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Oomen PGA, Dijkstra S, Hofstra LM, Nijhuis MM, Verbon A, Mudrikova T, Wensing AMJ, Hoepelman AIM, Van Welzen BJ. Integrated analysis of viral blips, residual viremia, and associated factors in people with HIV: Results from a retrospective cohort study. J Med Virol 2023; 95:e29178. [PMID: 37861450 DOI: 10.1002/jmv.29178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
The etiology of viral blips is not yet fully elucidated. One of the hypotheses is that blips reflect variations in residual viremia (RV) near the detectability threshold. In this study, we evaluated whether RV is associated with viral blips and which factors are associated with RV. All treatment regimens in 2010-2020 consisting of two nucleos(-t)ide reverse transcriptase inhibitors and one anchor (integrase strand transfer inhibitor [INSTI], non-nucleoside reverse transcriptase inhibitor [NNRTI], or protease inhibitor [PI]) in people with HIV (PWH) were evaluated for RV (detectable viremia <50 cp/mL) and blips (isolated viral loads [VLs] 50-499 cp/mL between measurements <50 cp/mL). All medical records were reviewed and regimens in which a VL ≥ 50 cp/mL was deemed to result from non-adherence (based on the documented conclusion by the treating physician) were excluded. Factors associated with blips and RV were identified using generalized linear mixed models. In total, 24 518 VLs from 1658 PWH were analyzed. VLs were measured during INSTI- (n = 5119; 20.9%), PI- (n = 8935; 36.4%), and NNRTI-use (n = 10 464; 42.7%). VLs were categorized as blips in 1.4% (n = 332). The 24,186 non-blip VLs were RNAneg (no RV) (n = 15 326; 63.4%), 1-19 cp/mL (n = 6318; 26.1%), 20-49 cp/mL (n = 1620; 6.7%), or <50 cp/mL with an unknown RV level (n = 922; 3.8%). In 193/1658 PWH (11.6%), the RV level was RNAneg in all VLs assessed. RV 1-19 cp/mL and 20-49 cp/mL (vs. RNAneg ) were significantly associated with subsequent viral blips (respective odds ratio 2.66 and 4.90 [95% confidence intervals: 1.98-3.58 and 3.41-7.04]). Zenith VL and use of PIs (vs. INSTIs/NNRTIs) were associated with higher RV and blip odds. This large cohort study showed that blips were associated with higher preceding RV. Both the anchor type and factors previously linked to the latent viral reservoir were associated with RV, suggesting blips having a multifactorial origin.
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Affiliation(s)
- Patrick G A Oomen
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Suzan Dijkstra
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - L Marije Hofstra
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique M Nijhuis
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Annelies Verbon
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tania Mudrikova
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Translational Virology, University Medical Center Utrecht, Utrecht, The Netherlands
- Ezintsha, Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andy I M Hoepelman
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Berend J Van Welzen
- Department of Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
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2
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Plantinga NL, van Lanschot MCJ, Raven CFH, Schuurman R, Rirash AF, van Deursen B, Boland GJ, Siksma TO, Fries E, Mostert M, Thijsen SFT, Hofstra LM. Integrated surveillance of human respiratory viruses in addition to SARS-CoV-2 in a public testing facility in the Netherlands. J Clin Virol 2023; 158:105346. [PMID: 36502623 PMCID: PMC9699712 DOI: 10.1016/j.jcv.2022.105346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/04/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND SARS-CoV-2 prevention measures impact the circulation of other respiratory viruses. Surveillance in the network of general practitioners is hampered by widespread testing for SARS-CoV-2 in public testing facilities. OBJECTIVES To evaluate integrated community surveillance of SARS-CoV-2 and other respiratory viruses and describe epidemiological trends. STUDY DESIGN Respiratory surveillance was set up within an existing SARS-CoV-2 public testing facility. Community-dwelling (a)symptomatic persons provided consent for completion of a questionnaire and additional testing on residual material from swabs taken for SARS-CoV-2 RT-PCR (Allplex Seegene). Daily, a random subset was tested for sixteen respiratory viruses by multiplex realtime PCRs (Seegene). RESULTS Between October 6th (week 40) 2021 and April 22nd (week 16) 2022, 3,969 subjects were tested. The weekly median age ranged from 23 to 39 years. The prevalence of respiratory symptoms ranged from 98.5% (week 40) to 27.4% (week 1). The prevalence of detection of any respiratory virus (including SARS-CoV-2), ranged from 19.6% in week 49 to 75.3% in week 14. SARS-CoV-2 prevalence ranged from 2.2% (week 40) to 63.3% (week 14). Overall, SARS-CoV-2 was detected most frequently (27.3%), followed by rhinoviruses (14.6%, range 3.5-47.8%) and seasonal coronaviruses (3.7%, range 0-10.4%, mostly 229E and OC43). Influenzavirus was detected in 3.0% of participants from week 6 onwards. CONCLUSIONS Integrated respiratory viral surveillance within public testing facilities is feasible and informative. Prevalences may be affected by changes in SARS-CoV-2 prevention and testing policies. Population characteristics help to interpret trends over time. Integrated surveillance may inform policymakers and hospitals for adequate response measures during respiratory seasons.
