21 results on '"Chaudron, Sandra E"'
Search Results
2. Impact of an electronic alert on prescription patterns of meropenem, voriconazole and caspofungin
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Chok, Lionel, Kusejko, Katharina, Eberhard, Nadia, Chaudron, Sandra E., Saleschus, Dirk, Kocher, Claudine, Kouyos, Roger D., Weber, Rainer, and Kuster, Stefan P.
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- 2021
- Full Text
- View/download PDF
3. Absence of Proviral Human Immunodeficiency Virus (HIV) Type 1 Evolution in Early-Treated Individuals With HIV Switching to Dolutegravir Monotherapy During 48 Weeks.
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Jörimann, Lisa, Tschumi, Jasmin, Zeeb, Marius, Leemann, Christine, Schenkel, Corinne D, Neumann, Kathrin, Chaudron, Sandra E, Zaheri, Maryam, Frischknecht, Paul, Neuner-Jehle, Nadia, Kuster, Herbert, Braun, Dominique L, Grube, Christina, Kouyos, Roger, Metzner, Karin J, Günthard, Huldrych F, and (SHCS), for the Swiss HIV Cohort Study
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HIV ,MONONUCLEAR leukocytes ,DOLUTEGRAVIR ,POLYMERASE chain reaction ,CLINICAL trials - Abstract
Human immunodeficiency virus type 1 (HIV-1) infection is treated with antiretroviral therapy (ART), usually consisting of 2–3 different drugs, referred to as combination ART (cART). Our recent randomized clinical trial comparing a switch to dolutegravir monotherapy with continuation of cART in early-treated individuals demonstrated sustained virological suppression over 48 weeks. Here, we characterize the longitudinal landscape of the HIV-1 reservoir in these participants, with particular attention to potential differences between treatment groups regarding evidence of evolution as a proxy for low-level replication. Near full-length HIV-1 proviral polymerase chain reaction and next-generation sequencing was applied to longitudinal peripheral blood mononuclear cell samples to assess proviral evolution and the potential emergence of drug resistance mutations (DRMs). Neither an increase in genetic distance nor diversity over time was detected in participants of both treatment groups. Single proviral analysis showed high proportions of defective proviruses and low DRM numbers. No evidence for evolution during dolutegravir monotherapy was found in these early-treated individuals. [ABSTRACT FROM AUTHOR]
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- 2023
- Full Text
- View/download PDF
4. HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected
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Nguyen, Huyen, Thorball, Christian W., Fellay, Jacques, Böni, Jürg, Yerly, Sabine, Perreau, Matthieu, Klimkait, Thomas, Kusejko, Katharina, Bachmann, Nadine, Chaudron, Sandra E., Paioni, Paolo, Thurnheer, Maria C., Battegay, Manuel, Cavassini, Matthias, Vernazza, Pietro, Bernasconi, Enos, Günthard, Huldrych F., and Kouyos, Roger
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- 2019
- Full Text
- View/download PDF
5. A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study
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Chaudron, Sandra E, Leemann, Christine, Kusejko, Katharina, Nguyen, Huyen, Tschumi, Nadine, Marzel, Alex, Huber, Michael, Böni, Jürg, Perreau, Matthieu, Klimkait, Thomas, Yerly, Sabine, Ramette, Alban, Hirsch, Hans H, Rauch, Andri, Calmy, Alexandra, Vernazza, Pietro, Bernasconi, Enos, Cavassini, Matthias, Metzner, Karin J, Kouyos, Roger D, Günthard, Huldrych F, and University of Zurich
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10028 Institute of Medical Virology ,10234 Clinic for Infectious Diseases ,2723 Immunology and Allergy ,610 Medicine & health ,2725 Infectious Diseases - Published
- 2022
6. The Interplay Between Replication Capacity of HIV-1 and Surrogate Markers of Disease
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Rindler, Audrey E, primary, Kusejko, Katharina, additional, Kuster, Herbert, additional, Neumann, Kathrin, additional, Leemann, Christine, additional, Zeeb, Marius, additional, Chaudron, Sandra E, additional, Braun, Dominique L, additional, Kouyos, Roger D, additional, Metzner, Karin J, additional, and Günthard, Huldrych F, additional
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- 2022
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7. Phylogenetic cluster analysis identifies virological and behavioral drivers of HIV transmission in MSM
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Bachmann, Nadine, Kusejko, Katharina, Nguyen, Huyen, Chaudron, Sandra E, Kadelka, Claus, Turk, Teja, Böni, Jürg, Perreau, Matthieu, Klimkait, Thomas, Yerly Ferrillo, Sabine, Battegay, Manuel, Rauch, Andri, Ramette, Alban, Vernazza, Pietro, Bernasconi, Enos, Cavassini, Matthias, Günthard, Huldrych F, Kouyos, Roger D, Swiss HIV Cohort Study, and University of Zurich
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ddc:616 ,Phylogenetics ,10028 Institute of Medical Virology ,10234 Clinic for Infectious Diseases ,drivers of transmission ,HIV transmission clusters ,610 Medicine & health ,MSM - Abstract
Identifying local outbreaks and their drivers is a key step towards curbing 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 ten years.
