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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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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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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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Hosokawa-Muto J, Sassa-O’Brien Y, Fujinami Y, Nakahara H. Analysis Comparison for Rapid Identification of Pathogenic Virus from Infected Tissue Samples. Diagnostics (Basel) 2022; 12:diagnostics12010196. [PMID: 35054363 PMCID: PMC8774399 DOI: 10.3390/diagnostics12010196] [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: 11/30/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
When examining infectious samples, rapid identification of the pathogenic agent is required for diagnosis and treatment or for investigating the cause of death. In our previous study, we applied exhaustive amplification using non-specific primers (the rapid determination system of viral genome sequences, the RDV method) to identify the causative virus via swab samples from a cat with a suspected viral infection. The purpose of the current study is to investigate suitable methods for the rapid identification of causative pathogens from infected tissue samples. First, the influenza virus was inoculated into mice to prepare infected tissue samples. RNA extracted from the mouse lung homogenates was transcribed into cDNA and then analyzed using the RDV method and next-generation sequencing, using MiSeq and MinION sequencers. The RDV method was unable to detect the influenza virus in the infected tissue samples. However, influenza virus reads were detected using next-generation sequencing. Comparing MiSeq and MinION, the time required for library and sequence preparation was shorter for MinION sequencing than for MiSeq sequencing. We conclude that when a causative virus needs to be rapidly identified from an infectious sample, MinION sequencing is currently the method of choice.
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Affiliation(s)
- Junji Hosokawa-Muto
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, Kashiwa 277-0882, Chiba, Japan; (Y.F.); (H.N.)
- Correspondence: ; Tel.: +81-4-7135-8001
| | - Yukiko Sassa-O’Brien
- Laboratory of Veterinary Infectious Disease, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Tokyo, Japan;
| | - Yoshihito Fujinami
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, Kashiwa 277-0882, Chiba, Japan; (Y.F.); (H.N.)
| | - Hiroaki Nakahara
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, Kashiwa 277-0882, Chiba, Japan; (Y.F.); (H.N.)
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Seeing the Woods for the Trees Again: Analyzing Evolutionary Diagrams in German and US University-Level Textbooks. EDUCATION SCIENCES 2021. [DOI: 10.3390/educsci11080367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phylogenetic trees are important tools for teaching and understanding evolution, yet students struggle to read and interpret them correctly. In this study, we extend a study conducted by Catley and Novick (2008) by investigating depictions of evolutionary trees in US textbooks. We investigated 1197 diagrams from 11 German and 11 United States university textbooks, conducting a cross-country comparison and comparing the results with data from the 2008 study. A coding manual was developed based on the 2008 study, with extensions focused on additional important aspects of evolutionary trees. The US and German books showed only a low number of significant differences, typically with very small impacts. In both samples, some characteristics that can render reading trees more difficult or foster misconceptions were found to be prevalent in various portions of the diagrams. Furthermore, US textbooks showed fewer problematic properties in our sample than in the 2008 sample. We conclude that evolutionary trees in US and German textbooks are represented comparably and that depictions in US textbooks have improved over the past 12 years. As students are confronted with comparable depictions of evolutionary relatedness, we argue that findings and materials from one country should easily be transferable to the other.
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Oliveira M, Mason-Buck G, Ballard D, Branicki W, Amorim A. Biowarfare, bioterrorism and biocrime: A historical overview on microbial harmful applications. Forensic Sci Int 2020; 314:110366. [PMID: 32683271 PMCID: PMC7305902 DOI: 10.1016/j.forsciint.2020.110366] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022]
Abstract
Microbial Forensics is a field that continues to grow in interest and application among the forensic community. This review, divided into two sections, covers several topics associated with this new field. The first section presents a historic overview concerning the use of microorganisms (or its product, i.e. toxins) as harmful biological agents in the context of biological warfare (biowarfare), bioterrorism, and biocrime. Each case is illustrated with the examination of case reports that span from prehistory to the present day. The second part of the manuscript is devoted to the role of MF and highlights the necessity to prepare for the pressing threat of the harmful use of biological agents as weapons. Preventative actions, developments within the field to ensure a timely and effective response and are discussed herein.
