1
|
Zhao J, Huang H, Lee S, Ragupathy V, Biswas S, Mbondji-wonje C, Wang X, Jiang A, Hewlett I. Identification, Genetic Characterization and Validation of Highly Diverse HIV-1 Viruses for Reference Panel Development. Viruses 2021; 13:v13071417. [PMID: 34372623 PMCID: PMC8310377 DOI: 10.3390/v13071417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
The continued diversification of HIV poses potentially significant challenges to HIV diagnostics and therapeutics. The dynamic evolution of emerging variants is highlighted in countries such as Cameroon in West Central Africa, where all known subtypes and circulating recombinant forms (CRFs) have been shown to be prevalent. We obtained several hundred HIV-positive plasma and viruses from this region for characterization and identification of highly divergent HIV strains. A total of 163 viral strains were cultured to high titers and high volumes using donor peripheral blood mononuclear cells (PBMCs). Initially, 101 viruses representing 59 strains were well characterized and categorized. Results showed that the viral load (VL) range was 0.36–398.9 × 107 copies/mL, p24 values was 0.2–1134 ng/mL. Phylogenetic analysis of thirty-six near full-length HIV-1 genomic sequences demonstrated that most recombinants were highly diverse CRF02 containing unique recombinant forms (URFs). There were seven viral isolates identified as pure subtype/sub-subtypes (F2, A1, G, and D), six as CRFs (CRF06, CRF18, and CRF22), and ten as URFs. These extensively characterized reagents reflect the current dynamic and complex HIV epidemic in Cameroon and provide valuable insights into the potential phylogenetic evolutionary trend of global HIV molecular epidemiology in the future. These materials may be useful for development of HIV validation and reference panels to evaluate the performance of serologic antigen and nucleic acid assays for their ability to detect and quantitate highly divergent HIV strains.
Collapse
Affiliation(s)
- Jiangqin Zhao
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
| | | | | | | | | | | | | | | | - Indira Hewlett
- Correspondence: (J.Z.); (I.H.); Tel.: +1-240-402-6746 (J.Z.); +1-240-402-9587 (I.H.)
| |
Collapse
|
2
|
Standardization of Nucleic Acid Tests: the Approach of the World Health Organization. J Clin Microbiol 2019; 57:JCM.01056-18. [PMID: 30257900 DOI: 10.1128/jcm.01056-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The first World Health Organization (WHO) international standards (ISs) for nucleic acid amplification techniques were established two decades ago, with the initial focus on blood screening for three major viral targets, i.e., hepatitis C virus, hepatitis B virus, and human immunodeficiency virus 1. These reference materials have subsequently found utility in the diagnosis and monitoring of a wide range of infectious diseases in clinical microbiology laboratories worldwide. WHO collaborating centers develop ISs and coordinate international studies for their evaluation. The WHO Expert Committee on Biological Standardization is responsible for the endorsement of new standardization projects and the establishment of new and replacement ISs. Potencies of ISs are defined in international units (IU); the reporting in IU for assays calibrated with an IS (or secondary standards traceable to the IS) facilitates comparability of results for different assays and determination of assay parameters such as analytical sensitivities.
Collapse
|
3
|
[Human immunodeficiency virus: position of Blood Working Group of the Federal Ministry of Health]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2016; 58:1351-70. [PMID: 26487384 DOI: 10.1007/s00103-015-2255-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
4
|
Human Immunodeficiency Virus (HIV). Transfus Med Hemother 2016; 43:203-22. [PMID: 27403093 PMCID: PMC4924471 DOI: 10.1159/000445852] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022] Open
|
5
|
Baylis SA, Chudy M, Nübling CM. Standardization of NAT for Blood-Borne Pathogens. Transfus Med Hemother 2015; 42:211-8. [PMID: 26557812 DOI: 10.1159/000435872] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
Assays based on nucleic acid amplification technology (NAT) are increasingly used for screening of blood and for diagnosis or monitoring of patients. Both regulatory requirements for blood screening and international recommendations for the treatment of patients are based on common reference materials available globally for the standardization of NAT assays. World Health Organization International Standards (WHO ISs) and International Reference Panels (WHO IRPs) are primary reference materials. The characterization and manufacture of WHO reference materials as well as their evaluation is performed on behalf of the WHO by collaborating centers; their establishment is decided upon by the WHO Expert Committee on Biological Standardization (ECBS). The potency of the first WHO IS is defined by the 'international unit' (IU) which should be maintained upon replacement of the IS. The IU, unlike copy number or genome equivalent, is defined by the IS with a physical existence, is available worldwide, and allows traceability and comparability of results. The anticipated use of WHO ISs is the calibration of secondary standards or the validation of essential assay features, e.g. limit of detection.