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- 2021
8. HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection
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Kok, Yik Lim, Vongrad, Valentina, Chaudron, Sandra E., Shilaih, Mohaned, Leemann, Christine, Neumann, Kathrin, Kusejko, Katharina, Di Giallonardo, Francesca, Kuster, Herbert, Braun, Dominique L., Kouyos, Roger D., Günthard, Huldrych F., Metzner, Karin J., University of Zurich, and Metzner, Karin J
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CD4-Positive T-Lymphocytes ,10028 Institute of Medical Virology ,Host Microbial Interactions ,Molecular biology ,Virus Integration ,T cells ,virus diseases ,HIV Infections ,610 Medicine & health ,2700 General Medicine ,Viral Load ,Lymphocyte Activation ,Virus Latency ,10234 Clinic for Infectious Diseases ,AIDS/HIV ,Antiretroviral Therapy, Highly Active ,Neoplasms ,Virology ,Disease Progression ,HIV-1 ,Humans ,Medicine ,Research Article ,Cell Proliferation - Abstract
HIV-1 is capable of integrating its genome into that of its host cell. We examined the influence of the activation state of CD4+ T cells, the effect of antiretroviral therapy (ART), and the clinical stage of HIV-1 infection on HIV-1 integration site features and selection. HIV-1 integration sites were sequenced from longitudinally sampled resting and activated CD4+ T cells from 12 HIV-1-infected individuals. In total, 589 unique HIV-1 integration sites were analyzed: 147, 391, and 51 during primary, chronic, and late presentation of HIV-1 infection, respectively. As early as during primary HIV-1 infection and independent of the activation state of CD4+ T cells collected on and off ART, HIV-1 integration sites were preferentially detected in recurrent integration genes, genes associated with clonal expansion of latently HIV-1-infected CD4+ T cells, cancer-related genes, and highly expressed genes. The preference for cancer-related genes was more pronounced at late stages of HIV-1 infection. Host genomic features of HIV-1 integration site selection remained stable during HIV-1 infection in both resting and activated CD4+ T cells. In summary, characteristic HIV-1 integration site features are preestablished as early as during primary HIV-1 infection and are found in both resting and activated CD4+ T cells.
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- 2021
9. 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
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Kusejko, Katharina, Marzel, Alex, Nguyen, Huyen, Chaudron, Sandra E, Bachmann, Nadine, Weber, Rainer, Bruggmann, Philip, Roth, Jan A, Bernasconi, Enos, Calmy, Alexandra, Cavassini, Matthias, Bregenzer, Andrea, Böni, Jürg, Yerly, Sabine, Klimkait, Thomas, Perreau, Matthieu, Walti, Laura N, Günthard, Huldrych F, Kouyos, Roger D, Swiss HIV Cohort Study, and University of Zurich
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10028 Institute of Medical Virology ,10234 Clinic for Infectious Diseases ,610 Medicine & health - Published
- 2020
10. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study.