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MESH Headings
- Bacterial Infections
- Biological Warfare/history
- Bioterrorism/history
- Crime/history
- Forensic Sciences
- HIV Infections
- High-Throughput Screening Assays
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Humans
- Machine Learning
- Microbiological Techniques
- Toxins, Biological/adverse effects
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.
| | | | - David Ballard
- King's Forensics, King's College London, London, United Kingdom
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology of the Jagiellonian University, Kraków, Poland
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal; Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Abstract
PURPOSE OF REVIEW Within-host diversity complicates transmission models because it recognizes that between-host virus phylogenies are not identical to the transmission history among the infected hosts. This review presents the biological and theoretical foundations for recent development in this field, and shows that modern phylodynamic methods are capable of inferring realistic transmission histories from HIV sequence data. RECENT FINDINGS Transmission of single or multiple genetic variants from a donor's HIV population results in donor-recipient phylogenies with combinations of monophyletic, paraphyletic, and polyphyletic patterns. Large-scale simulations and analyses of many real HIV datasets have established that transmission direction, directness, or common source often can be inferred based on HIV sequence data. Phylodynamic reconstruction of HIV transmissions that include within-host HIV diversity have recently been established and made available in several software packages. SUMMARY Phylodynamic methods that include realistic features of HIV genetic diversification have come of age, significantly improving inference of key epidemiological parameters. This opens the door to more accurate surveillance and better-informed prevention campaigns.
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Li WY, Huang SW, Wang SF, Liu HF, Chou CH, Wu SJ, Huang HD, Lu PL, Fann CSJ, Chen M, Chen YH, Chen YMA. Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2020; 54:596-605. [PMID: 32067946 DOI: 10.1016/j.jmii.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/21/2019] [Accepted: 12/26/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND/PURPOSE Intentional transmission of HIV-1 is a crime. Identifying the source of transmission between HIV-1 infected cases using phylogenetic analysis has limitations, including delayed examinations after the initiation of infection and ambiguity of phyletic relationships. This study was the first to introduce phylogenetic tree Results as forensic evidence in a trial in Taiwan. METHODS Three lawsuit cases from different district courts in Taiwan were chosen for this study. We identified the source of transmission between individuals in each lawsuit based on the maximum likelihood and Bayesian phylogenetic tree analyses using the HIV-1 sequences from molecular cloning and ultra-deep pyrosequencing (UDPS). Two gene regions of the HIV genome, env and gag, were involved. RESULTS The results of phylogenetic analysis using sequences from molecular cloning were clear and evidential enough in lawsuits 1 and 3. Due to the delayed sampling time, the result of sequences from molecular cloning in lawsuit 2 was ambiguous. Combined with the analyzed result of sequences from UDPS and epidemiological information, the source of transmission in lawsuit 2 was further identified. CONCLUSION Hence phylogenetic analyses cannot exclude the possibility of unsampled intermediaries, the data interpretation should be more careful and conservative, and it should not be considered as the only evidence for the source identification in a trial without epidemiological or serological information. The evaluation of the introduced UDPS method in the identification of transmission source has shown that the validity and evidential effects were still limited and need further optimization.
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Affiliation(s)
- Wei-You Li
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Szu-Wei Huang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Sheng-Fan Wang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsin-Fu Liu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Shang-Jung Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Po-Liang Lu
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Cathy S J Fann
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Marcelo Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Urology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Cosmetic Applications and Management, Mackay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Yen-Hsu Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Clinical Pharmacogenomics and Pharmacoproteomics Program, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
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9
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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10
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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11
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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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12
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Whole-genome sequencing of Neisseria gonorrhoeae in a forensic transmission case. Forensic Sci Int Genet 2019; 42:141-146. [PMID: 31319352 DOI: 10.1016/j.fsigen.2019.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/02/2019] [Accepted: 07/02/2019] [Indexed: 11/21/2022]
Abstract
Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission episode in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods. We obtained genomes of Neisseria gonorrhoeae from the victim, the suspect, and 29 unrelated controls. The analysis of the genomes revealed that the victim and suspect isolates had identical sequences in both the bacterial chromosome and the single plasmid present in them. One of the local controls was very similar (differing in only 2 SNPs) to the case sequences, but the remaining controls were very divergent. Additional cases of identity and very high similarity among controls were observed occasionally, pointing at recent transmission cases. These results were more discriminative than the previous molecular epidemiology analyses performed at the hospital's Microbiology Service, as Multi-Locus Sequence Typing (MLST) could not distinguish between the suspect/victim and the controls isolates, and Pulse Field Gel Electrophoresis (PFGE) was not able to distinguish between the suspect/victim and one of the local controls. These results lead us to conclude that complete bacterial genome sequences obtained with HTS technologies may be a valuable tool for establishing recent transmission cases and, although more studies are needed, they have a great potential for being used in forensic analyses.