Collapse
Affiliation(s)
- Sally A Baylis
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - Michael Chudy
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany
| | - C Micha Nübling
- Department of Virology, Paul-Ehrlich-Institut, Langen, Germany ; World Health Organization, Essential Medicines and Health Products Department, Geneva, Switzerland
| |
Collapse
|
6
|
Vetter BN, Orlowski V, Fransen K, Niederhauser C, Aubert V, Brandenberger M, Ciardo D, Dollenmaier G, Klimkait T, Regenass S, Schmid P, Schottstedt V, Suter-Riniker F, Yerly S, Shah C, Böni J, Schüpbach J. Generation of a recombinant Gag virus-like-particle panel for the evaluation of p24 antigen detection by diagnostic HIV tests. PLoS One 2014; 9:e111552. [PMID: 25343245 PMCID: PMC4208835 DOI: 10.1371/journal.pone.0111552] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/28/2014] [Indexed: 02/07/2023] Open
Abstract
Background Detection of HIV-1 p24 antigen permits early identification of primary HIV infection and timely intervention to limit further spread of the infection. Principally, HIV screening should equally detect all viral variants, but reagents for a standardised test evaluation are limited. Therefore, we aimed to create an inexhaustible panel of diverse HIV-1 p24 antigens. Methods We generated a panel of 43 recombinantly expressed virus-like particles (VLPs), containing the structural Gag proteins of HIV-1 subtypes A-H and circulating recombinant forms (CRF) CRF01_AE, CRF02_AG, CRF12_BF, CRF20_BG and group O. Eleven 4th generation antigen/antibody tests and five antigen-only tests were evaluated for their ability to detect VLPs diluted in human plasma to p24 concentrations equivalent to 50, 10 and 2 IU/ml of the WHO p24 standard. Three tests were also evaluated for their ability to detect p24 after heat-denaturation for immune-complex disruption, a pre-requisite for ultrasensitive p24 detection. Results Our VLP panel exhibited an average intra-clade p24 diversity of 6.7%. Among the 4th generation tests, the Abbott Architect and Siemens Enzygnost Integral 4 had the highest sensitivity of 97.7% and 93%, respectively. Alere Determine Combo and BioRad Access were least sensitive with 10.1% and 40.3%, respectively. Antigen-only tests were slightly more sensitive than combination tests. Almost all tests detected the WHO HIV-1 p24 standard at a concentration of 2 IU/ml, but their ability to detect this input for different subtypes varied greatly. Heat-treatment lowered overall detectability of HIV-1 p24 in two of the three tests, but only few VLPs had a more than 3-fold loss in p24 detection. Conclusions The HIV-1 Gag subtype panel has a broad diversity and proved useful for a standardised evaluation of the detection limit and breadth of subtype detection of p24 antigen-detecting tests. Several tests exhibited problems, particularly with non-B subtypes.
Collapse
Affiliation(s)
- Beatrice N. Vetter
- Swiss National Center for Retroviruses (SNCR), Institute of Medical Virology, University of Zürich, Zürich, Switzerland
- * E-mail:
| | - Vanessa Orlowski
- Swiss National Center for Retroviruses (SNCR), Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Katrien Fransen
- Institute of Tropical Medicine (ITG), Clinical Science, Antwerp, Belgium
| | | | - Vincent Aubert
- University Hospital, Service of Immunology and Allergy, CHUV, Lausanne, Switzerland
| | | | | | | | - Thomas Klimkait
- Department Biomedicine, Haus Petersplatz, University of Basel, Basel, Switzerland
| | | | - Patrick Schmid
- Department of Infectious Diseases, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland
| | | | | | - Sabine Yerly
- University Hospitals (HUG), Laboratory of Virology, Genève, Switzerland
| | - Cyril Shah
- Swiss National Center for Retroviruses (SNCR), Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Jürg Böni
- Swiss National Center for Retroviruses (SNCR), Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Jörg Schüpbach
- Swiss National Center for Retroviruses (SNCR), Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| |
Collapse
|
7
|
Zhao X, Chen X, Zhang Y, He X, Li W, Shi L, Chen X, Xu Z, Zhong N, Ji G, Yang L, Wang J. Development and evaluation of reverse-transcription loop-mediated isothermal amplification for rapid detection of human immunodeficiency virus type 1. Indian J Med Microbiol 2013. [PMID: 23183461 DOI: 10.4103/0255-0857.103757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE The objective of this study was to establish a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method for rapid detection of human immunodeficiency virus type 1 (HIV-1). MATERIALS AND METHODS The HIV-1 integrase gene region was selected because it was a conserved part of the HIV-1 genome. Six primers specific to eight regions of the HIV-1 integrase gene were designed. A total of 171 samples (18 HIV-1 confirmed positive samples and 153 serum specimens were collected in this study) were tested by RT-LAMP and reverse-transcription polymerase chain reaction (RT-PCR). After amplification in an isothermal water bath for 45 min, samples containing HIV-1 generated the expected ladder-like products while other viruses generated no product. RESULTS The sensitivity and specificity of the RT-LAMP assay were evaluated by comparison with RT-PCR. The assay was significantly more sensitive than normal gel-based RT-PCR. CONCLUSION Because it is specific and simple, the RT-LAMP assay can be widely applied in clinical laboratories for rapid detection of HIV-1.
