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Calderón LCL, Cabanne GS, Marcos A, Novo SG, Torres C, Perez AM, Pybus OG, König GA. Phylodynamic analysis of foot-and-mouth disease virus evolution in Mar Chiquita, Argentina. Arch Virol 2024; 169:101. [PMID: 38630189 DOI: 10.1007/s00705-024-06028-0] [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: 09/25/2023] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10- 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread.
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Affiliation(s)
| | - Gustavo S Cabanne
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Buenos Aires, Argentina
| | - Andrea Marcos
- Coordinación general de Epidemiología y Análisis de Riesgo, SENASA, Buenos Aires, Argentina
| | - Sabrina Galdo Novo
- DGLYCT - Dirección de Laboratorio Animal, SENASA, Buenos Aires, Argentina
| | - Carolina Torres
- Instituto de Investigaciones en Bacteriología y Virología Molecular FFyB, UBA, Buenos Aires, Argentina
| | - Andrés M Perez
- Department of Veterinary Population Medicine, UMN, St Paul, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina.
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Kabir A, Kamboh AA, Abubakar M, Baloch H, Nizamani ZA. Foot-and-mouth disease virus dynamics in border areas of Pakistan with Afghanistan. Mol Biol Rep 2024; 51:370. [PMID: 38411732 DOI: 10.1007/s11033-024-09262-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/17/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Foot and mouth disease (FMD) is a highly contagious disease that impacts cloven-hoofed animals globally. The illegal trade of livestock between the border regions of Pakistan and Afghanistan can contribute to the spread of this disease. This study focuses on investigating the outbreaks of FMD that occurred in this area from June 2020 to May 2021. METHODS RESULTS: A total of 233 epithelial tissue samples were collected, and 77% were found positive for FMDV through an antigen-detection by ELISA and molecular conformation through RT-PCR. The study found three serotypes of FMDV dominating in the border area of Pakistan with Afghanistan: O, A, and Asia-1. The outbreak activity was peaked between August/September followed by July/October 2020. Phylogenetic analysis conducted using the VP1 region sequence showed that serotype O isolates belonged to the Middle East-South Asia (ME-SA) topotype, PanAsia-2 lineage, and ANT-10 sub-lineage, while serotype Asia-1 isolates belonged to a novel lineage BD-18.The highest prevalence of serotype O of FMDV was found in cattle and buffalo of 1-2 year age group, while the highest outbreak ratio of serotype O was recorded in goats of 0-1 year age group and sheep of > 2 year age group. The serotype O was more prevalent in male than female sheep. The type A was more prevalent in females of sheep and goats than their corresponding males. The serotype Asia-1 was more prevalent in females of cattle and sheep than their corresponding males. The outbreak epidemiology of FMD varied significantly between various regions, months of study, animal species, age groups, and gender. CONCLUSIONS The study found that FMD outbreaks in the border area of Pakistan and Afghanistan were diverse and complicated, and that different types of FMDV were circulating. The study recommended effective actions to stop FMD transmission in this area.
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Affiliation(s)
- Abdul Kabir
- Department, of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, 70060, Pakistan
| | - Asghar Ali Kamboh
- Department, of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, 70060, Pakistan.
| | | | - Hasina Baloch
- Department, of Veterinary Microbiology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, 70060, Pakistan
| | - Zaheer Ahmed Nizamani
- Department of Veterinary Pathology, Faculty of Animal Husbandry and Veterinary Sciences, Sindh Agriculture University, Tandojam, 70060, Pakistan
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Specht IOA, Petros BA, Moreno GK, Brock-Fisher T, Krasilnikova LA, Schifferli M, Yang K, Cronan P, Glennon O, Schaffner SF, Park DJ, MacInnis BL, Ozonoff A, Fry B, Mitzenmacher MD, Varilly P, Sabeti PC. Inferring Viral Transmission Pathways from Within-Host Variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.14.23297039. [PMID: 37873325 PMCID: PMC10593003 DOI: 10.1101/2023.10.14.23297039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA. We then demonstrate that our reconstruction approach infers transmissions more accurately than two leading methods on synthetic data, as well as in a controlled outbreak of bovine respiratory syncytial virus and an epidemiologically-investigated SARS-CoV-2 outbreak in South Africa. Finally, we apply our transmission reconstruction tool to 5,692 outbreaks among the 134,682 Massachusetts genomes. Our methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, and provide an adaptable mathematical framework for tracking within-host evolution.
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Affiliation(s)
- Ivan O. A. Specht
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard College, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Brittany A. Petros
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA
- Harvard/MIT MD-PhD Program, Boston, MA 02115, USA
- Systems, Synthetic, and Quantitative Biology PhD Program, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Gage K. Moreno
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Taylor Brock-Fisher
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Lydia A. Krasilnikova
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | | | - Paul Cronan
- Fathom Information Design, Boston, MA 02114, USA
| | | | | | - Daniel J. Park
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bronwyn L. MacInnis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Al Ozonoff
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ben Fry
- Fathom Information Design, Boston, MA 02114, USA
| | - Michael D. Mitzenmacher
- Department of Computer Science, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Patrick Varilly
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Pardis C. Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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4
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Robert A, Tsui Lok Hei J, Watson CH, Gsell PS, Hall Y, Rambaut A, Longini IM, Sakoba K, Kucharski AJ, Touré A, Danmadji Nadlaou S, Saidou Barry M, Fofana TO, Lansana Kaba I, Sylla L, Diaby ML, Soumah O, Diallo A, Niare A, Diallo A, Eggo RM, Caroll MW, Henao-Restrepo AM, Edmunds WJ, Hué S. Quantifying the value of viral genomics when inferring who infected whom in the 2014-16 Ebola virus outbreak in Guinea. Virus Evol 2023; 9:vead007. [PMID: 36926449 PMCID: PMC10013732 DOI: 10.1093/ve/vead007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Transmission trees can be established through detailed contact histories, statistical or phylogenetic inference, or a combination of methods. Each approach has its limitations, and the extent to which they succeed in revealing a 'true' transmission history remains unclear. In this study, we compared the transmission trees obtained through contact tracing investigations and various inference methods to identify the contribution and value of each approach. We studied eighty-six sequenced cases reported in Guinea between March and November 2015. Contact tracing investigations classified these cases into eight independent transmission chains. We inferred the transmission history from the genetic sequences of the cases (phylogenetic approach), their onset date (epidemiological approach), and a combination of both (combined approach). The inferred transmission trees were then compared to those from the contact tracing investigations. Inference methods using individual data sources (i.e. the phylogenetic analysis and the epidemiological approach) were insufficiently informative to accurately reconstruct the transmission trees and the direction of transmission. The combined approach was able to identify a reduced pool of infectors for each case and highlight likely connections among chains classified as independent by the contact tracing investigations. Overall, the transmissions identified by the contact tracing investigations agreed with the evolutionary history of the viral genomes, even though some cases appeared to be misclassified. Therefore, collecting genetic sequences during outbreak is key to supplement the information contained in contact tracing investigations. Although none of the methods we used could identify one unique infector per case, the combined approach highlighted the added value of mixing epidemiological and genetic information to reconstruct who infected whom.
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Affiliation(s)
- Alexis Robert
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Joseph Tsui Lok Hei
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Conall H Watson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Epidemic Diseases Research Group Oxford, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7LG, UK
| | | | - Yper Hall
- UK Health Security Agency, Manor Farm Rd, Porton Down, Salisbury SP4 0JG, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Ira M Longini
- Department of Biostatistics, University of Florida, 2004 Mowry Road, 5th Floor CTRB, Gainesville, FL 32611-7450, USA
| | - Keïta Sakoba
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Adam J Kucharski
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Alhassane Touré
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | | | | | | | - Lansana Sylla
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | - Ousmane Soumah
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Abdourahime Diallo
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | - Amadou Niare
- World Health Organization Ebola Vaccination Team, Sonfonia T.7, Conakry, Guinea
| | | | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Miles W Caroll
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, UK
| | | | - W John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
| | - Stéphane Hué
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 6HT, UK
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5
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Johnson PCD, Hägglund S, Näslund K, Meyer G, Taylor G, Orton RJ, Zohari S, Haydon DT, Valarcher JF. Evaluating the potential of whole-genome sequencing for tracing transmission routes in experimental infections and natural outbreaks of bovine respiratory syncytial virus. Vet Res 2022; 53:107. [PMID: 36510312 PMCID: PMC9746130 DOI: 10.1186/s13567-022-01127-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022] Open
Abstract
Bovine respiratory syncytial virus (BRSV) is a major cause of respiratory disease in cattle. Genomic sequencing can resolve phylogenetic relationships between virus populations, which can be used to infer transmission routes and potentially inform the design of biosecurity measures. Sequencing of short (<2000 nt) segments of the 15 000-nt BRSV genome has revealed geographic and temporal clustering of BRSV populations, but insufficient variation to distinguish viruses collected from herds infected close together in space and time. This study investigated the potential for whole-genome sequencing to reveal sufficient genomic variation for inferring transmission routes between herds. Next-generation sequencing (NGS) data were generated from experimental infections and from natural outbreaks in Jämtland and Uppsala counties in Sweden. Sufficient depth of coverage for analysis of consensus and sub-consensus sequence diversity was obtained from 47 to 20 samples respectively. Few (range: 0-6 polymorphisms across the six experiments) consensus-level polymorphisms were observed along experimental transmissions. A much higher level of diversity (146 polymorphic sites) was found among the consensus sequences from the outbreak samples. The majority (144/146) of polymorphisms were between rather than within counties, suggesting that consensus whole-genome sequences show insufficient spatial resolution for inferring direct transmission routes, but might allow identification of outbreak sources at the regional scale. By contrast, within-sample diversity was generally higher in the experimental than the outbreak samples. Analyses to infer known (experimental) and suspected (outbreak) transmission links from within-sample diversity data were uninformative. In conclusion, analysis of the whole-genome sequence of BRSV from experimental samples discriminated between circulating isolates from distant areas, but insufficient diversity was observed between closely related isolates to aid local transmission route inference.