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Wu J, Hu Z, Yao H, Wang H, Lei Y, Zhong P, Feng Y, Xing H, Shen Y, Jin L, Liu A, Qin Y, Miao L, Su B, Zhang Y, Guo H. The inference of HIV-1 transmission direction between HIV-1 positive couples based on the sequences of HIV-1 quasi-species. BMC Infect Dis 2019; 19:566. [PMID: 31253127 PMCID: PMC6599307 DOI: 10.1186/s12879-019-4163-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 06/04/2019] [Indexed: 11/22/2022] Open
Abstract
Background To infer transmission direction of a HIV transmission chain is helpful not only in legal jurisdiction but also in precise intervention to prevent HIV spread. Recently, the direction of transmission is inferred by whether paraphyletic-monophyletic (PM) or a combination of paraphyletic and polyphyletic (PP) topologies is observed or not between the sequences of source and recipient in the phylogenetic tree. However, paraphyly between them often declines over time and may disappear between spouses due to bidirectional transmission after primary infection. In this study, our aim is to test the reliability of inferring HIV transmission direction between epidemiologically linked HIV-1 positive couples using whether or not paraphyly is observed in phylogenetic tree. Methods HIV quasi-species were sequenced using PCR product clones, and then Bayesian analysis of molecular sequences with MCMC was employed to construct phylogenetic relationship of env, gag, pol gene fragments of HIV-1 positive couples using BEAST software. Results Our results showed that all sequences of seven couples except pol sequences of couple 12 and 13 form their own monophyletic cluster in phylogenetic tree including the closest control sequences from GenBank or other studies on local samples, which are supported by significant Bayesian posterior probabilities more than 0.9932. Of seven couples, paraphyly is only observed in phylogenetic tree constructed with env and pol gene sequences of three couples and gag gene sequences of four couples. Paraphyly is not observed in half of HIV positive couples. Pol sequences of couple 13 is separated by Blast selected controls; pol sequences of couple 12 in phylogenetic tree is supported by a lower Bayesian posterior value. Conclusion Paraphyly relationship between sequences of donator and recipient is only observed among partial HIV-1 positive couples with epidemiological link. Phylogenetic relationship is not always the same when various gene regions of HIV are used to conduct phylogenetic analysis. The combination of phylogenetic analysis based on various gene regions of HIV and enough epidemiology investigation is essential when inferring transmission direction of HIV in a transmission chain or in one couple. However, while observed paraphyly can be used to infer transmission direction in HIV-1 positive couple, no observed paraphyly cannot deny it.
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Affiliation(s)
- Jianjun Wu
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Zhongwang Hu
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Hui Yao
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Hai Wang
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Yanhua Lei
- Hefei Prefecture Center for Disease Control and Prevention, 86 Liu'an Road, Hefei, China
| | - Ping Zhong
- Shanghai Municipal Center for Disease Control and Prevention, 1380 Zhongshan West Road, Shanghai, China
| | - Yi Feng
- Chinese Center for Disease Control and Prevention, 155 Changbei Road, Beijing, China
| | - Hui Xing
- Chinese Center for Disease Control and Prevention, 155 Changbei Road, Beijing, China
| | - Yuelan Shen
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Lin Jin
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Aiwen Liu
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Yizu Qin
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Lifeng Miao
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China
| | - Bin Su
- Anhui Provincial Center for Disease Control and Prevention, 12560 Fanhuadadao, Hefei, China.
| | - Yibo Zhang
- Department of Hospital Infection Control, Shanghai Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hongxiong Guo
- Jiangsu Provincial Center for Disease Control and Prevention, 172 Jiangsu Road, Nanjing, China.
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14
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Hosokawa-Muto J, Sakai H, Sassa Y, Fujinami Y, Kishimoto M, Nakahara H. Rapid detection of pathogenic virus genome sequence from throat and nasal swab samples using an exhaustive gene amplification method. Forensic Sci Med Pathol 2019; 15:399-403. [PMID: 31250258 DOI: 10.1007/s12024-019-00128-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2019] [Indexed: 12/01/2022]
Abstract
Rapid identification of pathogenic agents is important in response to the emergence of biocrime and bioterrorism, to facilitate appropriate confinement and treatment. As the rapid determination system of viral genome sequences (RDV method) using exhaustive gene amplification is useful for rapid identification, we examined whether this method could be applied to forensic samples. To detect pathogenic virus in a cat with suspected viral infections, fluid swab samples were applied to the RDV method. The following steps were performed: viral propagation, extraction of the viral genome, amplification of the first library, fragmentation of the library, amplification of the second library using non-specific primer sets, and direct sequencing of the amplicon. To confirm the viruses detected by this method, we performed conventional PCR using virus-specific primers. We detected pathogenic virus genome sequences from the swab samples and confirmed infection with these viruses. In addition, we directly detected a viral genome sequence from the nasal swab sample without the viral propagation step. The RDV method is infrequently used in forensic analysis. This method is practicable with equipment existing in a normal laboratory and is useful for rapid detection and identification of pathogenic viruses in forensic samples. This method would also be applicable to the detection of bacteria and fungi.
