Drivers of HIV-1 transmission: The Portuguese case
Autoři:
Andrea-Clemencia Pineda-Peña aff001; Marta Pingarilho aff001; Guangdi Li aff003; Bram Vrancken aff004; Pieter Libin aff004; Perpétua Gomes aff006; Ricardo Jorge Camacho aff004; Kristof Theys aff004; Ana Barroso Abecasis aff001;
Působiště autorů:
Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
aff001; Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC) and Basic Sciences Department, Universidad del Rosario, Bogotá, Colombia
aff002; Department of Metabolism and Endocrinology, Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, National Clinical Research Center for Metabolic Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
aff003; Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
aff004; Artificial Intelligence Lab, Department of Computer Science, Vrije Universiteit Brussel, Brussels, Belgium
aff005; Laboratório de Biologia Molecular (LMCBM, SPC, CHLO-HEM), Lisbon, Portugal
aff006; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz, Caparica, Portugal
aff007
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0218226
Souhrn
Background
Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines.
Methods
Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses.
Results
In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001).
Discussion
TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes.
Klíčová slova:
Antimicrobial resistance – Europe – HIV-1 – Phylogenetic analysis – Portugal – Portuguese people – Sequence analysis
Zdroje
1. European Centre for Disease Prevention and Control, World Health Organization. Regional Office for Europe. HIV/AIDS surveillance in Europe 2018. 2017 Data.
2. Cortes Martins H, Aldir I. Infeção VIH e SIDA: a situação em Portugal a 31 de dezembro de 2017 [Internet]. Lisboa: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP; 2018 Nov. Report No.: 149. Available: http://hdl.handle.net/10400.18/5666
3. Ragonnet-Cronin ML, Shilaih M, Günthard HF, Hodcroft EB, Böni J, Fearnhill E, et al. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland. Sci Rep. 2016;6: 32251. doi: 10.1038/srep32251 27642070
4. Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, et al. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol. 2016;2: vew010. doi: 10.1093/ve/vew010 27774303
5. Pineda-Peña A-C, Theys K, Stylianou DC, Demetriades I, SPREAD/ESAR Program, Abecasis AB, et al. HIV-1 Infection in Cyprus, the Eastern Mediterranean European Frontier: A Densely Sampled Transmission Dynamics Analysis from 1986 to 2012. Sci Rep. 2018;8: 1702. doi: 10.1038/s41598-017-19080-5 29374182
6. Pineda-Peña A-C, Schrooten Y, Vinken L, Ferreira F, Li G, Trovão NS, et al. Trends and predictors of transmitted drug resistance (TDR) and clusters with TDR in a local Belgian HIV-1 epidemic. PLoS ONE. 2014;9: e101738. doi: 10.1371/journal.pone.0101738 25003369
7. Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, et al. Social and Genetic Networks of HIV-1 Transmission in New York City. PLoS Pathog. 2017;13: e1006000. doi: 10.1371/journal.ppat.1006000 28068413
8. Conselho Científico do Programa Nacional para a Infeção VIH/SIDA. Recomendações Portuguesas para o tratamento da infeção por VIH-1 e VIH-2 (2016 versão 1.0). Programa Nacional para a Infeção VIH/SIDA;
9. EACS European AIDS Clinical Society. European Guidelines for treatment of HIV-positive adults in Europe version 9.1. [Internet]. European AIDS Clinical Society (EACS); 2018. Available: http://www.eacsociety.org
10. Wittkop L, Günthard HF, de Wolf F, Dunn D, Cozzi-Lepri A, de Luca A, et al. Effect of transmitted drug resistance on virological and immunological response to initial combination antiretroviral therapy for HIV (EuroCoord-CHAIN joint project): a European multicohort study. Lancet Infect Dis. 2011;11: 363–371. doi: 10.1016/S1473-3099(11)70032-9 21354861
11. Palma AC, Araújo F, Duque V, Borges F, Paixão MT, Camacho R, et al. Molecular epidemiology and prevalence of drug resistance-associated mutations in newly diagnosed HIV-1 patients in Portugal. Infect Genet Evol. 2007;7: 391–398. doi: 10.1016/j.meegid.2007.01.009 17360244
12. UNAIDS. Joint United Nations Programme on HIV/AIDS. Global AIDS Update 2018—Miles to Go: Closing Gaps, Breaking Barriers, Righting Injustices. 2018.