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Affiliation(s)
- Paul C D Johnson
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Sara Hägglund
- HPIG. Unit of Ruminant Medicine. Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Katarina Näslund
- Department of Microbiology, National Veterinary Institute, SVA, Uppsala, Sweden
| | - Gilles Meyer
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Siamak Zohari
- Department of Microbiology, National Veterinary Institute, SVA, Uppsala, Sweden
| | - Daniel T Haydon
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Jean François Valarcher
- HPIG. Unit of Ruminant Medicine. Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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6
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Stockdale JE, Liu P, Colijn C. The potential of genomics for infectious disease forecasting. Nat Microbiol 2022; 7:1736-1743. [PMID: 36266338 DOI: 10.1038/s41564-022-01233-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/18/2022] [Indexed: 11/09/2022]
Abstract
Genomic technologies have led to tremendous gains in understanding how pathogens function, evolve and interact. Pathogen diversity is now measurable at high precision and resolution, in part because over the past decade, sequencing technologies have increased in speed and capacity, at decreased cost. Alongside this, the use of models that can forecast emergence and size of infectious disease outbreaks has risen, highlighted by the coronavirus disease 2019 pandemic but also due to modelling advances that allow for rapid estimates in emerging outbreaks to inform monitoring, coordination and resource deployment. However, genomics studies have remained largely retrospective. While they contain high-resolution views of pathogen diversification and evolution in the context of selection, they are often not aligned with designing interventions. This is a missed opportunity because pathogen diversification is at the core of the most pressing infectious public health challenges, and interventions need to take the mechanisms of virulence and understanding of pathogen diversification into account. In this Perspective, we assess these converging fields, discuss current challenges facing both surveillance specialists and modellers who want to harness genomic data, and propose next steps for integrating longitudinally sampled genomic data with statistical learning and interpretable modelling to make reliable predictions into the future.
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Affiliation(s)
- Jessica E Stockdale
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada.
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7
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Skums P, Mohebbi F, Tsyvina V, Baykal PI, Nemira A, Ramachandran S, Khudyakov Y. SOPHIE: Viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework. Cell Syst 2022; 13:844-856.e4. [PMID: 36265470 PMCID: PMC9590096 DOI: 10.1016/j.cels.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 01/26/2023]
Abstract
Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed for phylogenetic inference of transmission histories, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, although common source outbreaks violate this assumption. We propose a maximum likelihood framework, SOPHIE, based on the integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modeled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity, and accurately infers transmissions without case-specific epidemiological data.
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Affiliation(s)
- Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, GA, USA.
| | - Fatemeh Mohebbi
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Vyacheslav Tsyvina
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Pelin Icer Baykal
- Department of Biosystems Science & Engineering, ETH Zurich, Basel, Switzerland
| | - Alina Nemira
- Department of Computer Science, Georgia State University, Atlanta, GA, USA
| | - Sumathi Ramachandran
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yury Khudyakov
- Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, GA, USA
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8
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Alamil M, Thébaud G, Berthier K, Soubeyrand S. Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics. Front Microbiol 2022; 13:983938. [PMID: 36274731 PMCID: PMC9581327 DOI: 10.3389/fmicb.2022.983938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has opened the route for a deep assessment of within-host genetic diversity that can be used, e.g., to characterize microbial communities and to infer transmission links in infectious disease outbreaks. The performance of such characterizations and inferences cannot be analytically assessed in general and are often grounded on computer-intensive evaluations. Then, being able to simulate within-host genetic diversity across time under various demo-genetic assumptions is paramount to assess the performance of the approaches of interest. In this context, we built an original model that can be simulated to investigate the temporal evolution of genotypes and their frequencies under various demo-genetic assumptions. The model describes the growth and the mutation of genotypes at the nucleotide resolution conditional on an overall within-host viral kinetics, and can be tuned to generate fast non-equilibrium demo-genetic dynamics. We ran simulations of this model and computed classic diversity indices to characterize the temporal variation of within-host genetic diversity (from high-throughput amplicon sequences) of virus populations under three demographic kinetic models of viral infection. Our results highlight how demographic (viral load) and genetic (mutation, selection, or drift) factors drive variations in within-host diversity during the course of an infection. In particular, we observed a non-monotonic relationship between pathogen population size and genetic diversity, and a reduction of the impact of mutation on diversity when a non-specific host immune response is activated. The large variation in the diversity patterns generated in our simulations suggests that the underlying model provides a flexible basis to produce very diverse demo-genetic scenarios and test, for instance, methods for the inference of transmission links during outbreaks.
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Affiliation(s)
- Maryam Alamil
- INRAE, BioSP, Avignon, France
- Department of Mathematics and Computer Science, Alfaisal University, Riyadh, Saudi Arabia
- *Correspondence: Maryam Alamil ;
| | - Gaël Thébaud
- PHIM Plant Health Institute, INRAE, Univ Montpellier, CIRAD, Institut Agro, IRD, Montpellier, France
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9
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Strong R, McCleary S, Grierson S, Choudhury B, Steinbach F, Crooke HR. Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK. Front Microbiol 2022; 13:909396. [PMID: 35836425 PMCID: PMC9274199 DOI: 10.3389/fmicb.2022.909396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak via full genome sequencing will be beneficial.
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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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11
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Leavitt SV, Lee RS, Sebastiani P, Horsburgh CR, Jenkins HE, White LF. Estimating the relative probability of direct transmission between infectious disease patients. Int J Epidemiol 2021; 49:764-775. [PMID: 32211747 DOI: 10.1093/ije/dyaa031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/07/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Estimating infectious disease parameters such as the serial interval (time between symptom onset in primary and secondary cases) and reproductive number (average number of secondary cases produced by a primary case) are important in understanding infectious disease dynamics. Many estimation methods require linking cases by direct transmission, a difficult task for most diseases. METHODS Using a subset of cases with detailed genetic and/or contact investigation data to develop a training set of probable transmission events, we build a model to estimate the relative transmission probability for all case-pairs from demographic, spatial and clinical data. Our method is based on naive Bayes, a machine learning classification algorithm which uses the observed frequencies in the training dataset to estimate the probability that a pair is linked given a set of covariates. RESULTS In simulations, we find that the probabilities estimated using genetic distance between cases to define training transmission events are able to distinguish between truly linked and unlinked pairs with high accuracy (area under the receiver operating curve value of 95%). Additionally, only a subset of the cases, 10-50% depending on sample size, need to have detailed genetic data for our method to perform well. We show how these probabilities can be used to estimate the average effective reproductive number and apply our method to a tuberculosis outbreak in Hamburg, Germany. CONCLUSIONS Our method is a novel way to infer transmission dynamics in any dataset when only a subset of cases has rich contact investigation and/or genetic data.
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Affiliation(s)
- Sarah V Leavitt
- School of Public Health, Department of Biostatistics, Boston University, Boston, MA, USA
| | - Robyn S Lee
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.,University of Toronto Dalla Lana School of Public Health Epidemiology Division, Toronto, ON, Canada
| | - Paola Sebastiani
- School of Public Health, Department of Biostatistics, Boston University, Boston, MA, USA
| | - C Robert Horsburgh
- School of Public Health, Department of Epidemiology, Boston University, Boston, MA, USA
| | - Helen E Jenkins
- School of Public Health, Department of Biostatistics, Boston University, Boston, MA, USA
| | - Laura F White
- School of Public Health, Department of Biostatistics, Boston University, Boston, MA, USA
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12
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Yamamoto T, Sawai K, Nishi T, Fukai K, Kato T, Hayama Y, Murato Y, Shimizu Y, Yamaguchi E. Subgrouping and analysis of relationships between classical swine fever virus identified during the 2018-2020 epidemic in Japan by a novel approach using shared genomic variants. Transbound Emerg Dis 2021; 69:1166-1177. [PMID: 33730417 DOI: 10.1111/tbed.14076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF) is a worldwide devastating disease of the pig industry caused by classical swine fever virus (CSFV). In September 2018, an outbreak of CSF occurred in Japan where the disease had been eradicated and was officially designated a CSF-free country since 2015. Following the detection of the first 2018 case on a farm in Gifu Prefecture, the disease spread among both farm pigs and wild boars and still continues. Epigenome analysis using whole-genome information is helpful in identifying the infection route, but the current approaches provide an insufficient resolution. In this study, a novel method of using single-nucleotide variants (SNVs) was employed to identify the associations among 158 isolates (65 from farms and 93 from wild boars). The identified groups of CSFV strains were plotted in different colours on a map, identifying the location where each strain was collected. The lack of an SNV set shared between the index case and the other strains suggested the first infection in Japan during the outbreak occurred in wild boars, not at the index farm. For the Atsumi Peninsula outbreaks, where nine farms were found infected within a 10-km radius area, the farm strains were assembled into three groups, suggesting these outbreaks resulted from at least three different infection events in this area. For the infections in the area around Saitama Prefecture, an area remote from the epicentre, strains from both the farms and wild boars were identified as being in the same group, suggesting they resulted from one viral introduction. Likewise, seven infected farms in Okinawa Prefecture, almost 1,500 km from Gifu Prefecture, were identified as being in a common, but separate group. By demonstrating the variety of transmission routes and possibility of long-distance infection, these results will help improve disease control measures.
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Affiliation(s)
- Takehisa Yamamoto
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Kotaro Sawai
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Tatsuya Nishi
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Katsuhiko Fukai
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Tomoko Kato
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Yoko Hayama
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yoshinori Murato
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yumiko Shimizu
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Emi Yamaguchi
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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13
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Kombe IK, Agoti CN, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission. Sci Rep 2021; 11:1463. [PMID: 33446831 PMCID: PMC7809427 DOI: 10.1038/s41598-021-81078-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group.
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Affiliation(s)
- Ivy K Kombe
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Patrick K Munywoki
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Disease and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4 7AL, UK
| | - Graham F Medley
- Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
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14
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Schlosser F, Brockmann D. Finding disease outbreak locations from human mobility data. EPJ DATA SCIENCE 2021; 10:52. [PMID: 34692370 PMCID: PMC8525067 DOI: 10.1140/epjds/s13688-021-00306-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/05/2021] [Indexed: 05/09/2023]
Abstract
UNLABELLED Finding the origin location of an infectious disease outbreak quickly is crucial in mitigating its further dissemination. Current methods to identify outbreak locations early on rely on interviewing affected individuals and correlating their movements, which is a manual, time-consuming, and error-prone process. Other methods such as contact tracing, genomic sequencing or theoretical models of epidemic spread offer help, but they are not applicable at the onset of an outbreak as they require highly processed information or established transmission chains. Digital data sources such as mobile phones offer new ways to find outbreak sources in an automated way. Here, we propose a novel method to determine outbreak origins from geolocated movement data of individuals affected by the outbreak. Our algorithm scans movement trajectories for shared locations and identifies the outbreak origin as the most dominant among them. We test the method using various empirical and synthetic datasets, and demonstrate that it is able to single out the true outbreak location with high accuracy, requiring only data of N = 4 individuals. The method can be applied to scenarios with multiple outbreak locations, and is even able to estimate the number of outbreak sources if unknown, while being robust to noise. Our method is the first to offer a reliable, accurate out-of-the-box approach to identify outbreak locations in the initial phase of an outbreak. It can be easily and quickly applied in a crisis situation, improving on previous manual approaches. The method is not only applicable in the context of disease outbreaks, but can be used to find shared locations in movement data in other contexts as well. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1140/epjds/s13688-021-00306-6.