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Ramirez, Jessy J Duran, Ballouz, Tala, Nguyen, Huyen, Kusejko, Katharina, Chaudron, Sandra E, Huber, Michael, Hirsch, Hans H, Perreau, Matthieu, Ramette, Alban, Yerly, Sabine, Cavassini, Matthias, Stöckle, Marcel, Furrer, Hansjakob, Vernazza, Pietro, Bernasconi, Enos, Günthard, Huldrych F, Kouyos, Roger D, Study, Swiss HIV Cohort, Duran Ramirez, Jessy J, and Swiss HIV Cohort Study
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PUBLIC health surveillance ,HIV ,MEN who have sex with men ,COHORT analysis ,MOLECULAR clusters - Abstract
Background: In Switzerland, HIV-1 transmission among men who have sex with men (MSM) has been dominated by subtype B, whilst non-B subtypes are commonly attributed to infections acquired abroad among heterosexuals. Here, we evaluated the temporal trends of non-B subtypes and the characteristics of molecular transmission clusters (MTCs) among MSM.Methods: Sociodemographic and clinical data and partial pol sequences were obtained from participants enrolled in the Swiss HIV Cohort Study. For non-B subtypes, maximum likelihood trees were constructed, from which Swiss MTCs were identified and analyzed by transmission group.Results: Non-B subtypes were identified in 8.1% (416/5116) of MSM participants. CRF01_AE was the most prevalent strain (3.5%), followed by subtype A (1.2%), F (1.1%), CRF02_AG (1.1%), C (0.9%), and G (0.3%). Between 1990 and 2019, an increase in the proportion of newly diagnosed individuals (0/123 [0%] to 11/32 [34%]) with non-B subtypes in MSM was found. Across all non-B subtypes, the majority of MSM MTCs were European. Larger MTCs were observed for MSM than heterosexuals.Conclusions: We found a substantial increase in HIV-1 non-B subtypes among MSM in Switzerland and the occurrence of large MTCs, highlighting the importance of molecular surveillance in guiding public health strategies targeting the HIV-1 epidemic. [ABSTRACT FROM AUTHOR]- Published
- 2022
- Full Text
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11. A systematic phylogenetic approach to study the interaction of HIV-1 with coinfections, non-communicable and opportunistic diseases
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Kusejko, Katharina, Bachmann, Nadine, Chaudron, Sandra E, Nguyen, Huyen, Braun, Dominique L, Hampel, Benjamin, Battegay, Manuel, Bernasconi, Enos, Calmy, Alexandra, Cavassini, Matthias, Hoffmann, Matthias, Böni, Jürg, Yerly, Sabine, Klimkait, Thomas, Perreau, Matthieu, Rauch, Andri, Günthard, Huldrych F, and Kouyos, Roger D
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610 Medicine & health - Abstract
To systematically test whether coinfections spread along the HIV-1 transmission network and whether similarities of 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's sarcoma, clustered significantly, suggesting transmission of these infections along the HIV-1 transmission network. The clustering of patients with neurocognitive complaints, however, 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 infectious conditions 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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- 2019
- Full Text
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12. Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of Human Immunodeficiency Virus Transmission in Men Who Have Sex With Men.
- Author
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Bachmann, Nadine, Kusejko, Katharina, Nguyen, Huyen, Chaudron, Sandra E, Kadelka, Claus, Turk, Teja, Böni, Jürg, Perreau, Matthieu, Klimkait, Thomas, Yerly, Sabine, Battegay, Manuel, Rauch, Andri, Ramette, Alban, Vernazza, Pietro, Bernasconi, Enos, Cavassini, Matthias, Günthard, Huldrych F, Kouyos, Roger D, and Study, Swiss HIV Cohort
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HIV infection epidemiology ,HIV infection transmission ,HIV infection risk factors ,DECISION trees ,DISEASE clusters ,PHYLOGENY ,REGRESSION analysis ,EPIDEMICS ,MEN who have sex with men ,CLUSTER analysis (Statistics) ,HIV ,POISSON distribution - 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. [ABSTRACT FROM AUTHOR]
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- 2021
- Full Text
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13. A Systematic Phylogenetic Approach to Study the Interaction of HIV-1 With Coinfections, Noncommunicable Diseases, and Opportunistic Diseases.