13. Ssemwanga D, Lihana RW, Ugoji C, Abimiku A, Nkengasong J, Dakum P, et al. Update on HIV-1 acquired and transmitted drug resistance in Africa. AIDS Rev. 2015;17: 3–20. 25427100
14. Abecasis AB, Wensing AMJ, Paraskevis D, Vercauteren J, Theys K, Van de Vijver DAMC, et al. HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics. Retrovirology. 2013;10: 7. doi: 10.1186/1742-4690-10-7 23317093
15. Esteves A, Parreira R, Venenno T, Franco M, Piedade J, Germano De Sousa J, et al. Molecular epidemiology of HIV type 1 infection in Portugal: high prevalence of non-B subtypes. AIDS Res Hum Retroviruses. 2002;18: 313–325. doi: 10.1089/088922202753519089 11897032
16. Libin P, Beheydt G, Deforche K, Imbrechts S, Ferreira F, Van Laethem K, et al. RegaDB: community-driven data management and analysis for infectious diseases. Bioinformatics. 2013;29: 1477–1480. doi: 10.1093/bioinformatics/btt162 23645815
17. Bennett DE, Camacho RJ, Otelea D, Kuritzkes DR, Fleury H, Kiuchi M, et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS ONE. 2009;4: e4724. doi: 10.1371/journal.pone.0004724 19266092
18. Alcantara LCJ, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, et al. A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res. 2009;37: W634–642. doi: 10.1093/nar/gkp455 19483099
19. Pineda-Peña A-C, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, et al. Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools. Infect Genet Evol. 2013;19: 337–348. doi: 10.1016/j.meegid.2013.04.032 23660484
20. Struck D, Lawyer G, Ternes A-M, Schmit J-C, Bercoff DP. COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification. Nucleic Acids Res. 2014;42: e144. doi: 10.1093/nar/gku739 25120265
21. Bártolo I, Abecasis AB, Borrego P, Barroso H, McCutchan F, Gomes P, et al. Origin and epidemiological history of HIV-1 CRF14_BG. PLoS ONE. 2011;6: e24130. doi: 10.1371/journal.pone.0024130 21969855
22. Kuiken C, Korber B, Shafer RW. HIV sequence databases. AIDS Rev. 2003;5: 52–61. 12875108
23. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32: 1792–1797. doi: 10.1093/nar/gkh340 15034147
24. Libin P, Deforche K, Abecasis AB, Theys K. VIRULIGN: fast codon-correct alignment and annotation of viral genomes. Bioinformatics. 2018; doi: 10.1093/bioinformatics/bty851 30295730
25. Ragonnet-Cronin M, Hodcroft E, Hué S, Fearnhill E, Delpech V, Brown AJL, et al. Automated analysis of phylogenetic clusters. BMC Bioinformatics. 2013;14: 317. doi: 10.1186/1471-2105-14-317 24191891
26. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 2012;29: 1969–1973. doi: 10.1093/molbev/mss075 22367748
27. Rambaut A, Lam TT, Max Carvalho L, Pybus OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2: vew007. doi: 10.1093/ve/vew007 27774300
28. Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 2013;30: 713–724. doi: 10.1093/molbev/mss265 23180580
29. Yebra G, Holguín A, Pillay D, Hué S. Phylogenetic and demographic characterization of HIV-1 transmission in Madrid, Spain. Infect Genet Evol. 2013;14: 232–239. doi: 10.1016/j.meegid.2012.12.006 23291408
30. Esteves A, Parreira R, Piedade J, Venenno T, Franco M, Germano de Sousa J, et al. Spreading of HIV-1 subtype G and envB/gagG recombinant strains among injecting drug users in Lisbon, Portugal. AIDS Res Hum Retroviruses. 2003;19: 511–517. doi: 10.1089/088922203766774568 12892060
31. Direção-Geral da Saúde. Programa diz não a uma seringa em segunda mão, Kit Prevenção. Programa Nacional para a Infeção VIH/SIDA; 2013.
32. Hofstra LM, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, et al. Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe. Clin Infect Dis. 2016;62: 655–663. doi: 10.1093/cid/civ963 26620652
33. Pingarilho M, Pineda-Peña A-C, Gomes P, Pimentel VF, Libin P, Theys K, et al. BEST HOPE—Cohort of newly diagnosed patients in Portugal. XI congresso nacional de VIH/SIDA e XIII congresso nacional de Doenças Infecciosas e Microbiologia clínica 2016; 2016; Coimbra, Portugal.
34. Brenner B, Wainberg MA, Roger M. Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions. AIDS. 2013;27: 1045–1057. doi: 10.1097/QAD.0b013e32835cffd9 23902920
Článek vyšel v časopise
PLOS One
2019 Číslo 9
- Jak a kdy u celiakie začíná reakce na lepek? Možnou odpověď poodkryla čerstvá kanadská studie
- Pomůže v budoucnu s triáží na pohotovostech umělá inteligence?
- Spermie, vajíčka a mozky – „jednohubky“ z výzkumu 2024/38
- Infekce se v Americe po příjezdu Kolumba šířily nesrovnatelně déle, než se traduje
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
Nejčtenější v tomto čísle
- Graviola (Annona muricata) attenuates behavioural alterations and testicular oxidative stress induced by streptozotocin in diabetic rats
- CH(II), a cerebroprotein hydrolysate, exhibits potential neuro-protective effect on Alzheimer’s disease
- Comparison between Aptima Assays (Hologic) and the Allplex STI Essential Assay (Seegene) for the diagnosis of Sexually transmitted infections
- Assessment of glucose-6-phosphate dehydrogenase activity using CareStart G6PD rapid diagnostic test and associated genetic variants in Plasmodium vivax malaria endemic setting in Mauritania
Zvyšte si kvalifikaci online z pohodlí domova
Všechny kurzy