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Affiliation(s)
- N L Plantinga
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands.
| | - M C J van Lanschot
- Department of Infectious Diseases, Public Health Service Utrecht region, Netherlands
| | - C F H Raven
- Department of Infectious Diseases, Public Health Service Utrecht region, Netherlands
| | - R Schuurman
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands
| | - A F Rirash
- Department of Infectious Diseases, Public Health Service Utrecht region, Netherlands
| | - B van Deursen
- Department of Infectious Diseases, Public Health Service Utrecht region, Netherlands
| | - G J Boland
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands
| | - T O Siksma
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands
| | - E Fries
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands
| | - M Mostert
- Department of Medical Microbiology, Diakonessenhuis Utrecht, Netherlands
| | - S F T Thijsen
- Department of Medical Microbiology, Diakonessenhuis Utrecht, Netherlands
| | - L M Hofstra
- Department of Medical Microbiology, University Medical Center Utrecht, Netherlands
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3
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Dijkstra S, Hofstra LM, Mudrikova T, Wensing AMJ, Oomen PGA, Hoepelman AIM, van Welzen BJ. Lower Incidence of HIV-1 Blips Observed During Integrase Inhibitor-Based Combination Antiretroviral Therapy. J Acquir Immune Defic Syndr 2022; 89:575-582. [PMID: 34966148 DOI: 10.1097/qai.0000000000002898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/06/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND As the nature of viral blips remains unclear, their occurrence often leads to uncertainty. This study compares blip incidence rates during treatment with different combination antiretroviral therapy anchors. SETTING Retrospective cohort study in a tertiary hospital. METHODS All antiretroviral regimens between 2010 and 2020 containing 2 nucleos(-t)ide reverse transcriptase inhibitors and 1 anchor in virologically suppressed people living with HIV (PLWH) from our center were evaluated for the occurrence of blips [isolated viral loads (VLs) 50-499 copies/mL between measurements <50 copies/mL]. Factors associated with blips were identified using multivariable generalized estimating equation-based negative binomial models. The relationship between blips and either persistent low-level viremia (consecutive VLs ≥ 50 copies/mL not classified as failure) or virologic failure (consecutive VLs ≥ 200 or 1 VL ≥ 500 copies/mL) was also evaluated. RESULTS In total, 308 blips occurred during 3405 treatment courses in 1661 PLWH. Compared with a non-nucleoside reverse transcriptase inhibitor anchor, blip incidence was higher for protease inhibitors (incidence rate ratio 1.37; 95% confidence interval 1.05 to 1.78) and lower for integrase inhibitors (INSTIs) (incidence rate ratio 0.64; 95% confidence interval: 0.43 to 0.96). In addition, blips were associated with higher zenith VL, higher VL test frequency, and shorter time since antiretroviral therapy initiation. PLWH experiencing blips were more likely to demonstrate persistent low-level viremia but not virologic failure. Blips led to extra consultations and measurements. CONCLUSIONS INSTI-based regimens display a low number of blips. Although we found no correlation with virologic failure, the occurrence of blips led to an increased clinical burden. Further research is needed to elucidate the implications and underlying mechanisms of these findings.
