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Kipfer ET, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. eLife 2023; 12:RP89035. [PMID: 37988285 PMCID: PMC10662946 DOI: 10.7554/elife.89035] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the coronavirus disease 2019 pandemic, already established methods were challenged by the large genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Tatjana Kipfer
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Martin J Lett
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Christopher MR Lang
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, MattenstrasseBaselSwitzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of BaselBaselSwitzerland
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Kipfer E, Hauser D, Lett MJ, Otte F, Urda L, Zhang Y, Lang CMR, Chami M, Mittelholzer C, Klimkait T. Rapid cloning-free mutagenesis of new SARS-CoV-2 variants using a novel reverse genetics platform. bioRxiv 2023:2023.05.11.540343. [PMID: 37292682 PMCID: PMC10245781 DOI: 10.1101/2023.05.11.540343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reverse genetic systems enable the engineering of RNA virus genomes and are instrumental in studying RNA virus biology. With the recent outbreak of the COVID-19 pandemic, already established methods were challenged by the large genome of SARS-CoV-2. Herein we present an elaborated strategy for the rapid and straightforward rescue of recombinant plus-stranded RNA viruses with high sequence fidelity, using the example of SARS-CoV-2. The strategy called CLEVER (CLoning-free and Exchangeable system for Virus Engineering and Rescue) is based on the intracellular recombination of transfected overlapping DNA fragments allowing the direct mutagenesis within the initial PCR-amplification step. Furthermore, by introducing a linker fragment - harboring all heterologous sequences - viral RNA can directly serve as a template for manipulating and rescuing recombinant mutant virus, without any cloning step. Overall, this strategy will facilitate recombinant SARS-CoV-2 rescue and accelerate its manipulation. Using our protocol, newly emerging variants can quickly be engineered to further elucidate their biology. To demonstrate its potential as a reverse genetics platform for plus-stranded RNA viruses, the protocol has been successfully applied for the cloning-free rescue of recombinant Chikungunya and Dengue virus.
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Affiliation(s)
- Enja Kipfer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - David Hauser
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Martin J. Lett
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Fabian Otte
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Lorena Urda
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Christopher M. R. Lang
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Mittelholzer
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, 4009 Basel, Switzerland
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Seeburg U, Urda L, Otte F, Lett MJ, Caimi S, Mittelholzer C, Klimkait T. Virus Inactivation by Formaldehyde and Common Lysis Buffers. Viruses 2023; 15:1693. [PMID: 37632035 PMCID: PMC10458352 DOI: 10.3390/v15081693] [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: 07/12/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Numerous mammalian viruses are routinely analyzed in clinical diagnostic laboratories around the globe or serve as indispensable model systems in viral research. Potentially infectious viral entities are handled as blood, biopsies, or cell and tissue culture samples. Countless protocols describe methods for virus fixation and inactivation, yet for many, a formal proof of safety and completeness of inactivation remains to be shown. While modern nucleic acid extraction methods work quite effectively, data are largely lacking on possible residual viral infectivity, e.g., when assessed after extended culture times, which maximizes the sensitivity for low levels of residual infectiousness. Therefore, we examined the potency and completeness of inactivation procedures on virus-containing specimens when applying commonly used fixatives like formaldehyde or nucleic acid extraction/lysis buffers. Typical representatives of different virus classes, including RNA and DNA viruses, enveloped and non-enveloped, such as adenovirus, enterovirus, lentivirus, and coronavirus, were used, and the reduction in the in vitro infectiousness was assessed for standard protocols. Overall, a 30-minute incubation with formaldehyde at room temperature effectively inactivated all tested enveloped and non-enveloped viruses. Full inactivation of HIV-1 and ECHO-11 was also achieved with all buffers in the test, whereas for SARS-CoV-2 and AdV-5, only five of the seven lysis buffers were fully effective under the tested conditions.
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Otte F, Zhang Y, Spagnuolo J, Thielen A, Däumer M, Wiethe C, Stoeckle M, Kusejko K, Klein F, Metzner KJ, Klimkait T. Revealing viral and cellular dynamics of HIV-1 at the single-cell level during early treatment periods. Cell Rep Methods 2023; 3:100485. [PMID: 37426753 PMCID: PMC10326345 DOI: 10.1016/j.crmeth.2023.100485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 01/30/2023] [Accepted: 04/28/2023] [Indexed: 07/11/2023]
Abstract
While combination therapy completely suppresses HIV-1 replication in blood, functional virus persists in CD4+ T cell subsets in non-peripheral compartments that are not easily accessible. To fill this gap, we investigated tissue-homing properties of cells that transiently appear in the circulating blood. Through cell separation and in vitro stimulation, the HIV-1 "Gag and Envelope reactivation co-detection assay" (GERDA) enables sensitive detection of Gag+/Env+ protein-expressing cells down to about one cell per million using flow cytometry. By associating GERDA with proviral DNA and polyA-RNA transcripts, we corroborate the presence and functionality of HIV-1 in critical body compartments utilizing t-distributed stochastic neighbor embedding (tSNE) and density-based spatial clustering of applications with noise (DBSCAN) clustering with low viral activity in circulating cells early after diagnosis. We demonstrate transcriptional HIV-1 reactivation at any time, potentially giving rise to intact, infectious particles. With single-cell level resolution, GERDA attributes virus production to lymph-node-homing cells with central memory T cells (TCMs) as main players, critical for HIV-1 reservoir eradication.
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Affiliation(s)
- Fabian Otte
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Yuepeng Zhang
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
| | - Julian Spagnuolo
- Experimental Immunology, Department Biomedicine, University of Basel, 4056 Basel, Switzerland
| | | | | | | | - Marcel Stoeckle
- Infectiology, University Hospital Basel, 4031 Basel, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Karin J. Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, and Institute of Medical Virology, University of Zurich, 8091 Zurich, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine, University of Basel, 4009 Basel, Switzerland
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Mnzava D, Okuma J, Ndege R, Kimera N, Ntamatungiro A, Nyuri A, Byakuzana T, Abilahi F, Mayeka P, Temba E, Fanuel T, Glass TR, Klimkait T, Vanobberghen F, Weisser M. Decentralization of viral load testing to improve HIV care and treatment cascade in rural Tanzania: observational study from the Kilombero and Ulanga Antiretroviral Cohort. BMC Infect Dis 2023; 23:222. [PMID: 37029356 PMCID: PMC10081287 DOI: 10.1186/s12879-023-08155-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/13/2023] [Indexed: 04/09/2023] Open
Abstract
INTRODUCTION Monitoring HIV viral load (HVL) in people living with HIV (PLHIV) on antiretroviral therapy (ART) is recommended by the World Health Organization. Implementation of HVL testing programs have been affected by logistic and organizational challenges. Here we describe the HVL monitoring cascade in a rural setting in Tanzania and compare turnaround times (TAT) between an on-site and a referral laboratory. METHODS In a nested study of the prospective Kilombero and Ulanga Antiretroviral Cohort (KIULARCO) we included PLHIV aged ≥ 15 years, on ART for ≥ 6 months after implementation of routine HVL monitoring in 2017. We assessed proportions of PLHIV with a blood sample taken for HVL, whose results came back, and who were virally suppressed (HVL < 1000 copies/mL) or unsuppressed (HVL ≥ 1000 copies/mL). We described the proportion of PLHIV with unsuppressed HVL and adequate measures taken as per national guidelines and outcomes among those with low-level viremia (LLV; 100-999 copies/mL). We compare TAT between on-site and referral laboratories by Wilcoxon rank sum tests. RESULTS From 2017 to 2020, among 4,454 PLHIV, 4,238 (95%) had a blood sample taken and 4,177 (99%) of those had a result. Of those, 3,683 (88%) were virally suppressed. In the 494 (12%) unsuppressed PLHIV, 425 (86%) had a follow-up HVL (102 (24%) within 4 months and 158 (37%) had virologic failure. Of these, 103 (65%) were already on second-line ART and 32/55 (58%) switched from first- to second-line ART after a median of 7.7 months (IQR 4.7-12.7). In the 371 (9%) PLHIV with LLV, 327 (88%) had a follow-up HVL. Of these, 267 (82%) resuppressed to < 100 copies/ml, 41 (13%) had persistent LLV and 19 (6%) had unsuppressed HVL. The median TAT for return of HVL results was 21 days (IQR 13-39) at the on-site versus 59 days (IQR 27-99) at the referral laboratory (p < 0.001) with PLHIV receiving the HVL results after a median of 91 days (IQR 36-94; similar for both laboratories). CONCLUSION Robust HVL monitoring is achievable in remote resource-limited settings. More focus is needed on care models for PLHIV with high viral loads to timely address results from routine HVL monitoring.
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Affiliation(s)
- Dorcas Mnzava
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
| | - James Okuma
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Robert Ndege
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
- St. Francis Referral Hospital, Ifakara, United Republic of Tanzania
| | - Namvua Kimera
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
| | - Alex Ntamatungiro
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
| | - Amina Nyuri
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
| | | | - Faraji Abilahi
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania
| | - Paul Mayeka
- USAID Boresha Afya, Morogoro, United Republic of Tanzania
| | - Emmy Temba
- USAID Boresha Afya, Morogoro, United Republic of Tanzania
| | - Teddy Fanuel
- USAID Boresha Afya, Morogoro, United Republic of Tanzania
| | - Tracy Renée Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, Molecular Virology, University of Basel, Basel, Switzerland
| | - Fiona Vanobberghen
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Maja Weisser
- Ifakara Health Institute, Ifakara Branch, Ifakara, United Republic of Tanzania.
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, CH, Basel, Switzerland.
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Labarile M, Loosli T, Zeeb M, Kusejko K, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Battegay M, Rauch A, Calmy A, Notter J, Bernasconi E, Fux C, Günthard HF, Pasin C, Kouyos RD, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Quantifying and Predicting Ongoing Human Immunodeficiency Virus Type 1 Transmission Dynamics in Switzerland Using a Distance-Based Clustering Approach. J Infect Dis 2023; 227:554-564. [PMID: 36433831 DOI: 10.1093/infdis/jiac457] [Citation(s) in RCA: 1] [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] [Received: 08/03/2022] [Revised: 11/11/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Despite effective prevention approaches, ongoing human immunodeficiency virus 1 (HIV-1) transmission remains a public health concern indicating a need for identifying its drivers. METHODS We combined a network-based clustering method using evolutionary distances between viral sequences with statistical learning approaches to investigate the dynamics of HIV transmission in the Swiss HIV Cohort Study and to predict the drivers of ongoing transmission. RESULTS We found that only a minority of clusters and patients acquired links to new infections between 2007 and 2020. While the growth of clusters and the probability of individual patients acquiring new links in the transmission network was associated with epidemiological, behavioral, and virological predictors, the strength of these associations decreased substantially when adjusting for network characteristics. Thus, these network characteristics can capture major heterogeneities beyond classical epidemiological parameters. When modeling the probability of a newly diagnosed patient being linked with future infections, we found that the best predictive performance (median area under the curve receiver operating characteristic AUCROC = 0.77) was achieved by models including characteristics of the network as predictors and that models excluding them performed substantially worse (median AUCROC = 0.54). CONCLUSIONS These results highlight the utility of molecular epidemiology-based network approaches for analyzing and predicting ongoing HIV transmission dynamics. This approach may serve for real-time prospective assessment of HIV transmission.
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Affiliation(s)
- Marco Labarile
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Tom Loosli
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Marius Zeeb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.,Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Manuel Battegay
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Julia Notter
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Christoph Fux
- Department of Infectious Diseases, Kantonsspital Aarau, Aarau, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chloé Pasin
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital 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, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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Brown JA, Nsakala BL, Mokhele K, Rakuoane I, Muhairwe J, Glass TR, Amstutz A, Tschumi N, Belus JM, Klimkait T, Labhardt ND. Dolutegravir in real life: Self-reported mental and physical health outcomes after transitioning from efavirenz- to dolutegravir-based antiretroviral therapy in a prospective cohort study in Lesotho. HIV Med 2023; 24:153-162. [PMID: 35730213 DOI: 10.1111/hiv.13352] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/31/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION HIV programmes across many countries in Africa have recently transitioned people living with HIV from efavirenz (EFV)- to dolutegravir (DTG)-containing antiretroviral therapy (ART). As both drugs are associated with neuropsychiatric adverse effects, this study assessed the mental health and HIV/ART-associated symptoms of people living with HIV before and after transition to DTG. METHODS The prospective DO-REAL cohort enrolled people starting DTG-based ART in Lesotho from February to December 2020. For this analysis within DO-REAL, we included adults changing from tenofovir disoproxil fumarate (TDF)/lamivudine (3TC)/EFV to TDF/3TC/DTG within first-line therapy. At transition and 16 weeks thereafter, participants completed the Patient Health Questionnaire-9 (PHQ-9; depression screening), the 12-item Short-Form Health Survey (SF-12; mental and physical health), and a modified HIV Symptom Index (mHSI; HIV/ART-related symptoms). We also assessed weight change. We used McNemar tests with Bonferroni corrections to assess binary outcomes. CLINICALTRIALS gov: NCT04238767. RESULTS Among 1228 participants, 1131 completed follow-up. Of these, 60.0% were female, the median age was 46 years (interquartile range [IQR] 38-55), and the median time taking ART was 5.7 years (IQR 3.5-8.9). No change was observed for weight or overall PHQ-9 or SF-12 outcomes. However, three mHSI items decreased at follow-up: 'feeling sad/down/depressed' (bothered 6.0% vs. 3.3% of participants at least 'a little' before vs. after transition; adjusted p = 0.048); 'feeling nervous/anxious' (7.4% vs. 3.4%; adjusted p = 0.0009); and 'nightmares, strange/vivid dreams' (6.3% vs. 3.5%; adjusted p = 0.027). Individual PHQ-9 or SF-12 items also improved. Being symptom free across all measures increased from 5.1% to 11.4% (p < 0.0001). CONCLUSIONS We observed no negative impacts and potential moderate improvements with DTG, providing further support for the rollout of DTG.
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Affiliation(s)
- Jennifer A Brown
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Molecular Virology Group, Department of Biomedicine, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Kuena Mokhele
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | | | - Tracy R Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Alain Amstutz
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,University Hospital Basel, Basel, Switzerland
| | - Nadine Tschumi
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jennifer M Belus
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,University of Maryland, College Park, Maryland, USA
| | - Thomas Klimkait
- Molecular Virology Group, Department of Biomedicine, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus D Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,University Hospital Basel, Basel, Switzerland
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Stöger L, Katende A, Mapesi H, Kalinjuma AV, van Essen L, Klimkait T, Battegay M, Weisser M, Letang E. Persistent High Burden and Mortality Associated With Advanced HIV Disease in Rural Tanzania Despite Uptake of World Health Organization "Test and Treat" Guidelines. Open Forum Infect Dis 2022; 9:ofac611. [PMID: 36540386 PMCID: PMC9757676 DOI: 10.1093/ofid/ofac611] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Information about burden, characteristics, predictors, and outcomes of advanced human immunodeficiency virus disease (AHD) is scarce in rural settings of sub-Saharan Africa. Human immunodeficiency virus (HIV) infections and associated deaths remain high despite specific guidelines issued by the World Health Organization (WHO). METHODS Burden of AHD and 6-month death/loss to follow-up (LTFU) were described among 2498 antiretroviral therapy (ART)-naive nonpregnant people with HIV (PWH) aged >15 years enrolled in the Kilombero Ulanga Antiretroviral Cohort in rural Tanzania between 2013 and 2019. Baseline characteristics associated with AHD and predictors of death/LTFU among those with AHD were analyzed using multivariate logistic and Cox regression, respectively. RESULTS Of the PWH, 62.2% had AHD at diagnosis (66.8% before vs 55.7% after national uptake of WHO "test and treat" guidelines in 2016). At baseline, older age, male sex, lower body mass index, elevated aminotransferase aspartate levels, severe anemia, tachycardia, decreased glomerular filtration rate, clinical complaints, impaired functional status, and enrollment into care before 2018 were independently associated with AHD. Among people with AHD, incidence of mortality, and LTFU were 16 and 34 per 100 person-years, respectively. WHO clinical stage 3 or 4, CD4 counts <100 cells/µL, severe anemia, tachypnea, and liver disease were associated with death/LTFU. CONCLUSIONS More than 50% of PWH enrolled in our cohort after test and treat implementation still had AHD at diagnosis. Increasing HIV testing and uptake and implementation of the WHO-specific guidelines on AHD for prevention, diagnosis, treatment of opportunistic infections, and reducing the risks of LTFU are urgently needed to reduce morbidity and mortality.