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Affiliation(s)
- Junji Hosokawa-Muto
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan.
| | - Hiroki Sakai
- Laboratory of Veterinary Pathology, Joint Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Yukiko Sassa
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Yoshihito Fujinami
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Mai Kishimoto
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Hiroaki Nakahara
- Fifth Biology Section, First Department of Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
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15
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Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO. HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens. Mol Biol Evol 2019; 35:1812-1819. [PMID: 29401317 DOI: 10.1093/molbev/msy016] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoe-leather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, that is, on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from www.github.com/veg/hivtrace, along with the accompanying result visualization module from www.github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens.
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Affiliation(s)
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Andrew J Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, CA
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16
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Mutenherwa F, Wassenaar DR, de Oliveira T. Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research. J Empir Res Hum Res Ethics 2018; 14:61-77. [PMID: 30486713 DOI: 10.1177/1556264618809608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The use of phylogenetics in HIV molecular epidemiology has considerably increased our ability to understand the origin, spread, and characteristics of HIV epidemics. Despite its potential to advance knowledge on HIV transmission dynamics, the ethical issues associated with HIV molecular epidemiology have received minimal attention. In-depth interviews were conducted with scientists from diverse backgrounds to explore their perspectives on ethical issues associated with phylogenetic analysis of HIV genetic data as applied to HIV transmission dynamics studies. The Emanuel framework was used as the analytical framework. Favorable risk-benefit ratio and informed consent were the most invoked ethical principles and fair participant selection the least. Fear of loss of privacy and disclosure of HIV transmission were invariably cited as key ethical concerns. As HIV sequence data become increasingly available, comprehensive guidelines should be developed to guide its access, sharing and use, cognizant of the potential harms that may result.
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Affiliation(s)
- Farirai Mutenherwa
- 1 University of KwaZulu-Natal, South Africa.,2 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Tulio de Oliveira
- 1 University of KwaZulu-Natal, South Africa.,2 KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,3 Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
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17
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Environmental microbiology: Perspectives for legal and occupational medicine. Leg Med (Tokyo) 2018; 35:34-43. [DOI: 10.1016/j.legalmed.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/09/2018] [Accepted: 09/23/2018] [Indexed: 11/18/2022]
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18
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Affiliation(s)
- Amy Willis
- Department of Biostatistics, University of Washington, Seattle, WA
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19
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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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20
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The Transmission and Evolution of HIV-1 Quasispecies within One Couple: a Follow-up Study based on Next-Generation Sequencing. Sci Rep 2018; 8:1404. [PMID: 29362487 PMCID: PMC5780463 DOI: 10.1038/s41598-018-19783-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/04/2018] [Indexed: 11/09/2022] Open
Abstract
Next-generation sequencing (NGS) has been successfully used to trace HIV-1 infection. In this study, we investigated the transmission and evolution of HIV-1 quasispecies in a couple infected through heterosexual behavior. A heterosexual couple in which both partners were infected with HIV-1 was followed up for 54 months. Blood samples including whole-blood and plasma samples, were collected at various time points. After HIV-1 subtyping, NGS (Miseq platform) was used to sequence the env region of the HIV-1 quasispecies. Genetic distances were calculated, and phylogenetic trees were generated. We found both partners were infected with HIV-1 subtype circulating recombinant form (CRF), CRF65_cpx. The quasispecies distribution was relatively tightly clustered in the phylogenetic tree during early infection. Over time, the distribution of HIV-1 quasispecies gradually became more dispersed at 12th months, with a progressive increase in gene diversity. By 37th months, the sequences obtained for both partners formed different clusters in the phylogenetic tree. These results suggest that the HIV-1 contact tracing results generated by the Miseq platform may be more reliable than other conventional sequencing methods, which can provide important information about the transmission and evolution of HIV-1. Our findings may help to better target preventative interventions for promoting public health.
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21
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Fujimoto K, Coghill LM, Weier CA, Hwang LY, Kim JY, Schneider JA, Metzker ML, Brown JM. Short Communication: Lack of Support for Socially Connected HIV-1 Transmission Among Young Adult Black Men Who Have Sex with Men. AIDS Res Hum Retroviruses 2017; 33:935-940. [PMID: 28398775 DOI: 10.1089/aid.2016.0228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We explore the phylogenetic relationships among HIV sequences sampled from young adult black men who have sex with men (YAB-MSM), who are connected through peer referral/social ties and who attend common venues. Using 196 viral sequences sampled from the peripheral blood mononuclear cells of 10 individuals, our preliminary phylogenetic results indicate that these socially connected YAB-MSM are infected with distantly related viruses and provide no evidence for viral transmission between network members. Our results suggest that HIV-prevention strategies that target young adult MSM should extend beyond their network members and local community.