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Affiliation(s)
- Suzan Dijkstra
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
| | - L Marije Hofstra
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, the Netherlands; and
| | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, the Netherlands; and
- Ezinthsa, WITS RHI University of the Witwatersrand, Johannesburg, South-Africa
| | - Patrick G A Oomen
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Andy I M Hoepelman
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Berend J van Welzen
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
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4
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Rümke LW, Groenveld FC, van Os YMG, Praest P, Tanja AAN, de Jong DTCM, Symons J, Schuurman R, Reinders T, Hofstra LM, Nierkens S, Thijsen SFT, Heron M, Lebbink RJ, Beekman JM, Nijhuis M, Wensing AMJ. In-depth Characterization of Vaccine Breakthrough Infections With SARS-CoV-2 Among Health Care Workers in a Dutch Academic Medical Center. Open Forum Infect Dis 2022; 9:ofab553. [PMID: 34988250 PMCID: PMC8714358 DOI: 10.1093/ofid/ofab553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/03/2021] [Indexed: 11/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 infection after coronavirus disease 2019 vaccination raises concerns about the emergence of vaccine escape variants. Here we characterize 14 breakthrough infections among 5860 fully vaccinated Dutch health care workers ≥14 days after the final dose of vaccination with either BNT162b2, mRNA-1273, or Ad26.COV2.S. These breakthrough infections presented with regular B.1.1.7 (Alpha) and B.1.617.2 (Delta) variants and high viral loads, despite normal vaccine-induced B- and T-cell immune responses detected by live virus neutralization assays and ELISpot. High-risk exposure settings, such as in households, indicate a potential risk of viral transmission despite full vaccination.
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Affiliation(s)
- Lidewij W Rümke
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Femke C Groenveld
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Yvonne M G van Os
- Occupational Health Office, Department of Human Resources, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Patrique Praest
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anniek A N Tanja
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dorien T C M de Jong
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jori Symons
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob Schuurman
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tessa Reinders
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - L Marije Hofstra
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Steven F T Thijsen
- Department of Medical Microbiology & Immunology, Utrecht, the Netherlands
| | - Michiel Heron
- Department of Medical Microbiology & Immunology, Utrecht, the Netherlands
| | - Robert-Jan Lebbink
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, the Netherlands.,Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, the Netherlands
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
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5
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Steens JA, Zhu Y, Taylor DW, Bravo JPK, Prinsen SHP, Schoen CD, Keijser BJF, Ossendrijver M, Hofstra LM, Brouns SJJ, Shinkai A, van der Oost J, Staals RHJ. SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation. Nat Commun 2021; 12:5033. [PMID: 34413302 PMCID: PMC8376896 DOI: 10.1038/s41467-021-25337-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Characteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3' end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5' end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.
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Affiliation(s)
- Jurre A. Steens
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands ,Scope Biosciences, Wageningen, The Netherlands
| | - Yifan Zhu
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - David W. Taylor
- grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, University of Texas at Austin, Austin, TX USA ,grid.89336.370000 0004 1936 9924Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX USA ,grid.89336.370000 0004 1936 9924Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX USA ,grid.89336.370000 0004 1936 9924LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX USA
| | - Jack P. K. Bravo