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Affiliation(s)
- Frank Schlosser
- Department of Physics, Humboldt-University of Berlin, Newtonstr. 15, 12489 Berlin, Germany
- Complex Systems Group, Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany
| | - Dirk Brockmann
- Institute for Theoretical Biology, Humboldt-University of Berlin, Philippstr. 13, 10115 Berlin, Germany
- Complex Systems Group, Robert Koch-Institute, Nordufer 20, 13353 Berlin, Germany
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15
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Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations. Sci Rep 2020; 10:21980. [PMID: 33319838 PMCID: PMC7738532 DOI: 10.1038/s41598-020-78900-3] [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: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022] Open
Abstract
Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful methods include ‘phylodynamic approaches’ that integrate evolutionary and epidemiological data. However, they are typically computationally intensive, require extensive data, and are best applied when there is a strong molecular clock signal and substantial pathogen diversity. To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemic Mycobacterium bovis (the causative agent of bovine/zoonotic tuberculosis, bTB) infection. Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks. However, the method can be sensitive to assumptions about within-host evolution.
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16
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Montazeri H, Little S, Legha MM, Beerenwinkel N, DeGruttola V. Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times. Stat Appl Genet Mol Biol 2020; 19:/j/sagmb.ahead-of-print/sagmb-2019-0026/sagmb-2019-0026.xml. [PMID: 33085643 PMCID: PMC8212962 DOI: 10.1515/sagmb-2019-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/16/2020] [Indexed: 11/15/2022]
Abstract
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks. Such research can aid in the development of appropriate interventions and in the design of studies to evaluate them. Several computational methods have been proposed to infer transmission chains from sequence data; however, existing methods do not generally reliably reconstruct transmission trees because genetic sequence data or inferred phylogenetic trees from such data contain insufficient information for accurate estimation of transmission chains. Here, we show by simulation studies that incorporating infection times, even when they are uncertain, can greatly improve the accuracy of reconstruction of transmission trees. To achieve this improvement, we propose a Bayesian inference methods using Markov chain Monte Carlo that directly draws samples from the space of transmission trees under the assumption of complete sampling of the outbreak. The likelihood of each transmission tree is computed by a phylogenetic model by treating its internal nodes as transmission events. By a simulation study, we demonstrate that accuracy of the reconstructed transmission trees depends mainly on the amount of information available on times of infection; we show superiority of the proposed method to two alternative approaches when infection times are known up to specified degrees of certainty. In addition, we illustrate the use of a multiple imputation framework to study features of epidemic dynamics, such as the relationship between characteristics of nodes and average number of outbound edges or inbound edges, signifying possible transmission events from and to nodes. We apply the proposed method to a transmission cluster in San Diego and to a dataset from the 2014 Sierra Leone Ebola virus outbreak and investigate the impact of biological, behavioral, and demographic factors.
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Affiliation(s)
- Hesam Montazeri
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Susan Little
- Department of Medicine, University of California San Diego, California, USA
| | - Mozhgan Mozaffari Legha
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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17
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Graystock P, Ng WH, Parks K, Tripodi AD, Muñiz PA, Fersch AA, Myers CR, McFrederick QS, McArt SH. Dominant bee species and floral abundance drive parasite temporal dynamics in plant-pollinator communities. Nat Ecol Evol 2020; 4:1358-1367. [PMID: 32690902 PMCID: PMC7529964 DOI: 10.1038/s41559-020-1247-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 06/15/2020] [Indexed: 12/30/2022]
Abstract
Pollinator reductions can leave communities less diverse and potentially at increased risk of infectious diseases. Species-rich plant and bee communities have high species turnover, making the study of disease dynamics challenging. To address how temporal dynamics shape parasite prevalence in plant and bee communities, we screened >5,000 bees and flowers over an entire growing season for five common bee microparasites (Nosema ceranae, Nosema bombi, Crithidia bombi, Crithidia expoeki and neogregarines). Over 110 bee species and 89 flower species were screened, revealing that 42% of bee species (12.2% individual bees) and 70% of flower species (8.7% individual flowers) had at least one parasite in or on them, respectively. Some common flowers (for example, Lychnis flos-cuculi) harboured multiple parasite species whilst others (for example, Lythrum salicaria) had few. Significant temporal variation of parasite prevalence in bees was linked to bee diversity, bee and flower abundance and community composition. Specifically, we found that bee communities had the highest prevalence late in the season, when social bees (Bombus spp. and Apis mellifera) were dominant and bee diversity was lowest. Conversely, prevalence on flowers was lowest late in the season when floral abundance was highest. Thus turnover in the bee community impacted community-wide prevalence, and turnover in the plant community impacted when parasite transmission was likely to occur at flowers. These results imply that efforts to improve bee health will benefit from the promotion of high floral numbers to reduce transmission risk, maintaining bee diversity to dilute parasites and monitoring the abundance of dominant competent hosts.
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Affiliation(s)
- Peter Graystock
- Department of Entomology, Cornell University, Ithaca, NY, USA.
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot, UK.
- Department of Entomology, University of California Riverside, Riverside, CA, USA.
| | - Wee Hao Ng
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Kyle Parks
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | | | - Paige A Muñiz
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Ashley A Fersch
- Department of Entomology, Cornell University, Ithaca, NY, USA
| | - Christopher R Myers
- Center for Advanced Computing, and Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, CA, USA
| | - Scott H McArt
- Department of Entomology, Cornell University, Ithaca, NY, USA
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18
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Firestone SM, Hayama Y, Lau MSY, Yamamoto T, Nishi T, Bradhurst RA, Demirhan H, Stevenson MA, Tsutsui T. Transmission network reconstruction for foot-and-mouth disease outbreaks incorporating farm-level covariates. PLoS One 2020; 15:e0235660. [PMID: 32667952 PMCID: PMC7363093 DOI: 10.1371/journal.pone.0235660] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 06/22/2020] [Indexed: 11/19/2022] Open
Abstract
Transmission network modelling to infer 'who infected whom' in infectious disease outbreaks is a highly active area of research. Outbreaks of foot-and-mouth disease have been a key focus of transmission network models that integrate genomic and epidemiological data. The aim of this study was to extend Lau's systematic Bayesian inference framework to incorporate additional parameters representing predominant species and numbers of animals held on a farm. Lau's Bayesian Markov chain Monte Carlo algorithm was reformulated, verified and pseudo-validated on 100 simulated outbreaks populated with demographic data Japan and Australia. The modified model was then implemented on genomic and epidemiological data from the 2010 outbreak of foot-and-mouth disease in Japan, and outputs compared to those from the SCOTTI model implemented in BEAST2. The modified model achieved improvements in overall accuracy when tested on the simulated outbreaks. When implemented on the actual outbreak data from Japan, infected farms that held predominantly pigs were estimated to have five times the transmissibility of infected cattle farms and be 49% less susceptible. The farm-level incubation period was 1 day shorter than the latent period, the timing of the seeding of the outbreak in Japan was inferred, as were key linkages between clusters and features of farms involved in widespread dissemination of this outbreak. To improve accessibility the modified model has been implemented as the R package 'BORIS' for use in future outbreaks.
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Affiliation(s)
- Simon M. Firestone
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Max S. Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Tatsuya Nishi
- Exotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Tokyo, Japan
| | - Richard A. Bradhurst
- Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne, Parkville, VIC, Australia
| | - Haydar Demirhan
- Mathematical Sciences Discipline, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Mark A. Stevenson
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
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Abstract
MOTIVATION The combination of genomic and epidemiological data holds the potential to enable accurate pathogen transmission history inference. However, the inference of outbreak transmission histories remains challenging due to various factors such as within-host pathogen diversity and multi-strain infections. Current computational methods ignore within-host diversity and/or multi-strain infections, often failing to accurately infer the transmission history. Thus, there is a need for efficient computational methods for transmission tree inference that accommodate the complexities of real data. RESULTS We formulate the direct transmission inference (DTI) problem for inferring transmission trees that support multi-strain infections given a timed phylogeny and additional epidemiological data. We establish hardness for the decision and counting version of the DTI problem. We introduce Transmission Tree Uniform Sampler (TiTUS), a method that uses SATISFIABILITY to almost uniformly sample from the space of transmission trees. We introduce criteria that prioritize parsimonious transmission trees that we subsequently summarize using a novel consensus tree approach. We demonstrate TiTUS's ability to accurately reconstruct transmission trees on simulated data as well as a documented HIV transmission chain. AVAILABILITY AND IMPLEMENTATION https://github.com/elkebir-group/TiTUS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Palash Sashittal
- Department of Aerospace Engineering, University of Illinois at Urbana-Champaign, Urbama, IL 61801, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbama, IL 61801, USA
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20
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Polonsky JA, Baidjoe A, Kamvar ZN, Cori A, Durski K, Edmunds WJ, Eggo RM, Funk S, Kaiser L, Keating P, de Waroux OLP, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J, Jombart T. Outbreak analytics: a developing data science for informing the response to emerging pathogens. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180276. [PMID: 31104603 PMCID: PMC6558557 DOI: 10.1098/rstb.2018.0276] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2018] [Indexed: 12/16/2022] Open
Abstract
Despite continued efforts to improve health systems worldwide, emerging pathogen epidemics remain a major public health concern. Effective response to such outbreaks relies on timely intervention, ideally informed by all available sources of data. The collection, visualization and analysis of outbreak data are becoming increasingly complex, owing to the diversity in types of data, questions and available methods to address them. Recent advances have led to the rise of outbreak analytics, an emerging data science focused on the technological and methodological aspects of the outbreak data pipeline, from collection to analysis, modelling and reporting to inform outbreak response. In this article, we assess the current state of the field. After laying out the context of outbreak response, we critically review the most common analytics components, their inter-dependencies, data requirements and the type of information they can provide to inform operations in real time. We discuss some challenges and opportunities and conclude on the potential role of outbreak analytics for improving our understanding of, and response to outbreaks of emerging pathogens. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'. This theme issue is linked with the earlier issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'.
