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Nascimento FF, Mehta SR, Little SJ, Volz EM. Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology. AIDS 2024; 38:865-873. [PMID: 38126363 PMCID: PMC10994139 DOI: 10.1097/qad.0000000000003820] [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: 03/07/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data. METHODS We simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively. RESULTS Consensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network. CONCLUSION Source attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.
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Affiliation(s)
- Fabrícia F. Nascimento
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Sanjay R. Mehta
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | - Susan J. Little
- Division of Infectious Diseases, University of California San Diego, San Diego, CA, USA
| | - Erik M. Volz
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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2
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Stadelman-Behar AM, Gehre MN, Atallah L, Clarke T, Leonso AA, Jojola F, Zheng H, Jia H, Lyss SB, Switzer WM, Grytdal SP, Durham M, Salas NM, Sievers M, Smelser C. Investigation of Presumptive HIV Transmission Associated with Receipt of Platelet-Rich Plasma Microneedling Facials at a Spa Among Former Spa Clients - New Mexico, 2018-2023. MMWR. MORBIDITY AND MORTALITY WEEKLY REPORT 2024; 73:372-376. [PMID: 38662678 PMCID: PMC11065465 DOI: 10.15585/mmwr.mm7316a3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
HIV transmitted through cosmetic injection services via contaminated blood has not been previously documented. During summer 2018, the New Mexico Department of Health (NMDOH) was notified of a diagnosis of HIV infection in a woman with no known HIV risk factors who reported exposure to needles from cosmetic platelet-rich plasma microneedling facials (vampire facials) received at a spa in spring 2018. An investigation of the spa's services began in summer 2018, and NMDOH and CDC identified four former spa clients, and one sexual partner of a spa client, all of whom received HIV infection diagnoses during 2018-2023, despite low reported behavioral risks associated with HIV acquisition. Nucleotide sequence analysis revealed highly similar HIV strains among all cases. Although transmission of HIV via unsterile injection practices is a known risk, determining novel routes of HIV transmission among persons with no known HIV risk factors is important. This investigation identified an HIV cluster associated with receipt of cosmetic injection services at an unlicensed facility that did not follow recommended infection control procedures or maintain client records. Requiring adequate infection control practices and maintenance of client records at spa facilities offering cosmetic injection services can help prevent the transmission of HIV and other bloodborne pathogens and ensure adequate traceback and notification in the event of adverse clinical outcomes, respectively.
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3
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Csete J, Elliott R, Bernard EJ. So many harms, so little benefit: a global review of the history and harms of HIV criminalisation. Lancet HIV 2023; 10:e52-e61. [PMID: 36202138 DOI: 10.1016/s2352-3018(22)00248-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/07/2022]
Abstract
Since the early years of HIV, many jurisdictions have criminalised HIV non-disclosure, potential or perceived exposure, and transmission. Many of these laws and prosecutions are without a scientific basis and reflect an inaccurate understanding of HIV-related risk and harm. Numerous studies of HIV criminal prosecutions show that women, sex workers, racial minorities, gay and bisexual men, transgender people, immigrants, and Indigenous people are disproportionately charged and convicted, often resulting in long custodial sentences. Data from molecular HIV surveillance, used to track HIV outbreaks in marginalised populations, are prone to be misused in HIV criminal cases. Scientific consensus statements and international standards have helped to guide advocacy to repeal or reform a number of these laws, resulting in fewer prosecutions in some jurisdictions. Many successful reform efforts have been led by people living with HIV and are notable at a moment of reckoning on racism and inequality in global health.
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Affiliation(s)
- Joanne Csete
- Department of Population and Family Health, Columbia University Mailman School of Public Health, New York, NY, USA.
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4
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Chao E, Chato C, Vender R, Olabode AS, Ferreira RC, Poon AFY. Molecular source attribution. PLoS Comput Biol 2022; 18:e1010649. [PMID: 36395093 PMCID: PMC9671344 DOI: 10.1371/journal.pcbi.1010649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Elisa Chao
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Reid Vender
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- School of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- * E-mail:
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5
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Gussler JW, Campo DS, Dimitrova Z, Skums P, Khudyakov Y. Primary case inference in viral outbreaks through analysis of intra-host variant population. BMC Bioinformatics 2022; 23:62. [PMID: 35135469 PMCID: PMC8822801 DOI: 10.1186/s12859-022-04585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Investigation of outbreaks to identify the primary case is crucial for the interruption and prevention of transmission of infectious diseases. These individuals may have a higher risk of participating in near future transmission events when compared to the other patients in the outbreak, so directing more transmission prevention resources towards these individuals is a priority. Although the genetic characterization of intra-host viral populations can aid the identification of transmission clusters, it is not trivial to determine the directionality of transmissions during outbreaks, owing to complexity of viral evolution. Here, we present a new computational framework, PYCIVO: primary case inference in viral outbreaks. This framework expands upon our earlier work in development of QUENTIN, which builds a probabilistic disease transmission tree based on simulation of evolution of intra-host hepatitis C virus (HCV) variants between cases involved in direct transmission during an outbreak. PYCIVO improves upon QUENTIN by also adding a custom heterogeneity index and identifying the scenario when the primary case may have not been sampled. Results These approaches were validated using a set of 105 sequence samples from 11 distinct HCV transmission clusters identified during outbreak investigations, in which the primary case was epidemiologically verified. Both models can detect the correct primary case in 9 out of 11 transmission clusters (81.8%). However, while QUENTIN issues erroneous predictions on the remaining 2 transmission clusters, PYCIVO issues a null output for these clusters, giving it an effective prediction accuracy of 100%. To further evaluate accuracy of the inference, we created 10 modified transmission clusters in which the primary case had been removed. In this scenario, PYCIVO was able to correctly identify that there was no primary case in 8/10 (80%) of these modified clusters. This model was validated with HCV; however, this approach may be applicable to other microbial pathogens. Conclusions PYCIVO improves upon QUENTIN by also implementing a custom heterogeneity index which empowers PYCIVO to make the important ‘No primary case’ prediction. One or more samples, possibly including the primary case, may have not been sampled, and this designation is meant to account for these scenarios.
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Affiliation(s)
- J Walker Gussler
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30333, USA.,Department of Computer Science, Georgia State University, 1 Park Place NE, Atlanta, GA, 30303, USA
| | - David S Campo
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30333, USA.
| | - Zoya Dimitrova
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30333, USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, 1 Park Place NE, Atlanta, GA, 30303, USA
| | - Yury Khudyakov
- Centers for Disease Control and Prevention, 1600 Clifton Rd, Atlanta, GA, 30333, USA
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6
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Zhang J, Fan Q, Luo M, Yao J, Pan X, Li X. Phylogenetic evidence of HIV-1 transmission linkage between two men who have sex with men. Virol J 2021; 18:106. [PMID: 34059082 PMCID: PMC8166102 DOI: 10.1186/s12985-021-01573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
Background In China, an HIV-infected man (complainant; P2) alleged that another man (defendant; P1) had unlawfully infected him with HIV through unprotected homosexual contact in 2018. Methods We employed epidemiological, serological and phylogenetic analyses to investigate the transmission linkage between two men who have sex with men (MSM). Partial segments of three HIV-1 gene regions (gag, pol, and env) were amplified and sequenced by cloning. Maximum-likelihood (ML) and Bayesian methods were used to determine the direction and estimate the timing of transmission. Local control sequences and database control sequences were also used in the phylogenetic analysis. Results It indicated that P2 underwent HIV seroconversion after P1 was diagnosed as HIV positive. The time to the most recent common ancestor (tMRCA) estimates consistently showed that P1 most likely became HIV-1 infected at an earlier date than P2. P1 and P2 were infected with the same HIV-1 CRF01_AE subtype according to segments of all three gene regions (gag, pol, and env). All three genetic regions of P1 have been subject to more potential selective forces than those of P2, indicating a longer evolutionary history. Bayesian and ML trees showed similar paraphyletic-monophyletic topologies of gag and env, with the virus from P1 located at the root, which supported a P1-to-P2 transmission direction. Conclusions Phylogenetic investigations can elucidate HIV transmission linkage and might empower its use in the opposition of the intentional transmission of HIV-1 as a forensic tool.
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Affiliation(s)
- Jiafeng Zhang
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399, Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Qin Fan
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399, Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Mingyu Luo
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399, Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Jiaming Yao
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399, Binsheng Road, Hangzhou, 310051, Zhejiang, China
| | - Xiaohong Pan
- Department of HIV/AIDS & STD Control and Prevention, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399, Binsheng Road, Hangzhou, 310051, Zhejiang, China.
| | - Xingguang Li
- Department of Technology R&D, Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, Zhejiang, China.
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7
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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] [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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8
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Bernard EJ, McClelland A, Cardell B, Chung C, Castro-Bojorquez M, French M, Hursey D, Khanna N, Minalga MB, Spieldenner A, Strub S. We Are People, Not Clusters! THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:1-4. [PMID: 32945744 DOI: 10.1080/15265161.2020.1809550] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
| | | | - Barb Cardell
- Colorado Organizations and Individuals Responding to HIV/AIDS
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9
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Rose R, Hall M, Redd AD, Lamers S, Barbier AE, Porcella SF, Hudelson SE, Piwowar-Manning E, McCauley M, Gamble T, Wilson EA, Kumwenda J, Hosseinipour MC, Hakim JG, Kumarasamy N, Chariyalertsak S, Pilotto JH, Grinsztejn B, Mills LA, Makhema J, Santos BR, Chen YQ, Quinn TC, Fraser C, Cohen MS, Eshleman SH, Laeyendecker O. Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort. J Infect Dis 2019; 220:1406-1413. [PMID: 30590741 PMCID: PMC6761953 DOI: 10.1093/infdis/jiy734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission. METHODS For 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the partner) were closest to the root. DoT was also assessed using maximum parsimony to infer ancestral node states for 100 bootstrap trees. RESULTS DoT was predicted correctly for both single-pair and subtype-specific trees in 22 pairs (67%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples. CONCLUSIONS Phylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.