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Affiliation(s)
- Linda Stöger
- ISGlobal, Hospital Clinic, Universitat de Barcelona, Barcelona, Spain
| | | | - Herry Mapesi
- Ifakara Health Institute, Ifakara, Tanzania,Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Aneth V Kalinjuma
- Ifakara Health Institute, Ifakara, Tanzania,Faculty of Health Sciences, Department of Epidemiology and Biostatistics, University of the Witwatersrand, School of Public Health, Johannesburg, South Africa
| | - Liselot van Essen
- Gerion, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Thomas Klimkait
- Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Manuel Battegay
- Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Maja Weisser
- Ifakara Health Institute, Ifakara, Tanzania,Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland,Swiss Tropical and Public Health Institute, Basel, Switzerland,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Emilio Letang
- Correspondence: Emilio Letang, MD, MPH, PhD, Barcelona Institute for Global Health, Rosselló 132, 4.1, Barcelona 08036, Spain ()
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Hamusonde K, Nicca D, Günthard HF, Stöckle M, Darling KEA, Calmy A, Bernasconi E, Haerry D, Schmid P, Kouyos RD, Rauch A, Salazar-Vizcaya L, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Jackson-Perry D, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Labhardt N, Leuzinger K, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Notter J, Paioni P, Pantaleo G, Perreau M, Rauch A, Salazar-Vizcaya L, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Weisser M, Yerly S. Triggers of Change in Sexual Behavior Among People With HIV: The Swiss U U Statement and COVID-19 Compared. J Infect Dis 2022; 227:407-411. [PMID: 36408629 PMCID: PMC9891402 DOI: 10.1093/infdis/jiac459] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
We assessed changes in sexual behavior among people with human immunodeficiency virus (HIV) over 20 years. Condom use with stable partners steadily declined from over 90 to 29 since the Swiss U U statement, with similar trajectories between men who have sex with men (MSM) and heterosexuals. Occasional partnership remained higher among MSM compared to heterosexuals even during coronavirus disease 2019 (COVID-19) social distancing.
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Affiliation(s)
- Kalongo Hamusonde
- Correspondence: K. Hamusonde, Msc, Bern University Hospital, Inselspital, Universitätsklinik für Infektiologie, Personalhaus 6, Bern 3010, Switzerland ()
| | - Dunja Nicca
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, 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
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Katharine E A Darling
- Service of Infectious Diseases, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Ente Ospedaliero Cantonale, University of Southern Switzerland, Lugano, Switzerland
| | | | - Patrick Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, 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
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10
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Bosetti D, Mugglin C, Calmy A, Cavassini M, Stöckle M, Braun D, Notter J, Haerry D, Hampel B, Kovari H, Bernasconi E, Wandeler G, Rauch A, Aebi-Popp K, Anagnostopoulos A, Battegay M, Bernasconi E, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Hachfeld A, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Kusejko K, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Nemeth J, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Wandeler G, Yerly S. Risk Factors and Incidence of Sexually Transmitted Infections in the Swiss HIV Cohort Study. Open Forum Infect Dis 2022; 9:ofac592. [PMID: 36504700 PMCID: PMC9728517 DOI: 10.1093/ofid/ofac592] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022] Open
Abstract
Background Sexually transmitted infections (STIs) are common among people with human immunodeficiency virus (PWH), but there are limited data about risk factors and incidence of STIs in large, representative cohort studies. Methods We assessed incidence and risk factors of STIs reported by treating physicians within the Swiss HIV Cohort Study (SHCS). Sexually transmitted infections and demographic, clinical, and behavioral characteristics were prospectively collected at 6-month follow-up visits between October 2017 and November 2019. We used multilevel Poisson regression to assess incidence rate ratios of different STIs. Results Among 10 140 study participants, a total of 1634 STIs in 1029 SHCS participants were reported over 17 766 person-years of follow up (PYFUP). The overall incidence of any reported STI was 91.9 per 1000 PYFU (95% confidence interval [CI], 85.8 -98.5). Among the 1634 STI episodes, there were 573 (35.1%) incident cases of syphilis, 497 gonorrhea (30.4%), and 418 chlamydia (25.6%). Men who have sex with men (MSM) younger than 50 years represented 21% of the study population, but accounted for 61% of reported STIs. Male sex (adjusted incidence rate ratio [aIRR], 2.03; 95% CI, 1.36-3.02), MSM (aIRR, 3.62; 95% CI, 2.88-4.55), age group 18-34 years (aIRR, 1.78; 95% CI, 1.51-2.10), history of sexual relationships with occasional partners (aIRR, 6.87; 95% CI, 5.40-8.73), and reporting injecting drug use (aIRR, 2.48; 95% CI, 1.91-3.23) were associated with a higher risk of incident STIs. Conclusions Sexually transmitted infections were frequent among PWH and varied considerably between age and risk groups. Screening programs and recommendations for STI testing need to be adapted according to risk factors and demographic characteristics.
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Affiliation(s)
| | - Catrina Mugglin
- Correspondence: Catrina Mugglin, MSc, MD, PhD, Inselspital, Bern University Hospital, Freiburgstrasse, CH-3010 Bern, Switzerland ()
| | - Alexandra Calmy
- HIV/AIDS Unit, Department of Infectious Diseases, Geneva, Switzerland
| | - Matthias Cavassini
- University Hospital of Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Dominique Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Julia Notter
- Division of Infectious Diseases and Hospital Epidemiology, St. Gallen, Switzerland
| | | | - Benjamin Hampel
- Department of Public and Global Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland,Checkpoint Zurich, Zurich, Switzerland
| | - Helen Kovari
- Zentrum für Infektionskrankheiten, Klinik im Park, Zurich, Switzerland
| | - Enos Bernasconi
- Ente Ospedaliero Cantonale, Lugano, University of Geneva, and University of Southern Switzerland, Lugano, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital of Geneva, University of Geneva, Geneva, Switzerland
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11
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Chaudron SE, Leemann C, Kusejko K, Nguyen H, Tschumi N, Marzel A, Huber M, Böni J, Perreau M, Klimkait T, Yerly S, Ramette A, Hirsch HH, Rauch A, Calmy A, Vernazza P, Bernasconi E, Cavassini M, Metzner KJ, Kouyos RD, Günthard HF. A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study. J Infect Dis 2022; 226:1256-1266. [PMID: 35485458 DOI: 10.1093/infdis/jiac166] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/27/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studying human immunodeficiency virus type 1 (HIV-1) superinfection is important to understand virus transmission, disease progression, and vaccine design. But detection remains challenging, with low sampling frequencies and insufficient longitudinal samples. METHODS Using the Swiss HIV Cohort Study (SHCS), we developed a molecular epidemiology screening for superinfections. A phylogeny built from 22 243 HIV-1 partial polymerase sequences was used to identify potential superinfections among 4575 SHCS participants with longitudinal sequences. A subset of potential superinfections was tested by near-full-length viral genome sequencing (NFVGS) of biobanked plasma samples. RESULTS Based on phylogenetic and distance criteria, 325 potential HIV-1 superinfections were identified and categorized by their likelihood of being detected as superinfections due to sample misidentification. NFVGS was performed for 128 potential superinfections; of these, 52 were confirmed by NFVGS, 15 were not confirmed, and for 61 sampling did not allow confirming or rejecting superinfection because the sequenced samples did not include the relevant time points causing the superinfection signal in the original screen. Thus, NFVGS could support 52 of 67 adequately sampled potential superinfections. CONCLUSIONS This cohort-based molecular approach identified, to our knowledge, the largest population of confirmed superinfections, showing that, while rare with a prevalence of 1%-7%, superinfections are not negligible events.
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Affiliation(s)
- Sandra E Chaudron
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christine Leemann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huyen Nguyen
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nadine Tschumi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Alex Marzel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Schulthess Klinik, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.,Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland.,Division of Infectious Diseases and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pietro Vernazza
- Clinic for Infectiology and Hospital Hygiene, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Service for Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital 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, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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12
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Nadeau S, Thorball CW, Kouyos R, Günthard HF, Böni J, Yerly S, Perreau M, Klimkait T, Rauch A, Hirsch HH, Cavassini M, Vernazza P, Bernasconi E, Fellay J, Mitov V, Stadler T. A phylogeny-aware GWAS framework to correct for heritable pathogen effects on infectious disease traits. Mol Biol Evol 2022; 39:6654835. [PMID: 35921544 PMCID: PMC9366186 DOI: 10.1093/molbev/msac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. However, pathogen effects on a trait can be heritable from donor to recipient in transmission chains. Thus, residuals in GWAS association tests for host genetic effects may not be independent due to shared pathogen ancestry. We propose a new method to estimate and remove heritable pathogen effects on a trait based on the pathogen phylogeny prior to host GWAS, thus restoring independence of samples. In simulations, we show this additional step can increase GWAS power to detect truly associated host variants when pathogen effects are highly heritable, with strong phylogenetic correlations. We applied our framework to data from two different host-pathogen systems, HIV in humans and X. arboricola in A. thaliana. In both systems, the heritability and thus phylogenetic correlations turn out to be low enough such that qualitative results of GWAS do not change when accounting for the pathogen shared ancestry through a correction step. This means that previous GWAS results applied to these two systems should not be biased due to shared pathogen ancestry. In summary, our framework provides additional information on the evolutionary dynamics of traits in pathogen populations and may improve GWAS if pathogen effects are highly phylogenetically correlated amongst individuals in a cohort.
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Affiliation(s)
- Sarah Nadeau
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Roger Kouyos
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases, Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Hans H Hirsch
- Department of Biomedicine, University of Basel, Basel, Switzerland.,Division of Clinical Virology, University Hospital Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Jacques Fellay
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.,Global Health Institute, School of Life Sciences, École Polytechnique FÉdÉrale de Lausanne, Lausanne, Switzerland
| | - Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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13
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Kusejko K, Tschumi N, Chaudron SE, Nguyen H, Battegay M, Bernasconi E, Böni J, Huber M, Calmy A, Cavassini M, Egle A, Grabmeier-Pfistershammer K, Haas B, Hirsch H, Klimkait T, Öllinger A, Perreau M, Ramette A, Flury BB, Sarcletti M, Scherrer A, Schmid P, Yerly S, Zangerle R, Günthard HF, Kouyos RD. Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics. J Acquir Immune Defic Syndr 2022; 90:e4-e12. [PMID: 35298446 PMCID: PMC9394492 DOI: 10.1097/qai.0000000000002949] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/23/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Phylogenetic analyses of 2 or more countries allow to detect differences in transmission dynamics of local HIV-1 epidemics beyond differences in demographic characteristics. METHODS A maximum-likelihood phylogenetic tree was built using pol -sequences of the Swiss HIV Cohort Study (SHCS) and the Austrian HIV Cohort Study (AHIVCOS), with international background sequences. Three types of phylogenetic cherries (clusters of size 2) were analyzed further: (1) domestic cherries; (2) international cherries; and (3) SHCS/AHIVCOS-cherries. Transmission group and ethnicities observed within the cherries were compared with the respective distribution expected from a random distribution of patients on the phylogeny. RESULTS The demographic characteristics of the AHIVCOS (included patients: 3'141) and the SHCS (included patients: 12'902) are very similar. In the AHIVCOS, 36.5% of the patients were in domestic cherries, 8.3% in international cherries, and 7.0% in SHCS/AHIVCOS cherries. Similarly, in the SHCS, 43.0% of the patients were in domestic cherries, 8.2% in international cherries, and 1.7% in SHCS/AHIVCOS cherries. Although international cherries in the SHCS were dominated by heterosexuals with men who have sex with men being underrepresented, the opposite was the case for the AHIVCOS. In both cohorts, cherries with one patient belonging to the transmission group intravenous drug user and the other one non-intravenous drug user were underrepresented. CONCLUSIONS In both cohorts, international HIV transmission plays a major role in the local epidemics, mostly driven by men who have sex with men in the AHIVOS, and by heterosexuals in the SHCS, highlighting the importance of international collaborations to understand global HIV transmission links on the way to eliminate HIV.
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Affiliation(s)
- Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nadine Tschumi
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Sandra E. Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, University of Geneva and University of Southern Switzerland, Lugano, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexander Egle
- Department of Internal Medicine III with Haematology, Medical Oncology, Haemostaseology, Infectiology and Rheumatology, Oncologic Center, Paracelsus Medical University, Salzburg, Austria
| | | | - Bernhard Haas
- Institute of Hospital Hygiene and Microbiology, Styrian Hospital Corporation, The Styrian Healthcare Company, Graz, Austria
| | - Hans Hirsch
- Molecular Virology, Department of Biomedicine–Petersplatz, University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine–Petersplatz, University of Basel, Basel, Switzerland
| | - Angela Öllinger
- Department of Dermatology, Kepler University Hospital, Linz, Austria
| | - Matthieu Perreau
- Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alban Ramette
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Baharak Babouee Flury
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland; and
| | - Mario Sarcletti
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St. Gallen, Switzerland; and
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Robert Zangerle
- Department of Dermatology, Venereology and Allergology, Medical University of Innsbruck, Innsbruck, Austria
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital 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, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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14
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Emamzadeh Yazdi S, Heyman HM, Prinsloo G, Klimkait T, Meyer JJM. Identification of Anti-HIV Biomarkers of Helichrysum Species by NMR-Based Metabolomic Analysis. Front Pharmacol 2022; 13:904231. [PMID: 35935828 PMCID: PMC9355245 DOI: 10.3389/fphar.2022.904231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022] Open
Abstract
Several species of the Helichrysum genus have been used ethnobotanically to treat conditions that we today know have been caused by viral infections. Since HIV is a modern disease with no ethnobotanical history, we commenced with a study on the anti-HIV activity of several Helichrysum species. Drug discovery of small molecules from natural resources that is based on the integration of chemical and biological activity by means of metabolomical analyses, enables faster and a more cost-effective path to identify active compounds without the need for a long process of bioassay-guided fractionation. This study used metabolomics to identify anti-HIV compounds as biomarkers from 57 Helichrysum species in a combined study of the chemical and biological data of two previous studies. In the OPLS-DA and hierarchical cluster analyses, anti-HIV activity data was included as a secondary observation, which assisted in the correlation of the phytochemical composition and biological activity of the samples. Clear grouping revealed similarity in chemical composition and bioactivity of the samples. Based on the biological activity of polar extracts, there was a distinct phytochemical difference between active and non-active groups of extracts. This NMR-based metabolomic investigation showed that the chlorogenic acids, compounds with cinnamoyl functional groups, and quinic acid were the most prominent compounds in the Helichrysum species with anti-HIV activity. This study further revealed that the chlorogenic acid type compounds and quinic acid are biomarkers for anti-HIV activity.