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Affiliation(s)
- Jonathan A. Polonsky
- Department of Health Emergency Information and Risk Assessment, World Health Organization, Avenue Appia 20, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva, Switzerland
| | - Amrish Baidjoe
- Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG, UK
| | - Zhian N. Kamvar
- Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG, UK
| | - Anne Cori
- Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG, UK
| | - Kara Durski
- Department of Infectious Hazard Management, World Health Organization, Avenue Appia 20, 1211 Geneva, Switzerland
| | - W. John Edmunds
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Laurent Kaiser
- Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, 1211 Geneva, Switzerland
| | - Patrick Keating
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- UK Public Health Rapid Support Team, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Olivier le Polain de Waroux
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- UK Public Health Rapid Support Team, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- Public Health England, Wellington House, 133–155 Waterloo Road, London SE1 8UG, UK
| | - Michael Marks
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Paula Moraga
- Centre for Health Informatics, Computing and Statistics (CHICAS), Lancaster Medical School, Lancaster University, Lancaster LA1 4YW, UK
| | - Oliver Morgan
- Department of Health Emergency Information and Risk Assessment, World Health Organization, Avenue Appia 20, 1211 Geneva, Switzerland
| | - Pierre Nouvellet
- Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG, UK
- School of Life Sciences, University of Sussex, Sussex House, Brighton BN1 9RH, UK
| | - Ruwan Ratnayake
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Chrissy H. Roberts
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Jimmy Whitworth
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- UK Public Health Rapid Support Team, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Thibaut Jombart
- Department of Infectious Disease Epidemiology, School of Public Health, MRC Centre for Global Infectious Disease Analysis, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place London W2 1PG, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
- UK Public Health Rapid Support Team, London School of Hygiene and Tropical Medicine, Keppel St, London WC1E 7HT, UK
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Hayama Y, Firestone SM, Stevenson MA, Yamamoto T, Nishi T, Shimizu Y, Tsutsui T. Reconstructing a transmission network and identifying risk factors of secondary transmissions in the 2010 foot-and-mouth disease outbreak in Japan. Transbound Emerg Dis 2019; 66:2074-2086. [PMID: 31131968 DOI: 10.1111/tbed.13256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 11/27/2022]
Abstract
Research aimed at understanding transmission networks, representing a network of "who infected whom" for an infectious disease outbreak, have been actively conducted in recent years. Transmission network models incorporating epidemiological and genetic data are valuable for elucidating disease transmission pathways. In this study, we reconstructed the transmission network of the foot-and-mouth disease (FMD) epidemic in Japan in 2010, and explored farm-level risk factors associated with increased risk of secondary transmission. A published, systematic Bayesian transmission network model was applied to epidemiological data of 292 infected farms and whole genome sequence data of 104 of the infected farms. This model can make inferences for known infected farms even lacking genetic data. After estimating the consensus network, the accuracy of the network was examined by comparison with epidemiological data. Then, risk factors inferred to have been sources of secondary transmission were explored using zero-inflated Poisson regression model. As far as we are aware, this study represents the largest FMD outbreak transmission network to be published by such means combining epidemiological and genetic data. The consensus network reasonably generated the epidemiological links, which were estimated from the actual epidemiological investigation. Among 292 farms, 101 farms (35%) were inferred to have been the sources of secondary transmission, and amongst these farms, the median number of secondary cases was 2 (min:1-max:18) farms. The farm-type (small and large -sized pig farms), the number of days from onset to notification, and the number of susceptible farms within a 1-km radius were significantly associated with secondary transmission. Transmission network modelling enabled inference of the connections between infected farms during the FMD epidemic and identified important factors for controlling the risk of secondary transmission. This study demonstrated that the predominant susceptible species held on a farm, farm size, and animal density were associated with increased onwards transmission.
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Affiliation(s)
- Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Simon M Firestone
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark A Stevenson
- Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, Asia-Pacific Centre for Animal Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Tatsuya Nishi
- Exotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Yumiko Shimizu
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Japan
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22
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Lau MSY, Grenfell BT, Worby CJ, Gibson GJ. Model diagnostics and refinement for phylodynamic models. PLoS Comput Biol 2019; 15:e1006955. [PMID: 30951528 PMCID: PMC6469796 DOI: 10.1371/journal.pcbi.1006955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/17/2019] [Accepted: 03/18/2019] [Indexed: 11/29/2022] Open
Abstract
Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Development of such tools is essential for model criticism, refinement, and calibration. The idea of utilising latent residuals for model assessment has already been exploited in general spatio-temporal epidemiological settings. Specifically, by proposing appropriately designed non-centered, re-parameterizations of a given epidemiological process, one can construct latent residuals with known sampling distributions which can be used to quantify evidence of model mis-specification. In this paper, we extend this idea to formulate a novel model-diagnostic framework for phylodynamic models. Using simulated examples, we show that our framework may effectively detect a particular form of mis-specification in a phylodynamic model, particularly in the event of superspreading. We also exemplify our approach by applying the framework to a dataset describing a local foot-and-mouth (FMD) outbreak in the UK, eliciting strong evidence against the assumption of no within-host-diversity in the outbreak. We further demonstrate that our framework can facilitate model calibration in real-life scenarios, by proposing a within-host-diversity model which appears to offer a better fit to data than one that assumes no within-host-diversity of FMD virus. Integrated modelling of conventional epidemiological data and modern genomic data (i.e. phylodynamics) has made significant progress in recent years, due to the ever-increasing availability of genomic data and development of statistical methods. However, there is a lack of tools for carrying out effective diagnostics for phylodynamic models. We propose a novel model diagnostic framework that involves a latent residual process which is a priori independent of model assumptions and which can be used to quantify, and reveal the nature of, model inadequacy. Our results suggest that our framework may systematically detect deviation from a particular model assumption and greatly facilitate subsequent model calibration.
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Affiliation(s)
- Max S. Y. Lau
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- * E-mail:
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
- Fogarty International Center, National Institute of Health, Bethesda, MD, USA
| | | | - Gavin J. Gibson
- Maxwell Institute for Mathematical Sciences, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK
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23
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Gilbertson MLJ, Fountain-Jones NM, Craft ME. Incorporating genomic methods into contact networks to reveal new insights into animal behavior and infectious disease dynamics. BEHAVIOUR 2019; 155:759-791. [PMID: 31680698 DOI: 10.1163/1568539x-00003471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Utilization of contact networks has provided opportunities for assessing the dynamic interplay between pathogen transmission and host behavior. Genomic techniques have, in their own right, provided new insight into complex questions in disease ecology, and the increasing accessibility of genomic approaches means more researchers may seek out these tools. The integration of network and genomic approaches provides opportunities to examine the interaction between behavior and pathogen transmission in new ways and with greater resolution. While a number of studies have begun to incorporate both contact network and genomic approaches, a great deal of work has yet to be done to better integrate these techniques. In this review, we give a broad overview of how network and genomic approaches have each been used to address questions regarding the interaction of social behavior and infectious disease, and then discuss current work and future horizons for the merging of these techniques.
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Affiliation(s)
- Marie L J Gilbertson
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nicholas M Fountain-Jones
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
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24
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Firestone SM, Hayama Y, Bradhurst R, Yamamoto T, Tsutsui T, Stevenson MA. Reconstructing foot-and-mouth disease outbreaks: a methods comparison of transmission network models. Sci Rep 2019; 9:4809. [PMID: 30886211 PMCID: PMC6423326 DOI: 10.1038/s41598-019-41103-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022] Open
Abstract
A number of transmission network models are available that combine genomic and epidemiological data to reconstruct networks of who infected whom during infectious disease outbreaks. For such models to reliably inform decision-making they must be transparently validated, robust, and capable of producing accurate predictions within the short data collection and inference timeframes typical of outbreak responses. A lack of transparent multi-model comparisons reduces confidence in the accuracy of transmission network model outputs, negatively impacting on their more widespread use as decision-support tools. We undertook a formal comparison of the performance of nine published transmission network models based on a set of foot-and-mouth disease outbreaks simulated in a previously free country, with corresponding simulated phylogenies and genomic samples from animals on infected premises. Of the transmission network models tested, Lau’s systematic Bayesian integration framework was found to be the most accurate for inferring the transmission network and timing of exposures, correctly identifying the source of 73% of the infected premises (with 91% accuracy for sources with model support >0.80). The Structured COalescent Transmission Tree Inference provided the most accurate inference of molecular clock rates. This validation study points to which models might be reliably used to reconstruct similar future outbreaks and how to interpret the outputs to inform control. Further research could involve extending the best-performing models to explicitly represent within-host diversity so they can handle next-generation sequencing data, incorporating additional animal and farm-level covariates and combining predictions using Ensemble methods and other approaches.
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Affiliation(s)
- Simon M Firestone
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Yoko Hayama
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Richard Bradhurst
- Centre of Excellence for Biosecurity Risk Analysis, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Takehisa Yamamoto
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Toshiyuki Tsutsui
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, 305-0856, Japan
| | - Mark A Stevenson
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
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25
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Miller JK, Chen J, Sundermann A, Marsh JW, Saul MI, Shutt KA, Pacey M, Mustapha MM, Harrison LH, Dubrawski A. Statistical outbreak detection by joining medical records and pathogen similarity. J Biomed Inform 2019; 91:103126. [PMID: 30771483 PMCID: PMC6424617 DOI: 10.1016/j.jbi.2019.103126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/05/2019] [Accepted: 02/06/2019] [Indexed: 01/08/2023]
Abstract
We present a statistical inference model for the detection and characterization of outbreaks of hospital associated infection. The approach combines patient exposures, determined from electronic medical records, and pathogen similarity, determined by whole-genome sequencing, to simultaneously identify probable outbreaks and their root-causes. We show how our model can be used to target isolates for whole-genome sequencing, improving outbreak detection and characterization even without comprehensive sequencing. Additionally, we demonstrate how to learn model parameters from reference data of known outbreaks. We demonstrate model performance using semi-synthetic experiments.
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Affiliation(s)
- James K Miller
- Auton Lab, Carnegie Mellon University, Pittsburgh, PA, United States.
| | - Jieshi Chen
- Auton Lab, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Alexander Sundermann
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States; Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Jane W Marsh
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States
| | - Melissa I Saul
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Kathleen A Shutt
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States
| | - Marissa Pacey
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States
| | - Mustapha M Mustapha
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States
| | - Lee H Harrison
- Infectious Diseases Epidemiology Research Unit, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, United States
| | - Artur Dubrawski
- Auton Lab, Carnegie Mellon University, Pittsburgh, PA, United States
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26
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Liao SJ, Marshall J, Hazelton ML, French NP. Extending statistical models for source attribution of zoonotic diseases: a study of campylobacteriosis. J R Soc Interface 2019; 16:20180534. [PMID: 30958154 PMCID: PMC6364659 DOI: 10.1098/rsif.2018.0534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
Preventing and controlling zoonoses through the design and implementation of public health policies requires a thorough understanding of transmission pathways. Modelling jointly the epidemiological data and genetic information of microbial isolates derived from cases provides a methodology for tracing back the source of infection. In this paper, the attribution probability for human cases of campylobacteriosis for each source, conditional on the extent to which each case resides in a rural compared to urban environment, is estimated. A model that incorporates genetic data and evolutionary processes is applied alongside a newly developed genetic-free model. We show that inference from each model is comparable except for rare microbial genotypes. Further, the effect of 'rurality' may be modelled linearly on the logit scale, with increasing rurality leading to the increasing likelihood of ruminant-sourced campylobacteriosis.