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Affiliation(s)
| | - Matthew Hall
- Big Data Institute, University of Oxford, United Kingdom
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | - Sarah E Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Marybeth McCauley
- Science Facilitation Department, Durham, Chapel Hill, North Carolina
| | - Theresa Gamble
- Science Facilitation Department, Durham, Chapel Hill, North Carolina
| | - Ethan A Wilson
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, Washington
| | | | - Mina C Hosseinipour
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | - Jose H Pilotto
- Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
- Laboratorio de AIDS e Imunologia Molecular (IOC/Fiocruz), Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-INI-Fiocruz, Rio de Janeiro, Brazil
| | - Lisa A Mills
- Centers for Disease Control and Prevention (CDC) Division of HIV/AIDS Prevention/KEMRI–CDC Research and Public Health Collaboration HIV Research Branch, Kisumu, Kenya
| | | | - Breno R Santos
- Servico de Infectologia, Hospital Nossa Senhora da Conceicao/GHC, Porto Alegre, Brazil
| | - Ying Q Chen
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, Washington
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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10
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Ciccozzi M, Lai A, Zehender G, Borsetti A, Cella E, Ciotti M, Sagnelli E, Sagnelli C, Angeletti S. The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review. J Med Virol 2019; 91:1707-1724. [PMID: 31243773 DOI: 10.1002/jmv.25526] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022]
Abstract
In the last decade, the phylogenetic approach is recurrent in molecular evolutionary analysis. On 12 May, 2019, about 2 296 213 papers are found, but typing "phylogeny" or "epidemiology AND phylogeny" only 199 804 and 20 133 are retrieved, respectively. Molecular epidemiology in infectious diseases is widely used to define the source of infection as so as the ancestral relationships of individuals sampled from a population. Coalescent theory and phylogeographic analysis have had scientific application in several, recent pandemic events, and nosocomial outbreaks. Hepatitis viruses and immunodeficiency virus (human immunodeficiency virus) have been largely studied. Phylogenetic analysis has been recently applied on Polyomaviruses so as in the more recent outbreaks due to different arboviruses type as Zika and chikungunya viruses discovering the source of infection and the geographic spread. Data on sequences isolated by the microorganism are essential to apply the phylogenetic tools and research in the field of infectious disease phylodinamics is growing up. There is the need to apply molecular phylogenetic and evolutionary methods in areas out of infectious diseases, as translational genomics and personalized medicine. Lastly, the application of these tools in vaccine strategy so as in antibiotic and antiviral researchers are encouraged.
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Affiliation(s)
- Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, Roma, Italy
| | - Eleonora Cella
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marco Ciotti
- Laboratory of Molecular Virology, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
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11
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Coltart CEM, Hoppe A, Parker M, Dawson L, Amon JJ, Simwinga M, Geller G, Henderson G, Laeyendecker O, Tucker JD, Eba P, Novitsky V, Vandamme AM, Seeley J, Dallabetta G, Harling G, Grabowski MK, Godfrey-Faussett P, Fraser C, Cohen MS, Pillay D. Ethical considerations in global HIV phylogenetic research. Lancet HIV 2018; 5:e656-e666. [PMID: 30174214 PMCID: PMC7327184 DOI: 10.1016/s2352-3018(18)30134-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/28/2018] [Accepted: 06/06/2018] [Indexed: 01/01/2023]
Abstract
Phylogenetic analysis of pathogens is an increasingly powerful way to reduce the spread of epidemics, including HIV. As a result, phylogenetic approaches are becoming embedded in public health and research programmes, as well as outbreak responses, presenting unique ethical, legal, and social issues that are not adequately addressed by existing bioethics literature. We formed a multidisciplinary working group to explore the ethical issues arising from the design of, conduct in, and use of results from HIV phylogenetic studies, and to propose recommendations to minimise the associated risks to both individuals and groups. We identified eight key ethical domains, within which we highlighted factors that make HIV phylogenetic research unique. In this Review, we endeavoured to provide a framework to assist researchers, public health practitioners, and funding institutions to ensure that HIV phylogenetic studies are designed, done, and disseminated in an ethical manner. Our conclusions also have broader relevance for pathogen phylogenetics.
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Affiliation(s)
| | - Anne Hoppe
- Division of Infection and Immunity, University College London, London, UK.
| | - Michael Parker
- The Wellcome Centre for Ethics and Humanities (Ethox), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liza Dawson
- Division of AIDS, National Institutes of Health, Bethesda, MD, USA
| | - Joseph J Amon
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | | | - Gail Geller
- Berman Institute of Bioethics and School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Gail Henderson
- Center for Genomics and Society, Department of Social Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Oliver Laeyendecker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph D Tucker
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Patrick Eba
- Community Support, Social Justice and Inclusion Department, Geneva, Switzerland; School of Law, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Vladimir Novitsky
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven-University of Leuven, Leuven, Belgium; Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Janet Seeley
- Africa Health Research Institute, KwaZulu-Natal, South Africa; Department of Global Health and Development, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Guy Harling
- Institute for Global Health, University College London, London, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - M Kate Grabowski
- Department of Pathology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Rakai Community Cohort Study, Rakai Health Sciences Program, Kalisizo, Uganda
| | - Peter Godfrey-Faussett
- Joint United Nations Programme on HIV/AIDS, Geneva, Switzerland; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Myron S Cohen
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA; Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, KwaZulu-Natal, South Africa
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12
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Leitner T, Romero-Severson E. Phylogenetic patterns recover known HIV epidemiological relationships and reveal common transmission of multiple variants. Nat Microbiol 2018; 3:983-988. [PMID: 30061758 PMCID: PMC6442454 DOI: 10.1038/s41564-018-0204-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/22/2018] [Indexed: 11/09/2022]
Abstract
The growth of human immunodeficiency virus (HIV) sequence databases resulting from drug resistance testing has motivated efforts using phylogenetic methods to assess how HIV spreads1-4. Such inference is potentially both powerful and useful for tracking the epidemiology of HIV and the allocation of resources to prevention campaigns. We recently used simulation and a small number of illustrative cases to show that certain phylogenetic patterns are associated with different types of epidemiological linkage5. Our original approach was later generalized for large next-generation sequencing datasets and implemented as a free computational pipeline6. Previous work has claimed that direction and directness of transmission could not be established from phylogeny because one could not be sure that there were no intervening or missing links involved7-9. Here, we address this issue by investigating phylogenetic patterns from 272 previously identified HIV transmission chains with 955 transmission pairs representing diverse geography, risk groups, subtypes, and genomic regions. These HIV transmissions had known linkage based on epidemiological information such as partner studies, mother-to-child transmission, pairs identified by contact tracing, and criminal cases. We show that the resulting phylogeny inferred from real HIV genetic sequences indeed reveals distinct patterns associated with direct transmission contra transmissions from a common source. Thus, our results establish how to interpret phylogenetic trees based on HIV sequences when tracking who-infected-whom, when and how genetic information can be used for improved tracking of HIV spread. We also investigate limitations that stem from limited sampling and genetic time-trends in the donor and recipient HIV populations.
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Affiliation(s)
- Thomas Leitner
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - Ethan Romero-Severson
- Theoretical Biology and Biophysics Group, MS K710, Los Alamos National Laboratory, Los Alamos, NM, USA
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13
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Barré‐Sinoussi F, Abdool Karim SS, Albert J, Bekker L, Beyrer C, Cahn P, Calmy A, Grinsztejn B, Grulich A, Kamarulzaman A, Kumarasamy N, Loutfy MR, El Filali KM, Mboup S, Montaner JSG, Munderi P, Pokrovsky V, Vandamme A, Young B, Godfrey‐Faussett P. Expert consensus statement on the science of HIV in the context of criminal law. J Int AIDS Soc 2018; 21:e25161. [PMID: 30044059 PMCID: PMC6058263 DOI: 10.1002/jia2.25161] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 06/21/2018] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Globally, prosecutions for non-disclosure, exposure or transmission of HIV frequently relate to sexual activity, biting, or spitting. This includes instances in which no harm was intended, HIV transmission did not occur, and HIV transmission was extremely unlikely or not possible. This suggests prosecutions are not always guided by the best available scientific and medical evidence. DISCUSSION Twenty scientists from regions across the world developed this Expert Consensus Statement to address the use of HIV science by the criminal justice system. A detailed analysis of the best available scientific and medical research data on HIV transmission, treatment effectiveness and forensic phylogenetic evidence was performed and described so it may be better understood in criminal law contexts. Description of the possibility of HIV transmission was limited to acts most often at issue in criminal cases. The possibility of HIV transmission during a single, specific act was positioned along a continuum of risk, noting that the possibility of HIV transmission varies according to a range of intersecting factors including viral load, condom use, and other risk reduction practices. Current evidence suggests the possibility of HIV transmission during a single episode of sex, biting or spitting ranges from no possibility to low possibility. Further research considered the positive health impact of modern antiretroviral therapies that have improved the life expectancy of most people living with HIV to a point similar to their HIV-negative counterparts, transforming HIV infection into a chronic, manageable health condition. Lastly, consideration of the use of scientific evidence in court found that phylogenetic analysis alone cannot prove beyond reasonable doubt that one person infected another although it can be used to exonerate a defendant. CONCLUSIONS The application of up-to-date scientific evidence in criminal cases has the potential to limit unjust prosecutions and convictions. The authors recommend that caution be exercised when considering prosecution, and encourage governments and those working in legal and judicial systems to pay close attention to the significant advances in HIV science that have occurred over the last three decades to ensure current scientific knowledge informs application of the law in cases related to HIV.
