albany, NY
| | | | - Judith Wethers
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Monica M. Parker
- Wadsworth Center, New York State Department of Health, Albany, NY
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Neutralizing epitopes in the membrane-proximal region of HIV-1 gp41: genetic variability and co-variation. Immunol Lett 2006; 106:180-6. [PMID: 16859756 DOI: 10.1016/j.imlet.2006.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2006] [Accepted: 06/08/2006] [Indexed: 10/24/2022]
Abstract
Recent investigations on the passive immunization have proved that neutralizing antibodies directed to the membrane-proximal region of HIV-1 gp41 are potent anti-viral components, so this region is thought to be an attractive target for AIDS vaccine. Three key neutralizing epitopes, ELDKWA (aa662-667), NWFDIT (aa671-676) and ERDRDR (aa739-744) have been mapped in this region. In this study, their genetic variability and co-variation was evaluated. There exists marked shift in the predominant sequence patterns on these three neutralizing epitopes over time. Compared with subtype B, non-B clades exhibit significant genetic variability and co-variation on these three epitopes. Among HIV-1 strains isolated in recent 5 years, about one third displays epitope variants simultaneously on three epitopes. The newly isolated strains with co-variations on several neutralizing epitopes ought to be of strict surveillance in clinical treatment, and those frequent epitope variants should also be considered in vaccine design.
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19
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Akouamba BS, Viel J, Charest H, Merindol N, Samson J, Lapointe N, Brenner BG, Lalonde R, Harrigan PR, Boucher M, Soudeyns H. HIV-1 genetic diversity in antenatal cohort, Canada. Emerg Infect Dis 2005; 11:1230-4. [PMID: 16102312 PMCID: PMC3320510 DOI: 10.3201/eid1108.040877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We studied HIV genetic diversity in a cohort of 127 pregnant, HIV-infected women who received prenatal care at Sainte-Justine Hospital in Montreal, Canada, between 1999 and 2003. Clade assignments were derived by phylogenetic analysis of amplified pol sequences. Genotyping was successful in 103 of 127 women, 59 (57.3%) of whom were infected with clade B HIV-1, and 44 (42.7%) with nonclade B viruses, including subtypes A, C, D, F, G, and H. Four sequences remained unassigned. Forty-three of 44 women infected with non-clade B viruses were newcomers from sub-Saharan Africa, and subtype identity was consistent with those circulating in their countries of origin. These results highlight the epidemiologic importance of non-B HIV-1 in antenatal populations in a large North American urban center, underscore the influence of population movements on clade intermixing, and identify a group of patients who could be targeted for surveillance and drug therapy followup.
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Affiliation(s)
- Bertine S. Akouamba
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Janique Viel
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
| | - Hugues Charest
- Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Natacha Merindol
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | | | - Normand Lapointe
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Bluma G. Brenner
- Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | | | - P. Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Marc Boucher
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
| | - Hugo Soudeyns
- Hôpital Sainte-Justine, Montreal, Quebec, Canada
- Université de Montréal, Montreal, Quebec, Canada
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Achkar JM, Burda ST, Konings FAJ, Urbanski MM, Williams CAU, Seifen D, Kahirimbanyi MN, Vogler M, Parta M, Lupatkin HC, Zolla-Pazner S, Nyambi PN. Infection with HIV type 1 group M non-B subtypes in individuals living in New York City. J Acquir Immune Defic Syndr 2005; 36:835-44. [PMID: 15213568 DOI: 10.1097/00126334-200407010-00011] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To document infection with HIV type 1 (HIV-1) group M non-B subtypes in individuals living in New York City. DESIGN From October 1999 through April 2003, HIV-1-seropositive individuals were selected from 3 clinics in New York City based on having risk factors for infection with HIV-1 non-B subtypes. METHODS HIV-1 RNA was extracted from plasma samples, and partial gag, pol, or env genes were amplified by PCR analysis. The infecting HIV-1 group M subtype was determined based on results of either heteroduplex mobility assay or sequencing and phylogenetic analysis. RESULTS Ninety-seven subjects were enrolled in the study. Of the 97 subjects, 91 (94%) were selected based on having emigrated from a non-European country, while 6 (6%) were native United States citizens. Subtypes were successfully determined in 53 (55%) of the 97 plasma samples tested. The subtypes in 2 plasma samples were unclassifiable. HIV-1 infections were classified as those due to the following group M subtypes: A (n = 4; 7%), B (n = 12; 22%), C (n = 8; 15%), F (n = 2; 4%), CRF01_AE-like (n = 7; 13%), CRF02_AG-like (n = 19; 34%), an intersubtype recombinant form G/A (n = 1; 2%), and unclassifiable viruses (n = 2; 4%). CONCLUSION This study reveals infection with a broad variety of HIV-1 group M subtypes mostly in the immigrant population of New York City as well as how several non-B subtypes are being introduced into the United States.
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Affiliation(s)
- Jacqueline M Achkar
- Department of Medicine, New York University School of Medicine, NY 10010, USA.
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Swanson P, de Mendoza C, Joshi Y, Golden A, Hodinka RL, Soriano V, Devare SG, Hackett J. Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT. J Clin Microbiol 2005; 43:3860-8. [PMID: 16081923 PMCID: PMC1233972 DOI: 10.1128/jcm.43.8.3860-3868.2005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2004] [Revised: 04/22/2005] [Accepted: 05/06/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions.
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Affiliation(s)
- Priscilla Swanson
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Carmen de Mendoza
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Yagnya Joshi
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Alan Golden
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Richard L. Hodinka
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Vincent Soriano
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Sushil G. Devare
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - John Hackett
- Abbott Laboratories, AIDS Research and Retrovirus Discovery, Abbott Park, Illinois 60064, Instituto de Salud Carlos III, Service of Infectious Diseases, Madrid, Spain, Clinical Virology Laboratory, Children's Hospital of Philadelphia, and Departments of Pediatrics and Pathology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
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22
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Slobod KS, Coleclough C, Brown SA, Stambas J, Zhan X, Surman S, Jones BG, Zirkel A, Freiden PJ, Brown B, Sealy R, Bonsignori M, Hurwitz JL. Clade, Country and Region-specific HIV-1 Vaccines: Are they necessary? AIDS Res Ther 2005; 2:3. [PMID: 15860130 PMCID: PMC1112584 DOI: 10.1186/1742-6405-2-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 04/28/2005] [Indexed: 11/22/2022] Open
Abstract
Today, scientists are often encouraged to custom-design vaccines based on a particular country or clade. Here, we review the scientific literature and then suggest that the overwhelming endeavor to produce a unique vaccine for every world region or virus subtype may not be necessary.
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Affiliation(s)
- Karen S Slobod
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pediatrics, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
| | - Chris Coleclough
- Department of Immunology, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pathology, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
| | - Scott A Brown
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - John Stambas
- Department of Microbiology and Immunology, University of Melbourne, Vic 3010, Australia
| | - Xiaoyan Zhan
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Sherri Surman
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Bart G Jones
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Amy Zirkel
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Pamela J Freiden
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Brita Brown
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Robert Sealy
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
| | - Mattia Bonsignori
- Department of Immunology, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Clinical and Biological Sciences, University of Insubria, Varese, 21100, Italy
| | - Julia L Hurwitz
- Department of Infectious Diseases, St Jude Children's Research Hospital, 332 N. Lauderdale, Memphis, TN 38105 USA
- Department of Pathology, College of Medicine, 899 Madison Ave., University of Tennessee, Memphis, TN 38163 USA
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