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Balakrishna S, Loosli T, Zaheri M, Frischknecht P, Huber M, Kusejko K, Yerly S, Leuzinger K, Perreau M, Ramette A, Wymant C, Fraser C, Kellam P, Gall A, Hirsch HH, Stoeckle M, Rauch A, Cavassini M, Bernasconi E, Notter J, Calmy A, Günthard HF, Metzner KJ, Kouyos RD. Frequency matters: comparison of drug resistance mutation detection by Sanger and next-generation sequencing in HIV-1. J Antimicrob Chemother 2023; 78:656-664. [PMID: 36738248 DOI: 10.1093/jac/dkac430] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/18/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is gradually replacing Sanger sequencing (SS) as the primary method for HIV genotypic resistance testing. However, there are limited systematic data on comparability of these methods in a clinical setting for the presence of low-abundance drug resistance mutations (DRMs) and their dependency on the variant-calling thresholds. METHODS To compare the HIV-DRMs detected by SS and NGS, we included participants enrolled in the Swiss HIV Cohort Study (SHCS) with SS and NGS sequences available with sample collection dates ≤7 days apart. We tested for the presence of HIV-DRMs and compared the agreement between SS and NGS at different variant-calling thresholds. RESULTS We included 594 pairs of SS and NGS from 527 SHCS participants. Males accounted for 80.5% of the participants, 76.3% were ART naive at sample collection and 78.1% of the sequences were subtype B. Overall, we observed a good agreement (Cohen's kappa >0.80) for HIV-DRMs for variant-calling thresholds ≥5%. We observed an increase in low-abundance HIV-DRMs detected at lower thresholds [28/417 (6.7%) at 10%-25% to 293/812 (36.1%) at 1%-2% threshold]. However, such low-abundance HIV-DRMs were overrepresented in ART-naive participants and were in most cases not detected in previously sampled sequences suggesting high sequencing error for thresholds <3%. CONCLUSIONS We found high concordance between SS and NGS but also a substantial number of low-abundance HIV-DRMs detected only by NGS at lower variant-calling thresholds. Our findings suggest that a substantial fraction of the low-abundance HIV-DRMs detected at thresholds <3% may represent sequencing errors and hence should not be overinterpreted in clinical practice.
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Affiliation(s)
- Suraj Balakrishna
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Paul Frischknecht
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Karoline Leuzinger
- Clinical Virology Division, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Chris Wymant
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Kellam
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Astrid Gall
- Excellence in Life Sciences (EMBO), Heidelberg, Germany
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Marcel Stoeckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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2
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Rindler AE, Kusejko K, Kuster H, Neumann K, Leemann C, Zeeb M, Chaudron SE, Braun DL, Kouyos RD, Metzner KJ, Günthard HF. The interplay between replication capacity of HIV-1 and surrogate markers of disease. J Infect Dis 2022; 226:1057-1068. [PMID: 35299248 DOI: 10.1093/infdis/jiac100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HIV-1 replication capacity (RC) of transmitted/founder viruses may influence the further course of HIV-1 infection. METHODS Replication capacities (RCs) of 355 whole genome primary HIV-1 isolates derived from samples acquired during acute and recent primary HIV-1 infection (PHI) were determined using a novel high throughput infection assay in primary cells. The RCs were used to elucidate potential factors that could be associated with RC during PHI. RESULTS Increased RC was found to be associated with increased set point viral load (VL), and significant differences in RCs among 13 different HIV-1 subtypes were discerned. Notably, we observed an increase in RCs for primary HIV-1 isolates of HIV-1 subtype B over a 17-year period. Associations were not observed between RC and CD4 count at sample date of RC measurement, CD4 recovery after initiation of antiretroviral treatment (ART), CD4 decline in untreated individuals, and acute retroviral syndrome severity scores. DISCUSSION These findings highlight that RCs of primary HIV-1 isolates acquired during the acute and recent phase of infection are more associated with viral factors, i.e., set point VL, than with host factors. Furthermore, we observed a temporal increase in RC for HIV-1 subtype B viruses over a period of 17 years.
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Affiliation(s)
- Audrey E Rindler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Herbert Kuster
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Morozov V, Lagaye S, Morozov A. The TZM-bl Reporter Cell Line Expresses Kynureninase That Can Neutralize 2F5-like Antibodies in the HIV-1 Neutralization Assay. Int J Mol Sci 2022; 23:ijms23020641. [PMID: 35054825 PMCID: PMC8775840 DOI: 10.3390/ijms23020641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Induction of broadly neutralizing antibodies targeting ectodomain of the transmembrane (TM) glycoprotein gp41 HIV-1 provides a basis for the development of a universal anti-viral vaccine. The HeLa cell-derived TZM-bl reporter cell line is widely used for the estimation of lentiviruses neutralization by immune sera. The cell line is highly permissive to infection by most strains of HIV, SIV, and SHIV. Here we demonstrated that TZM-bl cells express a 48 kDa non-glycosylated protein (p48) recognized by broadly neutralizing monoclonal antibody (mAb) 2F5 targeting the ELDKWA (aa 669–674) epitope of gp41TM of HIV-1. A significant amount of p48 was found in the cell supernatant. The protein was identified as human kynureninase (KYNU), which has the ELDKWA epitope. The protein is further called “p48 KYNU”. The HIV-1 neutralization by mAb 2F5 and 4E10 in the presence of p48KYNU was tested on Jurkat and TZM-bl cells. It was demonstrated that p48KYNU reduces neutralization by 2F5-like antibodies, but it has almost no effect on mAb 4E10. Therefore, p48KYNU can attenuate HIV-1 neutralization by 2F5-like antibodies and hence create false-negative results. Thus, previously tested immune sera that recognized the ELDKWA-epitope and demonstrated a “weak neutralization” of HIV-1 in TZM-bl assay should be reevaluated.
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Affiliation(s)
- Vladimir Morozov
- Institute of Human Virology, University of Maryland, Baltimore, MD 21201, USA
- Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
- Correspondence: (V.M.); (A.M.)
| | - Sylvie Lagaye
- Centre de Recherche Saint-Antoine (CRSA), INSERM—UMR-S 938/Sorbonne Université, CEDEX 12, 75571 Paris, France;
| | - Alexey Morozov
- Laboratory of Regulation of Intracellular Proteolysis, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Correspondence: (V.M.); (A.M.)
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