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Affiliation(s)
| | - Salim S Abdool Karim
- Mailman School of Public HealthColumbia UniversityNew YorkNYUSA
- Centre for the AIDS Program of Research in South AfricaUniversity of KwaZulu‐NatalDurbanSouth Africa
- Weill Medical CollegeCornell UniversityNew YorkNYUSA
| | - Jan Albert
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Linda‐Gail Bekker
- Institute of Infectious Disease and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
| | - Chris Beyrer
- Department of EpidemiologyCenter for AIDS Research and Center for Public Health and Human RightsJohn Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
| | - Pedro Cahn
- Infectious Diseases UnitJuan A. Fernandez Hospital Buenos AiresCABAArgentina
- Buenos Aires University Medical SchoolBuenos AiresArgentina
- Fundación HuéspedBuenos AiresArgentina
| | - Alexandra Calmy
- Infectious DiseasesGeneva University HospitalGenevaSwitzerland
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas‐FiocruzFiocruz, Rio de JaneiroBrazil
| | - Andrew Grulich
- Kirby InstituteUniversity of New South WalesSydneyNSWAustralia
| | | | | | - Mona R Loutfy
- Women's College Research InstituteTorontoCanada
- Women's College HospitalTorontoCanada
- Department of MedicineUniversity of TorontoTorontoCanada
| | - Kamal M El Filali
- Infectious Diseases UnitIbn Rochd Universtiy HospitalCasablancaMorocco
| | - Souleymane Mboup
- Institut de Recherche en Santéde Surveillance Epidemiologique et de FormationsDakarSenegal
| | - Julio SG Montaner
- Faculty of MedicineUniversity of British ColumbiaVancouverCanada
- BC Centre for Excellence in HIV/AIDSVancouverCanada
| | - Paula Munderi
- International Association of Providers of AIDS CareKampalaUganda
| | - Vadim Pokrovsky
- Russian Peoples’ Friendship University (RUDN‐ University)MoscowRussian Federation
- Central Research Institute of EpidemiologyFederal Service on Customers’ Rights Protection and Human Well‐being SurveillanceMoscowRussian Federation
| | - Anne‐Mieke Vandamme
- KU LeuvenDepartment of Microbiology and ImmunologyRega Institute for Medical Research, Clinical and Epidemiological VirologyLeuvenBelgium
- Center for Global Health and Tropical MedicineUnidade de MicrobiologiaInstituto de Higiene e Medicina TropicalUniversidade Nova de LisboaLisbonPortugal
| | - Benjamin Young
- International Association of Providers of AIDS CareWashingtonDCUSA
| | - Peter Godfrey‐Faussett
- UNAIDSGenevaSwitzerland
- Department of Infectious and Tropical DiseasesLondon School of Hygiene and Tropical MedicineLondonEngland
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14
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Saigal P, Weait M, Poulton M. Criminalisation of HIV transmission: an overview for clinicians. Sex Transm Infect 2018; 94:399-400. [PMID: 29720386 DOI: 10.1136/sextrans-2017-053456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/14/2018] [Accepted: 04/04/2018] [Indexed: 11/03/2022] Open
Affiliation(s)
- Priyanka Saigal
- Department of Sexual Health and HIV, King's College Hospital, London, UK
| | - Matthew Weait
- Faculty of Humanities and Social Sciences, University of Portsmouth, Portsmouth, UK
| | - Mary Poulton
- Department of Sexual Health and HIV, King's College Hospital, London, UK
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15
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Abstract
: Because HIV is a fast-evolving virus, HIV genomic sequences of several individuals can be used to investigate whether they belong to a transmission network. Since the infamous 'Florida dentist case' in the beginning of the 1990s, phylogenetic analyses has been recurrently used in court settings as a forensic tool in HIV transmission investigations, for example cases where one or more complainants allege that a defendant has unlawfully infected them with HIV. Such cases can arise both in the context of HIV-specific criminal laws - in countries where transmission of HIV infection is specifically criminalized - or in the context of general laws, for example, by applying physical or sexual assault laws to HIV-related cases. Although phylogenetic analysis as a forensic technique for HIV transmission investigations has become common in several countries, the methodologies have not yet been standardized, sometimes giving rise to unwarranted conclusions. In this literature review, we revisit HIV court case investigations published in the scientific literature, as well as the methodological aspects important for the application and standardization of phylogenetic analyses methods as a forensic tool. Phylogenetic methodologies are improving quickly, such that more recently, phylogenetic relatedness, directionality of transmission and timing of nodes in the tree are used to assess whether the phylogenetic transmission analysis is consistent with or contradicting the charges. We find that there has been a lack of consistency between methods used in court case investigations and that it is essential to define guidelines to be used by phylogenetic forensic experts in HIV transmission cases in court.
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16
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Campbell EM, Jia H, Shankar A, Hanson D, Luo W, Masciotra S, Owen SM, Oster AM, Galang RR, Spiller MW, Blosser SJ, Chapman E, Roseberry JC, Gentry J, Pontones P, Duwve J, Peyrani P, Kagan RM, Whitcomb JM, Peters PJ, Heneine W, Brooks JT, Switzer WM. Detailed Transmission Network Analysis of a Large Opiate-Driven Outbreak of HIV Infection in the United States. J Infect Dis 2017; 216:1053-1062. [PMID: 29029156 PMCID: PMC5853229 DOI: 10.1093/infdis/jix307] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/27/2017] [Indexed: 11/13/2022] Open
Abstract
In January 2015, an outbreak of undiagnosed human immunodeficiency virus (HIV) infections among persons who inject drugs (PWID) was recognized in rural Indiana. By September 2016, 205 persons in this community of approximately 4400 had received a diagnosis of HIV infection. We report results of new approaches to analyzing epidemiologic and laboratory data to understand transmission during this outbreak. HIV genetic distances were calculated using the polymerase region. Networks were generated using data about reported high-risk contacts, viral genetic similarity, and their most parsimonious combinations. Sample collection dates and recency assay results were used to infer dates of infection. Epidemiologic and laboratory data each generated large and dense networks. Integration of these data revealed subgroups with epidemiologic and genetic commonalities, one of which appeared to contain the earliest infections. Predicted infection dates suggest that transmission began in 2011, underwent explosive growth in mid-2014, and slowed after the declaration of a public health emergency. Results from this phylodynamic analysis suggest that the majority of infections had likely already occurred when the investigation began and that early transmission may have been associated with sexual activity and injection drug use. Early and sustained efforts are needed to detect infections and prevent or interrupt rapid transmission within networks of uninfected PWID.