- grid.89336.370000 0004 1936 9924Department of Molecular Biosciences, University of Texas at Austin, Austin, TX USA
| | | | - Cor D. Schoen
- grid.4818.50000 0001 0791 5666BioInteractions and Plant Health, Wageningen Plant Research, Wageningen, The Netherlands
| | | | | | - L. Marije Hofstra
- grid.7692.a0000000090126352Virology, Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stan J. J. Brouns
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
| | - Akeo Shinkai
- grid.472717.0RIKEN SPring-8 Center, Sayo, Hyogo, Japan ,grid.7597.c0000000094465255Present Address: RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - John van der Oost
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Raymond H. J. Staals
- grid.4818.50000 0001 0791 5666Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
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6
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Hofstra LM, Sánchez Rivas E, Nijhuis M, Bank LEA, Wilkinson E, Kelly K, Mudrikova T, Schuurman R, de Oliveira T, de Kort J, Wensing AMJ. High Rates of Transmission of Drug-resistant HIV in Aruba Resulting in Reduced Susceptibility to the WHO Recommended First-line Regimen in Nearly Half of Newly Diagnosed HIV-infected Patients. Clin Infect Dis 2017; 64:1092-1097. [PMID: 28329390 PMCID: PMC5848377 DOI: 10.1093/cid/cix056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/24/2017] [Indexed: 11/22/2022] Open
Abstract
Background. In Western countries emergence of human immunodeficiency virus (HIV) drug resistance has tremendously decreased, and transmission of drug resistance has merely stabilized in recent years. However, in many endemic settings with limited resources rates of emerging and transmitted drug resistance are not regularly assessed. Methods. We performed a survey including all HIV-infected individuals who received resistance testing in 2010–2015 in Aruba, a highly endemic HIV area in the Caribbean. Transmitted HIV drug resistance was determined using World Health Organization (WHO) criteria. Transmission dynamics were investigated using phylogenetic analyses. In a subset, baseline samples were re-analyzed using next generation sequencing (NGS). Results. Baseline resistance testing was performed in 104 newly diagnosed untreated individuals (54% of all newly diagnosed individuals in 2010–2015): 86% were men, 39% were foreign-born, and 22% had AIDS at diagnosis. And 33% (95% CI: 24–42%) was infected with a drug-resistant HIV variant. The prevalence of resistance to non-nucleoside reverse transcriptase inhibitors (NNRTIs) reached 45% (95% CI: 27–64%) in 2015, all based on the prevalence of mutation K103N. NGS did not demonstrate additional minority K103N-variants compared to routine resistance testing. K103N-harboring strains were introduced into the therapy-unexposed population via at least 6 independent transmissions epidemiologically linked to the surrounding countries. Virological failure of the WHO-recommended first-line NNRTI-based regimen was higher in the presence of K103N. Conclusions. The prevalence of resistant HIV in Aruba has increased to alarming levels, compromising the WHO-recommended first-line regimen. As adequate surveillance as advocated by the WHO is limited, the Caribbean region could face an unidentified rise of NNRTI-resistant HIV.
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Affiliation(s)
- L Marije Hofstra
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.,Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Elena Sánchez Rivas
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Monique Nijhuis
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Leonie E A Bank
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.,Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, The Netherlands
| | - Eduan Wilkinson
- Africa Centre for Population Health, Myeki, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Karina Kelly
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Tania Mudrikova
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, The Netherlands
| | - Rob Schuurman
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Tulio de Oliveira
- Africa Centre for Population Health, Myeki, South Africa.,School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, Republic of South Africa
| | - Jaclyn de Kort
- Department of Internal Medicine, Dr Horacio E. Oduber Hospital, Oranjestad, Aruba
| | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
