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An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes. PLoS One 2018; 13:e0206409. [PMID: 30427878 PMCID: PMC6235296 DOI: 10.1371/journal.pone.0206409] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 01/11/2023] Open
Abstract
For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (Kameris) that operates on k-mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences (n = 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.
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Evaluation of Hologic Aptima HIV-1 Quant Dx Assay on the Panther System on HIV Subtypes. J Clin Microbiol 2016; 54:2575-81. [PMID: 27510829 DOI: 10.1128/jcm.01350-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/02/2016] [Indexed: 11/20/2022] Open
Abstract
Quantitation of the HIV-1 viral load in plasma is the current standard of care for clinical monitoring of HIV-infected individuals undergoing antiretroviral therapy. This study evaluated the analytical and clinical performances of the Aptima HIV-1 Quant Dx assay (Hologic, San Diego, CA) for monitoring viral load by using 277 well-characterized subtype samples, including 171 cultured virus isolates and 106 plasma samples from 35 countries, representing all major HIV subtypes, recombinants, and circulating recombinant forms (CRFs) currently in circulation worldwide. Linearity of the Aptima assay was tested on each of 6 major HIV-1 subtypes (A, B, C, D, CRF01_AE, and CRF02_AG) and demonstrated an R(2) value of ≥0.996. The performance of the Aptima assay was also compared to those of the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 v.2 (CAP/CTM) and Abbott m2000 RealTime HIV-1 (RealTime) assays on all subtype samples. The Aptima assay values averaged 0.21 log higher than the CAP/CTM values and 0.30 log higher than the RealTime values, and the values were >0.4 log higher than CAP/CTM values for subtypes F and G and than RealTime values for subtypes C, F, and G and CRF02_AG. Two samples demonstrated results with >1-log differences from RealTime results. When the data were adjusted by the average difference, 94.9% and 87.0% of Aptima results fell within 0.5 log of the CAP/CTM and RealTime results, respectively. The linearity and accuracy of the Aptima assay in correctly quantitating all major HIV-1 subtypes, coupled with the completely automated format and high throughput of the Panther system, make this system well suited for reliable measurement of viral load in the clinical laboratory.
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Sanchez AM, DeMarco CT, Hora B, Keinonen S, Chen Y, Brinkley C, Stone M, Tobler L, Keating S, Schito M, Busch MP, Gao F, Denny TN. Development of a contemporary globally diverse HIV viral panel by the EQAPOL program. J Immunol Methods 2014; 409:117-30. [PMID: 24447533 DOI: 10.1016/j.jim.2014.01.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/07/2013] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
Abstract
The significant diversity among HIV-1 variants poses serious challenges for vaccine development and for developing sensitive assays for screening, surveillance, diagnosis, and clinical management. Recognizing a need to develop a panel of HIV representing the current genetic and geographic diversity NIH/NIAID contracted the External Quality Assurance Program Oversight Laboratory (EQAPOL) to isolate, characterize and establish panels of HIV-1 strains representing global diverse subtypes and circulating recombinant forms (CRFs), and to make them available to the research community. HIV-positive plasma specimens and previously established isolates were collected through a variety of collaborations with a preference for samples from acutely/recently infected persons. Source specimens were cultured to high-titer/high-volume using well-characterized cryopreserved PBMCs from National y donors. Panel samples were stored as neat culture supernatant or diluted into defibrinated plasma. Characterization for the final expanded virus stocks included viral load, p24 antigen, infectivity (TCID), sterility, coreceptor usage, and near full-length genome sequencing. Viruses are made available to approved, interested laboratories using an online ordering application. The current EQAPOL Viral Diversity panel includes 100 viral specimens representing 6 subtypes (A, B, C, D, F, and G), 2 sub-subtypes (F1 and F2), 7 CRFs (01, 02, 04, 14, 22, 24, and 47), 19 URFs and 3 group O viruses from 22 countries. The EQAPOL Viral Diversity panel is an invaluable collection of well-characterized reagents that are available to the scientific community, including researchers, epidemiologists, and commercial manufacturers of diagnostics and pharmaceuticals to support HIV research, as well as diagnostic and vaccine development.
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Affiliation(s)
| | | | - Bhavna Hora
- Duke University Medical Center, Durham, NC, USA
| | | | - Yue Chen
- Duke University Medical Center, Durham, NC, USA
| | | | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Leslie Tobler
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Sheila Keating
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Marco Schito
- HJF-DAIDS, A Division of The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, USA
| | | | - Feng Gao
- Duke University Medical Center, Durham, NC, USA.