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Affiliation(s)
- Kayo Fujimoto
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Lyndon M. Coghill
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | | | - Lu-Yu Hwang
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Ju Yeong Kim
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | | | | | - Jeremy M. Brown
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
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22
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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23
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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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24
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Wang N, Tang Z, Li Y, Xie P, Shao Y. Molecular linkage tracing of HIV-1 transmission events in seroconcordant couples in Guangxi Province, Southeastern China. SPRINGERPLUS 2016; 5:2015. [PMID: 27942427 PMCID: PMC5124024 DOI: 10.1186/s40064-016-3578-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 10/19/2016] [Indexed: 12/03/2022]
Abstract
Background Guangxi Province in Southeastern China has one of the highest HIV-1 infection and transmission rates in stable couples. However, the mode of transmission at the molecular level has seldom been reported amongst this group. It is important to investigate this issue to support the treatment-as-prevention approach and for efficient interventions. Methods HIV-1 subgenomic regions (1.2 kb of pol and a 660-bp env C2V5 fragment) were sequenced in 42 couples. A couple linkage assessment was performed by phylogenetic analysis of sequences and Bayesian analysis of genetic distances. A subset of pairs was selected for single-genome amplification. Results Thirty-five pairs (83.3 %, 35/42) were identified as linked, 3 pairs (7.1 %, 3/42) were identified as indeterminate, and 4 pairs (9.5 %) were identified as unlinked. The predominant intra-couple-transmitted HIV-1 subtype was CRF01_AE (80 %, 28/35). The median genetic distance of linked couples was 0.5 %. Conclusion The majority of HIV-1 transmission events in this study occurred within the partnership, and the predominant HIV-1 subtype was CRF01_AE. Further research on the mode of HIV transmission in other locations is needed. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-3578-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nidan Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing, People's Republic of China
| | - Zhenzhu Tang
- Guangxi Center for Disease Prevention and Control, Nanning, People's Republic of China
| | - Yijia Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing, People's Republic of China
| | - Peiyan Xie
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yiming Shao
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
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25
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Abstract
ABSTRACT
Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.
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26
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Abstract
Microbial forensics has been defined as the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes. Over the past 15 years, technology, particularly massively parallel sequencing, and bioinformatics advances now allow the characterization of microorganisms for a variety of human forensic applications, such as human identification, body fluid characterization, postmortem interval estimation, and biocrimes involving tracking of infectious agents. Thus, microbial forensics should be more broadly described as the discipline of applying scientific methods to the analysis of microbial evidence in criminal and civil cases for investigative purposes.
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Affiliation(s)
- Sarah E Schmedes
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Antti Sajantila
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Bruce Budowle
- Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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Paraskevis D, Nikolopoulos GK, Magiorkinis G, Hodges-Mameletzis I, Hatzakis A. The application of HIV molecular epidemiology to public health. INFECTION GENETICS AND EVOLUTION 2016; 46:159-168. [PMID: 27312102 DOI: 10.1016/j.meegid.2016.06.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 02/02/2023]
Abstract
HIV is responsible for one of the largest viral pandemics in human history. Despite a concerted global response for prevention and treatment, the virus persists. Thus, urgent public health action, utilizing novel interventions, is needed to prevent future transmission events, critical to eliminating HIV. For public health planning to prove effective and successful, we need to understand the dynamics of regional epidemics and to intervene appropriately. HIV molecular epidemiology tools as implemented in phylogenetic, phylodynamic and phylogeographic analyses have proven to be powerful tools in public health planning across many studies. Numerous applications with HIV suggest that molecular methods alone or in combination with mathematical modelling can provide inferences about the transmission dynamics, critical epidemiological parameters (prevalence, incidence, effective number of infections, Re, generation times, time between infection and diagnosis), or the spatiotemporal characteristics of epidemics. Molecular tools have been used to assess the impact of an intervention and outbreak investigation which are of great public health relevance. In some settings, molecular sequence data may be more readily available than HIV surveillance data, and can therefore allow for molecular analyses to be conducted more easily. Nonetheless, classic methods have an integral role in monitoring and evaluation of public health programmes, and should supplement emerging techniques from the field of molecular epidemiology. Importantly, molecular epidemiology remains a promising approach in responding to viral diseases.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - G K Nikolopoulos
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, United Kingdom
| | | | - A Hatzakis
- Hellenic Center for Diseases Control and Prevention, Maroussi, Greece
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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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Zhao Q, Zhang C, Jiang Y, Wen Y, Pan P, Li Y, Zhang G, Zhang L, Qiu M. Short Communication: Investigating a Chain of HIV Transmission Events Due to Homosexual Exposure and Blood Transfusion Based on a Next Generation Sequencing Method. AIDS Res Hum Retroviruses 2015; 31:1225-9. [PMID: 26355677 DOI: 10.1089/aid.2015.0178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This study investigates a chain of HIV transmission events due to homosexual exposure and blood transfusion in China. The MiSeq platform, a next generation sequencing (NGS) system, was used to obtain genetic details of the HIV-1 env region (336 base pairs). Evolutionary analysis combined with epidemiologic evidence suggests a transmission chain from patient T3 to T2 through homosexual exposure and subsequently to T1 through blood transfusion. More importantly, a phylogenetic study suggested a likely genetic bottleneck for HIV in homosexual transmission from T3 to T2, while T1 inherited the majority of variants from T2. The result from the MiSeq platform is consistent with findings from the epidemiologic survey. The MiSeq platform is a powerful tool for tracing HIV transmissions and intrapersonal evolution.