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Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, Van de Vijver DAMC, Åsjö B, Beshkov D, Coughlan S, Descamps D, Griskevicius A, Hamouda O, Horban A, Van Kasteren M, Kolupajeva T, Kostrikis LG, Liitsola K, Linka M, Mor O, Nielsen C, Otelea D, Paraskevis D, Paredes R, Poljak M, Puchhammer-Stöckl E, Sönnerborg A, Staneková D, Stanojevic M, Van Laethem K, Zazzi M, Zidovec Lepej S, Boucher CAB, Schmit JC, Wensing AMJ, Puchhammer-Stockl E, Sarcletti M, Schmied B, Geit M, Balluch G, Vandamme AM, Vercauteren J, Derdelinckx I, Sasse A, Bogaert M, Ceunen H, De Roo A, De Wit S, Echahidi F, Fransen K, Goffard JC, Goubau P, Goudeseune E, Yombi JC, Lacor P, Liesnard C, Moutschen M, Pierard D, Rens R, Schrooten Y, Vaira D, Vandekerckhove LPR, Van den Heuvel A, Van Der Gucht B, Van Ranst M, Van Wijngaerden E, Vandercam B, Vekemans M, Verhofstede C, Clumeck N, Van Laethem K, Beshkov D, Alexiev I, Lepej SZ, Begovac J, Kostrikis L, Demetriades I, Kousiappa I, Demetriou V, Hezka J, Linka M, Maly M, Machala L, Nielsen C, Jørgensen LB, Gerstoft J, Mathiesen L, Pedersen C, Nielsen H, Laursen A, Kvinesdal B, Liitsola K, Ristola M, Suni J, Sutinen J, Descamps D, Assoumou L, Castor G, Grude M, Flandre P, Storto A, Hamouda O, Kücherer C, Berg T, Braun P, Poggensee G, Däumer M, Eberle J, Heiken H, Kaiser R, Knechten H, Korn K, Müller H, Neifer S, Schmidt B, Walter H, Gunsenheimer-Bartmeyer B, Harrer T, Paraskevis D, Hatzakis A, Zavitsanou A, Vassilakis A, Lazanas M, Chini M, Lioni A, Sakka V, Kourkounti S, Paparizos V, Antoniadou A, Papadopoulos A, Poulakou G, Katsarolis I, Protopapas K, Chryssos G, Drimis S, Gargalianos P, Xylomenos G, Lourida G, Psichogiou M, Daikos GL, Sipsas NV, Kontos A, Gamaletsou MN, Koratzanis G, Sambatakou H, Mariolis H, Skoutelis A, Papastamopoulos V, Georgiou O, Panagopoulos P, Maltezos E, Coughlan S, De Gascun C, Byrne C, Duffy M, Bergin C, Reidy D, Farrell G, Lambert J, O'Connor E, Rochford A, Low J, Coakely P, O'Dea S, Hall W, Mor O, Levi I, Chemtob D, Grossman Z, Zazzi M, de Luca A, Balotta C, Riva C, Mussini C, Caramma I, Capetti A, Colombo MC, Rossi C, Prati F, Tramuto F, Vitale F, Ciccozzi M, Angarano G, Rezza G, Kolupajeva T, Vasins O, Griskevicius A, Lipnickiene V, Schmit JC, Struck D, Sauvageot N, Hemmer R, Arendt V, Michaux C, Staub T, Sequin-Devaux C, Wensing AMJ, Boucher CAB, van de Vijver DAMC, van Kessel A, van Bentum PHM, Brinkman K, Connell BJ, van der Ende ME, Hoepelman IM, van Kasteren M, Kuipers M, Langebeek N, Richter C, Santegoets RMWJ, Schrijnders-Gudde L, Schuurman R, van de Ven BJM, Åsjö B, Kran AMB, Ormaasen V, Aavitsland P, Horban A, Stanczak JJ, Stanczak GP, Firlag-Burkacka E, Wiercinska-Drapalo A, Jablonowska E, Maolepsza E, Leszczyszyn-Pynka M, Szata W, Camacho R, Palma C, Borges F, Paixão T, Duque V, Araújo F, Otelea D, Paraschiv S, Tudor AM, Cernat R, Chiriac C, Dumitrescu F, Prisecariu LJ, Stanojevic M, Jevtovic D, Salemovic D, Stanekova D, Habekova M, Chabadová Z, Drobkova T, Bukovinova P, Shunnar A, Truska P, Poljak M, Lunar M, Babic D, Tomazic J, Vidmar L, Vovko T, Karner P, Garcia F, Paredes R, Monge S, Moreno S, Del Amo J, Asensi V, Sirvent JL, de Mendoza C, Delgado R, Gutiérrez F, Berenguer J, Garcia-Bujalance S, Stella N, de Los Santos I, Blanco JR, Dalmau D, Rivero M, Segura F, Elías MJP, Alvarez M, Chueca N, Rodríguez-Martín C, Vidal C, Palomares JC, Viciana I, Viciana P, Cordoba J, Aguilera A, Domingo P, Galindo MJ, Miralles C, Del Pozo MA, Ribera E, Iribarren JA, Ruiz L, de la Torre J, Vidal F, Clotet B, Albert J, Heidarian A, Aperia-Peipke K, Axelsson M, Mild M, Karlsson A, Sönnerborg A, Thalme A, Navér L, Bratt G, Karlsson A, Blaxhult A, Gisslén M, Svennerholm B, Bergbrant I, Björkman P, Säll C, Mellgren Å, Lindholm A, Kuylenstierna N, Montelius R, Azimi F, Johansson B, Carlsson M, Johansson E, Ljungberg B, Ekvall H, Strand A, Mäkitalo S, Öberg S, Holmblad P, Höfer M, Holmberg H, Josefson P, Ryding U. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis 2015; 62:655-663. [PMID: 26620652 PMCID: PMC4741360 DOI: 10.1093/cid/civ963] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Transmitted human immunodeficiency virus drug resistance in Europe is stable at around 8%. The impact of baseline mutation patterns on susceptibility to antiretroviral drugs should be addressed using clinical guidelines. The impact on baseline susceptibility is largest for nonnucleoside reverse transcriptase inhibitors. Background. Numerous studies have shown that baseline drug resistance patterns may influence the outcome of antiretroviral therapy. Therefore, guidelines recommend drug resistance testing to guide the choice of initial regimen. In addition to optimizing individual patient management, these