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Parkin N, Bremer J, Bertagnolio S. Genotyping external quality assurance in the World Health Organization HIV drug resistance laboratory network during 2007-2010. Clin Infect Dis 2012; 54 Suppl 4:S266-72. [PMID: 22544186 DOI: 10.1093/cid/cir992] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The World Health Organization (WHO) has developed a global laboratory network to support human immunodeficiency virus drug resistance genotyping for public health surveillance in resource-limited countries. Blinded proficiency panels are an essential part of a genotyping quality-assurance program and are used to monitor the reliability of genotyping data in the WHO laboratory network. Laboratories in Europe, North America, Asia, Africa, and the Caribbean have tested panels annually since 2007; 103 of 131 submissions (79%) had >99% nucleotide sequence identity and resistance mutation concordance, compared with consensus. Most errors were associated with mixtures in the test specimen, leading to subjectivity in base-calling or amplification bias. Overall, genotyping assays used by the WHO laboratory network are reliable.
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Affiliation(s)
- Neil Parkin
- HIV Department, World Health Organization, Geneva, Switzerland.
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Manak M, Sina S, Anekella B, Hewlett I, Sanders-Buell E, Ragupathy V, Kim J, Vermeulen M, Stramer SL, Sabino E, Grabarczyk P, Michael N, Peel S, Garrett P, Tovanabutra S, Busch MP, Schito M. Pilot studies for development of an HIV subtype panel for surveillance of global diversity. AIDS Res Hum Retroviruses 2012; 28:594-606. [PMID: 22149143 DOI: 10.1089/aid.2011.0271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The continued global spread and evolution of HIV diversity pose significant challenges to diagnostics and vaccine strategies. NIAID partnered with the FDA, WRAIR, academia, and industry to form a Viral Panel Working Group to design and prepare a panel of well-characterized current and diverse HIV isolates. Plasma samples that had screened positive for HIV infection and had evidence of recently acquired infection were donated by blood centers in North and South America, Europe, and Africa. A total of 80 plasma samples were tested by quantitative nucleic acid tests, p24 antigen, EIA, and Western blot to assign a Fiebig stage indicative of approximate time from initial infection. Evaluation of viral load using FDA-cleared assays showed excellent concordance when subtype B virus was tested, but lower correlations for subtype C. Plasma samples were cocultivated with phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from normal donors to generate 30 viral isolates (50-80% success rate for samples with viral load >10,000 copies/ml), which were then expanded to 10(7)-10(9) virus copies per ml. Analysis of env sequences showed that sequences derived from cultured PBMCs were not distinguishable from those obtained from the original plasma. The pilot collection includes 30 isolates representing subtypes B, C, B/F, CRF04_cpx, and CRF02_AG. These studies will serve as a basis for the development of a comprehensive panel of highly characterized viral isolates that reflects the current dynamic and complex HIV epidemic, and will be made available through the External Quality Assurance Program Oversight Laboratory (EQAPOL).
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Affiliation(s)
- Mark Manak
- SeraCare Life Sciences, Inc., Gaithersburg, Maryland
| | - Silvana Sina
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Indira Hewlett
- U.S. Food and Drug Administration, CBER, Bethesda, Maryland
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Jerome Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Susan L. Stramer
- American Red Cross, Scientific Support Office, Gaithersburg, Maryland
| | - Ester Sabino
- Department of Infectious Disease/University of São Paulo, São Paulo, Brazil
| | - Piotr Grabarczyk
- Institute of Haematology and Blood Transfusion Medicine, Warsaw, Poland
| | - Nelson Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | - Sheila Peel
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Rockville, Maryland
| | | | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Rockville, Maryland
| | | | - Marco Schito
- Henry M. Jackson Foundation, Contractor to the Division of AIDS, NIH, Bethesda, Maryland
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Naidoo AF, Parboosing R, Gordon ML. Dual HIV Infection Uncommon in Patients on Antiretroviral Therapy in a Region with High HIV Prevalence. AIDS Res Hum Retroviruses 2009; 25:1225-30. [PMID: 20001312 DOI: 10.1089/aid.2009.0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dual HIV infection has been found in regions with high HIV prevalence and in populations infected with diverse strains of HIV. The prevalence of dual infection in KwaZulu-Natal (KZN), where there is a high prevalence of HIV and an influx of immigrants who may be infected with different HIV subtypes, is unknown. The aim of this study was to determine the prevalence of dual infection in KZN. Eighty-three samples were obtained from chronically infected patients on ARV treatment from sites throughout KZN. Subtyping of the samples was performed using the heteroduplex mobility assay (HMA). Twelve samples that had possible dual infection by HMA were cloned and sequenced. Phylogenetic analysis showed that there was no dual infection in these samples. Contrary to a previous study, we did not find dual infection in this region. The patients in our study may be different from those in the previous study in terms of transmission risk factors, treatment, and stage of infection (acute vs. chronic). This study may have important implications for vaccine development and for the pathogenesis and treatment of dual HIV infection.