Collapse
Affiliation(s)
- Xihong Zhao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430073; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510640, China
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol 2012; 50:3838-44. [PMID: 22993180 DOI: 10.1128/jcm.01516-12] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Whole HIV-1 genome sequences are pivotal for large-scale studies of inter- and intrahost evolution, including the acquisition of drug resistance mutations. The ability to rapidly and cost-effectively generate large numbers of HIV-1 genome sequences from different populations and geographical locations and determine the effect of minority genetic variants is, however, a limiting factor. Next-generation sequencing promises to bridge this gap but is hindered by the lack of methods for the enrichment of virus genomes across the phylogenetic breadth of HIV-1 and methods for the robust assembly of the virus genomes from short-read data. Here we report a method for the amplification, next-generation sequencing, and unbiased de novo assembly of HIV-1 genomes of groups M, N, and O, as well as recombinants, that does not require prior knowledge of the sequence or subtype. A sensitivity of at least 3,000 copies/ml was determined by using plasma virus samples of known copy numbers. We applied our novel method to compare the genome diversities of HIV-1 groups, subtypes, and genes. The highest level of diversity was found in the env, nef, vpr, tat, and rev genes and parts of the gag gene. Furthermore, we used our method to investigate mutations associated with HIV-1 drug resistance in clinical samples at the level of the complete genome. Drug resistance mutations were detected as both major variant and minor species. In conclusion, we demonstrate the feasibility of our method for large-scale HIV-1 genome sequencing. This will enable the phylogenetic and phylodynamic resolution of the ongoing pandemic and efficient monitoring of complex HIV-1 drug resistance genotypes.
Collapse
|
9
|
Performance evaluation of the new Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 for quantification of human immunodeficiency virus type 1 RNA. J Clin Microbiol 2010; 48:1195-200. [PMID: 20164281 DOI: 10.1128/jcm.01832-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite FDA approval and CE marking of commercial tests, manufacturer-independent testing of the technical aspects of newly developed tests is important. To evaluate the analytical performance and explore the clinical applicability of the new Roche COBAS AmpliPrep COBAS TaqMan HIV-1 test, version 2.0 (CAP/CTM v2.0), platform comparison was performed with the Roche CAP/CTM test, version 2.0, the COBAS Amplicor HIV-1 Monitor Test, version 1.5 (CAP/CA v1.5), the COBAS AmpliPrep COBAS TaqMan HIV-1 Test (CAP/CTM v1.0), and the Abbott m2000 RealTime HIV-1 assay on panels and diagnostic samples. Specificity was tested for HIV-2 samples. Furthermore, samples from HIV-1-seropositive individuals with CAP/CA v1.5-measured viral loads below 50 HIV-1 RNA copies per ml (cp/ml) and replicates of HIV-1-seronegative plasma were tested in a checkerboard analysis. CAP/CTM v2.0 is HIV-1 specific, with broad genotype inclusivity and no serious underquantification of viral load relative to the other assays used. Low viral loads below the threshold of quantification for CAP/CA v1.5 are observed with CAP/CTM v2.0. A CAP/CTM v2.0-measured viral load of >50 copies/ml in these samples correlated with therapy failure. In conclusion, CAP/CTM v2.0 is an accurate and reliable test for HIV-1 viral load measurement relative to the other assays used with respect to specificity, sensitivity, and genotype inclusivity.
Collapse
|
10
|
Abstract
Real-time RT-PCR has become the method of choice for automated detection of viral RNA target sequences in the clinical laboratory. Besides commercially available certified test systems, a variety of so-called in-house methods have been described in the literature. Generally, appropriate validation and continuous quality control are mandatory if these in-house-developed assays are used in clinical diagnostics. In this chapter, an in-house HIV-1 real-time RT-PCR assay for blood donor screening is described. The procedure includes the pooling of plasma samples, viral RNA isolation, and subsequent detection of amplification in real-time one-step RT-PCR. The validation considers the specificity, the sensitivity on HIV-1 genomic variants, and the robustness of the assay.