baseline resistance data enable transmitted drug resistance (TDR) to be surveyed for public health purposes. The SPREAD program systematically collects data to gain insight into TDR occurring in Europe since 2001. Methods. Demographic, clinical, and virological data from 4140 antiretroviral-naive human immunodeficiency virus (HIV)–infected individuals from 26 countries who were newly diagnosed between 2008 and 2010 were analyzed. Evidence of TDR was defined using the WHO list for surveillance of drug resistance mutations. Prevalence of TDR was assessed over time by comparing the results to SPREAD data from 2002 to 2007. Baseline susceptibility to antiretroviral drugs was predicted using the Stanford HIVdb program version 7.0. Results. The overall prevalence of TDR did not change significantly over time and was 8.3% (95% confidence interval, 7.2%–9.5%) in 2008–2010. The most frequent indicators of TDR were nucleoside reverse transcriptase inhibitor (NRTI) mutations (4.5%), followed by nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations (2.9%) and protease inhibitor mutations (2.0%). Baseline mutations were most predictive of reduced susceptibility to initial NNRTI-based regimens: 4.5% and 6.5% of patient isolates were predicted to have resistance to regimens containing efavirenz or rilpivirine, respectively, independent of current NRTI backbones. Conclusions. Although TDR was highest for NRTIs, the impact of baseline drug resistance patterns on susceptibility was largest for NNRTIs. The prevalence of TDR assessed by epidemiological surveys does not clearly indicate to what degree susceptibility to different drug classes is affected.
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Affiliation(s)
- L Marije Hofstra
- Luxembourg Institute of Health, Luxembourg.,Department of Virology, University Medical Center Utrecht, The Netherlands
| | | | - Jan Albert
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Federico Garcia
- Complejo Hospitalario Universitario de Granada, Instituto de Investigación IBS Granada; on behalf of Cohorte de Adultos de la Red de Investigación en SIDA, Spain
| | | | | | | | - Danail Beshkov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - Diane Descamps
- AP-HP Groupe hospitalier Bichat-Claude Bernard, IAME INSERM UMR 1137, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | | | | | | | | | | | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - Orna Mor
- National HIV Reference Laboratory, Chaim Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. dr. Matei Bals", Bucharest, Romania
| | | | | | - Mario Poljak
- Faculty of Medicine, Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Slovenia
| | | | - Anders Sönnerborg
- Karolinska Institute, Solna.,Karolinska University Hospital, Stockholm, Sweden
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Casadellà M, van Ham PM, Noguera-Julian M, van Kessel A, Pou C, Hofstra LM, Santos JR, Garcia F, Struck D, Alexiev I, Bakken Kran AM, Hoepelman AI, Kostrikis LG, Somogyi S, Liitsola K, Linka M, Nielsen C, Otelea D, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Staneková D, Stanojevic M, Van Laethem K, Zidovec Lepej S, Clotet B, Boucher CAB, Paredes R, Wensing AMJ. Primary resistance to integrase strand-transfer inhibitors in Europe. J Antimicrob Chemother 2015; 70:2885-8. [PMID: 26188038 DOI: 10.1093/jac/dkv202] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/16/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. METHODS This was a multicentre, cross-sectional study within the European SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score ≥ 10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65 samples were selected for 454 integrase sequencing. RESULTS For the population sequencing analysis, 278 samples were retrieved and successfully analysed. No signature resistance mutations to any of the InSTIs were detected. Eleven (4%) subjects had mutations at resistance-associated positions with an HIVdb score ≥ 10. Of the 56 samples successfully analysed with 454 sequencing, no InSTI signature mutations were detected, whereas integrase substitutions with an HIVdb score ≥ 10 were found in 8 (14.3%) individuals. CONCLUSIONS No signature InSTI-resistant variants were circulating in Europe before the introduction of InSTIs. However, polymorphisms contributing to InSTI resistance were not rare. As InSTI use becomes more widespread, continuous surveillance of primary InSTI resistance is warranted. These data will be key to modelling the kinetics of InSTI resistance transmission in Europe in the coming years.