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Affiliation(s)
- Qi Zhao
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Chen Zhang
- 2 National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yan Jiang
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yujie Wen
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Pinliang Pan
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Yang Li
- 2 National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Guiyun Zhang
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
| | - Lei Zhang
- 3 Research Center for Public Health, School of Medicine, Tsinghua University , Beijing, China
- 4 Melbourne Sexual Health Centre , Alfred Health, Melbourne, Victoria, Australia
- 5 Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University , Melbourne, Victoria, Australia
| | - Maofeng Qiu
- 1 National AIDS Reference Laboratory, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing, China
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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: 47] [Impact Index Per Article: 5.2] [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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Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL. Whole-genome sequencing in outbreak analysis. Clin Microbiol Rev 2015; 28:541-63. [PMID: 25876885 PMCID: PMC4399107 DOI: 10.1128/cmr.00075-13] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In addition to the ever-present concern of medical professionals about epidemics of infectious diseases, the relative ease of access and low cost of obtaining, producing, and disseminating pathogenic organisms or biological toxins mean that bioterrorism activity should also be considered when facing a disease outbreak. Utilization of whole-genome sequencing (WGS) in outbreak analysis facilitates the rapid and accurate identification of virulence factors of the pathogen and can be used to identify the path of disease transmission within a population and provide information on the probable source. Molecular tools such as WGS are being refined and advanced at a rapid pace to provide robust and higher-resolution methods for identifying, comparing, and classifying pathogenic organisms. If these methods of pathogen characterization are properly applied, they will enable an improved public health response whether a disease outbreak was initiated by natural events or by accidental or deliberate human activity. The current application of next-generation sequencing (NGS) technology to microbial WGS and microbial forensics is reviewed.
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Affiliation(s)
- Carol A Gilchrist
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen D Turner
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret F Riley
- Department of Public Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA School of Law, University of Virginia, Charlottesville, Virginia, USA Batten School of Leadership and Public Policy, University of Virginia, Charlottesville, Virginia, USA
| | - William A Petri
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Pathology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Erik L Hewlett
- Department of Medicine, School of Medicine, University of Virginia, Charlottesville, Virginia, USA Department of Microbiology, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
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Evaluation of the Universal Viral Transport system for long-term storage of virus specimens for microbial forensics. J Forensic Leg Med 2015; 34:29-33. [PMID: 26165655 DOI: 10.1016/j.jflm.2015.04.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/05/2015] [Accepted: 04/30/2015] [Indexed: 11/20/2022]
Abstract
Forensic microbial specimens, including bacteria and viruses, are collected at biocrime and bioterrorism scenes. Although it is preferable that the pathogens in these samples are alive and kept in a steady state, the samples may be stored for prolonged periods before analysis. Therefore, it is important to understand the effects of storage conditions on the pathogens contained within such samples. To evaluate the capacity to preserve viable virus and the viral genome, influenza virus was added to the transport medium of the Universal Viral Transport system and stored for over 3 months at various temperatures, after which virus titrations and quantitative analysis of the influenza hemagglutinin gene were performed. Although viable viruses became undetectable 29 days after the medium was stored at room temperature, viruses in the medium stored at 4°C were viable even after 99 days. A quantitative PCR analysis indicated that the hemagglutinin gene was maintained for 99 days at both 4°C and room temperature. Therefore, long-term storage at 4°C has little effect on viable virus and viral genes, so the Universal Viral Transport system can be useful for microbial forensics. This study provides important information for the handling of forensic virus specimens.