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Affiliation(s)
- Sih-Jing Liao
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Jonathan Marshall
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Martin L. Hazelton
- School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Nigel P. French
- mEpiLab, Infectious Disease Research Centre, School of Veterinary Science, Massey University, Palmerston North 4442, New Zealand
- New Zealand Food Safety Science & Research Centre, Massey University, Palmerston North 4442, New Zealand
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27
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Singh I, Deb R, Kumar S, Singh R, Andonissamy J, Smita S, Sengar GS, Kumar R, Ojha KK, Sahoo NR, Murali S, Chandran R, Nair RV, Lal SB, Mishra DC, Rai A. Deciphering foot-and-mouth disease (FMD) virus-host tropism. J Biomol Struct Dyn 2019; 37:4779-4789. [PMID: 30654708 DOI: 10.1080/07391102.2019.1567386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of Bos taurus, Gallus and Canis. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp 143RGD145 and at domain 676SIPLQ680 in alpha-integrin of B. taurus. Notably, in-silico site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and B. taurus integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, in-vitro analysis demonstrates the persistence of the putative tropism site 'SIPLQ' in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Indra Singh
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rajib Deb
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | - Sanjeev Kumar
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Rani Singh
- ICAR-Central Institute for Research on Cattle , Meerut , India
| | | | - Shuchi Smita
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | | | - Rajiv Kumar
- ICAR-Central Sheep and Wool Research Institute , Avikanagar , India
| | | | | | - S Murali
- ICAR-India National Bureau of Fish Genetic Resources , Lucknow , India
| | - Rejani Chandran
- ICAR-Central Institute of Fisheries Technology , Cochin , India
| | | | - S B Lal
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Dwijesh Chandra Mishra
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
| | - Anil Rai
- Centre for Agricultural Bio-Informatics ICAR-Indian Agricultural Statistics Research Institute , New Delhi , India
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28
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Tracking virus outbreaks in the twenty-first century. Nat Microbiol 2018; 4:10-19. [PMID: 30546099 PMCID: PMC6345516 DOI: 10.1038/s41564-018-0296-2] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 10/19/2018] [Indexed: 02/08/2023]
Abstract
Emerging viruses have the potential to impose substantial mortality, morbidity and economic burdens on human populations. Tracking the spread of infectious diseases to assist in their control has traditionally relied on the analysis of case data gathered as the outbreak proceeds. Here, we describe how many of the key questions in infectious disease epidemiology, from the initial detection and characterization of outbreak viruses, to transmission chain tracking and outbreak mapping, can now be much more accurately addressed using recent advances in virus sequencing and phylogenetics. We highlight the utility of this approach with the hypothetical outbreak of an unknown pathogen, ‘Disease X’, suggested by the World Health Organization to be a potential cause of a future major epidemic. We also outline the requirements and challenges, including the need for flexible platforms that generate sequence data in real-time, and for these data to be shared as widely and openly as possible. This Review Article describes how recent advances in viral genome sequencing and phylogenetics have enabled key issues associated with outbreak epidemiology to be more accurately addressed, and highlights the requirements and challenges for generating, sharing and using such data when tackling a viral outbreak.
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29
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Wang H, Hou P, Zhao G, Yu L, Gao YW, He H. Development and evaluation of serotype-specific recombinase polymerase amplification combined with lateral flow dipstick assays for the diagnosis of foot-and-mouth disease virus serotype A, O and Asia1. BMC Vet Res 2018; 14:359. [PMID: 30458768 PMCID: PMC6245561 DOI: 10.1186/s12917-018-1644-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Foot-and-mouth disease (FMD) caused by foot-and-mouth disease virus (FMDV) is one of the most highly infectious diseases in livestock, and leads to huge economic losses. Early diagnosis and rapid differentiation of FMDV serotype is therefore integral to the prevention and control of FMD. In this study, a series of serotype-specific reverse transcription recombinase polymerase amplification assays combined with lateral flow dipstick (RPA-LFD) were establish to differentiate FMDV serotypes A, O or Asia 1, respectively. Results The serotype-specific primers and probes of RPA-LFD were designed to target conserved regions of the FMDV VP1 gene sequence, and three primer and probe sets of serotype-specific RPA-LFD were selected for amplification of FMDV serotypes A, O or Asia 1, respectively. Following incubation at 38 °C for 20 min, the RPA amplification products could be visualized by LFD. Analytical sensitivity of the RPA assay was then determined with ten-fold serial dilutions of RNA of VP1 gene and the recombinant vector respectively containing VP1 gene from FMDV serotypes A, O or Asia1, the detection limits of these assays were 3 copies of plasmid DNA or 50 copies of viral RNA per reaction. Moreover, the specificity of the assay was assessed, and there was no cross reactions with other viruses leading to bovine vesicular lesions. Furthermore, 126 clinical samples were respectively detected with RPA-LFD and real-time PCR (rPCR), there was 98.41% concordance between the two assays, and two samples were positive by RPA-LFD but negative in rPCR, these were confirmed as FMDV-positive through viral isolation in BHK-21 cells. It showed that RPA-LFD assay was more sensitive than the rPCR method in this study. Conclusion The development of serotype-specific RPA-LFD assay provides a rapid, sensitive, and specific method for differentiation of FMDV serotype A, O or Asia1, respectively. It is possible that the serotype-specific RPA-LFD assay may be used as a integral protocol for field detection of FMDV.
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Affiliation(s)
- Hongmei Wang
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Peili Hou
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Guimin Zhao
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Li Yu
- Division of Livestock Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, 150001, China
| | - Yu-Wei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Military Veterinary Research Institute of Academy of Military Medical Sciences, Changchun, 130122, China.
| | - Hongbin He
- Ruminant Diseases Research Center, Key Laboratory of Animal Resistant Biology of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
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30
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Campbell F, Didelot X, Fitzjohn R, Ferguson N, Cori A, Jombart T. outbreaker2: a modular platform for outbreak reconstruction. BMC Bioinformatics 2018; 19:363. [PMID: 30343663 PMCID: PMC6196407 DOI: 10.1186/s12859-018-2330-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reconstructing individual transmission events in an infectious disease outbreak can provide valuable information and help inform infection control policy. Recent years have seen considerable progress in the development of methodologies for reconstructing transmission chains using both epidemiological and genetic data. However, only a few of these methods have been implemented in software packages, and with little consideration for customisability and interoperability. Users are therefore limited to a small number of alternatives, incompatible tools with fixed functionality, or forced to develop their own algorithms at considerable personal effort. RESULTS Here we present outbreaker2, a flexible framework for outbreak reconstruction. This R package re-implements and extends the original model introduced with outbreaker, but most importantly also provides a modular platform allowing users to specify custom models within an optimised inferential framework. As a proof of concept, we implement the within-host evolutionary model introduced with TransPhylo, which is very distinct from the original genetic model in outbreaker, and demonstrate how even complex model results can be successfully included with minimal effort. CONCLUSIONS outbreaker2 provides a valuable starting point for future outbreak reconstruction tools, and represents a unifying platform that promotes customisability and interoperability. Implemented in the R software, outbreaker2 joins a growing body of tools for outbreak analysis.
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Affiliation(s)
- Finlay Campbell
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Xavier Didelot
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Rich Fitzjohn
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
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31
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Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: the impact of recombination within the emerging O/ME-SA/Ind-2001 lineage. Sci Rep 2018; 8:14693. [PMID: 30279570 PMCID: PMC6168464 DOI: 10.1038/s41598-018-32693-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/31/2018] [Indexed: 11/08/2022] Open
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least 15 independent escapes during 2013–2017 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasise the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.
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32
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Skums P, Zelikovsky A, Singh R, Gussler W, Dimitrova Z, Knyazev S, Mandric I, Ramachandran S, Campo D, Jha D, Bunimovich L, Costenbader E, Sexton C, O'Connor S, Xia GL, Khudyakov Y. QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinformatics 2018; 34:163-170. [PMID: 29304222 DOI: 10.1093/bioinformatics/btx402] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/15/2017] [Indexed: 01/08/2023] Open
Abstract
Motivation Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use. Results The proposed framework QUasispecies Evolution, Network-based Transmission INference (QUENTIN) addresses the above challenges by evolutionary analysis of intra-host viral populations sampled by deep sequencing and Bayesian inference using general properties of social networks relevant to infection dissemination. This method allows inference of transmission direction even without the supporting case-specific epidemiological information, identify transmission clusters and reconstruct transmission history. QUENTIN was validated on experimental and simulated data, and applied to investigate HCV transmission within a community of hosts with high-risk behavior. It is available at https://github.com/skumsp/QUENTIN. Contact pskums@gsu.edu or alexz@cs.gsu.edu or rahul@sfsu.edu or yek0@cdc.gov. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pavel Skums
- Department of Computer Science, Georgia State University.,Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | | | - Rahul Singh
- Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA
| | - Walker Gussler
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Zoya Dimitrova
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Sergey Knyazev
- Department of Computer Science, Georgia State University
| | - Igor Mandric
- Department of Computer Science, Georgia State University
| | - Sumathi Ramachandran
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - David Campo
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Deeptanshu Jha
- Department of Computer Science, San Francisco State University, San Francisco, CA 94132, USA
| | - Leonid Bunimovich
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA 30313, USA
| | | | - Connie Sexton
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA.,Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Siobhan O'Connor
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA.,Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Guo-Liang Xia
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
| | - Yury Khudyakov
- Centers for Disease Control and Prevention, Division of Viral Hepatitis, Atlanta, GA 30303, USA
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De Maio N, Worby CJ, Wilson DJ, Stoesser N. Bayesian reconstruction of transmission within outbreaks using genomic variants. PLoS Comput Biol 2018; 14:e1006117. [PMID: 29668677 PMCID: PMC5927459 DOI: 10.1371/journal.pcbi.1006117] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 04/30/2018] [Accepted: 04/03/2018] [Indexed: 01/19/2023] Open
Abstract
Pathogen genome sequencing can reveal details of transmission histories and is a powerful tool in the fight against infectious disease. In particular, within-host pathogen genomic variants identified through heterozygous nucleotide base calls are a potential source of information to identify linked cases and infer direction and time of transmission. However, using such data effectively to model disease transmission presents a number of challenges, including differentiating genuine variants from those observed due to sequencing error, as well as the specification of a realistic model for within-host pathogen population dynamics. Here we propose a new Bayesian approach to transmission inference, BadTrIP (BAyesian epiDemiological TRansmission Inference from Polymorphisms), that explicitly models evolution of pathogen populations in an outbreak, transmission (including transmission bottlenecks), and sequencing error. BadTrIP enables the inference of host-to-host transmission from pathogen sequencing data and epidemiological data. By assuming that genomic variants are unlinked, our method does not require the computationally intensive and unreliable reconstruction of individual haplotypes. Using simulations we show that BadTrIP is robust in most scenarios and can accurately infer transmission events by efficiently combining information from genetic and epidemiological sources; thanks to its realistic model of pathogen evolution and the inclusion of epidemiological data, BadTrIP is also more accurate than existing approaches. BadTrIP is distributed as an open source package (https://bitbucket.org/nicofmay/badtrip) for the phylogenetic software BEAST2. We apply our method to reconstruct transmission history at the early stages of the 2014 Ebola outbreak, showcasing the power of within-host genomic variants to reconstruct transmission events. We present a new tool to reconstruct transmission events within outbreaks. Our approach makes use of pathogen genetic information, notably genetic variants at low frequency within host that are usually discarded, and combines it with epidemiological information of host exposure to infection. This leads to accurate reconstruction of transmission even in cases where abundant within-host pathogen genetic variation and weak transmission bottlenecks (multiple pathogen units colonising a new host at transmission) would otherwise make inference difficult due to the transmission history differing from the pathogen evolution history inferred from pathogen isolets. Also, the use of within-host pathogen genomic variants increases the resolution of the reconstruction of the transmission tree even in scenarios with limited within-outbreak pathogen genetic diversity: within-host pathogen populations that appear identical at the level of consensus sequences can be discriminated using within-host variants. Our Bayesian approach provides a measure of the confidence in different possible transmission histories, and is published as open source software. We show with simulations and with an analysis of the beginning of the 2014 Ebola outbreak that our approach is applicable in many scenarios, improves our understanding of transmission dynamics, and will contribute to finding and limiting sources and routes of transmission, and therefore preventing the spread of infectious disease.
