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Singer B, Di Nardo A, Hein J, Ferretti L. Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes. Mol Biol Evol 2024; 41:msae126. [PMID: 38922185 PMCID: PMC11251493 DOI: 10.1093/molbev/msae126] [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: 01/09/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterize their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterize the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.
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Affiliation(s)
- Benjamin Singer
- Department of Medicine, Stanford University, Stanford, CA, USA
| | | | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, UK
| | - Luca Ferretti
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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2
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Serwin K, Scheibe K, Urbańska A, Aksak-Wąs B, Karasińska-Cieślak M, Ząbek P, Siwak E, Cielniak I, Jabłonowska E, Wójcik-Cichy K, Jakubowski P, Bociąga-Jasik M, Witor A, Szymczak A, Szetela B, Parczewski M. Phylodynamic evolution of HIV-1 A6 sub-subtype epidemics in Poland. J Med Virol 2024; 96:e29482. [PMID: 38381668 DOI: 10.1002/jmv.29482] [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: 10/16/2023] [Revised: 01/24/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
The human immunodeficiency virus type 1 (HIV-1) A6 sub-subtype is highly prevalent in Eastern Europe. Over the past decade, the dissemination of the A6 lineage has been expanding in Poland. The recent Russian invasion of Ukraine may further escalate the spread of this sub-subtype. While evolutionary studies using viral sequences have been instrumental in identifying the HIV epidemic patterns, the origins, and dynamics of the A6 sub-subtype in Poland remain to be explored. We analyzed 1185 HIV-1 A6 pol sequences from Poland, along with 8318 publicly available sequences from other countries. For analyses, phylogenetic tree construction, population dynamics inference, Bayesian analysis, and discrete phylogeographic modeling were employed. Of the introduction events to Poland, 69.94% originated from Ukraine, followed by 29.17% from Russia. Most A6 sequences in Poland (53.16%) formed four large clades, with their introductions spanning 1993-2008. Central and Southern Polish regions significantly influenced migration events. Transmissions among men who have sex with men (MSM) emerged as the dominant risk group for virus circulation, representing 72.92% of migration events. Sequences from migrants were found primarily outside the large clades. Past migration from Ukraine has fueled the spread of the A6 sub-subtype and the current influx of war-displaced people maintains the growing national epidemic.
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Affiliation(s)
- Karol Serwin
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Bogusz Aksak-Wąs
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Malwina Karasińska-Cieślak
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Piotr Ząbek
- Department of Adults' Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Siwak
- Department of Adults' Infectious Diseases, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Cielniak
- Faculty of Medical Science, Collegium Medicum Cardinal Stefan Wyszynski University in Warsaw, Warsaw, Poland
| | - Elżbieta Jabłonowska
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | - Kamila Wójcik-Cichy
- Department of Infectious Diseases and Hepatology, Medical University of Łódź, Łódź, Poland
| | | | - Monika Bociąga-Jasik
- Department of Infectious and Tropical Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Adam Witor
- Regional Hospital, Out-Patient's Clinic for Immune Deficiency, Chorzów, Poland
| | - Aleksandra Szymczak
- Department of Infectious Diseases, Liver Disease and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Bartosz Szetela
- Department of Infectious Diseases, Liver Disease and Acquired Immune Deficiencies, Wroclaw Medical University, Wrocław, Poland
| | - Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
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3
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Chen Z, Lemey P, Yu H. Approaches and challenges to inferring the geographical source of infectious disease outbreaks using genomic data. THE LANCET. MICROBE 2024; 5:e81-e92. [PMID: 38042165 DOI: 10.1016/s2666-5247(23)00296-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 12/04/2023]
Abstract
Genomic data hold increasing potential in the elucidation of transmission dynamics and geographical sources of infectious disease outbreaks. Phylogeographic methods that use epidemiological and genomic data obtained from surveillance enable us to infer the history of spatial transmission that is naturally embedded in the topology of phylogenetic trees as a record of the dispersal of infectious agents between geographical locations. In this Review, we provide an overview of phylogeographic approaches widely used for reconstructing the geographical sources of outbreaks of interest. These approaches can be classified into ancestral trait or state reconstruction and structured population models, with structured population models including popular structured coalescent and birth-death models. We also describe the major challenges associated with sequencing technologies, surveillance strategies, data sharing, and analysis frameworks that became apparent during the generation of large-scale genomic data in recent years, extending beyond inference approaches. Finally, we highlight the role of genomic data in geographical source inference and clarify how this enhances understanding and molecular investigations of outbreak sources.