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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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Abstract
Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 PMCID: PMC4304655 DOI: 10.1097/qai.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Affiliation(s)
- Ann M. Dennis
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Tulio de Oliveira
- Wellcome Trust-Africa Centre for Health and Population Studies, University of Kwazula-Natal, ZA
| | - Deenan Pillay
- Division of Infection and Immunity, University College London, London, UK
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Myron S. Cohen
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC
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37
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Hartfield M, Murall CL, Alizon S. Clinical applications of pathogen phylogenies. Trends Mol Med 2014; 20:394-404. [DOI: 10.1016/j.molmed.2014.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 12/16/2022]
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Romero-Severson E, Skar H, Bulla I, Albert J, Leitner T. Timing and order of transmission events is not directly reflected in a pathogen phylogeny. Mol Biol Evol 2014; 31:2472-82. [PMID: 24874208 DOI: 10.1093/molbev/msu179] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of more than 1 host occur within hosts, not at the moment of transmission, predating the transmission events as described by the pretransmission interval. Second, the order in which nodes in a phylogeny occur may be reflective of the within-host dynamics rather than epidemiologic relationships. To investigate these phenomena, motivated by within-host diversity patterns, we developed a two-phase coalescent model that includes a transmission bottleneck followed by linear outgrowth to a maximum population size followed by either stabilization or decline of the population. The model predicts that the pretransmission interval shrinks compared with predictions based on constant population size or a simple transmission bottleneck. Because lineages coalesce faster in a small population, the probability of a pathogen phylogeny to resemble the transmission history depends on when after infection a donor transmits to a new host. We also show that the probability of inferring the incorrect order of multiple transmissions from the same host is high. Finally, we compare time of HIV-1 infection informed by genetic distances in phylogenies to independent biomarker data, and show that, indeed, the pretransmission interval biases phylogeny-based estimates of when transmissions occurred. We describe situations where caution is needed not to misinterpret which parts of a phylogeny that may indicate outbreaks and tight transmission clusters.
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Affiliation(s)
- Ethan Romero-Severson
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Helena Skar
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Ingo Bulla
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, SwedenDepartment of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM
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Som A. Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 2014; 16:536-48. [PMID: 24872401 DOI: 10.1093/bib/bbu015] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/05/2014] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic analysis is used to recover the evolutionary history of species, genes or proteins. Understanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. Moreover, it is important because of its wide applications that include understanding genome organization, epidemiological investigations, predicting protein functions, and deciding the genes to be analyzed in comparative studies. Despite immense progress in recent years, phylogenetic reconstruction involves many challenges that create uncertainty with respect to the true evolutionary relationships of the species or genes analyzed. One of the most notable difficulties is the widespread occurrence of incongruence among methods and also among individual genes or different genomic regions. Presence of widespread incongruence inhibits successful revealing of evolutionary relationships and applications of phylogenetic analysis. In this article, I concisely review the effect of various factors that cause incongruence in molecular phylogenies, the advances in the field that resolved some factors, and explore unresolved factors that cause incongruence along with possible ways for tackling them.
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40
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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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Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM. Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster. Mol Phylogenet Evol 2014; 75:126-37. [PMID: 24589520 DOI: 10.1016/j.ympev.2014.02.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 11/28/2022]
Abstract
Stochastic models of sequence evolution have been developed to reflect many biologically important processes, allowing for accurate phylogenetic reconstruction when an appropriate model is selected. However, commonly used models do not incorporate several potentially important biological processes. Spurious phylogenetic inference may result if these processes play an important role in the evolution of a dataset yet are not incorporated into assumed models. Few studies have attempted to assess the relative importance of multiple processes in producing spurious inferences. The application of phylogenetic methods to infer the source of HIV-1 transmission clusters depends upon accurate phylogenetic results, yet there are several relevant unmodeled biological processes (e.g., recombination and convergence) that may cause complications. Here, through analyses of HIV-1 env sequences from a small, forensically important transmission cluster, we tease apart the impact of these processes and present evidence suggesting that convergent evolution and high rates of insertions and deletions (causing alignment uncertainty) led to spurious phylogenetic signal with forensic relevance. Previous analyses show paraphyly of HIV-1 lineages sampled from an individual who, based on non-phylogenetic evidence, had never acted as a source of infection for others in this transmission cluster. If true, this pattern calls into question assumptions underlying phylogenetic approaches to source and recipient identification. By systematically assessing the contribution of different unmodeled processes, we demonstrate that removal of sites likely influenced by strong positive selection both reduces the alignment-wide signal supporting paraphyly of viruses sampled from this individual and eliminates support for the effects of recombination. Additionally, the removal of ambiguously aligned sites alters strongly supported relationships among viruses sampled from different individuals. These observations highlight the need to jointly consider multiple unmodeled evolutionary processes and motivate a phylogenomic perspective when inferring viral transmission histories.
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Affiliation(s)
- Vinson P Doyle
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - John J Andersen
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Bradley J Nelson
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Michael L Metzker
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, and Cell and Molecular Biology Program, Baylor College of Medicine, Houston, TX, USA
| | - Jeremy M Brown
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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Sajantila A. Molecular clocks ticking in the court room. INVESTIGATIVE GENETICS 2014; 5:4. [PMID: 24581009 PMCID: PMC3938035 DOI: 10.1186/2041-2223-5-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/20/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Antti Sajantila
- Department of Forensic Medicine, Hjelt Institute, University of Helsinki, P,O,Box 40, 00014 Helsinki, Finland.