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Affiliation(s)
- Nicola De Maio
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Colin J Worby
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Daniel J Wilson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Abstract
Transmissibility is the defining characteristic of infectious diseases. Quantifying transmission matters for understanding infectious disease epidemiology and designing evidence-based disease control programs. Tracing individual transmission events can be achieved by epidemiological investigation coupled with pathogen typing or genome sequencing. Individual infectiousness can be estimated by measuring pathogen loads, but few studies have directly estimated the ability of infected hosts to transmit to uninfected hosts. Individuals' opportunities to transmit infection are dependent on behavioral and other risk factors relevant given the transmission route of the pathogen concerned. Transmission at the population level can be quantified through knowledge of risk factors in the population or phylogeographic analysis of pathogen sequence data. Mathematical model-based approaches require estimation of the per capita transmission rate and basic reproduction number, obtained by fitting models to case data and/or analysis of pathogen sequence data. Heterogeneities in infectiousness, contact behavior, and susceptibility can have substantial effects on the epidemiology of an infectious disease, so estimates of only mean values may be insufficient. For some pathogens, super-shedders (infected individuals who are highly infectious) and super-spreaders (individuals with more opportunities to transmit infection) may be important. Future work on quantifying transmission should involve integrated analyses of multiple data sources.
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35
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Campbell F, Strang C, Ferguson N, Cori A, Jombart T. When are pathogen genome sequences informative of transmission events? PLoS Pathog 2018; 14:e1006885. [PMID: 29420641 PMCID: PMC5821398 DOI: 10.1371/journal.ppat.1006885] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 02/21/2018] [Accepted: 01/18/2018] [Indexed: 01/19/2023] Open
Abstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data. The increasing availability of genetic sequence data has sparked an interest in using pathogen whole genome sequences to reconstruct the history of individual transmission events in an infectious disease outbreak. However, such methodologies rely on pathogen genomes mutating rapidly enough to discriminate between infected individuals, an assumption that remains to be investigated. To determine pathogen outbreaks for which genetic data is expected to be informative of transmission events, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating pathogen genome sequences sampled from transmission pairs. We characterise transmission divergence of ten major outbreak causing pathogens using simulations and find significant variation between diseases, with viral outbreaks generally exhibiting higher transmission divergence than bacterial ones. We reconstruct these outbreaks using the R-packages outbreaker and phybreak and find that genetic sequence data, though useful for rapidly evolving pathogens, provides little to no information about outbreaks with low transmission divergence, such as Streptococcus pneumoniae and Shigella sonnei. Our results demonstrate the need to incorporate other sources of outbreak data, such as contact tracing data and spatial location data, into outbreak reconstruction tools.
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Affiliation(s)
- Finlay Campbell
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Camilla Strang
- Centre for Preventive Medicine, Department of Epidemiology and Disease Surveillance, Animal Health Trust, Suffolk, United Kingdom
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
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36
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Jamal SM, Belsham GJ. Molecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus. INFECTION GENETICS AND EVOLUTION 2018; 59:84-98. [PMID: 29412184 DOI: 10.1016/j.meegid.2018.01.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 02/07/2023]
Abstract
Foot-and-mouth disease virus (FMDV) is responsible for one of the most economically important infectious diseases of livestock. The virus spreads very easily and continues to affect many countries (mainly in Africa and Asia). The risks associated with the introduction of FMDV result in major barriers to trade in animals and their products. Seven antigenically distinct forms of the virus are known, called serotypes, but serotype C has not been detected anywhere for many years and may now be extinct. The serotypes have been further divided into topotypes (except for serotype Asia-1 viruses, which comprise a single topotype), genotypes, lineages and sub-lineages, which are usually restricted to specific geographical regions. However, sometimes, trans-regional spread of some strains occurs. Due to the error-prone replication of the RNA genome, the virus continuously evolves and new strains frequently arise (e.g. with modified antigenicity). Using nucleotide sequencing technologies, this rapid evolution of the viral genome can be followed. This allows the tracing of virus transmission pathways within an outbreak of disease if (near) full-length genome sequences can be generated. Furthermore, the movement of distinct virus lineages, from one country to another can be analyzed. Some important examples of the spread of new strains of FMD virus are described.
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Affiliation(s)
- Syed M Jamal
- Department of Biotechnology, University of Malakand, Chakdara, Dir (L), Khyber Pakhtunkhwa, Pakistan
| | - Graham J Belsham
- DTU National Veterinary Institute, Technical University of Denmark, Lindholm, Kalvehave 4771, Denmark.
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37
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Worby CJ, Lipsitch M, Hanage WP. Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. Am J Epidemiol 2017; 186:1209-1216. [PMID: 29149252 PMCID: PMC5860558 DOI: 10.1093/aje/kwx182] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/18/2017] [Indexed: 12/11/2022] Open
Abstract
Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection control. Genomic data shed new light on transmission dynamics and can be used to identify clusters of individuals likely to be linked by direct transmission. However, identification of individual routes of infection via single genome samples typically remains uncertain. We investigated the potential of deep sequence data to provide greater resolution on transmission routes, via the identification of shared genomic variants. We assessed several easily implemented methods to identify transmission routes using both shared variants and genetic distance, demonstrating that shared variants can provide considerable additional information in most scenarios. While shared-variant approaches identify relatively few links in the presence of a small transmission bottleneck, these links are highly accurate. Furthermore, we propose a hybrid approach that also incorporates phylogenetic distance to provide greater resolution. We applied our methods to data collected during the 2014 Ebola outbreak, identifying several likely routes of transmission. Our study highlights the power of data from deep sequencing of pathogens as a component of outbreak investigation and epidemiologic analyses.
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Affiliation(s)
- Colin J Worby
- Correspondence to Dr. Colin J. Worby, Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (e-mail: )
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38
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Lau MSY, Gibson GJ, Adrakey H, McClelland A, Riley S, Zelner J, Streftaris G, Funk S, Metcalf J, Dalziel BD, Grenfell BT. A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak. PLoS Comput Biol 2017; 13:e1005798. [PMID: 29084216 PMCID: PMC5679647 DOI: 10.1371/journal.pcbi.1005798] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/09/2017] [Accepted: 09/28/2017] [Indexed: 11/18/2022] Open
Abstract
In recent years there has been growing availability of individual-level spatio-temporal disease data, particularly due to the use of modern communicating devices with GPS tracking functionality. These detailed data have been proven useful for inferring disease transmission to a more refined level than previously. However, there remains a lack of statistically sound frameworks to model the underlying transmission dynamic in a mechanistic manner. Such a development is particularly crucial for enabling a general epidemic predictive framework at the individual level. In this paper we propose a new statistical framework for mechanistically modelling individual-to-individual disease transmission in a landscape with heterogeneous population density. Our methodology is first tested using simulated datasets, validating our inferential machinery. The methodology is subsequently applied to data that describes a regional Ebola outbreak in Western Africa (2014-2015). Our results show that the methods are able to obtain estimates of key epidemiological parameters that are broadly consistent with the literature, while revealing a significantly shorter distance of transmission. More importantly, in contrast to existing approaches, we are able to perform a more general model prediction that takes into account the susceptible population. Finally, our results show that, given reasonable scenarios, the framework can be an effective surrogate for susceptible-explicit individual models which are often computationally challenging. Availability of individual-level, spatio-temporal disease data (e.g. GPS locations of infected individuals) has been increasing in recent years, primarily due to the increased use of modern communication devices such as mobile phones. Such data create invaluable opportunities for researchers to study disease transmission on a more refined individual-to-individual level, facilitating the designs of potentially more effective control measures. However, the growing availability of such precise data has not been accompanied by development of statistically sound mechanistic frameworks. Developing such frameworks is an essential step for systematically extracting maximal information from data, in particular, evaluating the efficacy of individually-targeted control strategies and enabling forward epidemic prediction at the individual level. In this paper we develop a novel statistical framework that overcomes a few key limitations of existing approaches, enabling a machinery that can be used to infer the history of partially observed outbreaks and, more importantly, to produce a more comprehensive epidemic prediction. Our framework may also be a good surrogate for more computationally challenging individual-based models.