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Affiliation(s)
- Anneta Frances Naidoo
- Department of Virology, National Health Laboratory Services, University of KwaZulu-Natal, Durban, South Africa
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service/University of KwaZulu-Natal, Durban, South Africa
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Huang DD, Foley BT, Tolzmann CA, Ouma A, Bremer JW. Complex mosaic composition of near full-length genomes of two NED (NIH-ENVA-DOD) subtype panel HIV type 1 strains, BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC). AIDS Res Hum Retroviruses 2009; 25:1039-43. [PMID: 19795987 DOI: 10.1089/aid.2009.0078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Sequence characterization of the near full-length genomes of HIV-1 isolates BCF-Dioum and BCF-Kita, originating from the Democratic Republic of Congo (DRC), was continued. These NED panel isolates, contributed by F. Brun-Vezinet (ENVA-France), were first identified as subtypes G and H, respectively. Our earlier analyses of portions of their pol genes showed that both were likely to be intersubtype recombinants of different composition. This study analyzed the remainder of each genome, confirming them to be complex recombinants. The BCF-Dioum genome resembles CRF06_cpx strains found in West Africa, composed of subtypes A/G/J/K. The BCF-Kita genome is a unique complex recombinant A-F-G-H-K-U strain. These data support previous observations of the complexity of strains originating from the DRC. BCF-Dioum may be a suitable strain for standards and reagents since it matches a defined circulating recombinant form. Studies and reagents made from BCF-Kita should take into account its complex genome.
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Affiliation(s)
- Diana D. Huang
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Brian T. Foley
- HIV Sequence Database, Theoretical Biology and Biophysics Group (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Catlin A. Tolzmann
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - Annastasia Ouma
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
| | - James W. Bremer
- Department of Immunology/Microbiology, Rush Medical College, Chicago, Illinois 60612
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Jennings C, Fiscus SA, Crowe SM, Danilovic AD, Morack RJ, Scianna S, Cachafeiro A, Brambilla DJ, Schupbach J, Stevens W, Respess R, Varnier OE, Corrigan GE, Gronowitz JS, Ussery MA, Bremer JW. Comparison of two human immunodeficiency virus (HIV) RNA surrogate assays to the standard HIV RNA assay. J Clin Microbiol 2006; 43:5950-6. [PMID: 16333081 PMCID: PMC1317157 DOI: 10.1128/jcm.43.12.5950-5956.2005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus (HIV) RNA testing is the gold standard for monitoring antiretroviral therapy in HIV-infected patients. However, equipment and reagent costs preclude widespread use of the assay in resource-limited settings. The Perkin-Elmer Ultrasensitive p24 assay and the Cavidi Exavir Load assay both offer potentially simpler, less costly technologies for monitoring viral load. These assays were compared to the Roche Amplicor HIV-1 Monitor Test, v1.5, using panels of clinical samples (subtype B) from HIV-positive subjects and HIV-spiked samples (subtypes A, C, D, CRF_01AE, CRF_02AG, and F). The Ultrasensitive p24 assay detected 100% of the spiked samples with virus loads of >250,000 copies/ml and 61% of the clinical samples with virus loads of 219 to 288,850 copies/ml. Detection rates were improved substantially if an external lysis buffer was added to the procedure. The Cavidi assay detected 54 to 100% of spiked samples with virus loads >10,000 copies/ml and 68% of the clinical samples. These detection rates were also greatly improved with a newly implemented version of this kit. Coefficients of variation demonstrate good reproducibility for each of these kits. The results from the Cavidi v1.0, Cavidi v2.0, and Perkin-Elmer, and the Perkin-Elmer Plus external buffers all correlated well with the results from the Roche Monitor Test (r = 0.83 to 0.96, r = 0.84 to 0.99, r = 0.58 to 0.67, and r = 0.59 to 0.95, respectively). Thus, the use of these two assays for monitoring patients, together with less-frequent confirmation testing, offers a feasible alternative to frequent HIV RNA testing in resource-limited settings.
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Affiliation(s)
- Cheryl Jennings
- Rush Medical College, Department of Immunology/Microbiology, 1653 W. Congress Parkway, Chicago, IL 60612, USA.
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Travers SAA, Clewley JP, Glynn JR, Fine PEM, Crampin AC, Sibande F, Mulawa D, McInerney JO, McCormack GP. Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1. J Virol 2004; 78:10501-6. [PMID: 15367616 PMCID: PMC516391 DOI: 10.1128/jvi.78.19.10501-10506.2004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000. The majority of these sequences come from the Karonga District in Malawi and include some of the earliest known subtype C sequences. Linear regression analyses of sequence divergence estimates (with four different approaches) were plotted against sample year to estimate the year in which there was zero divergence from the reconstructed ancestral sequence. Here we suggest that the most recent common ancestor of subtype C appeared in the mid- to late 1960s. Sensitivity analyses, by which possible biases due to oversampling from one district were explored, gave very similar estimates.
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Affiliation(s)
- Simon A A Travers
- Biology Department, National University of Ireland, Maynooth, Maynooth, Co. Kildare, Ireland
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