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Kusejko, Katharina, Bachmann, Nadine, Chaudron, Sandra E, Nguyen, Huyen, Braun, Dominique L, Hampel, Benjamin, Battegay, Manuel, Bernasconi, Enos, Calmy, Alexandra, Cavassini, Matthias, Hoffmann, Matthias, Böni, Jürg, Yerly, Sabine, Klimkait, Thomas, Perreau, Matthieu, Rauch, Andri, Günthard, Huldrych F, Kouyos, Roger D, Study, Swiss HIV Cohort, and Swiss HIV Cohort Study
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NON-communicable diseases ,SYPHILIS ,MEDICAL virology ,BONE densitometry ,ETIOLOGY of diseases ,DISEASES - 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. [ABSTRACT FROM AUTHOR]
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- 2019
- Full Text
- View/download PDF
14. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study
- Author
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Duran Ramirez, Jessy J, Ballouz, Tala, Nguyen, Huyen, Kusejko, Katharina, Chaudron, Sandra E, Huber, Michael, Hirsch, Hans H, Perreau, Matthieu, Ramette, Alban, Yerly, Sabine, Cavassini, Matthias, Stöckle, Marcel, Furrer, Hansjakob, Vernazza, Pietro, Bernasconi, Enos, Günthard, Huldrych F, Kouyos, Roger D, Aebi-Popp, K, Anagnostopoulos, A, Battegay, M, Bernasconi, E, Böni, J, Braun, D L, Bucher, H C, Calmy, A, Cavassini, M, Ciuffi, A, Dollenmaier, G, Egger, M, Elzi, L, Fehr, J, Fellay, J, Furrer, H, A Fux, C, Günthard, H F, Haerry, D, Hasse, B, Hirsch, H H, Hoffmann, M, Hösli, I, Huber, M, Kahlert, C R, Kaiser, L, Keiser, O, Klimkait, T, Kouyos, R D, Kovari, H, Kusejko, K, Ledergerber, B, Martinetti, G, Martinez de Tejada, B, Marzolini, C, Metzner, K J, Müller, N, Nicca, D, Paioni, P, Pantaleo, G, Perreau, M, Rauch, A, Rudin, C, Schmid, P, Speck, R, Stöckle, M, Tarr, P, Trkola, A, Vernazza, P, Wandeler, G, Weber, R, Yerly, S, and University of Zurich
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Adult ,Male ,10028 Institute of Medical Virology ,medicine.medical_specialty ,Maximum likelihood ,Human immunodeficiency virus (HIV) ,HIV Infections ,610 Medicine & health ,Newly diagnosed ,medicine.disease_cause ,Men who have sex with men ,Cohort Studies ,10234 Clinic for Infectious Diseases ,03 medical and health sciences ,0302 clinical medicine ,HIV Seropositivity ,medicine ,Disease Transmission, Infectious ,Immunology and Allergy ,Humans ,030212 general & internal medicine ,MSM ,Prospective Studies ,Homosexuality, Male ,Phylogeny ,030304 developmental biology ,ddc:616 ,0303 health sciences ,Molecular Epidemiology ,Molecular epidemiology ,Transmission (medicine) ,business.industry ,Public health ,virus diseases ,10060 Epidemiology, Biostatistics and Prevention Institute (EBPI) ,3. Good health ,Non-B subtypes ,Infectious Diseases ,HIV-1 ,570 Life sciences ,biology ,business ,Transmission cluster ,610 Medizin und Gesundheit ,Switzerland ,Demography ,Cohort study ,570 Biowissenschaften ,Biologie - Abstract
Background In Switzerland, HIV-1 transmission among men who have sex with men (MSM) has been dominated by subtype B, whilst non-B subtypes are commonly attributed to infections acquired abroad among heterosexuals. Here, we evaluated the temporal trends of non-B subtypes and the characteristics of molecular transmission clusters (MTCs) among MSM. Methods Sociodemographic and clinical data and partial pol sequences were obtained from participants enrolled in the Swiss HIV Cohort Study. For non-B subtypes, maximum likelihood trees were constructed, from which Swiss MTCs were identified and analyzed by transmission group. Results Non-B subtypes were identified in 8.1% (416/5116) of MSM participants. CRF01_AE was the most prevalent strain (3.5%), followed by subtype A (1.2%), F (1.1%), CRF02_AG (1.1%), C (0.9%), and G (0.3%). Between 1990 and 2019, an increase in the proportion of newly diagnosed individuals (0/123 [0%] to 11/32 [34%]) with non-B subtypes in MSM was found. Across all non-B subtypes, the majority of MSM MTCs were European. Larger MTCs were observed for MSM than heterosexuals. Conclusions We found a substantial increase in HIV-1 non-B subtypes among MSM in Switzerland and the occurrence of large MTCs, highlighting the importance of molecular surveillance in guiding public health strategies targeting the HIV-1 epidemic.