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Affiliation(s)
- Max S. Y. Lau
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
| | - Gavin J. Gibson
- Maxwell Institute for Mathematical Sciences, Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh, United Kingdom
| | - Hola Adrakey
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Amanda McClelland
- International Federation of Red Cross and Red Crescent Societies, Geneva, Switzerland
| | - Steven Riley
- MRC Centre for Outbreak Analysis and Modelling, Department Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Jon Zelner
- School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - George Streftaris
- Maxwell Institute for Mathematical Sciences, Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh, United Kingdom
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jessica Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Benjamin D. Dalziel
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
- Department of Mathematics, Oregon State University, Corvallis, Oregon, United States of America
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
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39
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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40
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Klinkenberg D, Backer JA, Didelot X, Colijn C, Wallinga J. Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol 2017; 13:e1005495. [PMID: 28545083 PMCID: PMC5436636 DOI: 10.1371/journal.pcbi.1005495] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 04/03/2017] [Indexed: 01/22/2023] Open
Abstract
Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation. To properly resolve transmission events, these processes need to be taken into account. Recent years have seen much progress in theory and method development, but existing applications make simplifying assumptions that often break up the dependency between the four processes, or are tailored to specific datasets with matching model assumptions and code. To obtain a method with wider applicability, we have developed a novel approach to reconstruct transmission trees with sequence data. Our approach combines elementary models for transmission, case observation, within-host pathogen dynamics, and mutation, under the assumption that the outbreak is over and all cases have been observed. We use Bayesian inference with MCMC for which we have designed novel proposal steps to efficiently traverse the posterior distribution, taking account of all unobserved processes at once. This allows for efficient sampling of transmission trees from the posterior distribution, and robust estimation of consensus transmission trees. We implemented the proposed method in a new R package phybreak. The method performs well in tests of both new and published simulated data. We apply the model to five datasets on densely sampled infectious disease outbreaks, covering a wide range of epidemiological settings. Using only sampling times and sequences as data, our analyses confirmed the original results or improved on them: the more realistic infection times place more confidence in the inferred transmission trees. It is becoming easier and cheaper to obtain (whole genome) sequences of pathogen samples during outbreaks of infectious diseases. If all hosts during an outbreak are sampled, and these samples are sequenced, the small differences between the sequences (single nucleotide polymorphisms, SNPs) give information on the transmission tree, i.e. who infected whom, and when. However, correctly inferring this tree is not straightforward, because SNPs arise from unobserved processes including infection events, as well as pathogen growth and mutation within the hosts. Several methods have been developed in recent years, but often for specific applications or with limiting assumptions, so that they are not easily applied to new settings and datasets. We have developed a new model and method to infer transmission trees without putting prior limiting constraints on the order of unobserved events. The method is easily accessible in an R package implementation. We show that the method performs well on new and previously published simulated data. We illustrate applicability to a wide range of infectious diseases and settings by analysing five published datasets on densely sampled infectious disease outbreaks, confirming or improving the original results.
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Affiliation(s)
- Don Klinkenberg
- Department of Epidemiology and Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Jantien A. Backer
- Department of Epidemiology and Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Jacco Wallinga
- Department of Epidemiology and Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Statistics and Bio-Informatics, Leiden University Medical Center, Leiden, The Netherlands
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41
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Rasmussen DA, Kouyos R, Günthard HF, Stadler T. Phylodynamics on local sexual contact networks. PLoS Comput Biol 2017; 13:e1005448. [PMID: 28350852 PMCID: PMC5388502 DOI: 10.1371/journal.pcbi.1005448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/11/2017] [Accepted: 03/10/2017] [Indexed: 12/26/2022] Open
Abstract
Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks. We present a new framework for phylodynamics on local contact networks based on pairwise epidemiological models that track the status of pairs of nodes in the network rather than just individuals. Shifting our focus from individuals to pairs leads naturally to coalescent models that describe how lineages move through networks and the rate at which lineages coalesce. These pairwise coalescent models not only consider how network structure directly shapes pathogen phylogenies, but also how the relationship between phylogenies and contact networks changes depending on epidemic dynamics and the fraction of infected hosts sampled. By considering pathogen phylogenies in a probabilistic framework, these coalescent models can also be used to estimate the statistical properties of contact networks directly from phylogenies using likelihood-based inference. We use this framework to explore how much information phylogenies retain about the underlying structure of contact networks and to infer the structure of a sexual contact network underlying a large HIV-1 sub-epidemic in Switzerland. Phylodynamic models relate the branching pattern of a pathogen’s phylogenetic tree to the tree-like growth of an epidemic as it spreads through a host population. Such models are increasingly used to learn about the epidemiology of different pathogens. We extend current models to consider the structure of host contact networks—the web of physical interactions through which pathogens spread. By considering how local interactions among hosts shape the phylogeny of a pathogen, our models offer a “pathogen’s eye view” of these networks. Our models also provide a statistical framework that can be used to infer network structure directly from phylogenies, which we use to estimate the properties of a sexual contact network in Switzerland from a HIV phylogeny.
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Affiliation(s)
- David A. Rasmussen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail:
| | - Roger Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
- Institute of Medical Virology, University of Zürich, Zürich, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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42
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Spatial and temporal dynamics of superspreading events in the 2014-2015 West Africa Ebola epidemic. Proc Natl Acad Sci U S A 2017; 114:2337-2342. [PMID: 28193880 DOI: 10.1073/pnas.1614595114] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unprecedented scale of the Ebola outbreak in Western Africa (2014-2015) has prompted an explosion of efforts to understand the transmission dynamics of the virus and to analyze the performance of possible containment strategies. Models have focused primarily on the reproductive numbers of the disease that represent the average number of secondary infections produced by a random infectious individual. However, these population-level estimates may conflate important systematic variation in the number of cases generated by infected individuals, particularly found in spatially localized transmission and superspreading events. Although superspreading features prominently in first-hand narratives of Ebola transmission, its dynamics have not been systematically characterized, hindering refinements of future epidemic predictions and explorations of targeted interventions. We used Bayesian model inference to integrate individual-level spatial information with other epidemiological data of community-based (undetected within clinical-care systems) cases and to explicitly infer distribution of the cases generated by each infected individual. Our results show that superspreaders play a key role in sustaining onward transmission of the epidemic, and they are responsible for a significant proportion ([Formula: see text]61%) of the infections. Our results also suggest age as a key demographic predictor for superspreading. We also show that community-based cases may have progressed more rapidly than those notified within clinical-care systems, and most transmission events occurred in a relatively short distance (with median value of 2.51 km). Our results stress the importance of characterizing superspreading of Ebola, enhance our current understanding of its spatiotemporal dynamics, and highlight the potential importance of targeted control measures.
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43
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Abstract
The frequency and global impact of infectious disease outbreaks, particularly those caused by emerging viruses, demonstrate the need for a better understanding of how spatial ecology and pathogen evolution jointly shape epidemic dynamics. Advances in computational techniques and the increasing availability of genetic and geospatial data are helping to address this problem, particularly when both information sources are combined. Here, we review research at the intersection of evolutionary biology, human geography and epidemiology that is working towards an integrated view of spatial incidence, host mobility and viral genetic diversity. We first discuss how empirical studies have combined viral spatial and genetic data, focusing particularly on the contribution of evolutionary analyses to epidemiology and disease control. Second, we explore the interplay between virus evolution and global dispersal in more depth for two pathogens: human influenza A virus and chikungunya virus. We discuss the opportunities for future research arising from new analyses of human transportation and trade networks, as well as the associated challenges in accessing and sharing relevant spatial and genetic data.
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Affiliation(s)
- Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Andrew J Tatem
- Department of Geography and Environment, University of Southampton, Highfield, Southampton SO17 1BJ, UK Fogarty International Center, National Institutes of Health, Bethesda, MA, USA Flowminder Foundation, Stockholm, Sweden
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
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44
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Baele G, Suchard MA, Rambaut A, Lemey P. Emerging Concepts of Data Integration in Pathogen Phylodynamics. Syst Biol 2017; 66:e47-e65. [PMID: 28173504 PMCID: PMC5837209 DOI: 10.1093/sysbio/syw054] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/02/2016] [Indexed: 12/24/2022] Open
Abstract
Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.
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Affiliation(s)
- Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Kings Buildings, Edinburgh EH9 3FL, UK
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
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45
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Ray B, Ghedin E, Chunara R. Network inference from multimodal data: A review of approaches from infectious disease transmission. J Biomed Inform 2016; 64:44-54. [PMID: 27612975 PMCID: PMC7106161 DOI: 10.1016/j.jbi.2016.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 07/10/2016] [Accepted: 09/03/2016] [Indexed: 02/02/2023]
Abstract
Networks inference problems are commonly found in multiple biomedical subfields such as genomics, metagenomics, neuroscience, and epidemiology. Networks are useful for representing a wide range of complex interactions ranging from those between molecular biomarkers, neurons, and microbial communities, to those found in human or animal populations. Recent technological advances have resulted in an increasing amount of healthcare data in multiple modalities, increasing the preponderance of network inference problems. Multi-domain data can now be used to improve the robustness and reliability of recovered networks from unimodal data. For infectious diseases in particular, there is a body of knowledge that has been focused on combining multiple pieces of linked information. Combining or analyzing disparate modalities in concert has demonstrated greater insight into disease transmission than could be obtained from any single modality in isolation. This has been particularly helpful in understanding incidence and transmission at early stages of infections that have pandemic potential. Novel pieces of linked information in the form of spatial, temporal, and other covariates including high-throughput sequence data, clinical visits, social network information, pharmaceutical prescriptions, and clinical symptoms (reported as free-text data) also encourage further investigation of these methods. The purpose of this review is to provide an in-depth analysis of multimodal infectious disease transmission network inference methods with a specific focus on Bayesian inference. We focus on analytical Bayesian inference-based methods as this enables recovering multiple parameters simultaneously, for example, not just the disease transmission network, but also parameters of epidemic dynamics. Our review studies their assumptions, key inference parameters and limitations, and ultimately provides insights about improving future network inference methods in multiple applications.