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Affiliation(s)
- Simin Emamzadeh Yazdi
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- *Correspondence: Simin Emamzadeh Yazdi,
| | - Heino Martin Heyman
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Metabolon Inc., Morrisville, NC, United States
| | - Gerhard Prinsloo
- Department of Agriculture and Animal Health, University of South Africa (UNISA), Pretoria, South Africa
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
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15
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Muhairwe JA, Brown JA, Motaboli L, Nsakala BL, Lerotholi M, Amstutz A, Klimkait T, Glass TR, Labhardt ND. The Suboptimal Pediatric HIV Viral Load Cascade: Multidistrict Cohort Study Among Children Taking Antiretroviral Therapy in Lesotho, Southern Africa. Pediatr Infect Dis J 2022; 41:e75-e80. [PMID: 34862344 DOI: 10.1097/inf.0000000000003415] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Children living with HIV and taking antiretroviral therapy (ART) are a priority group for routine viral load (VL) monitoring. As per Lesotho guidelines, a VL ≥1000 copies/mL ("unsuppressed") should trigger adherence counseling and a follow-up VL; 2 consecutive unsuppressed VLs ("virologic failure") qualify for switching to second-line ART, with some exceptions. Here, we describe the pediatric VL cascade in Lesotho. METHODS In a prospective open cohort study comprising routine VL results from 22 clinics in Lesotho, we assessed outcomes along the VL cascade for children who had at least 1 VL test from January 2016 through June 2020. Data were censored on February 10, 2021. RESULTS In total, 1215 children received 5443 VL tests. The median age was 10 years (interquartile range 7-13) and 627/1215 (52%) were female; 362/1215 (30%) had at least 1 unsuppressed VL. A follow-up VL was available for 325/362 (90%), although only for 159/362 (44%) within 6 months of the first unsuppressed VL. Of those with a follow-up VL, 172/329 (53%) had virologic failure and 123/329 (37%) qualified for switching to second-line ART. Of these, 55/123 (45%) were ever switched, although only 9/123 (7%) were switched within 12 weeks of the follow-up VL. Delays were more pronounced in rural facilities. Overall, 100/362 (28%) children with an unsuppressed VL received a timely follow-up VL and, if required, a timely regimen switch. CONCLUSIONS Despite access to VL monitoring, clinical management was suboptimal. HIV programs should prioritize timely clinical action to maximize the benefits of VL monitoring.
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Affiliation(s)
- Josephine A Muhairwe
- From the SolidarMed, Partnerships for Health, Maseru, Lesotho
- Institute of Global Health, University of Geneva, Geneva, Switzerland
| | - Jennifer A Brown
- Department of Medicine, Swiss Tropical & Public Health Institute, Basel, Switzerland
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Alain Amstutz
- Department of Medicine, Swiss Tropical & Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Tracy R Glass
- Department of Medicine, Swiss Tropical & Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Niklaus D Labhardt
- Department of Medicine, Swiss Tropical & Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Urda L, Kreuter MH, Drewe J, Boonen G, Butterweck V, Klimkait T. The Petasites hybridus CO 2 Extract (Ze 339) Blocks SARS-CoV-2 Replication In Vitro. Viruses 2022; 14:v14010106. [PMID: 35062310 PMCID: PMC8781559 DOI: 10.3390/v14010106] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), has spread worldwide, affecting over 250 million people and resulting in over five million deaths. Antivirals that are effective are still limited. The antiviral activities of the Petasites hybdridus CO2 extract Ze 339 were previously reported. Thus, to assess the anti-SARS-CoV-2 activity of Ze 339 as well as isopetasin and neopetasin as major active compounds, a CPE and plaque reduction assay in Vero E6 cells was used for viral output. Antiviral effects were tested using the original virus (Wuhan) and the Delta variant of SARS-CoV-2. The antiviral drug remdesivir was used as control. Pre-treatment with Ze 339 in SARS-CoV-2-infected Vero E6 cells with either virus variant significantly inhibited virus replication with IC50 values of 0.10 and 0.40 μg/mL, respectively. The IC50 values obtained for isopetasin ranged between 0.37 and 0.88 μM for both virus variants, and that of remdesivir ranged between 1.53 and 2.37 μM. In conclusion, Ze 339 as well as the petasins potently inhibited SARS-CoV-2 replication in vitro of the Wuhan and Delta variants. Since time is of essence in finding effective treatments, clinical studies will have to demonstrate if Ze339 can become a therapeutic option to treat SARS-CoV-2 infections.
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Affiliation(s)
- Lorena Urda
- Department Biomedicine, University of Basel, Petersplatz 10, 4051 Basel, Switzerland
| | | | - Jürgen Drewe
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Georg Boonen
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Veronika Butterweck
- Medical Department, Max Zeller & Söhne AG, Seeblickstrasse 4, 8590 Romanshorn, Switzerland
| | - Thomas Klimkait
- Department Biomedicine, University of Basel, Petersplatz 10, 4051 Basel, Switzerland
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18
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Brown JA, Nsakala BL, Mokhele K, Rakuoane I, Muhairwe J, Urda L, Amstutz A, Tschumi N, Klimkait T, Labhardt ND. Viral suppression after transition from nonnucleoside reverse transcriptase inhibitor- to dolutegravir-based antiretroviral therapy: A prospective cohort study in Lesotho (DO-REAL study). HIV Med 2021; 23:287-293. [PMID: 34632682 PMCID: PMC9293184 DOI: 10.1111/hiv.13189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/25/2021] [Revised: 09/01/2021] [Accepted: 09/23/2021] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Since 2018, the World Health Organization has recommended dolutegravir (DTG)-containing antiretroviral therapy (ART) for most people living with HIV. Country programmes across Africa have subsequently transitioned from other, mostly nonnucleoside reverse transcriptase inhibitor (NNRTI)-based ART to DTG-based ART. This study aims to assess the virological impact of programmatic transitioning to DTG-based ART in Lesotho. METHODS The prospective Dolutegravir in Real-Life in Lesotho (DO-REAL) cohort enrols people living with HIV initiating or transitioning to DTG-based ART in Lesotho. Here, we present data from participants who transitioned from NNRTI- to DTG-based ART between February and December 2020. Blood samples collected at transition and at 16 weeks' follow-up (window 8-32 weeks) were used for viral load (VL) and resistance testing. RESULTS Among 1347 participants, follow-up data was available for 1225. The majority (60%) were female, median age at transition was 47 years [interquartile range (IQR): 38-56], and median (IQR) time since ART initiation was 5.9 (3.5-9.0) years. Among those with complete VL data, the rate of viral suppression to < 100 copies/mL was 1093/1116 (98%) before, 1073/1116 (96%) at, and 1098/1116 (98%) after transition. Even among those with a VL ≥ 100 copies/mL at transition, 42/44 (95%) achieved suppression to < 100 copies/mL at follow-up. Seven participants had a VL ≥ 1000 copies/mL at follow-up and did not harbour any integrase mutations associated with resistance to DTG. CONCLUSIONS The high levels of viral suppression observed are encouraging regarding virological outcomes upon programmatic transitioning from NNRTI- to DTG-based ART.
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Affiliation(s)
- Jennifer A Brown
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Kuena Mokhele
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | | | - Lorena Urda
- Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Nadine Tschumi
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology Group, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus D Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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19
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Amstutz A, Lejone TI, Khesa L, Kopo M, Kao M, Muhairwe J, Bresser M, Räber F, Klimkait T, Battegay M, Glass TR, Labhardt ND. Offering ART refill through community health workers versus clinic-based follow-up after home-based same-day ART initiation in rural Lesotho: The VIBRA cluster-randomized clinical trial. PLoS Med 2021; 18:e1003839. [PMID: 34673765 PMCID: PMC8568187 DOI: 10.1371/journal.pmed.1003839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/04/2021] [Accepted: 10/06/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Community-based antiretroviral therapy (ART) dispensing by lay workers is an important differentiated service delivery model in sub-Sahara Africa. However, patients new in care are generally excluded from such models. Home-based same-day ART initiation is becoming widespread practice, but linkage to the clinic is challenging. The pragmatic VIBRA (Village-Based Refill of ART) trial compared ART refill by existing lay village health workers (VHWs) versus clinic-based refill after home-based same-day ART initiation. METHODS AND FINDINGS The VIBRA trial is a cluster-randomized open-label clinical superiority trial conducted in 249 rural villages in the catchment areas of 20 health facilities in 2 districts (Butha-Buthe and Mokhotlong) in Lesotho. In villages (clusters) randomized to the intervention arm, individuals found to be HIV-positive during a door-to-door HIV testing campaign were offered same-day ART initiation with the option of refill by VHWs. The trained VHWs dispensed drugs and scheduled clinic visits for viral load measurement at 6 and 12 months. In villages randomized to the control arm, participants were offered same-day ART initiation with clinic-based ART refill. The primary outcome was 12-month viral suppression. Secondary endpoints included linkage and 12-month engagement in care. Analyses were intention-to-treat. The trial was registered on ClinicalTrials.gov (NCT03630549). From 16 August 2018 until 28 May 2019, 118 individuals from 108 households in 57 clusters in the intervention arm, and 139 individuals from 130 households in 60 clusters in the control arm, were enrolled (150 [58%] female; median age 36 years [interquartile range 30-48]; 200 [78%] newly diagnosed). In the intervention arm, 48/118 (41%) opted for VHW refill. At 12 months, 46/118 (39%) participants in the intervention arm and 64/139 (46%) in the control arm achieved viral suppression (adjusted risk difference -0.07 [95% CI -0.20 to 0.06]; p = 0.256). Arms were similar in linkage (adjusted risk difference 0.03 [-0.10 to 0.16]; p = 0.630), but engagement in care was non-significantly lower in the intervention arm (adjusted risk difference -0.12 [-0.23 to 0.003]; p = 0.058). Seven and 0 deaths occurred in the intervention and control arm, respectively. Of the intervention participants who did not opt for drug refill from the VHW at enrollment, 41/70 (59%) mentioned trust or conflict issues as the primary reason. Study limitations include a rather small sample size, 9% missing viral load measurements in the primary endpoint window, the low uptake of the VHW refill option in the intervention arm, and substantial migration among the study population. CONCLUSIONS The offer of village-based ART refill after same-day initiation led to similar outcomes as clinic-based refill. The intervention did not amplify the effect of home-based same-day ART initiation alone. The findings raise concerns about acceptance and safety of ART delivered by lay health workers after initiation in the community. TRIAL REGISTRATION Registered with Clinicaltrials.gov (NCT03630549).
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Affiliation(s)
- Alain Amstutz
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | | | | | | | | | | | - Moniek Bresser
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas Klimkait
- University of Basel, Basel, Switzerland
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Manuel Battegay
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Tracy Renée Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- * E-mail:
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20
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Brown JA, Amstutz A, Nsakala BL, Seeburg U, Vanobberghen F, Vanobberghen, Muhairwe J, Klimkait T, Daniel Labhardt N. Extensive drug resistance during low-level HIV viraemia while taking NNRTI-based ART supports lowering the viral load threshold for regimen switch in resource-limited settings: a pre-planned analysis from the SESOTHO trial. J Antimicrob Chemother 2021; 76:1294-1298. [PMID: 33599270 DOI: 10.1093/jac/dkab025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES WHO guidelines on ART define the HIV-1 viral load (VL) threshold for treatment failure at 1000 copies/mL. The Switch Either near Suppression Or THOusand (SESOTHO) trial, conducted in Lesotho from 2017 to 2020, found that patients with persistent viraemia below this threshold (100-999 copies/mL) benefit from switching to second-line ART. This pre-planned nested study assesses the prevalence of resistance-associated mutations (RAMs) in SESOTHO trial participants. METHODS The SESOTHO trial [registered at ClinicalTrials.gov (NCT03088241)] enrolled 80 persons taking NNRTI-based first-line ART with low-level HIV-1 viraemia (100-999 copies/mL) and randomized them (1:1) to switch to a PI-based second-line regimen (switch) or continue on first-line therapy (control). We sequenced relevant regions of the viral pol gene using plasma samples obtained at enrolment and 36 weeks. RAMs were classified with the Stanford HIV Drug Resistance Database. RESULTS Sequencing data were obtained for 37/80 (46%) participants at baseline and 26/48 (54%) participants without viral suppression to <50 copies/mL at 36 weeks (21 control participants and 5 switch participants). At baseline, 31/37 (84%) participants harboured high-level resistance to at least two drugs of their current regimen. At 36 weeks, 17/21 (81%) control participants harboured resistance to at least two drugs of their current regimen, while no PI-associated resistance was detected in the 5 switch participants with ongoing viraemia. CONCLUSIONS Among persons with low-level viraemia while taking NNRTI-based first-line ART enrolled in the SESOTHO trial, the majority harboured HIV-1 with RAMs that necessitate ART modification. These findings support lowering the VL threshold triggering a switch to second-line ART in future WHO guidelines.
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Affiliation(s)
- Jennifer Anne Brown
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Alain Amstutz
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | | | - Ulrike Seeburg
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Vanobberghen
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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21
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Bachmann N, Kusejko K, Nguyen H, Chaudron SE, Kadelka C, Turk T, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Ramette A, Vernazza P, Bernasconi E, Cavassini M, Günthard HF, Kouyos RD. Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of Human Immunodeficiency Virus Transmission in Men Who Have Sex With Men. Clin Infect Dis 2021; 72:2175-2183. [PMID: 32300807 DOI: 10.1093/cid/ciaa411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Identifying local outbreaks and their drivers is a key step toward curbing human immunodeficiency virus (HIV) transmission and potentially achieving HIV elimination. Such outbreaks can be identified as transmission clusters extracted from phylogenetic trees constructed of densely sampled viral sequences. In this study, we combined phylogenetic transmission clusters with extensive data on virological suppression and behavioral risk of cluster members to quantify the drivers of ongoing transmission over 10 years. METHODS Using the comprehensive Swiss HIV Cohort Study and its drug-resistance database, we reconstructed phylogenetic trees for each year between 2007 and 2017. We identified HIV transmission clusters dominated by men who have sex with men (MSM) and determined their annual growth. We used Poisson regression to assess if cluster growth was associated with a per-cluster infectivity and behavioral risk score. RESULTS Both infectivity and behavioral risk scores were significantly higher in growing MSM transmission clusters compared to nongrowing clusters (P ≤ .01). The fraction of transmission clusters without infectious members acquiring new infections increased significantly over the study period. The infectivity score was significantly associated with per-capita incidence of MSM transmission clusters in 8 years, while the behavioral risk score was significantly associated with per-capita incidence of MSM transmission clusters in 3 years. CONCLUSIONS We present a phylogenetic method to identify hotspots of ongoing transmission among MSM. Our results demonstrate the effectiveness of treatment as prevention at the population level. However, the significantly increasing number of new infections among transmission clusters without infectious members highlights a relative shift from diagnosed to undiagnosed individuals as drivers of HIV transmission in Swiss MSM.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Katharina Kusejko
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Huyen Nguyen
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Sandra E Chaudron
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Claus Kadelka
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Jürg Böni
- University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Andri Rauch
- Institute for Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital of St Gallen, St Gallen, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,University of Zurich, Institute of Medical Virology, Zurich, Switzerland
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22
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Glass TR, Günthard HF, Calmy A, Bernasconi E, Scherrer AU, Battegay M, Steffen A, Böni J, Yerly S, Klimkait T, Cavassini M, Furrer H. The Role of Human Immunodeficiency Virus (HIV) Asymptomatic Status When Starting Antiretroviral Therapy on Adherence and Treatment Outcomes and Implications for Test and Treat: The Swiss HIV Cohort Study. Clin Infect Dis 2021; 72:1413-1421. [PMID: 32157270 DOI: 10.1093/cid/ciaa239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/09/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Since the advent of universal test-and-treat , more people living with human immunodeficiency virus (PLHIV) initiating antiretroviral therapy (ART) are asymptomatic with a preserved immune system. We explored the impact of asymptomatic status on adherence and clinical outcomes. METHODS PLHIV registered in the Swiss HIV Cohort Study (SHCS) between 2003 and 2018 were included. We defined asymptomatic as Centers for Disease Control and Prevention stage A within 30 days of starting ART, non-adherence as any self-reported missed doses and viral failure as two consecutive viral load>50 copies/mL after >24 weeks on ART. Using logistic regression models, we measured variables associated with asymptomatic status and adherence and Cox proportional hazard models to assess association between symptom status and viral failure. RESULTS Of 7131 PLHIV, 76% started ART when asymptomatic and 1478 (22%) experienced viral failure after a median of 1.9 years (interquartile range, 1.1-4.2). In multivariable models, asymptomatic PLHIV were more likely to be younger, men who have sex with men, better educated, have unprotected sex, have a HIV-positive partner, have a lower viral load, and have started ART more recently. Asymptomatic status was not associated with nonadherence (odds ratio, 1.03 [95% confidence interval {CI}, .93-1.15]). Asymptomatic PLHIV were at a decreased risk of viral failure (adjusted hazard ratio, 0.87 [95% CI, .76-1.00]) and less likely to develop resistance (14% vs 27%, P < .001) than symptomatic PLHIV. CONCLUSIONS Despite concerns regarding lack of readiness, our study found no evidence of adherence issues or worse clinical outcomes in asymptomatic PLHIV starting ART.