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Affiliation(s)
- Ellsworth M Campbell
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Hongwei Jia
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anupama Shankar
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Debra Hanson
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Wei Luo
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Silvina Masciotra
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - S Michele Owen
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alexandra M Oster
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Romeo R Galang
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael W Spiller
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | | | | | | | - Joan Duwve
- Indiana State Department of Health, Indianapolis
- Indiana University Richard M. Fairbanks School of Public Health, Indianapolis
| | - Paula Peyrani
- Division of Infectious Diseases, University of Louisville, Kentucky
| | | | | | - Philip J Peters
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Walid Heneine
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John T Brooks
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - William M Switzer
- Division of HIV/AIDS Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
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17
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Bachmann N, Turk T, Kadelka C, Marzel A, Shilaih M, Böni J, Aubert V, Klimkait T, Leventhal GE, Günthard HF, Kouyos R. Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup. Retrovirology 2017; 14:33. [PMID: 28535768 PMCID: PMC5442860 DOI: 10.1186/s12977-017-0356-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/15/2017] [Indexed: 12/01/2022] Open
Abstract
Background Parent-offspring (PO) regression is a central tool to determine the heritability of phenotypic traits; i.e., the relative extent to which those traits are controlled by genetic factors. The applicability of PO regression to viral traits is unclear because the direction of viral transmission—who is the donor (parent) and who is the recipient (offspring)—is typically unknown and viral phylogenies are sparsely sampled. Methods We assessed the applicability of PO regression in a realistic setting using Ornstein–Uhlenbeck simulated data on phylogenies built from 11,442 Swiss HIV Cohort Study (SHCS) partial pol sequences and set-point viral load (SPVL) data from 3293 patients. Results We found that the misidentification of donor and recipient plays a minor role in estimating heritability and showed that sparse sampling does not influence the mean heritability estimated by PO regression. A mixed-effect model approach yielded the same heritability as PO regression but could be extended to clusters of size greater than 2 and allowed for the correction of confounding effects. Finally, we used both methods to estimate SPVL heritability in the SHCS. We employed a wide range of transmission pair criteria to measure heritability and found a strong dependence of the heritability estimates to these criteria. For the most conservative genetic distance criteria, for which heritability estimates are conceptually expected to be closest to true heritability, we found estimates ranging from 32 to 46% across different bootstrap criteria. For less conservative distance criteria, we found estimates ranging down to 8%. All estimates did not change substantially after adjusting for host-demographic factors in the mixed-effect model (±2%). Conclusions For conservative transmission pair criteria, both PO regression and mixed-effect models are flexible and robust tools to estimate the contribution of viral genetic effects to viral traits under real-world settings. Overall, we find a strong effect of viral genetics on SPVL that is not confounded by host demographics. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0356-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nadine Bachmann
- 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
| | - Claus Kadelka
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alex Marzel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Mohaned Shilaih
- Department 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
| | - Vincent Aubert
- Divisions of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - Thomas Klimkait
- Molecular Virology, Department Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - Gabriel E Leventhal
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, USA
| | - Huldrych F Günthard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Roger Kouyos
- 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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18
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Marzel A, Shilaih M, Turk T, Campbell NK, Yang WL, Böni J, Yerly S, Klimkait T, Aubert V, Furrer H, Calmy A, Battegay M, Cavassini M, Bernasconi E, Schmid P, Metzner KJ, Günthard HF, Kouyos RD. Mining for pairs: shared clinic visit dates identify steady HIV-positive partnerships. HIV Med 2017; 18:667-676. [PMID: 28378387 DOI: 10.1111/hiv.12507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES Here we examined the hypothesis that some stable HIV-infected partnerships can be found in cohort studies, as the patients frequently attend the clinic visits together. METHODS Using mathematical approximations and shuffling to derive the probabilities of sharing a given number of visits by chance, we identified and validated couples that may represent either transmission pairs or serosorting couples in a stable relationship. RESULTS We analysed 434 432 visits for 16 139 Swiss HIV Cohort Study patients from 1990 to 2014. For 89 pairs, the number of shared visits exceeded the number expected. Of these, 33 transmission pairs were confirmed on the basis of three criteria: an extensive phylogenetic tree, a self-reported steady HIV-positive partnership, and risk group affiliation. Notably, 12 of the validated transmission pairs (36%; 12 of 33) were of a mixed ethnicity with a large median age gap [17.5 years; interquartile range (IQR) 11.8-22 years] and these patients harboured HIV-1 of predominantly non-B subtypes, suggesting imported infections. CONCLUSIONS In the context of the surge in research interest in HIV transmission pairs, this simple method widens the horizons of research on within-pair quasi-species exchange, transmitted drug resistance and viral recombination at the biological level and targeted prevention at the public health level.
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Affiliation(s)
- A Marzel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - M Shilaih
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - T Turk
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - N K Campbell
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - W-L Yang
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - J Böni
- Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - S Yerly
- Laboratory of Virology, Geneva University Hospital, Geneva, Switzerland
| | - T Klimkait
- Molecular Virology, Department of Biomedicine-Petersplatz, University of Basel, Basel, Switzerland
| | - V Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, Lausanne, Switzerland
| | - H Furrer
- Department of Infectious Diseases, Berne University Hospital and University of Berne, Berne, Switzerland
| | - A Calmy
- Division of Infectious Diseases, Geneva University Hospital, Geneva, Switzerland
| | - M Battegay
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - M Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, Lausanne, Switzerland
| | - E Bernasconi
- Division of Infectious Diseases, Regional Hospital Lugano, Lugano, Switzerland
| | - P Schmid
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital, St. Gallen, Switzerland
| | - K J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - H F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - R D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, Swiss National Center for Retroviruses, University of Zurich, Zurich, Switzerland
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19
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Harsono D, Galletly CL, O'Keefe E, Lazzarini Z. Criminalization of HIV Exposure: A Review of Empirical Studies in the United States. AIDS Behav 2017; 21:27-50. [PMID: 27605364 PMCID: PMC5218970 DOI: 10.1007/s10461-016-1540-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This review of literature identifies and describes US empirical studies on the criminalization of HIV exposure, examines findings on key questions about these laws, highlights knowledge gaps, and sets a course for future research. Studies published between 1990 and 2014 were identified through key word searches of relevant electronic databases and discussions with experts. Twenty-five empirical studies were identified. Sixteen of these studies used quantitative methods with more than half of these being cross-sectional survey studies. Study samples included male and female HIV-positive persons, HIV-positive and -negative men who have sex with men, public health personnel, and medical providers. Research questions addressed awareness of and attitudes toward HIV exposure laws, potential influences of these laws on seropositive status disclosure for persons living with HIV, HIV testing for HIV-negative persons, safer sex practices for both groups, and associations between HIV exposure laws and HIV-related stigma. Surveys of the laws and studies of enforcement practices were also conducted. Attention should be shifted from examining attitudes about these laws to exploring their potential influence on public health practices and behaviors related to the HIV continuum of care. Studies examining enforcement and prosecution practices are also needed. Adapting a theoretical framework in future research may be useful in better understanding the influence of HIV exposure laws on HIV risk behaviors.
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Affiliation(s)
- Dini Harsono
- Center for Interdisciplinary Research on AIDS, Yale University, 135 College Street, Suite 200, New Haven, CT, 06510, USA.
| | - Carol L Galletly
- Center for AIDS Intervention Research, Medical College of Wisconsin, 2071 North Summit Avenue, Milwaukee, WI, 53202, USA
| | - Elaine O'Keefe
- Center for Interdisciplinary Research on AIDS, Yale University, 135 College Street, Suite 200, New Haven, CT, 06510, USA
| | - Zita Lazzarini
- Department of Community Medicine and Health Care, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
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20
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Siljic M, Salemovic D, Cirkovic V, Pesic-Pavlovic I, Ranin J, Todorovic M, Nikolic S, Jevtovic D, Stanojevic M. Forensic application of phylogenetic analyses - Exploration of suspected HIV-1 transmission case. Forensic Sci Int Genet 2016; 27:100-105. [PMID: 28024238 DOI: 10.1016/j.fsigen.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 12/05/2016] [Accepted: 12/18/2016] [Indexed: 11/28/2022]
Abstract
Transmission of human immunodeficiency virus (HIV) between individuals may have important legal implications and therefore may come to require forensic investigation based upon phylogenetic analysis. In criminal trials results of phylogenetic analyses have been used as evidence of responsibility for HIV transmission. In Serbia, as in many countries worldwide, exposure and deliberate transmission of HIV are criminalized. We present the results of applying state of the art phylogenetic analyses, based on pol and env genetic sequences, in exploration of suspected HIV transmission among three subjects: a man and two women, with presumed assumption of transmission direction from one woman to a man. Phylogenetic methods included relevant neighbor-joining (NJ), maximum likelihood (ML) and Bayesian methods of phylogenetic trees reconstruction and hypothesis testing, that has been shown to be the most sensitive for the reconstruction of epidemiological links mostly from sexually infected individuals. End-point limiting-dilution PCR (EPLD-PCR) assay, generating the minimum of 10 sequences per genetic region per subject, was performed to assess HIV quasispecies distribution and to explore the direction of HIV transmission between three subjects. Phylogenetic analysis revealed that the viral sequences from the three subjects were more genetically related to each other than to other strains circulating in the same area with the similar epidemiological profile, forming strongly supported transmission chain, which could be in favour of a priori hypothesis of one of the women infecting the man. However, in the EPLD based phylogenetic trees for both pol and env genetic region, viral sequences of one subject (man) were paraphyletic to those of two other subjects (women), implying the direction of transmission opposite to the a priori assumption. The dated tree in our analysis confirmed the clustering pattern of query sequences. Still, in the context of unsampled sequences and inherent limitations of the applied methods, we cannot unambiguously prove that HIV-1 transmission occurred directly between two individuals. Further exploration of the known and suspected transmission cases is needed in order to define methodologies and establish their reliability.
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Affiliation(s)
- Marina Siljic
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia
| | - Dubravka Salemovic
- Infectious and Tropical Diseases University Hospital, Clinical Center Serbia, HIV/AIDS Unit, Belgrade, Serbia
| | - Valentina Cirkovic
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia
| | - Ivana Pesic-Pavlovic
- Virology Laboratory, Microbiology Department, Clinical Center Serbia, Belgrade, Serbia
| | - Jovan Ranin
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia; Infectious and Tropical Diseases University Hospital, Clinical Center Serbia, HIV/AIDS Unit, Belgrade, Serbia
| | - Marija Todorovic
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia
| | - Slobodan Nikolic
- Institute of Forensic Medicine, University of Belgrade School of Medicine, Belgrade, Serbia
| | - Djordje Jevtovic
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia; Infectious and Tropical Diseases University Hospital, Clinical Center Serbia, HIV/AIDS Unit, Belgrade, Serbia
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, University of Belgrade School of Medicine, Belgrade, Serbia.
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Abstract
Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals' HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.