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Affiliation(s)
- M Casadellà
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - P M van Ham
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - M Noguera-Julian
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - A van Kessel
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | - C Pou
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - L M Hofstra
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - J R Santos
- HIV Unit, Hospital Universitari Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain
| | - F Garcia
- Complejo Hospitalario Univeristario de Granada, Instituto de Investigación IBS, Granada, Cohorte de Adultos de la Red de Investigación en SIDA (CoRIS) Spain
| | - D Struck
- Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - I Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | - A I Hoepelman
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
| | | | - S Somogyi
- Robert Koch-Institute, Berlin, Germany
| | - K Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - M Linka
- National Reference Laboratory for HIV/AIDS, National Institute of Public Health, Prague, Czech Republic
| | - C Nielsen
- Statens Serum Institut, Copenhagen, Denmark
| | - D Otelea
- National Institute for Infectious Diseases 'Prof. Dr. Matei Bals', Bucharest, Romania
| | - D Paraskevis
- National Retrovirus Reference Center, University of Athens, Athens, Greece
| | - M Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | - D Staneková
- Slovak Medical University, Bratislava, Slovakia
| | - M Stanojevic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - K Van Laethem
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Belgium
| | - S Zidovec Lepej
- University Hospital for Infectious Diseases 'Dr. Fran Mihaljevic', Zagreb, Croatia
| | - B Clotet
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - C A B Boucher
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - R Paredes
- IrsiCaixa AIDS Research Institute, Universitat Autònoma de Barcelona, Badalona, Catalonia, Spain Universitat de Vic-Universitat Central de Catalunya, Vic, Spain Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg
| | - A M J Wensing
- Department of Virology, Medical Microbiology, Utrecht Medical Centre, Utrecht, The Netherlands
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Hofstra LM, Nijhuis M, Pingen M, Mudrikova T, Riezebos-Brilman A, Simoons-Smit AM, Van Ham PM, Bierman WFW, Wensing AMJ. Evolution and viral characteristics of a long-term circulating resistant HIV-1 strain in a cluster of treatment-naive patients. J Antimicrob Chemother 2013; 68:1246-50. [PMID: 23467175 DOI: 10.1093/jac/dkt038] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Transmitted resistant HIV may revert to wild-type in the absence of drug pressure due to reduced replication capacity (RC). We observed eight therapy-naive patients infected with HIV harbouring four mutations at nucleoside reverse transcriptase inhibitor (NRTI) resistance-related positions: M41L, T69S, L210E and T215S. If partial reverted resistance patterns like these are detected at baseline, concerns for more extensive resistance in the quasispecies often directs selection of first-line combination antiretroviral therapy (cART) towards more complex regimens. METHODS Genotypic resistance testing and phylogenetic analysis was performed using pol sequences of 400 therapy-naive patients and 1322 patients with at least one NRTI-related mutation. Reverse transcriptase (RT) genes were cloned into a reference strain and RC was investigated. RESULTS Phylogenetic analysis showed that all eight patients are part of a transmission cluster (bootstrap value 92%). The patients resided in three distinct geographical regions and were either homosexually or heterosexually infected. Prior negative serology and analysis of base ambiguity demonstrated circulation for at least 7 years. In vivo evolution showed a mixture with wild-type (T215S/T) in only one untreated patient more than 6 years after diagnosis. The reverted resistance pattern did not confer a substantial reduction in RC compared with wild-type, explaining its persistence in vivo and long-term circulation in the population. Four patients started cART; three of them received quadruple cART. All patients showed good virological and immunological response. CONCLUSIONS Long-term circulation transcending distinct regions and transmission groups suggests reversion occurred in previous hosts in the transmission chain. Identification of clusters using epidemiological data and active-partner tracing may broaden therapeutic options in cases of transmitted resistance.
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Affiliation(s)
- L Marije Hofstra
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, Utrecht, The Netherlands
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