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Affiliation(s)
- Zhiyuan Chen
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, KU Leuven, Leuven, Belgium
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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4
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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Gregianini TS, Salvato RS, Barcellos RB, Godinho FM, Ruivo AP, de Melo VH, Schroder JA, Martiny FL, Möllmann EB, Favreto C, Baethgen LF, Ferreira VP, de Lima LE, Piazza CF, Machado TRM, Becker IM, Ramos RR, Frölich GC, Rossetti AF, Almeida LDC, Rodrigues TMA, Bragança IT, Campos AAS, Manzoni VB, Machado LC, da Silva LMI, de Oliveira ALS, Paiva MHS, Nunes ZMA, de Almeida PR, Demoliner M, Gularte JS, da Silva MS, Filippi M, Pereira VMDAG, Spilki FR, da Veiga ABG, Wallau GL. Chikungunya virus infection in the southernmost state of Brazil was characterised by self-limited transmission (2017-2019) and a larger 2021 outbreak. Mem Inst Oswaldo Cruz 2023; 118:e220259. [PMID: 37531506 PMCID: PMC10392894 DOI: 10.1590/0074-02760220259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Chikungunya is a mosquito-borne virus that has been causing large outbreaks in the Americas since 2014. In Brazil, Asian-Caribbean (AC) and East-Central-South-African (ECSA) genotypes have been detected and lead to large outbreaks in several Brazilian states. In Rio Grande do Sul (RS), the southernmost state of Brazil, the first cases were reported in 2016. OBJECTIVES AND METHODS We employed genome sequencing and epidemiological investigation to characterise the Chikungunya fever (CHIKF) burden in RS between 2017-2021. FINDINGS We detected an increasing CHIKF burden linked to travel associated introductions and communitary transmission of distinct lineages of the ECSA genotype during this period. MAIN CONCLUSIONS Until 2020, CHIKV introductions were most travel associated and transmission was limited. Then, in 2021, the largest outbreak occurred in the state associated with the introduction of a new ECSA lineage. CHIKV outbreaks are likely to occur in the near future due to abundant competent vectors and a susceptible population, exposing more than 11 million inhabitants to an increasing infection risk.
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Affiliation(s)
- Tatiana Schäffer Gregianini
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Richard Steiner Salvato
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Fernanda Marques Godinho
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Amanda Pellenz Ruivo
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Viviane Horn de Melo
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Júlio Augusto Schroder
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Fernanda Letícia Martiny
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Erica Bortoli Möllmann
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Cátia Favreto
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Divisão de Vigilância Epidemiológica, Porto Alegre, RS, Brasil
| | - Ludmila Fiorenzano Baethgen
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Vithoria Pompermaier Ferreira
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Lívia Eidt de Lima
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Cláudia Fasolo Piazza
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Taís Raquel Marcon Machado
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Irina Marieta Becker
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Raquel Rocha Ramos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Guilherme Carey Frölich
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Alana Fraga Rossetti
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Lucas da Cunha Almeida
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Tahiana Machado Antunes Rodrigues
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Isabella Tabelli Bragança
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | - Aline Alves Scarpellini Campos
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Divisão de Vigilância Ambiental, Porto Alegre, RS, Brasil
| | - Verônica Baú Manzoni
- Prefeitura de São Nicolau, Secretaria Municipal de Saúde, São Nicolau, RS, Brasil
| | - Lais Ceschini Machado
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - Luisa Maria Inácio da Silva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - André Luiz Sá de Oliveira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Núcleo de Estatística e Geoprocessamento, Recife, PE, Brasil
| | - Marcelo Henrique Santos Paiva
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
| | - Zenaida Marion Alves Nunes
- Secretaria Estadual da Saúde do Rio Grande do Sul, Centro Estadual de Vigilância em Saúde, Laboratório Central de Saúde Pública, Porto Alegre, RS, Brasil
| | | | - Meriane Demoliner
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, RS, Brasil
| | | | | | - Micheli Filippi
- Universidade Feevale, Laboratório de Microbiologia Molecular, Novo Hamburgo, RS, Brasil