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Affiliation(s)
- Tracy R Glass
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | | | - Manuel Battegay
- University of Basel, Basel, Switzerland.,Division of Infectious Diseases, University Hospital Basel, Basel, Switzerland
| | - Ana Steffen
- Division of Infectious Diseases, Kantonsspital St Gallen, St Gallen, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Thomas Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
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23
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Amstutz A, Brown JA, Ringera I, Muhairwe J, Lejone TI, Klimkait T, Glass TR, Labhardt ND. Engagement in Care, Viral Suppression, Drug Resistance, and Reasons for Nonengagement After Home-Based Same-Day Antiretroviral Therapy Initiation in Lesotho: A Two-Year Follow-up of the CASCADE Trial. Clin Infect Dis 2021; 71:2608-2614. [PMID: 31781759 PMCID: PMC7745003 DOI: 10.1093/cid/ciz1126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/15/2019] [Accepted: 11/13/2019] [Indexed: 12/02/2022] Open
Abstract
Background The CASCADE trial showed that compared with usual care (UC), offering same-day (SD) antiretroviral therapy (ART) during home-based human immunodeficiency virus testing improved engagement in care and viral suppression 12 months after diagnosis. However, questions remain regarding long-term outcomes and the risk of propagating drug resistance. Methods After completion of the primary endpoint at 12 months, participants not in care in both arms were traced and encouraged to access care. At 24 months, the following outcomes were assessed in both arms: engagement in care, viral suppression, and reasons for nonengagement. Furthermore, we explored the acquisition of drug resistance mutations (DRMs) among SD arm nonlinkers. Results At 24 months, 64% (88/137) in the SD arm vs 59% (81/137) in the UC arm were in care (absolute difference [AD], 5%; 95% confidence interval [CI], −6 to16; P = .38) and 57% (78/137) vs 54% (74/137) had documented viral suppression (AD, 3%; 95% CI, −9 to 15; P = .28). Among 36 participants alive and not in care at 24 months with ascertained status, the majority rejected contact with the health system or were unwilling to take ART. Among 8 interviewed SD arm nonlinkers, 6 had not initiated ART upon enrollment, and no acquired DRMs were detected. Two had taken the initial 30-day ART supply and acquired DRMs. Conclusions SD ART resulted in higher rates of engagement in care and viral suppression at 12 months but not at 24 months. Leveling off between both arms was driven by linkage beyond 12 months in the UC arm. We did not observe compensatory long-term disengagement in the SD arm. These long-term results endorse SD ART initiation policies. Clinical Trials Registration NCT02692027.
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Affiliation(s)
- Alain Amstutz
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Jennifer Anne Brown
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | - Thomas Klimkait
- University of Basel, Basel, Switzerland.,Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Tracy Renée Glass
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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24
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Marty N, Saeng-Aroon S, Heger E, Thielen A, Obermeier M, Pfeifer N, Kaiser R, Klimkait T. Adapting the geno2pheno[coreceptor] tool to HIV-1 subtype CRF01_AE by phenotypic validation using clinical isolates from South-East Asia. J Clin Virol 2021; 136:104755. [PMID: 33639408 DOI: 10.1016/j.jcv.2021.104755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/24/2020] [Accepted: 02/01/2021] [Indexed: 01/23/2023]
Abstract
OBJECTIVES Geno2pheno[coreceptor] is a widely used tool for the prediction of coreceptor usage (viral tropism) of HIV-1 samples. For HIV-1 CRF01_AE, a significant overcalling of X4-tropism is observed when using the standard settings of Geno2pheno[coreceptor]. The aim of this study was to provide the experimental backing for adaptations to the geno2pheno[coreceptor] algorithm in order to improve coreceptor usage predictions of clinical HIV-1 CRF01_AE isolates STUDY DESIGN: V3-sequences of 20 clinical HIV-1 subtype CRF01_AE samples were sequenced and analyzed by geno2pheno[coreceptor]. In parallel, coreceptor usage was determined for these samples by replicative phenotyping in human cells in the presence of specific X4- or R5-inhibitors. RESULTS The sole introduction of the CRF01_AE V3 region into a full-length otherwise subtype B provirus failed to produce replication-competent viral progeny. A successive genome-replacement strategy revealed that also CRF01_AE derived gag and pol sequences are necessary to generate HIV genomes with sufficient replication competence. Subsequent phenotypic analysis confirmed overcalling of X4-tropism for CRF01_AE viruses using the current version and the standard cut-off at 10% false positive rate (FPR) of geno2pheno[coreceptor]. Lowering the FPR cut-off to 2.5% reduced the X4-overcalling in our sample collection, while still allowing a safe administration of Maraviroc (MCV). CONCLUSION This study demonstrates the successful adjustment of geno2pheno[coreceptor] rules for subtype CRF01_AE. It also supports the unique strength of combining complementing methods, namely phenotyping and genotyping, for validating new bioinformatics tools prior to application in diagnostics.
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Affiliation(s)
- Nina Marty
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland.
| | - Siriphan Saeng-Aroon
- Hazardous Pathogen Laboratory, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Eva Heger
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | | | - Nico Pfeifer
- Max Planck Institute for Informatics, Saarland Informatics Campus E1 4, Saarbruecken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine-Petersplatz, University of Basel, Petersplatz 10, 4055 Basel, Switzerland
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25
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Brown JA, Mbunkah HA, Lejone TI, Ringera I, Cheleboi M, Klimkait T, Metzner KJ, Günthard HF, Labhardt ND, Kouyos RD, Tschumi N. Emergence of Human Immunodeficiency Virus-1 Drug Resistance During the 3-Month World Health Organization-Recommended Enhanced Adherence Counseling Period in the CART-1 Cohort Study. Open Forum Infect Dis 2021; 8:ofab046. [PMID: 34046513 PMCID: PMC8137466 DOI: 10.1093/ofid/ofab046] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/23/2022] Open
Abstract
Background In resource-limited settings, the World Health Organization recommends enhanced adherence counseling (EAC) for individuals with an unsuppressed human immunodeficiency virus (HIV)-1 viral load (VL) and to remeasure VL after 3 months to avoid unnecessary regimen switches. In cases in which this follow-up VL remains unsuppressed, a regimen switch is indicated. We aimed to assess levels of HIV-1 drug resistance before and after the EAC period among people with ongoing viremia (≥80 c/mL) after EAC. Methods We included adult participants of the CART-1 cohort study conducted in Lesotho who had a VL ≥80 c/mL after EAC. Paired plasma samples (before and after EAC) were analyzed by next-generation sequencing. We assessed the prevalence of resistance-associated mutations and viral susceptibility scores to each participant’s antiretroviral therapy (ART) regimen (range, 0–3; 3 indicates complete susceptibility). Results Among 93 participants taking nonnucleoside reverse-transcriptase inhibitor-based ART with an initial VL ≥1000 copies/mL who received a follow-up VL test after EAC, 76 still had a VL ≥80 copies/mL after EAC, and paired samples were available for 57 of 76. The number of individuals without full susceptibility to any drug in their regimen increased from 31 of 57 (54.4%) before to 36 of 57 (63.2%) after EAC. Median susceptibility scores dropped from 0.5 (interquartile range [IQR] = 0.25–) to 0.25 (IQR = 0.25–1) during the EAC period (P = .16). Conclusions Despite high levels of resistance before EAC, we observed a slight decline in susceptibility scores after EAC. The risk of further accumulation of resistance during EAC has to be balanced against the benefit of avoiding unnecessary switches in those with spontaneous resuppression after EAC.
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Affiliation(s)
- Jennifer A Brown
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Herbert A Mbunkah
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Thabo I Lejone
- SolidarMed, Swiss Organization for Health in Africa, Maseru, Lesotho
| | - Isaac Ringera
- SolidarMed, Swiss Organization for Health in Africa, Maseru, Lesotho
| | | | - Thomas Klimkait
- University of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niklaus D Labhardt
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Nadine Tschumi
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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26
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Abela IA, Scherrer AU, Böni J, Yerly S, Klimkait T, Perreau M, Hirsch HH, Furrer H, Calmy A, Schmid P, Cavassini M, Bernasconi E, Günthard HF. Emergence of Drug Resistance in the Swiss HIV Cohort Study Under Potent Antiretroviral Therapy Is Observed in Socially Disadvantaged Patients. Clin Infect Dis 2021; 70:297-303. [PMID: 30843028 DOI: 10.1093/cid/ciz178] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/28/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The rate of acquired human immunodeficiency virus type 1 (HIV-1) drug resistance (ADR) has fallen dramatically since introduction of combined antiretroviral therapy (cART) in Switzerland. However, clinical experience indicates that there are still patients at risk of newly acquiring drug resistance despite having access to cART. Here, we characterized risk factors for ADR, to improve patient care and prevent emergence of drug resistance and treatment failure. METHODS We performed a case-control study to identify risk factors for ADR in all patients starting their first cART in the Swiss HIV Cohort Study (SHCS) since 1996. The SHCS is highly representative and includes >75% of patients receiving ART in Switzerland. To this end, we implemented a systematic medical chart review to obtain more detailed information on additional parameters, which are not routinely collected in the SHCS. The collected data were analyzed using univariable and multivariable conditional logistic regression. RESULTS We included in our study 115 cases and 115 matched controls. Unemployment (multivariable odds ratio [mOR], 2.9 [95% confidence interval {CI}, 1.3-6.4]; P = .008), African origin (mOR, 3.0 [95% CI, 1.0-9.2]; P = .047), comedication with anti-infectives (mOR, 3.7 [95% CI, 1.0-12.6]; P = .045), and symptoms of mental illness (mOR, 2.6 [95% CI, 1.2-5.5]; P = .012) were associated with ADR in the multivariable model. CONCLUSIONS Although ADR has become very rare with cART due to new potent therapies, patients in socially challenging life situations or presenting with mental health issues are at higher risk for drug resistance. Prompt identification and adequate support of these patients before ADR will prevent treatment failure and HIV-1 transmission.
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Affiliation(s)
- Irene A Abela
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich.,Institute of Medical Virology, University of Zurich
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich.,Institute of Medical Virology, University of Zurich
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich
| | - Sabine Yerly
- Laboratory of Virology, Division of Infectious Diseases, Geneva University Hospitals
| | | | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne
| | - Hans H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospitals
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen
| | | | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich.,Institute of Medical Virology, University of Zurich
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27
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Reichmuth ML, Chaudron SE, Bachmann N, Nguyen H, Böni J, Metzner KJ, Perreau M, Klimkait T, Yerly S, Hirsch HH, Hauser C, Ramette A, Vernazza P, Cavassini M, Bernasconi E, Günthard HF, Kusejko K, Kouyos RD. Using longitudinally sampled viral nucleotide sequences to characterize the drivers of HIV-1 transmission. HIV Med 2020; 22:346-359. [PMID: 33368946 DOI: 10.1111/hiv.13030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/17/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Understanding the drivers of HIV-1 transmission is of importance for curbing the ongoing epidemic. Phylogenetic methods based on single viral sequences allow us to assess whether two individuals are part of the same viral outbreak, but cannot on their own assess who potentially transmitted the virus. We developed and assessed a molecular epidemiology method with the main aim to screen cohort studies for and to characterize individuals who are 'potential HIV-1 transmitters', in order to understand the drivers of HIV-1 transmission. METHODS We developed and validated a molecular epidemiology approach using longitudinally sampled viral Sanger sequences to characterize potential HIV-1 transmitters in the Swiss HIV Cohort Study. RESULTS Our method was able to identify 279 potential HIV-1 transmitters and allowed us to determine the main epidemiological and virological drivers of transmission. We found that the directionality of transmission was consistent with infection times for 72.9% of 85 potential HIV-1 transmissions with accurate infection date estimates. Being a potential HIV-1 transmitter was associated with risk factors including viral load [adjusted odds ratiomultivariable (95% confidence interval): 1.86 (1.49-2.32)], syphilis coinfection [1.52 (1.06-2.19)], and recreational drug use [1.45 (1.06-1.98)]. By contrast for the potential HIV-1 recipients, this association was weaker or even absent [1.18 (0.82-1.72), 0.89 (0.52-1.55) and 1.53 (0.98-2.39), respectively], indicating that inferred directionality of transmission is useful at the population level. CONCLUSIONS Our results indicate that longitudinally sampled Sanger sequences do not provide sufficient information to identify transmitters with high certainty at the individual level, but that they allow the drivers of transmission at the population level to be characterized.
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Affiliation(s)
- M L Reichmuth
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - S E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - N Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - H Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - J Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - K J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - M Perreau
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - T Klimkait
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - S Yerly
- Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - H H Hirsch
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.,Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - C Hauser
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - A Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - P Vernazza
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - M Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - E Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - H F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - K Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - R D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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28
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Amstutz A, Nsakala BL, Cheleboi M, Lejone TI, Hobbins MA, Battegay M, Klimkait T, Labhardt ND. Low rates of active hepatitis B and C infections among adults and children living with HIV and taking antiretroviral therapy: A multicenter screening study in Lesotho. J Med Virol 2020; 92:3857-3861. [PMID: 32369206 DOI: 10.1002/jmv.25970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/02/2020] [Indexed: 01/05/2023]
Abstract
Lesotho presents the second-highest adult human immunodeficiency virus (HIV) prevalence globally. Among people living with HIV, data on hepatitis B virus (HBV) or hepatitis C virus (HCV) coinfection are limited. We report HBV and HCV coinfection data from a multicentre cross-sectional study among adult and pediatric patients taking antiretroviral therapy in 10 health facilities in Lesotho. Among 1318 adults screened (68% female; median age, 44 years), 262 (20%) had immunologically controlled HBV infection, 99 (7.6%) tested anti-HBs positive and anti-HBc negative, indicating vaccination, and 57 (4.3%) had chronic HBV infection. Among the patients with chronic HBV infection, 15 tested hepatitis B envelope antigen (HBeAg) positive and eight had detectable HBV viremia (median, 2 477 400 copies/mL; interquartile range, 205-34 400 000) with a mean aspartate aminotransferase-to-platelet ratio index of 0.48 (SD, 0.40). Prevalence of HCV coinfection was 1.7% (22 of 1318), and only one patient had detectable HCV viremia. Among 162 pediatric patients screened, three (1.9%) had chronic HBV infection, whereby two also tested HBeAg-positive, and one had detectable HBV viral load (210 copies/mL). Six of 162 (3.7%) had anti-HCV antibodies, all with undetectable HCV viral loads. Overall prevalence of chronic HBV/HIV and HCV/HIV coinfection among adults and children was relatively low, comparable to earlier reports from the same region. But prevalence of immunologically controlled HBV infection among adults was high. Of those patients with chronic HBV infection, a minority had detectable HBV-DNA.
