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Avila-Rios S, García-Morales C, Reyes-Terán G, González-Rodríguez A, Matías-Florentino M, Mehta SR, Chaillon A. Phylodynamics of HIV in the Mexico City Metropolitan Region. J Virol 2022; 96:e0070822. [PMID: 35762759 PMCID: PMC9327710 DOI: 10.1128/jvi.00708-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/06/2022] [Indexed: 12/30/2022] Open
Abstract
Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.
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Affiliation(s)
- Santiago Avila-Rios
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Claudia García-Morales
- Center for Research in Infectious Diseases, National Institute of Respiratory Diseases, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the National Institutes of Health and High Specialty Hospitals, Ministry of Health, Mexico City, Mexico
| | | | | | - Sanjay R. Mehta
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
- Veterans Affairs Health System, San Diego, California, USA
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California, San Diego, San Diego, California, USA
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Olafsson S, Fridriksdottir RH, Love TJ, Tyrfingsson T, Runarsdottir V, Hansdottir I, Bergmann OM, Björnsson ES, Johannsson B, Sigurdardottir B, Löve A, Baldvinsdottir GE, Hernandez UB, Gudnason T, Heimisdottir M, Hellard M, Gottfredsson M. Cascade of care during the first 36 months of the treatment as prevention for hepatitis C (TraP HepC) programme in Iceland: a population-based study. Lancet Gastroenterol Hepatol 2021; 6:628-637. [PMID: 34171267 DOI: 10.1016/s2468-1253(21)00137-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND WHO has set targets to eliminate hepatitis C virus (HCV) infection as a global health threat by 2030 through a 65% reduction in HCV-related deaths and 80% reduction in HCV incidence. To achieve these goals, WHO set service coverage targets of 90% of the infected population being diagnosed and 80% of eligible patients being treated. In February, 2016, Iceland initiated a nationwide HCV elimination programme known as treatment as prevention for hepatitis C (TraP HepC), which aimed to maximise diagnosis and treatment access. This analysis reports on the HCV cascade of care in the first 3 years of the programme. METHODS This population-based study was done between Feb 10, 2016, and Feb 10, 2019. Participants aged 18 years or older with permanent residence in Iceland and PCR-confirmed HCV were offered direct-acting antiviral (DAA) therapy. The programme used a multidisciplinary team approach in which people who inject drugs were prioritised. Nationwide awareness campaigns, improved access to testing, and harm reduction services were scaled up simultaneously. The number of infected people in the national HCV registry was used in combination with multiple other data sources, including screening of low-risk groups and high-risk groups, to estimate the total number of HCV infections. The number of people diagnosed, linked to care, initiated on treatment, and cured were recorded during the study. This study is registered with ClinicalTrials.gov, NCT02647879. FINDINGS In February, 2016, at the onset of the programme, 760 (95% CI 690-851) individuals were estimated to have HCV infection, with 75 (95% CI 6-166) individuals undiagnosed. 682 individuals were confirmed to be HCV PCR positive. Over the next 3 years, 183 new infections (including 42 reinfections) were diagnosed, for a total of 865 infections in 823 individuals. It was estimated that more than 90% of all domestic HCV infections had been diagnosed as early as January, 2017. During the 3 years, 824 (95·3%) of diagnosed infections were linked to care, and treatment was initiated for 795 (96·5%) of infections linked to care. Cure was achieved for 717 (90·2%) of 795 infections. INTERPRETATION By using a multidisciplinary public health approach, involving tight integration with addiction treatment services, the core service coverage targets for 2030 set by WHO have been reached. These achievements position Iceland to be among the first nations to subsequently achieve the WHO goal of eliminating HCV as a public health threat. FUNDING The Icelandic Government and Gilead Sciences.
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Affiliation(s)
- Sigurdur Olafsson
- Department of Gastroenterology and Hepatology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland.
| | - Ragnheidur H Fridriksdottir
- Department of Gastroenterology and Hepatology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Thorvardur J Love
- Department of Science, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | | | | | - Ingunn Hansdottir
- Faculty of Psychology, School of Health Sciences, University of Iceland, Reykjavík, Iceland; SAA National Center for Addiction Medicine, Reykjavik, Iceland
| | - Ottar M Bergmann
- Department of Gastroenterology and Hepatology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Einar S Björnsson
- Department of Gastroenterology and Hepatology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Birgir Johannsson
- Department of Infectious Diseases, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Bryndis Sigurdardottir
- Department of Infectious Diseases, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Arthur Löve
- Department of Virology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland
| | - Gudrun E Baldvinsdottir
- Department of Virology, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | - Ubaldo Benitez Hernandez
- Department of Science, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Maria Heimisdottir
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland; Icelandic Health Insurance, Reykjavik, Iceland
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia; Department of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia
| | - Magnus Gottfredsson
- Department of Infectious Diseases, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Science, Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavík, Iceland
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Chaillon A, Smith DM. Phylogenetic analyses of SARS-CoV-2 B.1.1.7 lineage suggest a single origin followed by multiple exportation events versus convergent evolution. Clin Infect Dis 2021; 73:2314-2317. [PMID: 33772259 PMCID: PMC8083653 DOI: 10.1093/cid/ciab265] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/21/2022] Open
Abstract
The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) herald a new phase of the pandemic. This study used state-of-the-art phylodynamic methods to ascertain that the rapid rise of B.1.1.7 “Variant of Concern” most likely occurred by global dispersal rather than convergent evolution from multiple sources.