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The impact of criminalization of HIV non-disclosure on the healthcare engagement of women living with HIV in Canada: a comprehensive review of the evidence. J Int AIDS Soc 2015; 18:20572. [PMID: 26701080 PMCID: PMC4689876 DOI: 10.7448/ias.18.1.20572] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 12/12/2022] Open
Abstract
Introduction In 2012, the Supreme Court of Canada ruled that people living with HIV (PLWH) must disclose their HIV status to sexual partners prior to sexual activity that poses a “realistic possibility” of HIV transmission for consent to sex to be valid. The Supreme Court deemed that the duty to disclose could be averted if a person living with HIV both uses a condom and has a low plasma HIV-1 RNA viral load during vaginal sex. This is one of the strictest legal standards criminalizing HIV non-disclosure worldwide and has resulted in a high rate of prosecutions of PLWH in Canada. Public health advocates argue that the overly broad use of the criminal law against PLWH undermines efforts to engage individuals in healthcare and complicates gendered barriers to linkage and retention in care experienced by women living with HIV (WLWH). Methods We conducted a comprehensive review of peer-reviewed and non-peer-reviewed evidence published between 1998 and 2015 evaluating the impact of the criminalization of HIV non-disclosure on healthcare engagement of WLWH in Canada across key stages of the cascade of HIV care, specifically: HIV testing and diagnosis, linkage and retention in care, and adherence to antiretroviral therapy. Where available, evidence pertaining specifically to women was examined. Where these data were lacking, evidence relating to all PLWH in Canada or other international jurisdictions were included. Results and discussion Evidence suggests that criminalization of HIV non-disclosure may create barriers to engagement and retention within the cascade of HIV care for PLWH in Canada, discouraging access to HIV testing for some people due to fears of legal implications following a positive diagnosis, and compromising linkage and retention in healthcare through concerns of exposure of confidential medical information. There is a lack of published empirical evidence focused specifically on women, which is a concern given the growing population of WLWH in Canada, among whom marginalized and vulnerable women are overrepresented. Conclusions The threat of HIV non-disclosure prosecution combined with a heightened perception of surveillance may alter the environment within which women engage with healthcare services. Fully exploring the extent to which HIV criminalization represents a barrier to the healthcare engagement of WLWH is a public health priority.
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Campo DS, Xia GL, Dimitrova Z, Lin Y, Forbi JC, Ganova-Raeva L, Punkova L, Ramachandran S, Thai H, Skums P, Sims S, Rytsareva I, Vaughan G, Roh HJ, Purdy MA, Sue A, Khudyakov Y. Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings. J Infect Dis 2015; 213:957-65. [PMID: 26582955 DOI: 10.1093/infdis/jiv542] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/08/2015] [Indexed: 12/18/2022] Open
Abstract
Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections are associated with unsafe injection practices, drug diversion, and other exposures to blood and are difficult to detect and investigate. Here, we developed and validated a simple approach for molecular detection of HCV transmissions in outbreak settings. We obtained sequences from the HCV hypervariable region 1 (HVR1), using end-point limiting-dilution (EPLD) technique, from 127 cases involved in 32 epidemiologically defined HCV outbreaks and 193 individuals with unrelated HCV strains. We compared several types of genetic distances and calculated a threshold, using minimal Hamming distances, that identifies transmission clusters in all tested outbreaks with 100% accuracy. The approach was also validated on sequences obtained using next-generation sequencing from HCV strains recovered from 239 individuals, and findings showed the same accuracy as that for EPLD. On average, the nucleotide diversity of the intrahost population was 6.2 times greater in the source case than in any incident case, allowing the correct detection of transmission direction in 8 outbreaks for which source cases were known. A simple and accurate distance-based approach developed here for detecting HCV transmissions streamlines molecular investigation of outbreaks, thus improving the public health capacity for rapid and effective control of hepatitis C.
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Affiliation(s)
- David S Campo
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Guo-Liang Xia
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Zoya Dimitrova
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Yulin Lin
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joseph C Forbi
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lilia Ganova-Raeva
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lili Punkova
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sumathi Ramachandran
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Hong Thai
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pavel Skums
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Seth Sims
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Inna Rytsareva
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Gilberto Vaughan
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ha-Jung Roh
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael A Purdy
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Amanda Sue
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Yury Khudyakov
- Molecular Epidemiology and Bioinformatics Laboratory, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia
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Dodds C, Weait M, Bourne A, Egede S. Keeping confidence: HIV and the criminal law from HIV service providers' perspectives. CRITICAL PUBLIC HEALTH 2015; 25:410-426. [PMID: 26692653 PMCID: PMC4647852 DOI: 10.1080/09581596.2015.1019835] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/05/2015] [Indexed: 11/24/2022]
Abstract
We present qualitative research findings about how perceptions of criminal prosecutions for the transmission of HIV interact with the provision of high-quality HIV health and social care in England and Wales. Seven focus groups were undertaken with a total of 75 diverse professionals working in clinical and community-based services for people with HIV. Participants' understanding of the law in this area was varied, with many knowing the basic requirements for a prosecution, yet lacking confidence in the best way to communicate key details with those using their service. Prosecutions for HIV transmission have influenced, and in some instances, disrupted the provision of HIV services, creating ambivalence and concern among many providers about their new role as providers of legal information. The way that participants approached the topic with service users was influenced by their personal views on individual and shared responsibility for health, their concerns about professional liability and their degree of trust in non-coercive health promotion approaches to managing public health. These findings reveal an underlying ambivalence among many providers about how they regard the interface between criminal law, coercion and public health. It is also apparent that in most HIV service environments, meaningful exploration of practical ethical issues is relatively rare. The data presented here will additionally be of use to managers and providers of HIV services in order that they can provide consistent and confident support and advice to people with HIV.
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Affiliation(s)
- Catherine Dodds
- Sigma Research, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Adam Bourne
- Sigma Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Siri Egede
- Department of Sociology, University of Copenhagen, Copenhagen, Denmark
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25
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Chen M, Ma Y, Yang C, Yang L, Chen H, Dong L, Dai J, Jia M, Lu L. The combination of phylogenetic analysis with epidemiological and serological data to track HIV-1 transmission in a sexual transmission case. PLoS One 2015; 10:e0119989. [PMID: 25807147 PMCID: PMC4373787 DOI: 10.1371/journal.pone.0119989] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 01/24/2015] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To investigate the linkage of HIV transmission from a man to a woman through unprotected sexual contact without disclosing his HIV-positive status. METHODS Combined with epidemiological information and serological tests, phylogenetic analysis was used to test the a priori hypothesis of HIV transmission from the man to the woman. Control subjects, infected with HIV through heterosexual intercourse, from the same location were also sampled. Phylogenetic analyses were performed using the consensus gag, pol and env sequences obtained from blood samples of the man, the woman and the local control subjects. The env quasispecies of the man, the woman, and two controls were also obtained using single genome amplification and sequencing (SGA/S) to explore the paraphyletic relationship by phylogenetic analysis. RESULTS Epidemiological information and serological tests indicated that the man was infected with HIV-1 earlier than the woman. Phylogenetic analyses of the consensus sequences showed a monophyletic cluster for the man and woman in all three genomic regions. Furthermore, gag sequences of the man and woman shared a unique recombination pattern from subtype B and C, which was different from those of CRF07_BC or CRF08_BC observed in the local samples. These indicated that the viral sequences from the two subjects display a high level of similarity. Further, viral quasispecies from the man exhibited a paraphyletic relationship with those from the woman in the Bayesian and maximum-likelihood (ML) phylogenetic trees of the env region, which supported the transmission direction from the man to the woman. CONCLUSIONS In the context of epidemiological and serological evidence, the results of phylogenetic analyses support the transmission from the man to the woman.
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Affiliation(s)
- Min Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Yanling Ma
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Chaojun Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Li Yang
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Huichao Chen
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Lijuan Dong
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Jie Dai
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
| | - Manhong Jia
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
- * E-mail: (LL); (MJ)
| | - Lin Lu
- Center for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, Yunnan 650022, China
- College of Public Health, Kunming Medical University, Kunming, Yunnan 650500, China
- * E-mail: (LL); (MJ)
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26
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Davies A, Scott S, Badger S, Török ME, Peacock SJ. Public perceptions of bacterial whole-genome sequencing for tuberculosis. Trends Genet 2014; 31:58-60. [PMID: 25640860 DOI: 10.1016/j.tig.2014.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
Abstract
The ability to sequence a bacterial genome in less than 1 day represents a step change for clinical microbiology. Genomic data can be used to investigate suspected outbreaks and rapidly to identify multidrug-resistant organisms. We held an open public debate to explore public understanding and perceptions of bacterial whole-genome sequencing (WGS), which we describe here.
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Affiliation(s)
- Anna Davies
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Shirlene Badger
- Institute of Public Health, University of Cambridge, Cambridge, UK; PHG Foundation, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK; Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Trust Sanger Institute, Hinxton, UK; Public Health England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK; Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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27
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Poon AFY, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JSG, Harrigan PR. The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada. J Infect Dis 2014; 211:926-35. [PMID: 25312037 DOI: 10.1093/infdis/jiu560] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The diversification of human immunodeficiency virus (HIV) is shaped by its transmission history. We therefore used a population based province wide HIV drug resistance database in British Columbia (BC), Canada, to evaluate the impact of clinical, demographic, and behavioral factors on rates of HIV transmission. METHODS We reconstructed molecular phylogenies from 27,296 anonymized bulk HIV pol sequences representing 7747 individuals in BC-about half the estimated HIV prevalence in BC. Infections were grouped into clusters based on phylogenetic distances, as a proxy for variation in transmission rates. Rates of cluster expansion were reconstructed from estimated dates of HIV seroconversion. RESULTS Our criteria grouped 4431 individuals into 744 clusters largely separated with respect to risk factors, including large established clusters predominated by injection drug users and more-recently emerging clusters comprising men who have sex with men. The mean log10 viral load of an individual's phylogenetic neighborhood (composed of 5 other individuals with shortest phylogenetic distances) increased their odds of appearing in a cluster by >2-fold per log10 viruses per milliliter. CONCLUSIONS Hotspots of ongoing HIV transmission can be characterized in near real time by the secondary analysis of HIV resistance genotypes, providing an important potential resource for targeting public health initiatives for HIV prevention.