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Affiliation(s)
- Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | | | - Molisana Cheleboi
- Laboratory Services, St Charles Mission Hospital, Seboche, Butha-Buthe, Lesotho
| | - Thabo I Lejone
- SolidarMed, Partnerships for Health, Butha-Buthe, Lesotho
| | | | - Manuel Battegay
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Thomas Klimkait
- University of Basel, Basel, Switzerland
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Niklaus D Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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29
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Thorball CW, Borghesi A, Bachmann N, Von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Roth V, Kok YL, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Schmid P, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Fellay J. Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. J Acquir Immune Defic Syndr 2020; 85:517-524. [PMID: 33136754 DOI: 10.1097/qai.0000000000002473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The primary hurdle for the eradication of HIV-1 is the establishment of a latent viral reservoir early after primary infection. Here, we investigated the potential influence of human genetic variation on the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. SETTING Genome-wide association study and exome sequencing study to look for host genetic determinants of HIV-1 reservoir measurements in patients enrolled in the Swiss HIV Cohort Study, a nation-wide prospective observational study. METHODS We measured total HIV-1 DNA in peripheral blood mononuclear cells from study participants, as a proxy for the reservoir size at 3 time points over a median of 5.4 years, and searched for associations between human genetic variation and 2 phenotypic readouts: the reservoir size at the first time point and its decay rate over the study period. We assessed the contribution of common genetic variants using genome-wide genotyping data from 797 patients with European ancestry enrolled in the Swiss HIV Cohort Study and searched for a potential impact of rare variants and exonic copy number variants using exome sequencing data generated in a subset of 194 study participants. RESULTS Genome-wide and exome-wide analyses did not reveal any significant association with the size of the HIV-1 reservoir or its decay rate on suppressive antiretroviral treatment. CONCLUSIONS Our results point to a limited influence of human genetics on the size of the HIV-1 reservoir and its long-term dynamics in successfully treated individuals.
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Affiliation(s)
- Christian W Thorball
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Chantal Von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, Bern, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital of Lugano, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland; and
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital 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, Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
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Brown JA, Ringera I, Luoga E, Cheleboi M, Kimera N, Muhairwe J, Kayembe BP, Molapo Hlasoa M, Kabundi L, Yav CWD, Mothobi B, Thahane L, Amstutz A, Bachmann N, Mollel GJ, Bresser M, Glass TR, Paris DH, Klimkait T, Weisser M, Labhardt ND. Genotype-Informed Versus Empiric Management Of VirEmia (GIVE MOVE): study protocol of an open-label randomised clinical trial in children and adolescents living with HIV in Lesotho and Tanzania. BMC Infect Dis 2020; 20:773. [PMID: 33076866 PMCID: PMC7574572 DOI: 10.1186/s12879-020-05491-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 08/20/2020] [Accepted: 10/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Globally, the majority of people living with HIV have no or only limited access to HIV drug resistance testing to guide the selection of antiretroviral drugs. This is of particular concern for children and adolescents, who experience high rates of treatment failure. The GIVE MOVE trial assesses the clinical impact and cost-effectiveness of routinely providing genotypic resistance testing (GRT) to children and adolescents living with HIV who have an unsuppressed viral load (VL) while taking antiretroviral therapy (ART). Methods GIVE MOVE is an open-label randomised clinical trial enrolling children and adolescents (≥6 months to <19 years) living with HIV with a VL ≥400 copies/mL (c/mL) while taking first-line ART. Recruitment takes place at sites in Lesotho and Tanzania. Participants are randomised in a 1:1 allocation to a control arm receiving the standard of care (3 sessions of enhanced adherence counselling, a follow-up VL test, continuation of the same regimen upon viral resuppression or empiric selection of a new regimen upon sustained elevated viremia) and an intervention arm (GRT to inform onward treatment). The composite primary endpoint is the occurrence of any one or more of the following events during the 36 weeks of follow-up period: i) death due to any cause; ii) HIV- or ART-related hospital admission of ≥24 h duration; iii) new clinical World Health Organisation stage 4 event (excluding lymph node tuberculosis, stunting, oral or genital herpes simplex infection and oesophageal candidiasis); and iv) no documented VL <50 c/mL at 36 weeks follow-up. Secondary and exploratory endpoints assess additional health-related outcomes, and a nested study will assess the cost-effectiveness of the intervention. Enrolment of a total of 276 participants is planned, with an interim analysis scheduled after the first 138 participants have completed follow-up. Discussion This randomised clinical trial will assess if the availability of resistance testing improves clinical outcomes in children and adolescents with elevated viremia while taking ART. Trial registration This trial is registered with ClinicalTrials.gov (NCT04233242; registered 18.01.2020). More information: www.givemove.org.
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Affiliation(s)
- Jennifer Anne Brown
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Isaac Ringera
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | | | | | | | | | - Mosa Molapo Hlasoa
- Baylor College of Medicine Children's Foundation Lesotho, Maseru, Lesotho
| | - Lorraine Kabundi
- Baylor College of Medicine Children's Foundation Lesotho, Maseru, Lesotho
| | | | | | - Lineo Thahane
- Baylor College of Medicine Children's Foundation Lesotho, Maseru, Lesotho.,Baylor College of Medicine, Houston, TX, USA
| | - Alain Amstutz
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Nadine Bachmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Moniek Bresser
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Tracy Renée Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Daniel Henry Paris
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maja Weisser
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Ifakara, Tanzania.,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland. .,Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.
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Amstutz A, Lejone TI, Khesa L, Muhairwe J, Bresser M, Vanobberghen F, Kopo M, Kao M, Nsakala BL, Tlali K, Klimkait T, Battegay M, Labhardt ND, Glass TR. Home-based oral self-testing for absent and declining individuals during a door-to-door HIV testing campaign in rural Lesotho (HOSENG): a cluster-randomised trial. Lancet HIV 2020; 7:e752-e761. [PMID: 33045193 DOI: 10.1016/s2352-3018(20)30233-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/09/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND In sub-Saharan Africa, home-based HIV testing is validated and accepted, but coverage is low because household members are often absent during home-based testing campaigns. We aimed to measure the effect of a secondary distribution of oral-fluid HIV self-tests on coverage during home-based testing in rural Lesotho. METHODS The Home-Based Self-Testing (HOSENG) trial was a cluster-randomised, non-blinded superiority trial in rural villages in the catchment area of 20 health facilities of two districts in Lesotho (Butha-Buthe and Mokhotlong). Eligible villages had a consenting village chief and at least one registered village health worker; eligible households had a consenting representative aged 18 years or older. The HOSENG trial provided a recruitment platform for the interlinked Village-Based Refill of Antiretroviral Therapy (VIBRA) trial. Villages were randomly assigned 1:1:1:1 with block sizes of four to one of four groups: VIBRA control and HOSENG control; VIBRA control and HOSENG intervention; VIBRA intervention and HOSENG control; and VIBRA intervention and HOSENG intervention. Randomisation was stratified by district, village size, and access to the nearest health facility. An independent statistician was responsible for the computer-generated randomisation list. In the intervention group, oral-fluid HIV self-tests were left for absent or declining household members (aged ≥12 years) during a home visit from the HIV testing campaign team. One present household member was trained on self-test use. Distributed self-tests were followed up by village health workers. In control village clusters, absent or declining household members were referred to the clinic for HIV testing. The primary outcome was HIV testing coverage among all household members aged 12 years or older within 120 days, defined as a confirmed HIV test result or known status, reported in testing registers at the health facilities or on the follow-up forms of the village health worker. Adjusted random-effects logistic regression with individuals as the unit of analysis was used. This trial is registered with ClinicalTrials.gov, NCT03598686. FINDINGS Between July 26, 2018, and Dec 12, 2018, 3091 consenting households with 7816 household members aged 12 years or older were enrolled and randomly assigned (intervention: 57 village clusters, 1620 households, 4174 household members; control: 49 village clusters, 1471 households, 3642 household members). In the control group, 38 (3%) of 1455 initially absent or declining household members tested at a clinic within 120 days. In the intervention group, 841 (53%) of 1601 initially absent or declining household members had a confirmed status within 120 days; 12 (1%) of 841 tested at the clinic and 829 (99%) used their self-test kit. This resulted in a testing coverage of 2201 (60%) of 3642 in the control group versus 3386 (81%) of 4174 in the intervention group (odds ratio 3·00 [95% CI 2·52-3·59]; p<0·0001). INTERPRETATION Secondary distribution of oral-fluid HIV self-tests during home-based testing increases testing coverage substantially and thus presents a promising add-on during testing campaigns. FUNDING Swiss National Science Foundation.
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Affiliation(s)
- Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; University of Basel, Basel, Switzerland
| | | | - Lefu Khesa
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | - Moniek Bresser
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Fiona Vanobberghen
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Mathebe Kopo
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | - Mpho Kao
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | | | - Katleho Tlali
- SolidarMed, Partnerships for Health, Maseru, Lesotho
| | - Thomas Klimkait
- University of Basel, Basel, Switzerland; Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Tracy Renée Glass
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
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Amstutz A, Nsakala BL, Vanobberghen F, Muhairwe J, Glass TR, Namane T, Mpholo T, Battegay M, Klimkait T, Labhardt ND. Switch to second-line versus continued first-line antiretroviral therapy for patients with low-level HIV-1 viremia: An open-label randomized controlled trial in Lesotho. PLoS Med 2020; 17:e1003325. [PMID: 32936795 PMCID: PMC7494118 DOI: 10.1371/journal.pmed.1003325] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Current World Health Organization (WHO) antiretroviral therapy (ART) guidelines define virologic failure as two consecutive viral load (VL) measurements ≥1,000 copies/mL, triggering empiric switch to next-line ART. This trial assessed if patients with sustained low-level HIV-1 viremia on first-line ART benefit from a switch to second-line treatment. METHODS AND FINDINGS This multicenter, parallel-group, open-label, superiority, randomized controlled trial enrolled patients on first-line ART containing non-nucleoside reverse transcriptase inhibitors (NNRTI) with two consecutive VLs ≥100 copies/mL, with the second VL between 100-999 copies/mL, from eight clinics in Lesotho. Consenting participants were randomly assigned (1:1), stratified by facility, demographic group, and baseline VL, to either switch to second-line ART (switch group) or continued first-line ART (control group; WHO guidelines). The primary endpoint was viral suppression (<50 copies/mL) at 36 weeks. Analyses were by intention to treat, using logistic regression models, adjusted for demographic group and baseline VL. Between August 1, 2017, and August 7, 2019, 137 individuals were screened, of whom 80 were eligible and randomly assigned to switch (n = 40) or control group (n = 40). The majority of participants were female (54 [68%]) with a median age of 42 y (interquartile range [IQR] 35-51), taking tenofovir disoproxil fumarate/lamivudine/efavirenz (49 [61%]) and on ART for a median of 5.9 y (IQR 3.3-8.6). At 36 weeks, 22/40 (55%) participants in the switch versus 10/40 (25%) in the control group achieved viral suppression (adjusted difference 29%, 95% CI 8%-50%, p = 0.009). The switch group had significantly higher probability of viral suppression across different VL thresholds (<20, <100, <200, <400, and <600 copies/mL) but not for <1,000 copies/mL. Thirty-four (85%) participants in switch group and 21 (53%) in control group experienced at least one adverse event (AE) (p = 0.002). No hospitalization or death or other serious adverse events were observed. Study limitations include a follow-up period too short to observe differences in clinical outcomes, missing values in CD4 cell counts due to national stockout of reagents during the study, and limited generalizability of findings to other than NNRTI-based first-line ART regimens. CONCLUSIONS In this study, switching to second-line ART among patients with sustained low-level HIV-1 viremia resulted in a higher proportion of participants with viral suppression. These results endorse lowering the threshold for virologic failure in future WHO guidelines. TRIAL REGISTRATION The trial is registered at ClinicalTrials.gov, NCT03088241.