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15. Phylogenetic Cluster Analysis Identifies Virological and Behavioral Drivers of HIV Transmission in MSM
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Bachmann, Nadine, Kusejko, Katharina, Nguyen, Huyen, Chaudron, Sandra E, Kadelka, Claus, Turk, Teja, Böni, Jürg, Perreau, Matthieu, Klimkait, Thomas, Yerly, Sabine, Battegay, Manuel, Rauch, Andri, Ramette, Alban, Vernazza, Pietro, Bernasconi, Enos, Cavassini, Matthias, Günthard, Huldrych F, and Kouyos, Roger D
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570 Life sciences ,biology ,610 Medicine & health - Abstract
BACKGROUND Identifying local outbreaks and their drivers is a key step towards curbing 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 ten years. METHODS Using the comprehensive Swiss HIV Cohort Study and its drug-resistance database, we reconstructed phylogenetic trees for each year between 2007-2017. 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 non-growing clusters (p≤0.01). 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 eight years, while the behavioral risk score was significantly associated with per-capita incidence of MSM transmission clusters in three 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 highlight a relative shift from diagnosed to undiagnosed individuals as drivers of HIV transmission in Swiss MSM.
- Full Text
- View/download PDF
16. HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected
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Huyen Nguyen, Thorball, Christian W., Fellay, Jacques, Boni, Jurg, Yerly, Sabine, Perreau, Matthieu, Klimkait, Thomas, Kusejko, Katharina, Bachmann, Nadine, Chaudron, Sandra E., Paioni, Paolo, Thurnheer, Maria C., Battegay, Manuel, Cavassini, Matthias, Vernazza, Pietro, Bernasconi, Enos, Gunthard, Huldrych F., Kouyos, Roger, Anagnostopoulos, A., Braun, D. L., Bucher, H. C., Calmy, A., Ciuffi, A., Dollenmaier, G., Egger, M., Elzi, L., Fehr, J., Furrer, H., Fux, C. A., Haerry, D., Hasse, B., Hirsch, H. H., Hoffmann, M., Hosli, I., Huber, M., Kahlert, C., Kaiser, L., Keiser, O., Kouyos, R. D., Kovari, H., Ledergerber, B., Martinetti, G., de Tejada, B. Martinez, Marzolini, C., Metzner, K. J., Mueller, N., Nicca, D., Pantaleo, G., Rauch, A., Rudin, C., Scherrer, A. U., Schmid, P., Speck, R., Stockle, M., Tarr, P., Trkola, A., Wandeler, G., and Weber, R.