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Affiliation(s)
- Art F Y Poon
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
| | | | | | | | | | | | - Robert S Hogg
- BC Centre for Excellence in HIV/AIDS Faculty of Health Sciences, Simon Fraser University, Burnaby, Canada
| | - Julio S G Montaner
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
| | - P Richard Harrigan
- BC Centre for Excellence in HIV/AIDS Department of Medicine, University of British Columbia, Vancouver
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28
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Frost SDW, Pillay D. Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV. J Infect Dis 2014; 211:856-8. [PMID: 25312038 PMCID: PMC4340367 DOI: 10.1093/infdis/jiu563] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine and Institute of Public Health, University of Cambridge
| | - Deenan Pillay
- University College London, United Kingdom Africa Centre for Health and Population Studies, University of KwaZulu Natal, Durban, South Africa
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29
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Velsko SP, Osburn J, Allen J. Forensic interpretation of molecular variation on networks of disease transmission and genetic inheritance. Electrophoresis 2014; 35:3117-24. [PMID: 25137141 PMCID: PMC7159361 DOI: 10.1002/elps.201400205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/26/2014] [Accepted: 08/01/2014] [Indexed: 11/20/2022]
Abstract
This paper describes the inference‐on‐networks (ION) framework for forensic interpretat ION of molecular typing data in cases involving allegations of infectious microbial transmission, association of disease outbreaks with alleged sources, and identifying familial relationships using mitochondrial or Y chromosomal DNA. The framework is applicable to molecular typing data obtained using any technique, including those based on electrophoretic separations. A key insight is that the networks associated with disease transmission or DNA inheritance can be used to define specific testable relationships and avoid the ambiguity and subjectivity associated with the criteria used for inferring genetic relatedness now in use. We discuss specific applications of the framework to the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore and the 2001 foot‐and‐mouth disease virus (FMDV) outbreak in Great Britain.
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Affiliation(s)
- Stephan P Velsko
- Lawrence Livermore National Laboratory, Global Security Directorate, Livermore, CA, USA
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30
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31
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Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM. Using HIV networks to inform real time prevention interventions. PLoS One 2014; 9:e98443. [PMID: 24901437 PMCID: PMC4047027 DOI: 10.1371/journal.pone.0098443] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 05/02/2014] [Indexed: 11/19/2022] Open
Abstract
Objective To reconstruct the local HIV-1 transmission network from 1996 to 2011 and use network data to evaluate and guide efforts to interrupt transmission. Design HIV-1 pol sequence data were analyzed to infer the local transmission network. Methods We analyzed HIV-1 pol sequence data to infer a partial local transmission network among 478 recently HIV-1 infected persons and 170 of their sexual and social contacts in San Diego, California. A transmission network score (TNS) was developed to estimate the risk of HIV transmission from a newly diagnosed individual to a new partner and target prevention interventions. Results HIV-1 pol sequences from 339 individuals (52.3%) were highly similar to sequences from at least one other participant (i.e., clustered). A high TNS (top 25%) was significantly correlated with baseline risk behaviors (number of unique sexual partners and insertive unprotected anal intercourse (p = 0.014 and p = 0.0455, respectively) and predicted risk of transmission (p<0.0001). Retrospective analysis of antiretroviral therapy (ART) use, and simulations of ART targeted to individuals with the highest TNS, showed significantly reduced network level HIV transmission (p<0.05). Conclusions Sequence data from an HIV-1 screening program focused on recently infected persons and their social and sexual contacts enabled the characterization of a highly connected transmission network. The network-based risk score (TNS) was highly correlated with transmission risk behaviors and outcomes, and can be used identify and target effective prevention interventions, like ART, to those at a greater risk for HIV-1 transmission.
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Affiliation(s)
- Susan J. Little
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Sergei L. Kosakovsky Pond
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Christy M. Anderson
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Jason A. Young
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Joel O. Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Sanjay R. Mehta
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Susanne May
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
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32
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Chaillon A, Samleerat T, Zoveda F, Ballesteros S, Moreau A, Ngo-Giang-Huong N, Jourdain G, Gianella S, Lallemant M, Depaulis F, Barin F. Estimating the timing of mother-to-child transmission of the human immunodeficiency virus type 1 using a viral molecular evolution model. PLoS One 2014; 9:e90421. [PMID: 24717647 PMCID: PMC3981669 DOI: 10.1371/journal.pone.0090421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 01/30/2014] [Indexed: 11/19/2022] Open
Abstract
Background Mother-to-child transmission (MTCT) is responsible for most pediatric HIV-1 infections worldwide. It can occur during pregnancy, labor, or breastfeeding. Numerous studies have used coalescent and molecular clock methods to understand the epidemic history of HIV-1, but the timing of vertical transmission has not been studied using these methods. Taking advantage of the constant accumulation of HIV genetic variation over time and using longitudinally sampled viral sequences, we used a coalescent approach to investigate the timing of MTCT. Materials and Methods Six-hundred and twenty-two clonal env sequences from the RNA and DNA viral population were longitudinally sampled from nine HIV-1 infected mother-and-child pairs [range: 277–1034 days]. For each transmission pair, timing of MTCT was determined using a coalescent-based model within a Bayesian statistical framework. Results were compared with available estimates of MTCT timing obtained with the classic biomedical approach based on serial HIV DNA detection by PCR assays. Results Four children were infected during pregnancy, whereas the remaining five children were infected at time of delivery. For eight out of nine pairs, results were consistent with the transmission periods assessed by standard PCR-based assay. The discordance in the remaining case was likely confused by co-infection, with simultaneous introduction of multiple maternal viral variants at the time of delivery. Conclusions The study provided the opportunity to validate the Bayesian coalescent approach that determines the timing of MTCT of HIV-1. It illustrates the power of population genetics approaches to reliably estimate the timing of transmission events and deepens our knowledge about the dynamics of viral evolution in HIV-infected children, accounting for the complexity of multiple transmission events.
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Affiliation(s)
- Antoine Chaillon
- Université François-Rabelais, Institut National de la Santé et de la Recherche Médicale - Unité 966 et Laboratoire de Virologie, Centre Hopsitalier Universitaire Bretonneau, Tours, France
- University of California San Diego, Department of Pathology, San Diego, California, United States of America
- * E-mail:
| | - Tanawan Samleerat
- Université François-Rabelais, Institut National de la Santé et de la Recherche Médicale - Unité 966 et Laboratoire de Virologie, Centre Hopsitalier Universitaire Bretonneau, Tours, France
- Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - Faustine Zoveda
- Laboratoire Ecologie et Evolution, Centre National de la Recherche Scientifique - Unité Mixte de Recherche 7625- Ecole Normale Supérieure, Paris, France
| | - Sébastien Ballesteros
- Laboratoire Ecologie et Evolution, Centre National de la Recherche Scientifique - Unité Mixte de Recherche 7625- Ecole Normale Supérieure, Paris, France
| | - Alain Moreau
- Université François-Rabelais, Institut National de la Santé et de la Recherche Médicale - Unité 966 et Laboratoire de Virologie, Centre Hopsitalier Universitaire Bretonneau, Tours, France
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement, Chiang Mai, Thailand
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts, United States of America
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement, Chiang Mai, Thailand
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts, United States of America
| | - Sara Gianella
- University of California San Diego, Department of Pathology, San Diego, California, United States of America
| | - Marc Lallemant
- Institut de Recherche pour le Développement, Chiang Mai, Thailand
- Harvard School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts, United States of America
| | - Frantz Depaulis
- Laboratoire Ecologie et Evolution, Centre National de la Recherche Scientifique - Unité Mixte de Recherche 7625- Ecole Normale Supérieure, Paris, France
| | - Francis Barin
- Université François-Rabelais, Institut National de la Santé et de la Recherche Médicale - Unité 966 et Laboratoire de Virologie, Centre Hopsitalier Universitaire Bretonneau, Tours, France
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Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates. PLoS Comput Biol 2014; 10:e1003505. [PMID: 24699231 PMCID: PMC3974631 DOI: 10.1371/journal.pcbi.1003505] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/15/2014] [Indexed: 11/23/2022] Open
Abstract
Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the ‘store and retrieve’ hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation. Since its discovery three decades ago, the HIV epidemic has unfolded into one of the most devastating pandemics in human history. When HIV replication cannot be completely inhibited, the fast-evolving retrovirus continuously evades intra-host immune and drug selective pressure, but diversifies according to more neutral epidemiological dynamics at the interhost level. Limited evidence suggests that the virus may evolve faster in a single host than in a population of hosts, and various hypotheses have been put forward to explain this phenomenon. Here, we develop a new computational approach aimed at integrating host transmission information with pathogen genealogical reconstructions. We apply this approach to comprehensive sequence data sets sampled from a large HIV-1 subtype C transmission chain, and in addition to providing several insights into the reconstruction of HIV-1 transmissions histories and its associated population dynamics, we find that transmission decreases the HIV-1 evolutionary rate. The fact that we also identify this decline for substitutions that do not alter amino acid substitutions provides evidence against hypotheses that invoke selection forces. Instead, our findings support earlier reports that new infections start preferentially with less evolved variants, which may be stored in latently infected cells, and this may vary among different HIV-1 subtypes.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles Los Angeles, California, United States of America
| | - Alexei Drummond
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Anne-Mieke Vandamme
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Centro de Malária e Outras Doenças Tropicais Instituto de Higiene e Medicina Tropical and Unidade de Microbiologia, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Kristel Van Laethem
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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Field N, Cohen T, Struelens MJ, Palm D, Cookson B, Glynn JR, Gallo V, Ramsay M, Sonnenberg P, MacCannell D, Charlett A, Egger M, Green J, Vineis P, Abubakar I. Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement. THE LANCET. INFECTIOUS DISEASES 2014; 14:341-52. [DOI: 10.1016/s1473-3099(13)70324-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Iyengar A, Hadi S. Use of non-human DNA analysis in forensic science: a mini review. MEDICINE, SCIENCE, AND THE LAW 2014; 54:41-50. [PMID: 23929675 DOI: 10.1177/0025802413487522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Analysis of non-human DNA in forensic science, first reported about two decades ago, is now commonplace. Results have been used as evidence in court in a variety of cases ranging from abduction and murder to patent infringement and dog attack. DNA from diverse species, including commonly encountered pets such as dogs and cats, to plants, viruses and bacteria has been used and the sheer potential offered by such analyses has been proven. In this review, using case examples throughout, we detail the considerable literature in this field.