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Affiliation(s)
- Alain Amstutz
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | | | - Fiona Vanobberghen
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Tracy Renée Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Tilo Namane
- Motebang Government Hospital, Leribe, Lesotho
| | | | - Manuel Battegay
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- * E-mail:
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Bachmann N, von Braun A, Labhardt ND, Kadelka C, Günthard HF, Sekaggya-Wiltshire C, Castelnuovo B, Kambugu A, Lejone TI, Böni J, Yerly S, Perreau M, Klimkait T, Kouyos RD, Fehr J. Importance of routine viral load monitoring: higher levels of resistance at ART failure in Uganda and Lesotho compared with Switzerland. J Antimicrob Chemother 2020; 74:468-472. [PMID: 30476115 DOI: 10.1093/jac/dky436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/26/2018] [Indexed: 11/14/2022] Open
Abstract
Objectives Emerging resistance to antiretroviral drugs may jeopardize the achievements of improved access to ART. We compared the prevalence of different resistance mutations in HIV-infected adults with virological failure in a cohort with regular routine viral load (VL) monitoring (Switzerland) and cohorts with limited access to VL testing (Uganda and Lesotho). Methods We considered individuals who had genotypic resistance testing (GRT) upon virological failure (≥1000 copies/mL) and were on ART consisting of at least one NNRTI and two NRTIs. From Lesotho, individuals with two subsequent VLs ≥1000 copies/mL despite enhanced adherence counselling (n = 58) were included in the analysis. From Uganda, individuals with a single VL ≥1000 copies/mL (n = 120) were included in the analysis. From the Swiss HIV Cohort Study (SHCS), a population without history of monotherapy or dual therapy with the first GRT upon virological failure (n = 61) was selected. Results We found that 50.8% of individuals in the SHCS, 72.5% in Uganda and 81.0% in Lesotho harboured HIV with high-level resistance to at least two drugs from their current regimen. Stanford resistance scores were higher in Uganda compared with Switzerland for all drugs used in first-line treatment except zidovudine and tenofovir (P < 0.01) and higher in Lesotho compared with Uganda for all drugs used in first-line treatment except zidovudine (P < 0.01). Conclusions Frequent VL monitoring and possibly pretreatment GRT as done in the SHCS pays off by low levels of resistance even when treatment failure occurs. The high-level resistance patterns in Lesotho compared with Uganda could reflect a selection of strains with multiple resistance during enhanced adherence counselling.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Amrei von Braun
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Niklaus D Labhardt
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Claus Kadelka
- Department 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
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Barbara Castelnuovo
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Andrew Kambugu
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Thabo I Lejone
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, 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
| | - Jan Fehr
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Department of Public Health at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland
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Hampel B, Kusejko K, Kouyos RD, Böni J, Flepp M, Stöckle M, Conen A, Béguelin C, Künzler‐Heule P, Nicca D, Schmidt AJ, Nguyen H, Delaloye J, Rougemont M, Bernasconi E, Rauch A, Günthard HF, Braun DL, Fehr J, Anagnostopoulos A, Battegay M, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fellay J, Furrer H, Fux CA, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kovari H, Ledergerber B, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, Paioni P, Pantaleo G, Perreau M, Rudin C, Scherrer AU, Schmid P, Speck R, Tarr P, Trkola A, Vernazza P, Wandeler G, Weber R, Yerly S. Chemsex drugs on the rise: a longitudinal analysis of the Swiss HIV Cohort Study from 2007 to 2017. HIV Med 2020; 21:228-239. [DOI: 10.1111/hiv.12821] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2019] [Indexed: 12/22/2022]
Affiliation(s)
- B Hampel
- Division of Infectious Diseases and Hospital Epidemiology University Hospital Zurich University of Zurich Zurich Switzerland
- Institute of Medical Virology University of Zurich Zurich Switzerland
- Department of Public Health Epidemiology, Biostatistics and Public Health Institute University of Zurich Zurich Switzerland
| | - K 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
| | - RD 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
| | - J Böni
- Institute of Medical Virology University of Zurich Zurich Switzerland
| | - M Flepp
- Center of Infectious Diseases Zurich Zurich Switzerland
| | - M Stöckle
- Division of Infectious Diseases & Hospital Epidemiology University Hospital Basel University Basel Basel Switzerland
| | - A Conen
- Division of Infectious Diseases and Hospital Hygiene Cantonal Hospital Aarau Aarau Switzerland
| | - C Béguelin
- Department of Infectious Diseases Bern University Hospital University of Bern Bern Switzerland
| | - P Künzler‐Heule
- Institute of Nursing Science University of Basel, and University Hospital Basel Basel Switzerland
| | - D Nicca
- Institute of Nursing Science University of Basel, and University Hospital Basel Basel Switzerland
| | - AJ Schmidt
- Division of Infectious Diseases Cantonal Hospital St. Gallen St. Gallen Switzerland
| | - H Nguyen
- Division of Infectious Diseases and Hospital Epidemiology University Hospital Zurich University of Zurich Zurich Switzerland
- Institute of Medical Virology University of Zurich Zurich Switzerland
| | - J Delaloye
- Division of Infectious Diseases University Hospital Lausanne Lausanne Switzerland
| | - M Rougemont
- Division of Infectious Diseases University Hospital Geneva Geneva Switzerland
| | - E Bernasconi
- Division of Infectious Diseases Regional Hospital Lugano Lugano Switzerland
| | - A Rauch
- Department of Infectious Diseases Bern University Hospital University of Bern Bern Switzerland
| | - HF 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
| | - DL 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
| | - J Fehr
- Division of Infectious Diseases and Hospital Epidemiology University Hospital Zurich University of Zurich Zurich Switzerland
- Department of Public Health Epidemiology, Biostatistics and Public Health Institute University of Zurich Zurich Switzerland
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Surial B, Ledergerber B, Calmy A, Cavassini M, Günthard HF, Kovari H, Stöckle M, Bernasconi E, Schmid P, Fux CA, Furrer H, Rauch A, Wandeler G, Anagnostopoulos A, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Günthard HF, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert CR, Kaiser L, Keiser O, Klimkait T, Kouyos RD, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner KJ, Müller N, Nicca D, Paioni P, Pantaleo G, Perreau M, Rauch A, Rudin C, Scherrer AU, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Wandeler G, Weber R, Yerly S. Changes in Renal Function After Switching From TDF to TAF in HIV-Infected Individuals: A Prospective Cohort Study. J Infect Dis 2020; 222:637-645. [DOI: 10.1093/infdis/jiaa125] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
AbstractBackgroundReplacing tenofovir disoproxil fumarate (TDF) with tenofovir alafenamide (TAF) improves renal tubular markers in HIV-infected individuals but the impact on estimated glomerular filtration rate (eGFR) remains unclear.MethodsIn all participants from the Swiss HIV Cohort Study who switched from TDF to TAF-containing antiretroviral regimen or continued TDF, we estimated changes in eGFR and urine protein-to-creatinine ratio (UPCR) after 18 months using mixed-effect models.ResultsOf 3520 participants (26.6% women, median age 50 years), 2404 (68.5%) switched to TAF. Overall, 1664 (47.3%) had an eGFR <90 mL/min and 1087 (30.9%) an UPCR ≥15 mg/mmol. In patients with baseline eGFR ≥90 mL/min, eGFR decreased with the use of TDF and TAF (−1.7 mL/min). Switching to TAF was associated with increases in eGFR of 1.5 mL/min (95% confidence interval [CI], .5–2.5) if the baseline eGFR was 60–89 mL/min, and 4.1 mL/min (95% CI, 1.6–6.6) if <60 mL/min. In contrast, eGFR decreased by 5.8 mL/min (95% CI, 2.3–9.3) with continued use of TDF in individuals with baseline eGFR <60 mL/min. UPCR decreased after replacing TDF by TAF, independent of baseline eGFR.ConclusionsSwitching from TDF to TAF improves eGFR and proteinuria in patients with renal dysfunction.
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Affiliation(s)
- Bernard Surial
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alexandra Calmy
- Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital of Lausanne, University of Lausanne, Lausanne, 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
| | - Helen Kovari
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Marcel Stöckle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital of Lugano, Lugano, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital of St Gallen, St Gallen, Switzerland
| | - Christoph A Fux
- Division of Infectious Diseases, Cantonal Hospital of Aarau, Aarau, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Gilles Wandeler
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Carlisle LA, Turk T, Kusejko K, Metzner KJ, Leemann C, Schenkel CD, Bachmann N, Posada S, Beerenwinkel N, Böni J, Yerly S, Klimkait T, Perreau M, Braun DL, Rauch A, Calmy A, Cavassini M, Battegay M, Vernazza P, Bernasconi E, Günthard HF, Kouyos RD. Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection. J Infect Dis 2020; 220:254-265. [PMID: 30835266 DOI: 10.1093/infdis/jiz094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/01/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) genetic diversity increases over the course of infection and can be used to infer the time since infection and, consequently, infection recency, which are crucial for HIV-1 surveillance and the understanding of viral pathogenesis. METHODS We considered 313 HIV-infected individuals for whom reliable estimates of infection dates and next-generation sequencing (NGS)-derived nucleotide frequency data were available. Fractions of ambiguous nucleotides, obtained by population sequencing, were available for 207 samples. We assessed whether the average pairwise diversity calculated using NGS sequences provided a more exact prediction of the time since infection and classification of infection recency (<1 year after infection), compared with the fraction of ambiguous nucleotides. RESULTS NGS-derived average pairwise diversity classified an infection as recent with a sensitivity of 88% and a specificity of 85%. When considering only the 207 samples for which fractions of ambiguous nucleotides were available, the NGS-derived average pairwise diversity exhibited a higher sensitivity (90% vs 78%) and specificity (95% vs 67%) than the fraction of ambiguous nucleotides. Additionally, the average pairwise diversity could be used to estimate the time since infection with a mean absolute error of 0.84 years, compared with 1.03 years for the fraction of ambiguous nucleotides. CONCLUSIONS Viral diversity based on NGS data is more precise than that based on population sequencing in its ability to predict infection recency and provides an estimated time since infection that has a mean absolute error of <1 year.
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Affiliation(s)
- Louisa A Carlisle
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Teja Turk
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Corinne D Schenkel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Nadine Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Susana Posada
- Department of Biosystems Science and Engineering, ETH Zurich.,SIB Swiss Institute of Bioinformatics, University of Basel, Basel
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich.,SIB Swiss Institute of Bioinformatics, University of Basel, Basel
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich.,Swiss National Center for Retroviruses, University of Zurich, Zurich
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Geneva
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel
| | - Matthieu Perreau
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Geneva
| | | | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel
| | - Pietro Vernazza
- Division of Infectious Diseases, Cantonal Hospital St. Gallen, St. Gallen
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich.,Institute of Medical Virology, University of Zurich, Zurich
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Kusejko K, Bachmann N, Chaudron SE, Nguyen H, Braun DL, Hampel B, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD. A Systematic Phylogenetic Approach to Study the Interaction of HIV-1 With Coinfections, Noncommunicable Diseases, and Opportunistic Diseases. J Infect Dis 2020; 220:244-253. [PMID: 30835292 DOI: 10.1093/infdis/jiz093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/01/2019] [Indexed: 12/21/2022] Open
Abstract
To systematically test whether coinfections spread along the HIV-1 transmission network and whether similarities in HIV-1 genomes predict AIDS-defining illnesses and comorbidities, we analyzed the distribution of these variables on the HIV phylogeny of the densely sampled Swiss HIV Cohort Study. By combining different statistical methods, we could detect, quantify, and explain the clustering of diseases. Infectious conditions such as hepatitis C, but also Kaposi sarcoma, clustered significantly, suggesting transmission of these infections along the HIV-1 transmission network. The clustering of patients with neurocognitive complaints could not be completely explained by the clustering of patients with similar demographic risk factors, which suggests a potential impact of viral genetics. In summary, the consistent and robust signal for coinfections and comorbidities highlights the strong interaction of HIV-1 and other infections and shows the potential of combining phylogenetic methods to identify disease traits that are likely to be related to virus genetic factors.
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Affiliation(s)
- Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Nadine Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Sandra E Chaudron
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Benjamin Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital St Gallen, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Switzerland
| | | | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Switzerland
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Bircher RE, Ntamatungiro AJ, Glass TR, Mnzava D, Nyuri A, Mapesi H, Paris DH, Battegay M, Klimkait T, Weisser M. High failure rates of protease inhibitor-based antiretroviral treatment in rural Tanzania - A prospective cohort study. PLoS One 2020; 15:e0227600. [PMID: 31929566 PMCID: PMC6957142 DOI: 10.1371/journal.pone.0227600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 12/24/2019] [Indexed: 01/12/2023] Open
Abstract
Background Poor adherence to antiretroviral drugs and viral resistance are the main drivers of treatment failure in HIV-infected patients. In sub-Saharan Africa, avoidance of treatment failure on second-line protease inhibitor therapy is critical as treatment options are limited. Methods In the prospective observational study of the Kilombero & Ulanga Antiretroviral Cohort in rural Tanzania, we assessed virologic failure (viral load ≥1,000 copies/mL) and drug resistance mutations in bio-banked plasma samples 6–12 months after initiation of a protease inhibitor-based treatment regimen. Additionally, viral load was measured before start of protease inhibitor, a second time between 1–5 years after start, and at suspected treatment failure in patients with available bio-banked samples. We performed resistance testing if viral load was ≥1000 copies/ml. Risk factors for virologic failure were analyzed using logistic regression. Results In total, 252 patients were included; of those 56% were female and 21% children. Virologic failure occurred 6–12 months after the start of a protease inhibitor in 26/199 (13.1%) of adults and 7/53 of children (13.2%). The prevalence of virologic failure did not change over time. Nucleoside reverse transcriptase inhibitors drug resistance mutation testing performed at 6–12 months showed a positive signal in only 9/16 adults. No cases of resistance mutations for protease inhibitors were seen at this time. In samples taken between 1–5 years protease inhibitor resistance was demonstrated in 2/7 adults. In adult samples before protease inhibitor start, resistance to nucleoside reverse transcriptase inhibitors was detected in 30/41, and to non-nucleoside reverse-transcriptase inhibitors in 35/41 patients. In 15/16 pediatric samples, resistance to both drug classes but not for protease inhibitors was present. Conclusion Our study confirms high early failure rates in adults and children treated with protease inhibitors, even in the absence of protease inhibitors resistance mutations, suggesting an urgent need for adherence support in this setting.
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Affiliation(s)
- Rahel E. Bircher
- Ifakara Health Institute, Ifakara, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Molecular Virology, Department Biomedicine Petersplatz, University of Basel, Basel, Switzerland
| | | | - Tracy R. Glass
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | - Herry Mapesi
- Ifakara Health Institute, Ifakara, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- St. Francis Referral Hospital, Ifakara, Tanzania
| | - Daniel H. Paris
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Manuel Battegay
- University of Basel, Basel, Switzerland
- Departments of Medicine and Clinical Research, Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine Petersplatz, University of Basel, Basel, Switzerland
| | - Maja Weisser
- Ifakara Health Institute, Ifakara, Tanzania
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Departments of Medicine and Clinical Research, Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- * E-mail:
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Kusejko K, Marzel A, Nguyen H, Chaudron SE, Bachmann N, Weber R, Bruggmann P, Roth JA, Bernasconi E, Calmy A, Cavassini M, Bregenzer A, Böni J, Yerly S, Klimkait T, Perreau M, Walti LN, Günthard HF, Kouyos RD. Differences in social and mental well-being of long-term survivors among people who inject drugs and other participants in the Swiss HIV Cohort Study: 1980-2018. Antivir Ther 2020; 25:43-54. [PMID: 32235037 DOI: 10.3851/imp3347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND People living with HIV who were diagnosed before highly active antiretroviral therapy became available in 1996 and who survived at least 15 years after HIV diagnosis, termed long-term survivors (LTS), form a particularly vulnerable population. We study social, clinical and mental factors of LTS in the Swiss HIV Cohort Study, with a particular focus on people who inject drugs (PWID). METHODS We quantified differences between PWID LTS, and men who have sex with men (MSM) and heterosexual (HET) LTS. Using phylogenetic methods, we distinguished between heterosexual LTS who most likely shared a social network with PWID at the time of infection, termed clusteredHET, and those who did not, termed HET not clustered (HETnc). The analysis was performed using data collected at least 15 years post diagnosis. RESULTS Overall, 1,663 of 5,686 (29.2%) PWID were LTS. We found significant differences between PWID LTS and MSM/HETnc LTS regarding self-reported depression (59.4% versus 43.3%; odds ratio [OR]=1.8; P<0.001), incarceration (30.6% versus 7.0%; OR=6.9; P<0.001) and full work ability (25.4% versus 59.0%; OR=0.27; P<0.001). ClusteredHET were less vulnerable with respect to these variables than PWID LTS but more at risk compared with MSM/HETnc LTS, indicating that clusteredHET are closer to PWID with regard to social and mental aspects compared with all MSM/HETnc. CONCLUSIONS Even more than 15 years post HIV diagnosis, special care for HIV-positive PWID is needed, with emphasis on mental health and social integration of PWID LTS.
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Affiliation(s)
- 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
| | - Alex Marzel
- Department of Teaching, Research and Development, Schulthess Clinic, Zurich, Switzerland
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, 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
| | - Nadine Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Rainer Weber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Jan A Roth
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - Andrea Bregenzer
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - Laura N Walti
- Clinic for Infectious Diseases, Bern University Hospital, University of Bern, Bern, 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
| | - 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
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Labhardt ND, Ringera I, Lejone TI, Amstutz A, Klimkait T, Muhairwe J, Glass TR. Effect and cost of two successive home visits to increase HIV testing coverage: a prospective study in Lesotho, Southern Africa. BMC Public Health 2019; 19:1441. [PMID: 31676001 PMCID: PMC6825349 DOI: 10.1186/s12889-019-7784-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 05/02/2019] [Accepted: 10/16/2019] [Indexed: 11/10/2022] Open
Abstract
Background Home-based HIV testing and counselling (HB-HTC) is frequently used to increase awareness of HIV status in sub-Saharan Africa. Whereas acceptance of HB-HTC is usually high, testing coverage may remain low due to household members being absent during the home visits. This study assessed whether two consecutive visits, one during the week, one on the weekend, increase coverage. Methods The study was a predefined nested-study of the CASCADE-trial protocol and conducted in 62 randomly selected villages and 17 urban areas in Butha-Buthe district, Lesotho. HB-HTC teams visited each village/urban area twice: first during a weekday, followed by a weekend visit to catch-up for household members absent during the week. Primary outcome was HTC coverage after first and second visit. Coverage was defined as all individuals who knew their HIV status out of all household members (present and absent). Results HB-HTC teams visited 6665 households with 18,286 household members. At first visit, 69.2 and 75.4% of household members were encountered in rural and urban households respectively (p < 0.001) and acceptance for testing was 88.5% in rural and 79.5% in urban areas (p < 0.001), resulting in a coverage of 61.8 and 61.5%, respectively. After catch-up visit, the HTC coverage increased to 71.9% in rural and 69.4% in urban areas. The number of first time testers was higher at the second visit (47% versus 35%, p < 0.001). Direct cost per person tested and per person tested HIV positive were lower during weekdays (10.50 and 335 USD) than during weekends (20 and 1056 USD). Conclusions A catch-up visit on weekends increased the proportion of persons knowing their HIV status from 62 to 71% and reached more first-time testers. However, cost per person tested during catch-up visits was nearly twice the cost during first visit. Trial registration NCT02692027 (prospectively registered on February 21, 2016).