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Affiliation(s)
- A Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA, USA
| | - D M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA, USA
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Vrancken B, Zhao B, Li X, Han X, Liu H, Zhao J, Zhong P, Lin Y, Zai J, Liu M, Smith DM, Dellicour S, Chaillon A. Comparative Circulation Dynamics of the Five Main HIV Types in China. J Virol 2020; 94:e00683-20. [PMID: 32938762 PMCID: PMC7654276 DOI: 10.1128/jvi.00683-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/02/2020] [Indexed: 01/17/2023] Open
Abstract
The HIV epidemic in China accounts for 3% of the global HIV incidence. We compared the patterns and determinants of interprovincial spread of the five most prevalent circulating types. HIV pol sequences sampled across China were used to identify relevant transmission networks of the five most relevant HIV-1 types (B and circulating recombinant forms [CRFs] CRF01_AE, CRF07_BC, CRF08_BC, and CRF55_01B) in China. From these, the dispersal history across provinces was inferred. A generalized linear model (GLM) was used to test the association between migration rates among provinces and several measures of human mobility. A total of 10,707 sequences were collected between 2004 and 2017 across 26 provinces, among which 1,962 are newly reported here. A mean of 18 (minimum and maximum, 1 and 54) independent transmission networks involving up to 17 provinces were identified. Discrete phylogeographic analysis largely recapitulates the documented spread of the HIV types, which in turn, mirrors within-China population migration flows to a large extent. In line with the different spatiotemporal spread dynamics, the identified drivers thereof were also heterogeneous but are consistent with a central role of human mobility. The comparative analysis of the dispersal dynamics of the five main HIV types circulating in China suggests a key role of large population centers and developed transportation infrastructures as hubs of HIV dispersal. This advocates for coordinated public health efforts in addition to local targeted interventions.IMPORTANCE While traditional epidemiological studies are of great interest in describing the dynamics of epidemics, they struggle to fully capture the geospatial dynamics and factors driving the dispersal of pathogens like HIV as they have difficulties capturing linkages between infections. To overcome this, we used a discrete phylogeographic approach coupled to a generalized linear model extension to characterize the dynamics and drivers of the across-province spread of the five main HIV types circulating in China. Our results indicate that large urbanized areas with dense populations and developed transportation infrastructures are facilitators of HIV dispersal throughout China and highlight the need to consider harmonized country-wide public policies to control local HIV epidemics.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Bin Zhao
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xingguang Li
- Department of Hospital Office, The First People's Hospital of Fangchenggang, Fangchenggang, China
| | - Xiaoxu Han
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haizhou Liu
- Centre for Emerging Infectious Diseases, The State Key Laboratory of Virology, Wuhan Institute of Virology, University of Chinese Academy of Sciences, Wuhan, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Yi Lin
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention; Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Junjie Zai
- Immunology innovation Team, School of Medicine, Ningbo University, Ningbo, Zhejiang China
| | - Mingchen Liu
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, USA
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Vrancken B, Mehta SR, Ávila-Ríos S, García-Morales C, Tapia-Trejo D, Reyes-Terán G, Navarro-Álvarez S, Little SJ, Hoenigl M, Pines HA, Patterson T, Strathdee SA, Smith DM, Dellicour S, Chaillon A. Dynamics and Dispersal of Local HIV Epidemics Within San Diego and Across The San Diego-Tijuana Border. Clin Infect Dis 2020; 73:e2018-e2025. [PMID: 33079188 DOI: 10.1093/cid/ciaa1588] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Evolutionary analyses of well-annotated HIV sequence data can provide insights into viral transmission patterns and associated factors. Here, we explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) - Tijuana (Mexico) border region to identify factors that could help guide public health policy. METHODS HIV pol sequences were collected from people with HIV in San Diego County and from Tijuana between 1996-2018. A multistep phylogenetic approach was used to characterize the dynamics of spread. The contribution of geospatial factors and HIV risk group to the local dynamics were evaluated. RESULTS Phylogeographic analyses of the 2,034 sequences revealed an important contribution of local transmission in sustaining the epidemic, as well as a complex viral migration network across the region. Geospatial viral dispersal between San Diego communities occurred predominantly among men-who-have-sex with-men with central San Diego being the main source (34.9%) and recipient (39.5%) of migration events. HIV migration was more frequent from San Diego county towards Tijuana than vice versa. Migrations were best explained by driving time between locations. CONCLUSION The US-Mexico border may not be a major barrier to the spread of HIV, which may stimulate coordinated transnational intervention approaches. Whereas a focus on central San Diego has the potential to avert most spread, the substantial viral migration independent of central San Diego shows that county-wide efforts will be more effective. Combined, this work shows that epidemiological information gleaned from pathogen genomes can uncover mechanisms that underlie sustained spread and, in turn, can be a building block of public health decision making.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Herestraat, Leuven, Belgium
| | - Sanjay R Mehta
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Daniela Tapia-Trejo
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan, Colonia Sección XVI, CP, Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Coordinating Commission of the Mexican National Institutes of Health, Periférico Sur, Arenal Tepepan, Mexico City, Mexico
| | | | - Susan J Little
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Martin Hoenigl
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Heather A Pines
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Thomas Patterson
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Computational and Evolutionary Virology, KU Leuven, Herestraat, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, av. FD Roosevelt, Bruxelles, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, CA
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Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses 2020; 12:v12020182. [PMID: 32033422 PMCID: PMC7077180 DOI: 10.3390/v12020182] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.
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Affiliation(s)
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Correspondence:
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA;
| | - David R. Hillyard
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA;
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
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