| | | | | | | | - Gabriel Luz Wallau
- Fundação Oswaldo Cruz-Fiocruz, Instituto Aggeu Magalhães, Departamento de Entomologia e Núcleo de Bioinformática, Recife, PE, Brasil
- National Reference Centre for Tropical Infectious Diseases, Bernhard Nocht Institute for Tropical Medicine, Department of Arbovirology, WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Hamburg, Germany
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Franzo G, Legnardi M, Faustini G, Tucciarone CM, Cecchinato M. When Everything Becomes Bigger: Big Data for Big Poultry Production. Animals (Basel) 2023; 13:1804. [PMID: 37889739 PMCID: PMC10252109 DOI: 10.3390/ani13111804] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 08/13/2023] Open
Abstract
In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. Pollution and land erosion, competition for limited resources between animal and human nutrition, animal welfare concerns, limitations on the use of growth promoters and antimicrobial agents, and increasing risks and effects of animal infectious diseases and zoonoses are several topics that have received attention from authorities and the public. The increase in poultry production must be achieved mainly through optimization and increased efficiency. The increasing ability to generate large amounts of data ("big data") is pervasive in both modern society and the farming industry. Information accessibility-coupled with the availability of tools and computational power to store, share, integrate, and analyze data with automatic and flexible algorithms-offers an unprecedented opportunity to develop tools to maximize farm profitability, reduce socio-environmental impacts, and increase animal and human health and welfare. A detailed description of all topics and applications of big data analysis in poultry farming would be infeasible. Therefore, the present work briefly reviews the application of sensor technologies, such as optical, acoustic, and wearable sensors, as well as infrared thermal imaging and optical flow, to poultry farming. The principles and benefits of advanced statistical techniques, such as machine learning and deep learning, and their use in developing effective and reliable classification and prediction models to benefit the farming system, are also discussed. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking, and reconstruction of microorganisms' population dynamics, evolution, and spread. The benefits of the objective evaluation of the effectiveness of applied control strategies are also considered. Although human-artificial intelligence collaborations in the livestock sector can be frightening because they require farmers and employees in the sector to adapt to new roles, challenges, and competencies-and because several unknowns, limitations, and open-ended questions are inevitable-their overall benefits appear to be far greater than their drawbacks. As more farms and companies connect to technology, artificial intelligence (AI) and sensing technologies will begin to play a greater role in identifying patterns and solutions to pressing problems in modern animal farming, thus providing remarkable production-based and commercial advantages. Moreover, the combination of diverse sources and types of data will also become fundamental for the development of predictive models able to anticipate, rather than merely detect, disease occurrence. The increasing availability of sensors, infrastructures, and tools for big data collection, storage, sharing, and analysis-together with the use of open standards and integration with pathogen molecular epidemiology-have the potential to address the major challenge of producing higher-quality, more healthful food on a larger scale in a more sustainable manner, thereby protecting ecosystems, preserving natural resources, and improving animal and human welfare and health.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.); (G.F.); (C.M.T.); (M.C.)
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7
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Brintnell E, Poon A. Traversing missing links in the spread of HIV. eLife 2022; 11:82610. [PMID: 36178092 PMCID: PMC9525057 DOI: 10.7554/elife.82610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Combining clinical and genetic data can improve the effectiveness of virus tracking with the aim of reducing the number of HIV cases by 2030.
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Affiliation(s)
- Erin Brintnell
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Art Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Canada.,Department of Computer Science, Western University, London, Canada
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8
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Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan. Viruses 2022; 14:v14081634. [PMID: 35893699 PMCID: PMC9331208 DOI: 10.3390/v14081634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/16/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.