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Affiliation(s)
- Arati Iyengar
- School of Forensic & Investigative Sciences, University of Central Lancashire, Preston, UK
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Phillips M, Poulton M. HIV transmission, the Law and the work of the clinical team, January 2013. Int J STD AIDS 2013; 25:8-23. [PMID: 24047880 DOI: 10.1177/0956462413498338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Matthew Phillips
- Manchester Royal Infirmary, NHS North Western Deanery, Manchester, UK
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Vandamme AM, Pybus OG. Viral phylogeny in court: the unusual case of the Valencian anesthetist. BMC Biol 2013; 11:83. [PMID: 24059471 PMCID: PMC3717106 DOI: 10.1186/1741-7007-11-83] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 07/11/2013] [Indexed: 12/17/2022] Open
Abstract
A large and complex outbreak of hepatitis C virus in Valencia, Spain that began 25 years ago led to the prosecution and conviction of an anesthetist who was accused of infecting hundreds of his patients. Evolutionary analyses of viral gene sequences were presented as evidence in the trial, and these are now described in detail by González-Candelas and colleagues in a paper published in BMC Biology. Their study illustrates the challenges and opportunities that arise from the use of phylogenetic inference in criminal trials concerning virus transmission. See research article: http://www.biomedcentral.com/1741-7007/11/76
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Affiliation(s)
- Anne-Mieke Vandamme
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.
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Lazzarini Z, Galletly CL, Mykhalovskiy E, Harsono D, O'Keefe E, Singer M, Levine RJ. Criminalization of HIV transmission and exposure: research and policy agenda. Am J Public Health 2013; 103:1350-3. [PMID: 23763428 DOI: 10.2105/ajph.2013.301267] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
More than half of US jurisdictions have laws criminalizing knowing exposure to or transmission of HIV, yet little evidence supports these laws' effectiveness in reducing HIV incidence. These laws may undermine prevention efforts outlined in the US National HIV/AIDS Strategy, in which the United States has invested substantial federal funds. Future research should include studies of (1) the impact of US HIV exposure laws on public health systems and practices; (2) enforcement of these laws, including arrests, prosecutions, convictions, and sentencing; (3) alternatives to HIV exposure laws; and (4) direct and opportunity costs of enforcement. Policy efforts to mitigate potential negative impacts of these laws could include developing prosecutorial guidelines, modernized statutes, and model public health policies and protocols.
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Affiliation(s)
- Zita Lazzarini
- Division of Public Health Law and Bioethics, University of Connecticut Health Center, 263 Farmington Ave. MC-6325, Farmington, CT 06030-6325, USA.
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Ebbert MTW, Mallory MA, Wilson AR, Dooley SK, Hillyard DR. Application of a new informatics tool for contamination screening in the HIV sequencing laboratory. J Clin Virol 2013; 57:249-53. [PMID: 23583427 DOI: 10.1016/j.jcv.2013.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/14/2013] [Accepted: 03/16/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Current HIV-1 sequencing-based methods for detecting drug resistance-associated mutations are open and susceptible to contamination. Informatic identification of clinical sequences that are nearly identical to one another may indicate specimen-to-specimen contamination or another laboratory-associated issue. OBJECTIVES To design an informatic tool to rapidly identify potential contamination in the clinical laboratory using sequence analysis and to establish reference ranges for sequence variation in the HIV-1 protease and reverse transcriptase regions among a U.S. patient population. STUDY DESIGN We developed an open-source tool named HIV Contamination Detection (HIVCD). HIVCD was utilized to make pairwise comparisons of nearly 8000 partial HIV-1 pol gene sequences from patients across the United States and to calculate percent identities (PIDs) for each pair. ROC analysis and standard deviations of PID data were used to determine reference ranges for between-patient and within-patient comparisons and to guide selection of a threshold for identifying abnormally high PID between two unrelated sequences. RESULTS The PID reference range for between-patient comparisons ranged from 83.8 to 95.7% while within-patient comparisons ranged from 96 to 100%. Interestingly, 48% of between-patient sequence pairs with a PID>96.5 were geographically related. The selected threshold for abnormally high PIDs was 96 (AUC=0.993, sensitivity=0.980, specificity=0.999). During routine use, HIVCD identified a specimen mix-up and the source of contamination of a negative control. CONCLUSIONS In our experience, HIVCD is easily incorporated into laboratory workflow, useful for identifying potential laboratory errors, and contributes to quality testing. This type of analysis should be incorporated into routine laboratory practice.
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Affiliation(s)
- Mark T W Ebbert
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA.
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Sacks-Davis R, Daraganova G, Aitken C, Higgs P, Tracy L, Bowden S, Jenkinson R, Rolls D, Pattison P, Robins G, Grebely J, Barry A, Hellard M. Hepatitis C virus phylogenetic clustering is associated with the social-injecting network in a cohort of people who inject drugs. PLoS One 2012; 7:e47335. [PMID: 23110068 PMCID: PMC3482197 DOI: 10.1371/journal.pone.0047335] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 09/14/2012] [Indexed: 12/24/2022] Open
Abstract
It is hypothesized that social networks facilitate transmission of the hepatitis C virus (HCV). We tested for association between HCV phylogeny and reported injecting relationships using longitudinal data from a social network design study. People who inject drugs were recruited from street drug markets in Melbourne, Australia. Interviews and blood tests took place three monthly (during 2005-2008), with participants asked to nominate up to five injecting partners at each interview. The HCV core region of individual isolates was then sequenced and phylogenetic trees were constructed. Genetic clusters were identified using bootstrapping (cut-off: 70%). An adjusted Jaccard similarity coefficient was used to measure the association between the reported injecting relationships and relationships defined by clustering in the phylogenetic analysis (statistical significance assessed using the quadratic assignment procedure). 402 participants consented to participate; 244 HCV infections were observed in 238 individuals. 26 genetic clusters were identified, with 2-7 infections per cluster. Newly acquired infection (AOR = 2.03, 95% CI: 1.04-3.96, p = 0.037, and HCV genotype 3 (vs. genotype 1, AOR = 2.72, 95% CI: 1.48-4.99) were independent predictors of being in a cluster. 54% of participants whose infections were part of a cluster in the phylogenetic analysis reported injecting with at least one other participant in that cluster during the study. Overall, 16% of participants who were infected at study entry and 40% of participants with newly acquired infections had molecular evidence of related infections with at least one injecting partner. Likely transmission clusters identified in phylogenetic analysis correlated with reported injecting relationships (adjusted Jaccard coefficient: 0.300; p<0.001). This is the first study to show that HCV phylogeny is associated with the injecting network, highlighting the importance of the injecting network in HCV transmission.
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Affiliation(s)
- Rachel Sacks-Davis
- Centre for Population Health, Burnet Institute, Melbourne, Victoria, Australia.
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Killian MS, Vyas GN, Mehta R, Young K, Ebrahim O. Possible transmission of human immunodeficiency virus-1 infection from an elite controller to a patient who progressed to acquired immunodeficiency syndrome: a case report. J Med Case Rep 2012; 6:291. [PMID: 22967353 PMCID: PMC3469400 DOI: 10.1186/1752-1947-6-291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 06/08/2012] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Most individuals infected with human immunodeficiency virus-1, in the absence of antiretroviral therapy, exhibit persistent virus replication and declining CD4+ cell numbers, and progress to acquired immunodeficiency syndrome within 10 years of infection. Elite controllers are rare individuals with human immunodeficiency virus-1 infection who can maintain undetectable plasma virus levels and remain asymptomatic without antiretroviral therapy. It has been proposed that elite controllers benefit from being infected with attenuated human immunodeficiency virus-1 variants. CASE PRESENTATION A 31-year-old African woman presented with human immunodeficiency virus-1 infection during pregnancy and was diagnosed with acquired immunodeficiency syndrome. Subsequently, her husband, a 31-year-old African man, was tested and found to be seropositive for human immunodeficiency virus-1. His plasma human immunodeficiency virus-1 ribonucleic acid level was found to be below the limit of detection of the clinical assay. CONCLUSION This report provides evidence for the first described case of human immunodeficiency virus-1 infection possibly transmitted from an elite controller to a patient who progressed to acquired immunodeficiency syndrome. This observation strengthens the case against avirulence as a mechanism that protects elite controllers.
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Affiliation(s)
- Michael Scott Killian
- Department of Medicine, University of California San Francisco, 513 Parnassus Avenue, Box 1270, San Francisco, CA, 94143, USA.