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Affiliation(s)
- Niklaus Daniel Labhardt
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland. .,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Isaac Ringera
- SolidarMed, Swiss Organization for Health in Africa, Maseru, Lesotho
| | | | - Alain Amstutz
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Thomas Klimkait
- University of Basel, Basel, Switzerland.,Molecular Virology, Department of Biomedicine, Basel, Switzerland
| | | | - Tracy Renee Glass
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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Mkindi CG, Marandu EA, Masawa N, Bani F, Nyuri A, Byakuzana T, Klimkait T, Ding S, Pantaleo G, Battegay M, Orlova-Fink N, Weisser-Rohacek M, Daubenberger C. Safety and tolerance of lymph node biopsies from chronic HIV-1 volunteers in rural Tanzania. BMC Res Notes 2019; 12:561. [PMID: 31492170 PMCID: PMC6729032 DOI: 10.1186/s13104-019-4600-x] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/03/2019] [Indexed: 11/29/2022] Open
Abstract
Objective HIV-1 rapidly establishes a persistent infection that can be contained under life-long antiretroviral therapy (ART) but not cured. One major viral reservoir is the peripheral lymph node (LN) follicles. Studying the impact of novel HIV-1 treatment and vaccination approaches on cells residing in germinal centers is essential for rapid progress towards HIV-1 prevention and cure. Results We enrolled 9 asymptomatic adult volunteers with a newly diagnosed HIV-1 infection and CD4 T cell counts ≥ 350/ml. The patients underwent venous blood collection and inguinal lymph node excision surgery in parallel. Mononuclear cells were extracted from blood and tissues simultaneously. Participants were followed up regularly for 2 weeks until complete healing of the surgical wounds. All participants completed the lymph node excision surgery without clinical complications. Among the 9 volunteers, one elite controller was identified. The number of mononuclear cells recovered from lymph nodes ranged from 68 to 206 million and correlated positively with lymph node size. This is the first study to show that lymph node biopsy is a safe procedure and can be undertaken with local experts in rural settings. It provides a foundation for detailed immune response investigations during future clinical trials.
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Affiliation(s)
- Catherine Gerald Mkindi
- Department of Medical Parasitology and Infection Biology, Clinical Immunology, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | | | | | - Farida Bani
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Amina Nyuri
- Ifakara Health Institute, Bagamoyo, Tanzania
| | | | | | - Song Ding
- EuroVacc Foundation, Amsterdam, The Netherlands
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland.,Swiss Vaccine Research Institute, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Nina Orlova-Fink
- Department of Medical Parasitology and Infection Biology, Clinical Immunology, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | - Maja Weisser-Rohacek
- Department of Medical Parasitology and Infection Biology, Clinical Immunology, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania.,Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland. .,Ifakara Health Institute, Bagamoyo, Tanzania.
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Glass TR, Motaboli L, Nsakala B, Lerotholi M, Vanobberghen F, Amstutz A, Lejone TI, Muhairwe J, Klimkait T, Labhardt ND. The viral load monitoring cascade in a resource-limited setting: A prospective multicentre cohort study after introduction of routine viral load monitoring in rural Lesotho. PLoS One 2019; 14:e0220337. [PMID: 31461455 PMCID: PMC6713472 DOI: 10.1371/journal.pone.0220337] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/12/2019] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION For HIV-positive individuals on antiretroviral therapy (ART), the World Health Organization (WHO) recommends routine viral load (VL) monitoring. We report on the cascade of care in individuals with unsuppressed VL after introduction of routine VL monitoring in a district in Lesotho. MATERIALS AND METHODS In Butha-Buthe district 12 clinics (11 rural, 1 hospital) send samples for VL testing to the district laboratory. We included data from patients aged ≥15 years from Dec 1, 2015 to November 1, 2018. As per WHO guidelines VL <1000 copies/mL are considered suppressed, those ≥1000copies/mL unsuppressed. Patients with unsuppressed VL receive adherence counseling and follow-up VL within 8-12 weeks. Two consecutively unsuppressed VLs should trigger switch to second-line ART. For analysis of the VL monitoring cascade we defined care to be "according to guidelines" if patients with unsuppressed VL received a follow-up VL within <180 days and follow-up VL was either re-suppressed, or again unsuppressed and the individual was switched to second-line within 90 days. RESULTS For 9,949 individuals 24,948 VL tests were available. The majority were female (73%), median age 41 years (interquartile range 33-52), and 58% seen at rural clinics. Overall, 25% (260/1028) of individuals were managed according to guidelines: 40% (410/1028) had a follow-up VL within 180 days of their initial unsuppressed VL and 25% (260/1028) of those either re-suppressed or switched to second-line within 90 days. Female patients were more likely to have a follow-up VL done, (p = 0.015). In rural clinics rates of two consecutively unsuppressed VLs were higher than in the hospital (64% vs. 44%, p<0.001), and rural clinics were less likely to switch these patients to second-line (35% vs. 66%, p<0001). CONCLUSIONS Our data show that in a real-life setting availability of routine VL monitoring may not be exploited to its potential. A lack of timely follow-up after a first unsuppressed VL and reluctance to switch patients with confirmed virological failure, reduce the benefit of VL monitoring, i.e. in the rural clinics. Future studies will have to assess models of care which ensure that VL results are met with an action and make use of scalable innovative approaches.
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Affiliation(s)
- Tracy Renee Glass
- Swiss Tropical & Public Health Institute, Basel,
Switzerland
- University of Basel, Basel, Switzerland
| | - Lipontso Motaboli
- SolidarMed, Swiss Organisation for Health in Africa, Butha-Buthe,
Lesotho
| | - Bienvenu Nsakala
- SolidarMed, Swiss Organisation for Health in Africa, Butha-Buthe,
Lesotho
| | | | - Fiona Vanobberghen
- Swiss Tropical & Public Health Institute, Basel,
Switzerland
- University of Basel, Basel, Switzerland
| | - Alain Amstutz
- Swiss Tropical & Public Health Institute, Basel,
Switzerland
- University of Basel, Basel, Switzerland
- University Hospital Basel, Division of Infectious Diseases and Hospital
Epidemiology, Basel, Switzerland
| | | | - Josephine Muhairwe
- SolidarMed, Swiss Organisation for Health in Africa, Butha-Buthe,
Lesotho
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel,
Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Swiss Tropical & Public Health Institute, Basel,
Switzerland
- University of Basel, Basel, Switzerland
- University Hospital Basel, Division of Infectious Diseases and Hospital
Epidemiology, Basel, Switzerland
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Amstutz A, Lejone TI, Khesa L, Muhairwe J, Nsakala BL, Tlali K, Bresser M, Tediosi F, Kopo M, Kao M, Klimkait T, Battegay M, Glass TR, Labhardt ND. VIBRA trial - Effect of village-based refill of ART following home-based same-day ART initiation vs clinic-based ART refill on viral suppression among individuals living with HIV: protocol of a cluster-randomized clinical trial in rural Lesotho. Trials 2019; 20:522. [PMID: 31439004 PMCID: PMC6704675 DOI: 10.1186/s13063-019-3510-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 06/10/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND There is a need for evaluating community-based antiretroviral therapy (ART) delivery models to improve overall performance of HIV programs, specifically in populations that may have difficulties to access continuous care. This cluster-randomized clinical trial aims to evaluate the effectiveness of a multicomponent differentiated ART delivery model (VIBRA model) after home-based same-day ART initiation in remote villages in Lesotho, southern Africa. METHODS/DESIGN The VIBRA trial (VIllage-Based Refill of ART) is a cluster-randomized parallel-group superiority clinical trial conducted in two districts in Lesotho, southern Africa. Clusters (i.e., villages) are randomly assigned to either the VIBRA model or standard care. The clusters are stratified by district, village size, and village access to the nearest health facility. Eligible individuals (HIV-positive, aged 10 years or older, and not taking ART) identified during community-based HIV testing campaigns are offered same-day home-based ART initiation. The intervention clusters offer a differentiated ART delivery package with two features: (1) drug refills and follow-ups by trained and supervised village health workers (VHWs) and (2) the option of receiving individually tailored adherence reminders and notifications of viral load results via SMS. The control clusters will continue to receive standard care, i.e., collecting ART refills from a clinic and no SMS notifications. The primary endpoint is viral suppression 12 months after enrolment. Secondary endpoints include linkage to and engagement in care. Furthermore, safety and cost-effectiveness analyses plus qualitative research are planned. The minimum target sample size is 262 participants. The statistical analyses will follow the CONSORT guidelines. The VIBRA trial is linked to another trial, the HOSENG (HOme-based SElf-testiNG) trial, both of which are within the GET ON (GETing tOwards Ninety) research project. DISCUSSION The VIBRA trial is among the first to evaluate the delivery of ART by VHWs immediately after ART initiation. It assesses the entire HIV care cascade from testing to viral suppression. As most countries in sub-Saharan Africa have cadres like the VHW program in Lesotho, this model-if shown to be effective-has the potential to be scaled up. The system impact evaluation will provide valuable cost estimations, and the qualitative research will suggest how the model could be further modified to optimize its impact. TRIAL REGISTRATION Clinicaltrials.gov, NCT03630549 . Registered on 15 August 2018.
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Affiliation(s)
- Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
| | | | - Lefu Khesa
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
| | - Josephine Muhairwe
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
| | | | - Katleho Tlali
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
- Butha-Buthe Government Hospital, Butha-Buthe, Lesotho
| | - Moniek Bresser
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
| | - Fabrizio Tediosi
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
| | - Mathebe Kopo
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
| | - Mpho Kao
- SolidarMed, Swiss Organization for Health in Africa, Butha-Buthe, Lesotho
| | - Thomas Klimkait
- University of Basel, 4051 Basel, Switzerland
- Molecular Virology, Department of Biomedicine, University of Basel, 4051 Basel, Switzerland
| | - Manuel Battegay
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
| | - Tracy Renée Glass
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
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Amstutz A, Lejone TI, Khesa L, Muhairwe J, Nsakala BL, Tlali K, Bresser M, Vanobberghen F, Kopo M, Kao M, Klimkait T, Battegay M, Labhardt ND, Glass TR. The HOSENG trial - Effect of the provision of oral self-testing for absent and refusing individuals during a door-to-door HIV-testing campaign on testing coverage: protocol of a cluster-randomized clinical trial in rural Lesotho. Trials 2019; 20:496. [PMID: 31409421 PMCID: PMC6693145 DOI: 10.1186/s13063-019-3469-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/24/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND HIV-testing coverage remains below the targeted 90% despite efforts and resources invested. Home-based HIV-testing is a key approach endorsed by the World Health Organization (WHO), especially to reach individuals who might not seek testing otherwise. Although acceptance of testing during such campaigns is high, coverage remains low due to absent household members. This cluster-randomized trial aims to assess increase in testing coverage using oral HIV self-testing (HIVST) among individuals who are absent or decline testing during home-based HIV-testing. METHODS The HOSENG (HOme-based SElf-testiNG) trial is a cluster-randomized, parallel-group, superiority trial in two districts of Lesotho, Southern Africa. Clusters are stratified by district, village size, and village access to the nearest health facility. Cluster eligibility criteria include: village is in catchment area of one of the study facilities, village authority provides consent, and village has a registered, capable, and consenting village health worker (VHW). In intervention clusters, HIV self-tests are provided for eligible household members who are absent or decline HIV-testing in the presence of the campaign team. In control clusters, standard of care for absent and refusing individuals applies, i.e., referral to a health facility. The primary outcome is HIV-testing coverage among individuals aged 12 years or older within 120 days after enrollment. Secondary objectives include HIV-testing coverage among other age groups, and uptake of the different testing modalities. Statistical analyses will be conducted and reported in line with CONSORT guidelines. The HOSENG trial is linked to the VIBRA (Village-Based Refill of ART) trial. Together, they constitute the GET ON (GETting tOwards Ninety) research project. DISCUSSION The HOSENG trial tests whether oral HIVST may be an add-on during door-to-door testing campaigns towards achieving optimal testing coverage. The provision of oral self-test kits, followed up by VHWs, requires little additional human resources, finances and logistics. If cost-effective, this approach should inform home-based HIV-testing policies not only in Lesotho, but in similar high-prevalence settings. TRIAL REGISTRATION ClinicalTrials.gov, (ID: NCT03598686 ). Registered on 25 July 2018. More information is available at www.getonproject.wordpress.com .
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Affiliation(s)
- Alain Amstutz
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
| | | | - Lefu Khesa
- SolidarMed, Swiss Organization for Health in Africa, Maseru West, Lesotho
| | - Josephine Muhairwe
- SolidarMed, Swiss Organization for Health in Africa, Maseru West, Lesotho
| | | | - Katleho Tlali
- SolidarMed, Swiss Organization for Health in Africa, Maseru West, Lesotho
- Butha-Buthe Government Hospital, Butha-Buthe, Lesotho
| | - Moniek Bresser
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
| | - Fiona Vanobberghen
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
| | - Mathebe Kopo
- SolidarMed, Swiss Organization for Health in Africa, Maseru West, Lesotho
| | - Mpho Kao
- SolidarMed, Swiss Organization for Health in Africa, Maseru West, Lesotho
| | - Thomas Klimkait
- University of Basel, 4051 Basel, Switzerland
- Department of Biomedicine, University of Basel, 4051 Basel, Switzerland
| | - Manuel Battegay
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
| | - Niklaus Daniel Labhardt
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4051 Basel, Switzerland
| | - Tracy Renée Glass
- Clinical Research Unit, Department of Medicine, Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Switzerland
- University of Basel, 4051 Basel, Switzerland
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45
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Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nat Commun 2019; 10:3193. [PMID: 31324762 PMCID: PMC6642170 DOI: 10.1038/s41467-019-10884-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies. Here, Bachmann et al. provide data on long-term dynamics of the HIV-1 reservoir in 1,057 individuals on suppressive antiretroviral therapy and show that in 26.6% of individuals the reservoir increases. Viral blips and low-level viremia are significantly associated with a slower reservoir decay.