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9
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Phylodynamics and Coat Protein Analysis of Babaco Mosaic Virus in Ecuador. PLANTS 2022; 11:plants11131646. [PMID: 35807598 PMCID: PMC9268947 DOI: 10.3390/plants11131646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022]
Abstract
Babaco is a fast-growing herbaceous shrub with great commercial potential because of the organoleptic properties of its fruit. Babaco mosaic virus (BabMV) is a potexvirus in the family Alphaflexiviridae affecting babaco in all the provinces that produce this crop in Ecuador. BabMV was recently described but it has been affecting babaco for decades and, since many potexviruses are serologically indistinguishable, it may have been previously misidentified as papaya mosaic virus. Based on the coat protein (CP) gene, we aimed to study the distribution and epidemiological patterns of BabMV in babaco and chamburo over the years and to model its three-dimensional structure. Sequences of the CP were obtained from thirty-six isolates from plants collected in the main babaco-producing provinces of Ecuador between 2016 and 2021. The evolution rate of BabMV was estimated at 1.21 × 10−3 nucleotide substitutions site−1 year−1 and a time of origin of the most recent common ancestor around 1958.80. From molecular dynamics simulations, compared to other proteins of BabMV—RDRP, TGB1, and Alkb domain—the CP exhibited a higher flexibility with the C and N terminals as the most flexible regions. The reconstructed viral distribution provides dispersion patterns which have implications for control approaches of BabMV.
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10
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Dellicour S, Lemey P, Suchard MA, Gilbert M, Baele G. Accommodating sampling location uncertainty in continuous phylogeography. Virus Evol 2022; 8:veac041. [PMID: 35795297 PMCID: PMC9248920 DOI: 10.1093/ve/veac041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/22/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023] Open
Abstract
Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.
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Affiliation(s)
| | | | | | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, Bruxelles 1050, Belgium
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Phylodynamic Dispersal of SARS-CoV-2 Lineages Circulating across Polish-German Border Provinces. Viruses 2022; 14:v14050884. [PMID: 35632625 PMCID: PMC9143188 DOI: 10.3390/v14050884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction: The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evolved into a worldwide outbreak, with significant molecular evolution over time. Large-scale phylodynamic studies allow to map the virus spread and inform preventive strategies. Aim: This study investigates the extent of binational dispersal and dynamics of SARS-CoV-2 lineages between seven border provinces of the adjacent countries of Poland and Germany to reconstruct SARS-CoV-2 transmission networks. Methods: Following three pandemic waves from March 2020 to the end of May 2021, we analysed a dataset of 19,994 sequences divided into B.1.1.7|Alpha and non-Alpha lineage groups. We performed phylogeographic analyses using the discrete diffusion models to identify the pathways of virus spread. Results: Based on population dynamics inferences, in total, 673 lineage introductions (95% HPD interval 641−712) for non-Alpha and 618 (95% HPD interval 599−639) for B.1.1.7|Alpha were identified in the area. For non-Alpha lineages, 5.05% binational, 86.63% exclusively German, and 8.32% Polish clusters were found, with a higher frequency of international clustering observed for B.1.1.7|Alpha (13.11% for binational, 68.44% German and 18.45% Polish, p < 0.001). We identified key transmission hubs for the analysed lineages, namely Saxony, West Pomerania and Lower Silesia. Conclusions: Clustering patterns between Poland and Germany reflect the viral variant transmission dynamics at the international level in the borderline area. Tracing the spread of the virus between two adjacent large European countries may provide a basis for future intervention policies in cross-border cooperation efforts against the spread of the pandemics.
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12
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Louca S. The rates of global bacterial and archaeal dispersal. THE ISME JOURNAL 2022; 16:159-167. [PMID: 34282284 PMCID: PMC8692594 DOI: 10.1038/s41396-021-01069-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world. I find clear signs of continental-scale endemism, including strong correlations between phylogenetic divergence and geographic distance. However, the phylogenetic scale at which endemism generally occurs is extremely small, and most "species" (defined by an average nucleotide identity ≥ 95%) and even closely related strains (average nucleotide identity ≥ 99.9%) are globally distributed. Human-associated lineages display faster dispersal rates than other terrestrial lineages; the average net distance between any two human-associated cell lineages diverging 50 years ago is roughly 580 km. These results suggest that many previously reported global-scale microbial biogeographical patterns are likely the result of recent or current environmental filtering rather than geographic endemism. For human-associated lineages, estimated transition rates between Europe and North America are particularly high, and much higher than for non-human associated terrestrial lineages, highlighting the role that human movement plays in global microbial dispersal. Dispersal was slowest for hot spring- and terrestrial subsurface-associated lineages, indicating that these environments may act as "isolated islands" of microbial evolution.