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Abstract
OBJECTIVES Identifying the direction of transmission in transmission pairs is important both for forensic investigations and for the monitoring of HIV epidemics, however, reliable methods are not yet available due to the long time lag between infection and sampling in most real cases. DESIGNS Based on bottleneck effect and coreceptor switching, we aimed at identifying an estimator from sequences of viral gp120 proteins to determine transmission direction between transmission pairs. The estimator should be changed with HIV transmission but was independent of disease progression in an individual. METHODS Here, we present a novel and reliable approach for identifying transmission direction. We derived a set of conserved patterns, called common patterns, from the sequences of viruses, which differed in their coreceptor usage. The number of unique common patterns in viral sequences decreased with transmission but remained almost constant with the progress of disease in an individual. We used this number as an estimator to determine transmission direction in 73 transmission pairs for which the transmission direction was already known. RESULTS Our method predicted transmission direction with an accuracy of up to 94.5%. Of greater importance, our approach was not influenced by time lags between infection and sampling, and even transmission direction for transmission pairs with long time lags ranging from 2 years to more than 18 years were correctly determined. CONCLUSION Our approach for accurately determining transmission direction between transmission pairs is irrespective of the time lag between infection and sampling, which means a promising applications prospect.
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Castro-Nallar E, Crandall KA, Pérez-Losada M. Genetic diversity and molecular epidemiology of HIV transmission. Future Virol 2012. [DOI: 10.2217/fvl.12.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The high genetic diversity of HIV is one of its most significant features, as it has consequences in global distribution, vaccine design, therapy success, disease progression, transmissibility and viral load testing. Studying HIV diversity helps to understand its origins, migration patterns, current distribution and transmission events. New advances in sequencing technologies based on the parallel acquisition of data are now used to characterize within-host and population processes in depth. Additionally, we have seen similar advances in statistical methods designed to model the past history of lineages (the phylodynamic framework) to ultimately gain better insights into the evolutionary history of HIV. We can, for example, estimate population size changes, lineage dispersion over geographic areas and epidemiological parameters solely from sequence data. In this article, we review some of the evolutionary approaches used to study transmission patterns and processes in HIV and the insights gained from such studies.
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA
| | - Keith A Crandall
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA
| | - Marcos Pérez-Losada
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
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Castro-Nallar E, Pérez-Losada M, Burton GF, Crandall KA. The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol 2012; 62:777-92. [PMID: 22138161 PMCID: PMC3258026 DOI: 10.1016/j.ympev.2011.11.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/17/2011] [Accepted: 11/21/2011] [Indexed: 12/02/2022]
Abstract
Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).
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Affiliation(s)
- Eduardo Castro-Nallar
- Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA.
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Csete J, Elliott R. Criminalization of HIV transmission and exposure: in search of rights-based public health alternatives to criminal law. Future Virol 2011. [DOI: 10.2217/fvl.11.74] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of criminal law to address HIV transmission and exposure has been misguided and ineffective. Criminalization of HIV transmission and exposure raises difficult legal questions: what is the appropriate degree of mental culpability to trigger criminal prosecution? Is it appropriate for the law to equate nondisclosure of (known) HIV-positive status to a sexual partner with rape (as the law does in some jurisdictions)? Can it be justified to treat mere nondisclosure of HIV status as equivalent to the intent to cause harm? To what extent will the law recognize circumstances that mitigate harm, risk of harm and mental culpability, such as safer sex practices and low viral load, in mitigating the application of criminal sanctions? Sound guidance on avoiding the misuse of the criminal law in this area has been developed, but unfortunately many criminal laws in this area allow for prosecution even in cases where there is little justification. It is reasonable to expect that the use of these laws contributes to HIV-related stigma and discrimination, particularly when cases are portrayed sensationally in mass media. The harm caused by unjustified prosecutions and convictions and stigma is not counterbalanced by any evidence of public health benefits of this use of criminal law. These laws should urgently be repealed or reformed as part of a shift to strategies centered on human rights.
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Affiliation(s)
- Joanne Csete
- Columbia University Mailman School of Public Health, Heilbrunn Department of Population & Family Health, 60 Haven Avenue, #B2, New York, NY 10032, USA
| | - Richard Elliott
- Canadian HIV/AIDS Legal Network, 1240 Bay Street, Suite 600, Toronto M5R 2A7, Canada
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Transmission patterns of HIV and hepatitis C virus among networks of people who inject drugs. PLoS One 2011; 6:e22245. [PMID: 21799802 PMCID: PMC3140499 DOI: 10.1371/journal.pone.0022245] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 06/17/2011] [Indexed: 12/11/2022] Open
Abstract
Background The risk-related behaviours and practices associated with injection drug use remain a driver of HIV and hepatitis C virus (HCV) transmission throughout the world. Here we evaluated HIV and HCV transmission patterns in the context of social networks of injection drug users (IDU) recruited from a higher incidence region in order to better understand factors that contribute to ongoing transmission among IDU. Methods IDU recruited through a chain-referral method provided biological specimens for analysis. HIV and HCV positive specimens were sequenced and analyzed using phylogenetic methods (Neighbour-joining and Bayesian) and transmission patterns of HIV and HCV evaluated in the context of the recruitment networks. Results Among the 407 recruited IDU, HCV and HIV prevalence were 60.6% and 10.1%, respectively; 98% of HIV positive individuals were co-infected with HCV. Thirty-six percent of HCV sequences were associated with clusters, compared to 67% of HIV sequences. Four (16.7%) of the 24 HCV clusters contained membership separated by 2 or fewer recruitment cycles, compared to 10 (41.6%) derived from more than one recruitment component. Two (28.6%) of the 7 HIV clusters contained membership separated by 2 or fewer recruitment cycles while 6 (85.7%) were composed of inter component membership. Conclusions Few HIV and HCV transmissions coincided with the recruitment networks, suggesting that they occurred in a different social context or a context not captured by the recruitment network. However, among the complete cohort, a higher degree of HIV clustering indicates many are recent infections originating from within current social networks, whereas a larger proportion of HCV infections may have occurred earlier in injecting history and in the context of a different social environment.
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Dennin RH, Lafrenz M, Sinn A, Li LJ. Dilemma of concepts and strategies for the prevention of spread of HIV in relation to human behavior, law and human rights. J Zhejiang Univ Sci B 2011; 12:591-610. [PMID: 21726067 PMCID: PMC3134848 DOI: 10.1631/jzus.b1000434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 03/23/2011] [Indexed: 12/22/2022]
Abstract
The new prevalence data regarding the estimated global number of human immunodeficiency virus positive (HIV+) cases, i.e., including people who are either aware or unaware of their HIV infection in 2010, lead many to wonder why the increase in incidence has reached today's unprecedented level and escalated within such a short time. This, in spite of prevention campaigns in countries affected by HIV/acquired immune deficiency syndrome (AIDS) with their urgent messages aimed at preventing HIV transmission by promoting changes in individual's behavior. This article analyzes the background of the prevention strategies, in particular their political, social and legal concepts in terms of human rights, and reveals traits of human behavior not considered thus far. A radical reappraisal is necessary, at social and legislative levels, as well as options additional to current concepts. When ethical issues come up, they become blamed for outmoded moralistic positions. However, ignoring the reality has led to dire consequences from prioritizing individual human rights over society's collective need to prevent the spread of HIV.
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Affiliation(s)
- Reinhard H Dennin
- Institute of Medical Microbiology and Hygiene, University of Luebeck, Campus Luebeck, 160 Ratzeburger Allee, Luebeck D-23538, Germany.
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Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission. AIDS 2011; 25:1035-9. [PMID: 21505318 DOI: 10.1097/qad.0b013e3283467020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate whether time-measured phylogenetic analysis of longitudinal viral sequences can establish the direction and timing of HIV-1 transmission in an epidemiologically linked transmission cluster of three homosexual men. DESIGN An HIV-1-infected homosexual man (patient 1) and his long-term HIV-negative partner (patient 2) engaged in a triangular relationship with an additional partner (patient 3). On the basis of phylogenetic analysis of gag sequences, patient 3 was previously identified as the source for superinfection of patient 1 but the source of HIV-1 infection of patient 2, who seroconverted during the triangular relationship, remained unclear. Here, we set out to analyze newly obtained gag, pol and env sequences from all three patients to fully elucidate the transmission history in this epidemiologically linked cluster. METHODS Bayesian Markov Chain Monte Carlo (MCMC) phylogenetic analyses incorporating a relaxed clock model and a flexible Bayesian skyride tree prior were applied to the longitudinally obtained gag, pol and env sequences from all three patients. RESULTS Our time-measured evolutionary reconstructions convincingly supported transmission of HIV-1 from the new partner patient 3 to both patients 1 and 2. In addition, estimates of viral divergence times assisted in narrowing down the transmission intervals delineated by seroconversion estimates. CONCLUSION Our analysis implies that Bayesian MCMC phylogenetic reconstruction incorporating temporal information can indeed reveal the direction of multiple HIV-1 transmission events in an epidemiologically linked cluster and provide more detail on the timing of transmission.
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Abecasis AB, Geretti AM, Albert J, Power L, Weait M, Vandamme AM. Science in court: the myth of HIV fingerprinting. THE LANCET. INFECTIOUS DISEASES 2011; 11:78-9. [PMID: 21272786 DOI: 10.1016/s1473-3099(10)70283-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ana B Abecasis
- Instituto de Higiene e Medicina Tropical, Centro de Malária e Outras Doenças Tropicais, Universidade Nova de Lisboa, Lisbon, Portugal
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