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Affiliation(s)
- Nadine Bachmann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Chantal von Siebenthal
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Valentina Vongrad
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Teja Turk
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Kathrin Neumann
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, 4057 Basel, Switzerland
| | | | - Jaques Fellay
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Yik Lim Kok
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Alessandro Borghesi
- School of Life Sciences, EPFL, 1015, Lausanne, Switzerland.,Neonatal Intensive Care Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, 27100, Italy
| | - Sonali Parbhoo
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Mario Wieser
- Department of Mathematics and Computer Science, University of Basel, 4001, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Matthieu Perreau
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Thomas Klimkait
- Division Infection Diagnostics, Department Biomedicine-Petersplatz, University of Basel, 4001, Basel, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases and Laboratory of Virology, University Hospital Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Battegay
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, 4031, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, University Hospital Bern, 3010, Bern, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital of St. Gallen, 9007, St. Gallen, Switzerland
| | - Enos Bernasconi
- Infectious Diseases Service, Regional Hospital, 6900, Lugano, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1015, Lausanne, Switzerland
| | - Roger D Kouyos
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland. .,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland.
| | - Karin J Metzner
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, 8091, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
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46
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Bertels F, Marzel A, Leventhal G, Mitov V, Fellay J, Günthard HF, Böni J, Yerly S, Klimkait T, Aubert V, Battegay M, Rauch A, Cavassini M, Calmy A, Bernasconi E, Schmid P, Scherrer AU, Müller V, Bonhoeffer S, Kouyos R, Regoes RR. Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity. Mol Biol Evol 2019; 35:27-37. [PMID: 29029206 PMCID: PMC5850767 DOI: 10.1093/molbev/msx246] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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] [Indexed: 01/10/2023] Open
Abstract
Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as “per-parasite pathogenicity”. Using viral load and CD4+ T-cell measures from 2014 HIV-1 subtype B-infected individuals enrolled in the Swiss HIV Cohort Study, we investigated if virulence—measured as the rate of decline of CD4+ T cells—and per-parasite pathogenicity are heritable from donor to recipient. We estimated heritability by donor–recipient regressions applied to 196 previously identified transmission pairs, and by phylogenetic mixed models applied to a phylogenetic tree inferred from HIV pol sequences. Regressing the CD4+ T-cell declines and per-parasite pathogenicities of the transmission pairs did not yield heritability estimates significantly different from zero. With the phylogenetic mixed model, however, our best estimate for the heritability of the CD4+ T-cell decline is 17% (5–30%), and that of the per-parasite pathogenicity is 17% (4–29%). Further, we confirm that the set-point viral load is heritable, and estimate a heritability of 29% (12–46%). Interestingly, the pattern of evolution of all these traits differs significantly from neutrality, and is most consistent with stabilizing selection for the set-point viral load, and with directional selection for the CD4+ T-cell decline and the per-parasite pathogenicity. Our analysis shows that the viral genotype affects virulence mainly by modulating the per-parasite pathogenicity, while the indirect effect via the set-point viral load is minor.
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Affiliation(s)
- Frederic Bertels
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Venelin Mitov
- Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Sabine Yerly
- Division of Infectious Diseases, Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, University Hospital Lausanne, Lausanne, Switzerland
| | - Alexandra Calmy
- HIV/AIDS Unit, Infectious Disease Service, Geneva University Hospital, Geneva, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - Alexandra U Scherrer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
| | | | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roland R Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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47
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Romette JL, Prat CM, Gould EA, de Lamballerie X, Charrel R, Coutard B, Fooks AR, Bardsley M, Carroll M, Drosten C, Drexler JF, Günther S, Klempa B, Pinschewer D, Klimkait T, Avsic-Zupanc T, Capobianchi MR, Dicaro A, Ippolito G, Nitsche A, Koopmans M, Reusken C, Gorbalenya A, Raoul H, Bourhy H, Mettenleiter T, Reiche S, Batten C, Sabeta C, Paweska JT, Eropkin M, Zverev V, Hu Z, Mac Cullough S, Mirazimi A, Pradel F, Lieutaud P. The European Virus Archive goes global: A growing resource for research. Antiviral Res 2018; 158:127-134. [PMID: 30059721 PMCID: PMC7127435 DOI: 10.1016/j.antiviral.2018.07.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/21/2018] [Accepted: 07/23/2018] [Indexed: 11/28/2022]
Abstract
The European Virus Archive (EVA) was created in 2008 with funding from the FP7-EU Infrastructure Programme, in response to the need for a coordinated and readily accessible collection of viruses that could be made available to academia, public health organisations and industry. Within three years, it developed from a consortium of nine European laboratories to encompass associated partners in Africa, Russia, China, Turkey, Germany and Italy. In 2014, the H2020 Research and Innovation Framework Programme (INFRAS projects) provided support for the transformation of the EVA from a European to a global organization (EVAg). The EVAg now operates as a non-profit consortium, with 26 partners and 20 associated partners from 21 EU and non-EU countries. In this paper, we outline the structure, management and goals of the EVAg, to bring to the attention of researchers the wealth of products it can provide and to illustrate how end-users can gain access to these resources. Organisations or individuals who would like to be considered as contributors are invited to contact the EVAg coordinator, Jean-Louis Romette, at jean-louis.romette@univmed.fr.
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Affiliation(s)
- J L Romette
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France.
| | - C M Prat
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - E A Gould
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - X de Lamballerie
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - R Charrel
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
| | - B Coutard
- Architectures et Fonctions, des Macromolécules, Biologiques, Marseille, France
| | - A R Fooks
- Animal and Plant Health Agency, Weybridge, United Kingdom
| | - M Bardsley
- Animal and Plant Health Agency, Weybridge, United Kingdom
| | - M Carroll
- Department of Health-Special Pathogens Laboratory, Porton Down, United Kingdom
| | - C Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - J F Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, 10117 Berlin, Germany
| | - S Günther
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - B Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - D Pinschewer
- Department of Pathology and Immunology, University of Bales, Switzerland
| | - T Klimkait
- Department of Pathology and Immunology, University of Bales, Switzerland
| | - T Avsic-Zupanc
- Institute of Microbiology and Immunology, Lubljana, Slovenia
| | | | - A Dicaro
- UOC, Istituto Nazionale Malattie Infettive Roma, Italy
| | - G Ippolito
- UOC, Istituto Nazionale Malattie Infettive Roma, Italy
| | - A Nitsche
- Robert Koch Institut, Berlin, Germany
| | - M Koopmans
- ERASMUS Medical Center, Rotterdam, The Netherlands
| | - C Reusken
- ERASMUS Medical Center, Rotterdam, The Netherlands
| | - A Gorbalenya
- Leiden University Medical Center, Leiden, The Netherlands
| | - H Raoul
- Laboratoire Merieux, INSERM, Lyon, France
| | | | - T Mettenleiter
- Friedrich Loeffler Institut, Greifswald-Insel Riems, Germany
| | - S Reiche
- Friedrich Loeffler Institut, Greifswald-Insel Riems, Germany
| | - C Batten
- The Pirbright Institute, Pirbright, United Kingdom
| | - C Sabeta
- Onderstepoort Veterinary Institute, Praetoria, South Africa
| | - J T Paweska
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - M Eropkin
- Research Institute of Influenza, St. Petersburg, Russia
| | - V Zverev
- Mechnikov Scientific Research Institute for Vaccines and Sera, Moscow, Russia
| | - Z Hu
- Wuhan Institute of Virology, Wuhan, China
| | - S Mac Cullough
- Australian Animal Health Laboratory, Geelong, Australia Disease, Johannesburg, South Africa
| | | | - F Pradel
- Fondation Mérieux, réseau GABRIEL, Lyon, France
| | - P Lieutaud
- Unite des Virus Emergents (UVE: Aix Marseille Univ, IRD 190, INSERM 1207, IHU Méditerranée Infection), Marseille, France
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48
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Kusejko K, Kadelka C, Marzel A, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD. Inferring the age difference in HIV transmission pairs by applying phylogenetic methods on the HIV transmission network of the Swiss HIV Cohort Study. Virus Evol 2018; 4:vey024. [PMID: 30250751 PMCID: PMC6143731 DOI: 10.1093/ve/vey024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [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] [Indexed: 11/19/2022] Open
Abstract
Age-mixing patterns are of key importance for understanding the dynamics of human
immunodeficiency virus (HIV)-epidemics and target public health interventions. We use the
densely sampled Swiss HIV Cohort Study (SHCS) resistance database to study the age
difference at infection in HIV transmission pairs using phylogenetic methods. In addition,
we investigate whether the mean age difference of pairs in the phylogenetic tree is
influenced by sampling as well as by additional distance thresholds for including pairs.
HIV-1 pol-sequences of 11,922 SHCS patients and approximately 240,000 Los
Alamos background sequences were used to build a phylogenetic tree. Using this tree, 100
per cent down to 1 per cent of the tips were sampled repeatedly to generate pruned trees
(N = 500 for each sample proportion), of which pairs of SHCS patients
were extracted. The mean of the absolute age differences of the pairs, measured as the
absolute difference of the birth years, was analyzed with respect to this sample
proportion and a distance criterion for inclusion of the pairs. In addition, the
transmission groups men having sex with men (MSM), intravenous drug users (IDU), and
heterosexuals (HET) were analyzed separately. Considering the tree with all 11,922 SHCS
patients, 2,991 pairs could be extracted, with 954 (31.9 per cent) MSM-pairs, 635 (21.2
per cent) HET-pairs, 414 (13.8 per cent) IDU-pairs, and 352 (11.8 per cent) HET/IDU-pairs.
For all transmission groups, the age difference at infection was significantly
(P < 0.001) smaller for pairs in the tree compared with randomly assigned pairs,
meaning that patients of similar age are more likely to be pairs. The mean age difference
in the phylogenetic analysis, using a fixed distance of 0.05, was 9.2, 9.0, 7.3 and
5.6 years for MSM-, HET-, HET/IDU-, and IDU-pairs, respectively. Decreasing the cophenetic
distance threshold from 0.05 to 0.01 significantly decreased the mean age difference.
Similarly, repeated sampling of 100 per cent down to 1 per cent of the tips revealed an
increased age difference at lower sample proportions. HIV-transmission is age-assortative,
but the age difference of transmission pairs detected by phylogenetic analyses depends on
both sampling proportion and distance criterion. The mean age difference decreases when
using more conservative distance thresholds, implying an underestimation of
age-assortativity when using liberal distance criteria. Similarly, overestimation of the
mean age difference occurs for pairs from sparsely sampled trees, as it is often the case
in sub-Saharan Africa.
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Affiliation(s)
- Katharina Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Claus Kadelka
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Alex Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Manuel Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Petersgraben 4, CH-4031 Basel; University of Basel, Petersplatz 1, Basel, Switzerland
| | - Enos Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Via Tesserete 46, Lugano, Switzerland
| | - Alexandra Calmy
- Laboratory of Virology and Division of Infectious Diseases, Genève University Hospital, Rue Gabrielle-Perret-Gentil 4, CH-1205 Genève; University of Genève, 24 rue du Général-Dufour, Genève, Switzerland
| | - Matthias Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Rue du Bugnon 46, Lausanne, Switzerland
| | - Matthias Hoffmann
- Division of Infectious Diseases, Cantonal Hospital St Gallen, Rorschacher Strasse 95, St. Gallen, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Sabine Yerly
- Laboratory of Virology and Division of Infectious Diseases, Genève University Hospital, Rue Gabrielle-Perret-Gentil 4, CH-1205 Genève; University of Genève, 24 rue du Général-Dufour, Genève, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department of Biomedicine, University of Basel, Petersplatz 10, Basel, Switzerland
| | - Matthieu Perreau
- Division of Infectious Diseases, Lausanne University Hospital, Rue du Bugnon 46, Lausanne, Switzerland
| | - Andri Rauch
- Clinic for Infectious Diseases, Bern University Hospital, Freiburgstrasse 18, Bern; University of Bern, Hochschulstrasse 6, CH-3012 Bern, Switzerland
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, Rämistrasse 100, Zürich, Switzerland.,Institute of Medical Virology, University of Zürich, Winterthurerstrasse 190, Zürich, Switzerland
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49
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Braun DL, Hampel B, Kouyos R, Nguyen H, Shah C, Flepp M, Stöckle M, Conen A, Béguelin C, Künzler-Heule P, Nicca D, Schmid P, Delaloye J, Rougemont M, Bernasconi E, Rauch A, Günthard HF, Böni J, Fehr JS, Anagnostopoulos A, Battegay M, B E, B J, B DL, Bucher HC, Calmy A, Cavassini M, Ciuffi A, Dollenmaier G, Egger M, Elzi L, F JS, Fellay J, Furrer H, Fux CA, G HF, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Huber M, Kahlert C, Kaiser L, Keiser O, Klimkait T, K R, Kovari H, Ledergerber B, Martinetti G, Martinez de Tejada B, Marzolini C, Metzner KJ, Müller N, N D, Paioni P, Pantaleo G, Perreau M, R A, Rudin C, Scherrer AU, S P, Speck R, S M, Tarr P, Trkola A, Vernazza P, Wandeler G, Weber R, Yerly S. High Cure Rates With Grazoprevir-Elbasvir With or Without Ribavirin Guided by Genotypic Resistance Testing Among Human Immunodeficiency Virus/Hepatitis C Virus–coinfected Men Who Have Sex With Men. Clin Infect Dis 2018; 68:569-576. [DOI: 10.1093/cid/ciy547] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022] Open
Affiliation(s)
- Dominique L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich
| | - Benjamin Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich
| | - Huyen Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
| | - Cyril Shah
- Institute of Medical Virology, University of Zurich
| | | | - Marcel Stöckle
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University of Basel
| | - Anna Conen
- Division of Infectious Diseases and Hospital Hygiene, Cantonal Hospital Aarau
| | - Charles Béguelin
- Department of Infectious Diseases, Bern University Hospital, University of Bern
| | | | - Dunja Nicca
- Institute of Nursing Science, University Hospital Basel, University of Basel
| | - Patrick Schmid
- Division of Infectious Diseases, Cantonal Hospital St Gallen
| | - Julie Delaloye
- Intensive Care Unit, Department of Intensive Care Medicine, University of Lausanne and University Hospital Center
| | | | | | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital, University of Bern
| | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Institute of Medical Virology, University of Zurich
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich
| | - Jan S Fehr
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Switzerland
- Department Public Health, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Switzerland
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50
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Kusejko K, Marzel A, Hampel B, Bachmann N, Nguyen H, Fehr J, Braun DL, Battegay M, Bernasconi E, Calmy A, Cavassini M, Hoffmann M, Böni J, Yerly S, Klimkait T, Perreau M, Rauch A, Günthard HF, Kouyos RD. Quantifying the drivers of HIV transmission and prevention in men who have sex with men: a population model-based analysis in Switzerland. HIV Med 2018; 19:688-697. [PMID: 30051600 DOI: 10.1111/hiv.12660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Despite the huge success of antiretroviral therapy (ART), there is an ongoing HIV epidemic among men who have sex with men (MSM) in resource-rich countries. Understanding the driving factors underlying this process is important for curbing the epidemic. METHODS We simulated the HIV epidemic in MSM in Switzerland by stratifying a mathematical model by CD4 count, the care cascade and condom use. The model was parametrised with clinical, epidemiological and behavioural data from the Swiss HIV Cohort Study and surveys in the HIV-negative population. RESULTS According to our model, 3.4% of the cases that would otherwise have occurred in 2008-2015 were prevented by early initiation of ART. Only 0.6% of the cases were attributable to a change in condom use in the HIV-positive population, as less usage is mainly seen in virally suppressed MSM. Most new infections were attributable to transmission from recently infected undiagnosed individuals. It was estimated that doubling the diagnosis rate would have resulted in 11.8% fewer cases in 2001-2015. Moreover, it was estimated that introducing pre-exposure prophylaxis (PrEP) for 50% of those MSM not using condoms with occasional partners would have resulted in 22.6% fewer cases in 2012-2015. CONCLUSIONS By combining observational data on the relevant epidemiological and clinical processes with a mathematical model, we showed that the 'test and treat' approach is most effective in reducing the number of new cases. Only a moderate population-level effect was estimated for early initiation of ART and a weak effect for the change in condom use of diagnosed MSM. Protecting HIV-negative individuals who are not using condoms with PrEP was shown to have a major impact.
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Affiliation(s)
- K Kusejko
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - A Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - B Hampel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - N Bachmann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - H Nguyen
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - J Fehr
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - D L Braun
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - M Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - E Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - A Calmy
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - M Cavassini
- Division of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - M Hoffmann
- Division of Infectious Diseases, Cantonal Hospital St Gallen, St Gallen, Switzerland
| | - J Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - S Yerly
- Laboratory of Virology and Division of Infectious Diseases, Geneva University Hospital, University of Geneva, Geneva, Switzerland
| | - T Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - M Perreau
- Division of Immunology and Allergy, University of Lausanne, Lausanne, Switzerland
| | - A Rauch
- Clinic for Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - H F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - R D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
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