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Affiliation(s)
- Stilianos Louca
- grid.170202.60000 0004 1936 8008Department of Biology, University of Oregon, Eugene, OR USA ,grid.170202.60000 0004 1936 8008Institute of Ecology and Evolution, University of Oregon, Eugene, OR USA
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13
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Stadtmüller M, Laubner A, Rost F, Winkler S, Patrasová E, Šimůnková L, Reinhardt S, Beil J, Dalpke AH, Yi B. OUP accepted manuscript. Virus Evol 2022; 8:veac010. [PMID: 35494175 PMCID: PMC9048873 DOI: 10.1093/ve/veac010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution plays a significant role in shaping the dynamics of the coronavirus disease 2019 pandemic. To monitor the evolution of SARS-CoV-2 variants, through international collaborations, we performed genomic epidemiology analyses on a weekly basis with SARS-CoV-2 samples collected from a border region between Germany, Poland, and the Czech Republic in a global background. For identified virus mutant variants, active viruses were isolated and functional evaluations were performed to test their replication fitness and neutralization sensitivity against vaccine-elicited serum neutralizing antibodies. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. Of note, this B.1.1.7 sub-lineage is the predominant B.1.1.7 variant in several European countries such as Czech Republic, Austria, and Slovakia. The earliest samples belonging to this sub-lineage were detected in November 2020 in a few countries in the European continent, but not in the UK. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Gamma and Beta variants, respectively. Antibody neutralization assay of virus variant isolations has revealed that the variant with extra spike mutations is 3.2-fold less sensitive to vaccine-elicited antibodies as compared to the other B.1.1.7 variants tested, indicating potential for immune evasion, but it also exhibited reduced replication fitness, suggesting lower transmissibility. The wide spread of this B.1.1.7 sub-lineage was related to the pandemic waves in early 2021 in various European countries. These findings about the emergence, spread, evolution, infection, and transmission abilities of this B.1.1.7 sub-lineage add to our understanding about the pandemic development in Europe and highlight the importance of international collaboration on virus mutant surveillance.
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Affiliation(s)
| | - Alexa Laubner
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, Saxony 01307, Germany
| | - Fabian Rost
- DRESDEN concept Genome Center, Technische Universität Dresden, Fetscherstraße 105, Dresden, Saxony 01307, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, Fetscherstraße 105, Dresden, Saxony 01307, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, Technische Universität Dresden, Pfotenhauerstraße 108, Dresden, Saxony 01307, Germany
| | - Eva Patrasová
- Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Moskevská 15, Ústí nad Labem 400 01, Czech Republic
- Third Faculty of Medicine, Charles University in Prague, Ruská 2411/87, Prague 100 00, Czech Republic
| | - Lenka Šimůnková
- Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Moskevská 15, Ústí nad Labem 400 01, Czech Republic
| | | | - Johanna Beil
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, Technische Universität Dresden, Pfotenhauerstraße 108, Dresden, Saxony 01307, Germany
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, Dresden, Saxony 01307, Germany
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14
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Liu P, Song Y, Colijn C, MacPherson A. The impact of sampling bias on viral phylogeographic reconstruction. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000577. [PMID: 36962555 PMCID: PMC10021582 DOI: 10.1371/journal.pgph.0000577] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
Genomic epidemiology plays an ever-increasing role in our understanding of and response to the spread of infectious pathogens. Phylogeography, the reconstruction of the historical location and movement of pathogens from the evolutionary relationships among sampled pathogen sequences, can inform policy decisions related to viral movement among jurisdictions. However, phylogeographic reconstruction is impacted by the fact that the sampling and virus sequencing policies differ among jurisdictions, and these differences can cause bias in phylogeographic reconstructions. Here we assess the potential impacts of geographic-based sampling bias on estimated viral locations in the past, and on whether key viral movements can be detected. We quantify the effect of bias using simulated phylogenies with known geographic histories, and determine the impact of the biased sampling and of the underlying migration rate on the accuracy of estimated past viral locations. We find that overall, the accuracy of phylogeographic reconstruction is high, particularly when the migration rate is low. However, results depend on sampling, and sampling bias can have a large impact on the numbers and nature of estimated migration events. We apply these insights to the geographic spread of Ebolavirus in the 2014-2016 West Africa epidemic. This work highlights how sampling policy can both impact geographic inference and be optimized to best ensure the accuracy of specific features of geographic spread.