Collapse
Affiliation(s)
- Jens Müller
- Institute for Experimental Haematology and Transfusion Medicine, University of Bonn, Bonn, Germany.
| |
Collapse
|
11
|
Drexler JF, Kupfer B, Petersen N, Grotto RMT, Rodrigues SMC, Grywna K, Panning M, Annan A, Silva GF, Douglas J, Koay ESC, Smuts H, Netto EM, Simmonds P, Pardini MIDMC, Roth WK, Drosten C. A novel diagnostic target in the hepatitis C virus genome. PLoS Med 2009; 6:e31. [PMID: 19209955 PMCID: PMC2637920 DOI: 10.1371/journal.pmed.1000031] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 12/24/2008] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Detection and quantification of hepatitis C virus (HCV) RNA is integral to diagnostic and therapeutic regimens. All molecular assays target the viral 5'-noncoding region (5'-NCR), and all show genotype-dependent variation of sensitivities and viral load results. Non-western HCV genotypes have been under-represented in evaluation studies. An alternative diagnostic target region within the HCV genome could facilitate a new generation of assays. METHODS AND FINDINGS In this study we determined by de novo sequencing that the 3'-X-tail element, characterized significantly later than the rest of the genome, is highly conserved across genotypes. To prove its clinical utility as a molecular diagnostic target, a prototype qualitative and quantitative test was developed and evaluated multicentrically on a large and complete panel of 725 clinical plasma samples, covering HCV genotypes 1-6, from four continents (Germany, UK, Brazil, South Africa, Singapore). To our knowledge, this is the most diversified and comprehensive panel of clinical and genotype specimens used in HCV nucleic acid testing (NAT) validation to date. The lower limit of detection (LOD) was 18.4 IU/ml (95% confidence interval, 15.3-24.1 IU/ml), suggesting applicability in donor blood screening. The upper LOD exceeded 10(-9) IU/ml, facilitating viral load monitoring within a wide dynamic range. In 598 genotyped samples, quantified by Bayer VERSANT 3.0 branched DNA (bDNA), X-tail-based viral loads were highly concordant with bDNA for all genotypes. Correlation coefficients between bDNA and X-tail NAT, for genotypes 1-6, were: 0.92, 0.85, 0.95, 0.91, 0.95, and 0.96, respectively; X-tail-based viral loads deviated by more than 0.5 log10 from 5'-NCR-based viral loads in only 12% of samples (maximum deviation, 0.85 log10). The successful introduction of X-tail NAT in a Brazilian laboratory confirmed the practical stability and robustness of the X-tail-based protocol. The assay was implemented at low reaction costs (US$8.70 per sample), short turnover times (2.5 h for up to 96 samples), and without technical difficulties. CONCLUSION This study indicates a way to fundamentally improve HCV viral load monitoring and infection screening. Our prototype assay can serve as a template for a new generation of viral load assays. Additionally, to our knowledge this study provides the first open protocol to permit industry-grade HCV detection and quantification in resource-limited settings.
Collapse
Affiliation(s)
- Jan Felix Drexler
- Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- Institute of Virology, University of Bonn, Bonn, Germany
- Infectious Diseases Research Laboratory, University Hospital Prof. Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | - Bernd Kupfer
- Institute of Virology, University of Bonn, Bonn, Germany
| | - Nadine Petersen
- Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Rejane Maria Tommasini Grotto
- University of São Paulo State (UNESP), Botucatu Medical School, Blood Transfusion Centre - Molecular Biology Laboratory and Internal Medicine Department, Botucatu, São Paulo, Brazil
| | - Silvia Maria Corvino Rodrigues
- University of São Paulo State (UNESP), Botucatu Medical School, Blood Transfusion Centre - Molecular Biology Laboratory and Internal Medicine Department, Botucatu, São Paulo, Brazil
| | - Klaus Grywna
- Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Marcus Panning
- Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Augustina Annan
- Clinical Virology Group, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Giovanni Faria Silva
- University of São Paulo State (UNESP), Botucatu Medical School, Blood Transfusion Centre - Molecular Biology Laboratory and Internal Medicine Department, Botucatu, São Paulo, Brazil
| | - Jill Douglas
- Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Edinburgh, United Kingdom
| | - Evelyn S. C Koay
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore
- Molecular Diagnosis Centre, National University Hospital, Singapore
| | - Heidi Smuts
- Division Medical Virology/National Health Laboratory Service, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Eduardo M Netto
- Infectious Diseases Research Laboratory, University Hospital Prof. Edgard Santos, Federal University of Bahia, Salvador, Brazil
| | - Peter Simmonds
- Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Inês de Moura Campos Pardini
- University of São Paulo State (UNESP), Botucatu Medical School, Blood Transfusion Centre - Molecular Biology Laboratory and Internal Medicine Department, Botucatu, São Paulo, Brazil
| | | | - Christian Drosten
- Institute of Virology, University of Bonn, Bonn, Germany
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
12
|
Fryer JF, Minor PD. Standardisation of nucleic acid amplification assays used in clinical diagnostics: A report of the first meeting of the SoGAT Clinical Diagnostics Working Group. J Clin Virol 2009; 44:103-5. [DOI: 10.1016/j.jcv.2008.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
|