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concordance ,immune control ,transmission chains ,association ,virus diseases ,determinants ,restriction ,t-cell responses ,escape mutations ,hla ,coevolution ,evolution ,class-i ,mate choice - Abstract
Background: HIV's capacity to escape immune recognition by human leukocyte antigen (HLA) is a core component of HIV pathogenesis. A better understanding of the distribution of HLA class I in HIV-infected patients would improve our knowledge of pathogenesis in relation to the host HLA type and could better improve therapeutic strategies against HIV., Materials and Methods: Three hundred one to 325 transmission pairs and 469-496 clusters were identified for analysis among Swiss HIV Cohort Study (SHCS) participants using HIV pol sequences from the drug resistance database. HLA class I data were compiled at 3 specificity levels: 4-digit, 2-digit alleles, and HLA-B supertype. The analysis tabulated HLA-I homogeneity as 2 measures: the proportion of transmission pairs, which are HLA concordant, and the average percentage of allele matches within all clusters. These measures were compared with the mean value across randomizations with randomly assorted individuals., Results: We repeated the analysis for different HLA classification levels and separately for HLA-A,-B, and-C. Subanalyses by the risk group were performed for HLA-B. HLA-B showed significantly greater homogeneity in the transmission chains (2-digit clusters: 0.291 vs. 0.251, P value = 0.009; supertype clusters: 0.659 vs. 0.611, P value = 0.002; supertype pairs: 0.655 vs. 0.608, P value = 0.014). Risk group restriction caused the effect to disappear for men-who-have-sexwith- men but not for other risk groups. We also examined if protective HLA alleles B27 and B57 were under-or overrepresented in the transmission chains, although this yielded no significant pattern., Conclusions: The HLA-B alleles of patients within HIV-1 transmission chains segregate in homogenous clusters/pairs, potentially indicating preferential transmission among HLA-B concordant individuals.
17. A Systematic Molecular Epidemiology Screen Reveals Numerous Human Immunodeficiency Virus (HIV) Type 1 Superinfections in the Swiss HIV Cohort Study.
- Author
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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, and Günthard HF
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- Cohort Studies, Humans, Molecular Epidemiology, Phylogeny, Switzerland epidemiology, HIV Infections, HIV-1, Superinfection epidemiology, Vaccines
- 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., Competing Interests: Potential conflicts of interest. The institution of E. B. received fees for E. B. participation in advisory boards and travel grants from Gilead Sciences, MSD, ViiV Healthcare, Pfizer, AbbVie, and Sandoz. K. J. M. has received advisory board honoraria from Gilead Sciences; has received travel grants and honoraria from Gilead Sciences, Roche Diagnostics, GlaxoSmithKline, Merck Sharp & Dohme, Bristol-Myers Squibb, ViiV, and Abbott; the University of Zurich received research grants from Gilead Science, Novartis, Roche, and Merck Sharp & Dohme for studies for which K. J. M. serves as principal investigator. H. F. G. has received unrestricted research grants from Gilead Sciences and Roche; fees for data and safety monitoring board membership from Merck; consulting/advisory board membership fees from Gilead Sciences, Merck, and ViiV Healthcare; and grants from SystemsX, and the National Institutes of Health. The institution of H. F. G. received educational grants from Gilead Sciences, ViiV, MSD, AbbVie, and Sandoz. All other authors report no potential conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2022
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18. Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics.
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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, and Kouyos RD
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- Austria epidemiology, Cluster Analysis, Cohort Studies, Homosexuality, Male, Humans, Male, Phylogeny, Switzerland epidemiology, Epidemics, HIV Infections drug therapy, HIV Seropositivity epidemiology, HIV-1 genetics, Sexual and Gender Minorities, Substance Abuse, Intravenous epidemiology
- 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., Competing Interests: The authors have no conflicts of interest to disclose., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)
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- 2022
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19. Increasing Frequency and Transmission of HIV-1 Non-B Subtypes Among Men Who Have Sex With Men in the Swiss HIV Cohort Study.