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Affiliation(s)
- Pengyu Liu
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Yexuan Song
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ailene MacPherson
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
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15
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Deviatkin AA, Vakulenko YA, Dashian MA, Lukashev AN. Evaluating the Impact of Anthropogenic Factors on the Dissemination of Contemporary Cosmopolitan, Arctic, and Arctic-like Rabies Viruses. Viruses 2021; 14:66. [PMID: 35062270 PMCID: PMC8777955 DOI: 10.3390/v14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/29/2021] [Indexed: 11/16/2022] Open
Abstract
Rabies is a globally prevalent viral zoonosis that causes 59,000 deaths per year and has important economic consequences. Most virus spread is associated with the migration of its primary hosts. Anthropogenic dissemination, mainly via the transportation of rabid dogs, shaped virus ecology a few hundred years ago and is responsible for several current outbreaks. A systematic analysis of aberrant long-distance events in the steppe and Arctic-like groups of rabies virus was performed using statistical (Bayesian) phylogeography and plots of genetic vs. geographic distances. The two approaches produced similar results but had some significant differences and complemented each other. No phylogeographic analysis could be performed for the Arctic group because polar foxes transfer the virus across the whole circumpolar region at high velocity, and there was no correlation between genetic and geographic distances in this virus group. In the Arctic-like group and the steppe subgroup of the cosmopolitan group, a significant number of known sequences (15-20%) was associated with rapid long-distance transfers, which mainly occurred within Eurasia. Some of these events have been described previously, while others have not been documented. Most of the recent long-distance transfers apparently did not result in establishing the introduced virus, but a few had important implications for the phylogeographic history of rabies. Thus, human-mediated long-distance transmission of the rabies virus remains a significant threat that needs to be addressed.
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Affiliation(s)
- Andrei A. Deviatkin
- Laboratory of Molecular Biology and Biochemistry, Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia
| | - Yulia A. Vakulenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mariia A. Dashian
- Faculty of Biomedicine, Pirogov Medical University, 117997 Moscow, Russia;
| | - Alexander N. Lukashev
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia; (Y.A.V.); (A.N.L.)
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16
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Dellicour S, Gill MS, Faria NR, Rambaut A, Pybus OG, Suchard MA, Lemey P. Relax, Keep Walking - A Practical Guide to Continuous Phylogeographic Inference with BEAST. Mol Biol Evol 2021; 38:3486-3493. [PMID: 33528560 PMCID: PMC8321535 DOI: 10.1093/molbev/msab031] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Spatially explicit phylogeographic analyses can be performed with an inference framework that employs relaxed random walks to reconstruct phylogenetic dispersal histories in continuous space. This core model was first implemented 10 years ago and has opened up new opportunities in the field of phylodynamics, allowing researchers to map and analyze the spatial dissemination of rapidly evolving pathogens. We here provide a detailed and step-by-step guide on how to set up, run, and interpret continuous phylogeographic analyses using the programs BEAUti, BEAST, Tracer, and TreeAnnotator.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mandev S Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
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17
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Towards a more healthy conservation paradigm: integrating disease and molecular ecology to aid biological conservation †. J Genet 2021. [PMID: 33622992 PMCID: PMC7371965 DOI: 10.1007/s12041-020-01225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parasites, and the diseases they cause, are important from an ecological and evolutionary perspective because they can negatively affect host fitness and can regulate host populations. Consequently, conservation biology has long recognized the vital role that parasites can play in the process of species endangerment and recovery. However, we are only beginning to understand how deeply parasites are embedded in ecological systems, and there is a growing recognition of the important ways in which parasites affect ecosystem structure and function. Thus, there is an urgent need to revisit how parasites are viewed from a conservation perspective and broaden the role that disease ecology plays in conservation-related research and outcomes. This review broadly focusses on the role that disease ecology can play in biological conservation. Our review specifically emphasizes on how the integration of tools and analytical approaches associated with both disease and molecular ecology can be leveraged to aid conservation biology. Our review first concentrates on disease-mediated extinctions and wildlife epidemics. We then focus on elucidating how host–parasite interactions has improved our understanding of the eco-evolutionary dynamics affecting hosts at the individual, population, community and ecosystem scales. We believe that the role of parasites as drivers and indicators of ecosystem health is especially an exciting area of research that has the potential to fundamentally alter our view of parasites and their role in biological conservation. The review concludes with a broad overview of the current and potential applications of modern genomic tools in disease ecology to aid biological conservation.