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Affiliation(s)
- Bisakha Ray
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics & Systems Biology, USA; College of Global Public Health, New York University, USA
| | - Rumi Chunara
- Dept. of Computer Science and Engineering, Tandon School of Engineering, USA; College of Global Public Health, New York University, USA
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46
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Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, Lawyer G, Hamouda O, Struck D, Vercauteren J, Wensing A, Alexiev I, Åsjö B, Balotta C, Gomes P, Camacho RJ, Coughlan S, Griskevicius A, Grossman Z, Horban A, Kostrikis LG, Lepej SJ, Liitsola K, Linka M, Nielsen C, Otelea D, Paredes R, Poljak M, Puchhammer-Stöckl E, Schmit JC, Sönnerborg A, Staneková D, Stanojevic M, Stylianou DC, Boucher CAB, Nikolopoulos G, Vasylyeva T, Friedman SR, van de Vijver D, Angarano G, Chaix ML, de Luca A, Korn K, Loveday C, Soriano V, Yerly S, Zazzi M, Vandamme AM, Paraskevis D. The global spread of HIV-1 subtype B epidemic. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 46:169-179. [PMID: 27262355 PMCID: PMC5157885 DOI: 10.1016/j.meegid.2016.05.041] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/25/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) was discovered in the early 1980s when the virus had already established a pandemic. For at least three decades the epidemic in the Western World has been dominated by subtype B infections, as part of a sub-epidemic that traveled from Africa through Haiti to United States. However, the pattern of the subsequent spread still remains poorly understood. Here we analyze a large dataset of globally representative HIV-1 subtype B strains to map their spread around the world over the last 50years and describe significant spread patterns. We show that subtype B travelled from North America to Western Europe in different occasions, while Central/Eastern Europe remained isolated for the most part of the early epidemic. Looking with more detail in European countries we see that the United Kingdom, France and Switzerland exchanged viral isolates with non-European countries than with European ones. The observed pattern is likely to mirror geopolitical landmarks in the post-World War II era, namely the rise and the fall of the Iron Curtain and the European colonialism. In conclusion, HIV-1 spread through specific migration routes which are consistent with geopolitical factors that affected human activities during the last 50years, such as migration, tourism and trade. Our findings support the argument that epidemic control policies should be global and incorporate political and socioeconomic factors.
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Affiliation(s)
| | - Konstantinos Angelis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Ioannis Mamais
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Glenn Lawyer
- Department of Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Daniel Struck
- Centre de Recherche Public de la Sante, Luxembourg, Luxembourg
| | - Jurgen Vercauteren
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Annemarie Wensing
- Department of Virology, University Medical Center, Utrecht, The Netherlands
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Perpétua Gomes
- Molecular Biology Lab, LMCBM, SPC, HEM, Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal
| | - Ricardo J Camacho
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | | | | | | | | | - Snjezana J Lepej
- Department of Molecular Diagnostics and Flow Cytometry, University Hospital for Infectious Diseases "Dr. F. Mihaljevic", Zagreb, Croatia
| | - Kirsi Liitsola
- National Institute of Health and Welfare, Helsinki, Finland
| | - Marek Linka
- National Reference Laboratory of AIDS, National Institute of Health, Prague, Czech Republic
| | | | - Dan Otelea
- National Institute for Infectious Diseases "Prof. Dr. Matei Bals", Bucharest, Romania
| | | | - Mario Poljak
- Slovenian HIV/AIDS Reference Centre, University of Ljubljana, Faculty of Medicine, Ljubljana, Slovenia
| | | | | | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Divisions of Infectious Diseases and Clinical Virology, Karolinska Institute, Stockholm, Sweden
| | | | - Maja Stanojevic
- University of Belgrade Faculty of Medicine, Belgrade, Serbia
| | | | | | - Georgios Nikolopoulos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece
| | | | - Samuel R Friedman
- Institute of Infectious Diseases Research, National Development and Research Institutes, Inc., New York, USA
| | - David van de Vijver
- Eijkman Winkler Institute, Department of Virology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Andrea de Luca
- Institute of Clinical Infectious Diseases, Catholic university, Rome, Italy
| | - Klaus Korn
- University of Erlangen, Erlangen, Germany
| | - Clive Loveday
- International Clinical Virology Centre, Buckinghamshire, England, United Kingdom
| | | | | | | | - Anne-Mieke Vandamme
- Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Greece.
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47
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Vergne T, Fournié G, Markovich MP, Ypma RJF, Katz R, Shkoda I, Lublin A, Perk S, Pfeiffer DU. Transmission tree of the highly pathogenic avian influenza (H5N1) epidemic in Israel, 2015. Vet Res 2016; 47:109. [PMID: 27814754 PMCID: PMC5096331 DOI: 10.1186/s13567-016-0393-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/14/2016] [Indexed: 11/10/2022] Open
Abstract
The transmission tree of the Israeli 2015 epidemic of highly pathogenic avian influenza (H5N1) was modelled by combining the spatio-temporal distribution of the outbreaks and the genetic distance between virus isolates. The most likely successions of transmission events were determined and transmission parameters were estimated. It was found that the median infectious pressure exerted at 1 km was 1.59 times (95% CI 1.04, 6.01) and 3.54 times (95% CI 1.09, 131.75) higher than that exerted at 2 and 5 km, respectively, and that three farms were responsible for all seven transmission events.
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Affiliation(s)
- Timothée Vergne
- Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, Hatfield, UK.
| | - Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, Hatfield, UK
| | | | - Rolf J F Ypma
- Brain Mapping Unit, University of Cambridge, Cambridge, UK
| | - Ram Katz
- Veterinary Services, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | | | | | - Shimon Perk
- Veterinary Services, Ministry of Agriculture and Rural Development, Bet Dagan, Israel
| | - Dirk U Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Department of Production and Population Health, Royal Veterinary College, Hatfield, UK
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48
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Francis SS, Plucinski MM, Wallace AD, Riley LW. Genotyping Oral Commensal Bacteria to Predict Social Contact and Structure. PLoS One 2016; 11:e0160201. [PMID: 27684062 PMCID: PMC5042546 DOI: 10.1371/journal.pone.0160201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 07/17/2016] [Indexed: 02/04/2023] Open
Abstract
Social network structure is a fundamental determinant of human health, from infectious to chronic diseases. However, quantitative and unbiased approaches to measuring social network structure are lacking. We hypothesized that genetic relatedness of oral commensal bacteria could be used to infer social contact between humans, just as genetic relatedness of pathogens can be used to determine transmission chains of pathogens. We used a traditional, questionnaire survey-based method to characterize the contact network of the School of Public Health at a large research university. We then collected saliva from a subset of individuals to analyze their oral microflora using a modified deep sequencing multilocus sequence typing (MLST) procedure. We examined micro-evolutionary changes in the S. viridans group to uncover transmission patterns reflecting social network structure. We amplified seven housekeeping gene loci from the Streptococcus viridans group, a group of ubiquitous commensal bacteria, and sequenced the PCR products using next-generation sequencing. By comparing the generated S. viridans reads between pairs of individuals, we reconstructed the social network of the sampled individuals and compared it to the network derived from the questionnaire survey-based method. The genetic relatedness significantly (p-value < 0.001) correlated with social distance in the questionnaire-based network, and the reconstructed network closely matched the network derived from the questionnaire survey-based method. Oral commensal bacterial are thus likely transmitted through routine physical contact or shared environment. Their genetic relatedness can be used to represent a combination of social contact and shared physical space, therefore reconstructing networks of contact. This study provides the first step in developing a method to measure direct social contact based on commensal organism genotyping, potentially capable of unmasking hidden social networks that contribute to pathogen transmission.
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Affiliation(s)
- Stephen Starko Francis
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
- Division of Epidemiology and Biostatistics, University of California, San Francisco, California, United States of America
| | - Mateusz M. Plucinski
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
- Department of Environmental Science and Policy Management, University of California, Berkeley, California, United States of America
| | - Amelia D. Wallace
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
| | - Lee W. Riley
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, United States of America
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, United States of America
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49
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De Maio N, Wu CH, Wilson DJ. SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent. PLoS Comput Biol 2016; 12:e1005130. [PMID: 27681228 PMCID: PMC5040440 DOI: 10.1371/journal.pcbi.1005130] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/05/2016] [Indexed: 11/18/2022] Open
Abstract
Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients. Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our computationally efficient implementation of this model enables the inference of host-to-host transmission while accommodating within-host evolution and non-sampled hosts. SCOTTI is distributed as an open source package for the phylogenetic software BEAST2. We show that SCOTTI can generally infer transmission events even in the presence of considerable within-host variation, can account for the uncertainty associated with the possible presence of non-sampled hosts, and can efficiently use data from multiple samples of the same host, although there is some reduction in accuracy when samples are collected very close to the infection time. We illustrate the features of our approach by investigating transmission from genetic and epidemiological data in a Foot and Mouth Disease Virus (FMDV) veterinary outbreak in England and a Klebsiella pneumoniae outbreak in a Nepali neonatal unit. Transmission histories inferred with SCOTTI will be important in devising effective measures to prevent and halt transmission. We present a new tool, SCOTTI, to efficiently reconstruct transmission events within outbreaks. Our approach combines genetic information from infection samples with epidemiological information of patient exposure to infection. While epidemiological information has been traditionally used to understand who infected whom in an outbreak, detailed genetic information is increasingly becoming available with the steady progress of sequencing technologies. However, many complications, if unaccounted for, can affect the accuracy with which the transmission history is reconstructed. SCOTTI efficiently accounts for several complications, in particular within-patient genetic variation of the infectious organism, and non-sampled patients (such as asymptomatic patients). Thanks to these features, SCOTTI provides accurate reconstructions of transmission in complex scenarios, which will be important in finding and limiting the sources and routes of transmission, preventing the spread of infectious disease.
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Affiliation(s)
- Nicola De Maio
- Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Chieh-Hsi Wu
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Daniel J Wilson
- Institute for Emerging Infections, Oxford Martin School, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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50
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Lam TTY, Zhu H, Guan Y, Holmes EC. Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses. Annu Rev Genomics Hum Genet 2016; 17:193-218. [PMID: 27216777 DOI: 10.1146/annurev-genom-083115-022628] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The emergence and reemergence of rapidly evolving RNA viruses-particularly those responsible for respiratory diseases, such as influenza viruses and coronaviruses-pose a significant threat to global health, including the potential of major pandemics. Importantly, recent advances in high-throughput genome sequencing enable researchers to reveal the genomic diversity of these viral pathogens at much lower cost and with much greater precision than they could before. In particular, the genome sequence data generated allow inferences to be made on the molecular basis of viral emergence, evolution, and spread in human populations in real time. In this review, we introduce recent computational methods that analyze viral genomic data, particularly in combination with metadata such as sampling time, geographic location, and virulence. We then outline the insights these analyses have provided into the fundamental patterns and processes of evolution and emergence in human respiratory RNA viruses, as well as the major challenges in such genomic analyses.
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Affiliation(s)
- Tommy T-Y Lam
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Huachen Zhu
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yi Guan
- State Key Laboratory of Emerging Infectious Diseases and Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, China; , ,
- Joint Influenza Research Center and Joint Institute of Virology, Shantou University Medical College, Shantou 515041, China
- State Key Laboratory of Emerging Infectious Diseases (HKU-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen 518112, China
- Department of Microbiology, Guangxi Medical University, Nanning 530021, China
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia;
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