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Duran Ramirez JJ, Ballouz T, Nguyen H, Kusejko K, Chaudron SE, Huber M, Hirsch HH, Perreau M, Ramette A, Yerly S, Cavassini M, Stöckle M, Furrer H, Vernazza P, Bernasconi E, Günthard HF, and Kouyos RD
- Subjects
- Adult, Cohort Studies, Disease Transmission, Infectious, HIV Seropositivity epidemiology, HIV-1 genetics, HIV-1 isolation & purification, Humans, Male, Molecular Epidemiology, Phylogeny, Prospective Studies, Switzerland epidemiology, HIV Infections epidemiology, HIV Infections transmission, HIV Infections virology, HIV-1 classification, Homosexuality, Male statistics & numerical data
- Abstract
Background: In Switzerland, HIV-1 transmission among men who have sex with men (MSM) has been dominated by subtype B, whilst non-B subtypes are commonly attributed to infections acquired abroad among heterosexuals. Here, we evaluated the temporal trends of non-B subtypes and the characteristics of molecular transmission clusters (MTCs) among MSM., Methods: Sociodemographic and clinical data and partial pol sequences were obtained from participants enrolled in the Swiss HIV Cohort Study. For non-B subtypes, maximum likelihood trees were constructed, from which Swiss MTCs were identified and analyzed by transmission group., Results: Non-B subtypes were identified in 8.1% (416/5116) of MSM participants. CRF01_AE was the most prevalent strain (3.5%), followed by subtype A (1.2%), F (1.1%), CRF02_AG (1.1%), C (0.9%), and G (0.3%). Between 1990 and 2019, an increase in the proportion of newly diagnosed individuals (0/123 [0%] to 11/32 [34%]) with non-B subtypes in MSM was found. Across all non-B subtypes, the majority of MSM MTCs were European. Larger MTCs were observed for MSM than heterosexuals., Conclusions: We found a substantial increase in HIV-1 non-B subtypes among MSM in Switzerland and the occurrence of large MTCs, highlighting the importance of molecular surveillance in guiding public health strategies targeting the HIV-1 epidemic., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)
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- 2022
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20. 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.
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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, and Kouyos RD
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- Female, HIV Infections complications, HIV Infections etiology, HIV Long-Term Survivors statistics & numerical data, Humans, Male, Middle Aged, Prospective Studies, Psychology, Substance Abuse, Intravenous complications, Switzerland, Emotional Adjustment, HIV Infections psychology, HIV Long-Term Survivors psychology, Substance Abuse, Intravenous psychology
- 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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- 2020
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21. HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected.
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Nguyen H, Thorball CW, Fellay J, Böni J, Yerly S, Perreau M, Klimkait T, Kusejko K, Bachmann N, Chaudron SE, Paioni P, Thurnheer MC, Battegay M, Cavassini M, Vernazza P, Bernasconi E, Günthard HF, and Kouyos R
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- Humans, Switzerland epidemiology, Genetic Predisposition to Disease, HIV Infections genetics, HIV Infections transmission, HLA-A Antigens genetics, HLA-B Antigens genetics, HLA-C Antigens genetics
- Abstract
Background: HIV's capacity to escape immune recognition by human leukocyte antigen (HLA) is a core component of HIV pathogenesis. A better understanding of the distribution of HLA class I in HIV-infected patients would improve our knowledge of pathogenesis in relation to the host HLA type and could better improve therapeutic strategies against HIV., Materials and Methods: Three hundred one to 325 transmission pairs and 469-496 clusters were identified for analysis among Swiss HIV Cohort Study (SHCS) participants using HIV pol sequences from the drug resistance database. HLA class I data were compiled at 3 specificity levels: 4-digit, 2-digit alleles, and HLA-B supertype. The analysis tabulated HLA-I homogeneity as 2 measures: the proportion of transmission pairs, which are HLA concordant, and the average percentage of allele matches within all clusters. These measures were compared with the mean value across randomizations with randomly assorted individuals., Results: We repeated the analysis for different HLA classification levels and separately for HLA-A, -B, and -C. Subanalyses by the risk group were performed for HLA-B. HLA-B showed significantly greater homogeneity in the transmission chains (2-digit clusters: 0.291 vs. 0.251, P value = 0.009; supertype clusters: 0.659 vs. 0.611, P value = 0.002; supertype pairs: 0.655 vs. 0.608, P value = 0.014). Risk group restriction caused the effect to disappear for men-who-have-sex-with-men but not for other risk groups. We also examined if protective HLA alleles B27 and B57 were under- or overrepresented in the transmission chains, although this yielded no significant pattern., Conclusions: The HLA-B alleles of patients within HIV-1 transmission chains segregate in homogenous clusters/pairs, potentially indicating preferential transmission among HLA-B concordant individuals.
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- 2019
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