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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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Acquisition of HIV by African-born residents of Victoria, Australia: insights from molecular epidemiology. PLoS One 2013; 8:e84008. [PMID: 24391866 PMCID: PMC3877143 DOI: 10.1371/journal.pone.0084008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 11/11/2013] [Indexed: 11/19/2022] Open
Abstract
African-born Australians are a recognised "priority population" in Australia's Sixth National HIV/AIDS Strategy. We compared exposure location and route for African-born people living with HIV (PLHIV) in Victoria, Australia, with HIV-1 pol subtype from drug resistance assays and geographical origin suggested by phylogenetic analysis of env gene. Twenty adult HIV positive African-born Victorian residents were recruited via treating doctors. HIV exposure details were obtained from interviews and case notes. Viral RNA was extracted from participant stored plasma or whole blood. The env V3 region was sequenced and compared to globally representative reference HIV-1 sequences in the Los Alamos National Library HIV Database. Twelve participants reported exposure via heterosexual sex and two via iatrogenic blood exposures; four were men having sex with men (MSM); two were exposed via unknown routes. Eight participants reported exposure in their countries of birth, seven in Australia, three in other countries and two in unknown locations. Genotype results (pol) were available for ten participants. HIV env amplification was successful in eighteen cases. HIV-1 subtype was identified in all participants: eight both pol and env; ten env alone and two pol alone. Twelve were subtype C, four subtype B, three subtype A and one subtype CRF02_AG. Reported exposure location was consistent with the phylogenetic clustering of env sequences. African Australians are members of multiple transnational social and sexual networks influencing their exposure to HIV. Phylogenetic analysis may complement traditional surveillance to discern patterns of HIV exposure, providing focus for HIV prevention programs in mobile populations.
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Inferring the source of transmission with phylogenetic data. PLoS Comput Biol 2013; 9:e1003397. [PMID: 24367249 PMCID: PMC3868546 DOI: 10.1371/journal.pcbi.1003397] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 11/01/2013] [Indexed: 12/24/2022] Open
Abstract
Identifying the source of transmission using pathogen genetic data is complicated by numerous biological, immunological, and behavioral factors. A large source of error arises when there is incomplete or sparse sampling of cases. Unsampled cases may act as either a common source of infection or as an intermediary in a transmission chain for hosts infected with genetically similar pathogens. It is difficult to quantify the probability of common source or intermediate transmission events, which has made it difficult to develop statistical tests to either confirm or deny putative transmission pairs with genetic data. We present a method to incorporate additional information about an infectious disease epidemic, such as incidence and prevalence of infection over time, to inform estimates of the probability that one sampled host is the direct source of infection of another host in a pathogen gene genealogy. These methods enable forensic applications, such as source-case attribution, for infectious disease epidemics with incomplete sampling, which is usually the case for high-morbidity community-acquired pathogens like HIV, Influenza and Dengue virus. These methods also enable epidemiological applications such as the identification of factors that increase the risk of transmission. We demonstrate these methods in the context of the HIV epidemic in Detroit, Michigan, and we evaluate the suitability of current sequence databases for forensic and epidemiological investigations. We find that currently available sequences collected for drug resistance testing of HIV are unlikely to be useful in most forensic investigations, but are useful for identifying transmission risk factors. Molecular data from pathogens may be useful for identifying the source of infection and identifying pairs of individuals such that one host transmitted to the other. Inference of who acquired infection from whom is confounded by incomplete sampling, and given genetic data only, it is not possible to infer the direction of transmission in a transmission pair. Given additional information about an infectious disease epidemic, such as incidence of infection over time, and the proportion of hosts sampled, it is possible to correct for biases stemming from incomplete sampling of the infected host population. It may even be possible to infer the direction of transmission within a transmission pair if additional clinical, behavioral, and demographic covariates of the infected hosts are available. We consider the problem of identifying the source of infection using HIV sequence data collected for clinical purposes. We find that it is rarely possible to infer transmission pairs with high credibility, but such data may nevertheless be useful for epidemiological investigations and identifying risk factors for transmission.
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48
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Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. J Infect Dis 2013; 209:304-13. [PMID: 24151309 DOI: 10.1093/infdis/jit524] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is pandemic, but its contemporary global transmission network has not been characterized. A better understanding of the properties and dynamics of this network is essential for surveillance, prevention, and eventual eradication of HIV. Here, we apply a simple and computationally efficient network-based approach to all publicly available HIV polymerase sequences in the global database, revealing a contemporary picture of the spread of HIV-1 within and between countries. This approach automatically recovered well-characterized transmission clusters and extended other clusters thought to be contained within a single country across international borders. In addition, previously undescribed transmission clusters were discovered. Together, these clusters represent all known modes of HIV transmission. The extent of international linkage revealed by our comprehensive approach demonstrates the need to consider the global diversity of HIV, even when describing local epidemics. Finally, the speed of this method allows for near-real-time surveillance of the pandemic's progression.
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Affiliation(s)
- Cadhla Firth
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032; ,
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50
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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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