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18
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Jara M, Crespo R, Roberts DL, Chapman A, Banda A, Machado G. Development of a Dissemination Platform for Spatiotemporal and Phylogenetic Analysis of Avian Infectious Bronchitis Virus. Front Vet Sci 2021; 8:624233. [PMID: 34017870 PMCID: PMC8129014 DOI: 10.3389/fvets.2021.624233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/27/2021] [Indexed: 11/13/2022] Open
Abstract
Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.
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Affiliation(s)
- Manuel Jara
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Rocio Crespo
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - David L Roberts
- Department of Computer Science North Carolina State University, Raleigh, NC, United States
| | - Ashlyn Chapman
- Department of Computer Science North Carolina State University, Raleigh, NC, United States
| | - Alejandro Banda
- Poultry Research and Diagnostic Laboratory, College of Veterinary Medicine, Mississippi State University, Pearl, MS, United States
| | - Gustavo Machado
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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19
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Dellicour S, Hong SL, Vrancken B, Chaillon A, Gill MS, Maurano MT, Ramaswami S, Zappile P, Marier C, Harkins GW, Baele G, Duerr R, Heguy A. Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLoS Pathog 2021; 17:e1009571. [PMID: 34015049 PMCID: PMC8136714 DOI: 10.1371/journal.ppat.1009571] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
During the first phase of the COVID-19 epidemic, New York City rapidly became the epicenter of the pandemic in the United States. While molecular phylogenetic analyses have previously highlighted multiple introductions and a period of cryptic community transmission within New York City, little is known about the circulation of SARS-CoV-2 within and among its boroughs. We here perform phylogeographic investigations to gain insights into the circulation of viral lineages during the first months of the New York City outbreak. Our analyses describe the dispersal dynamics of viral lineages at the state and city levels, illustrating that peripheral samples likely correspond to distinct dispersal events originating from the main metropolitan city areas. In line with the high prevalence recorded in this area, our results highlight the relatively important role of the borough of Queens as a transmission hub associated with higher local circulation and dispersal of viral lineages toward the surrounding boroughs.
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Affiliation(s)
- Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego, California, United States of America
| | - Mandev S. Gill
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Matthew T. Maurano
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Sitharam Ramaswami
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Paul Zappile
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Christian Marier
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
| | - Gordon W. Harkins
- South African Medical Research Council Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, University of Leuven, Leuven, Belgium
| | - Ralf Duerr
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Adriana Heguy
- Department of Pathology, NYU Grossman School of Medicine, New York, New York, United States of America
- Genome Technology Center, Office for Science and Research, NYU Langone Health, New York, New York, United States of America
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20
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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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21
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Ssemwanga D, Bbosa N, Nsubuga RN, Ssekagiri A, Kapaata A, Nannyonjo M, Nassolo F, Karabarinde A, Mugisha J, Seeley J, Yebra G, Leigh Brown A, Kaleebu P. The Molecular Epidemiology and Transmission Dynamics of HIV Type 1 in a General Population Cohort in Uganda. Viruses 2020; 12:v12111283. [PMID: 33182587 PMCID: PMC7697205 DOI: 10.3390/v12111283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
The General Population Cohort (GPC) in south-western Uganda has a low HIV-1 incidence rate (<1%). However, new infections continue to emerge. In this research, 3796 HIV-1 pol sequences (GPC: n = 1418, non-GPC sites: n = 1223, Central Uganda: n = 1010 and Eastern Uganda: n = 145) generated between 2003–2015 were analysed using phylogenetic methods with demographic data to understand HIV-1 transmission in this cohort and inform the epidemic response. HIV-1 subtype A1 was the most prevalent strain in the GPC area (GPC and non-GPC sites) (39.8%), central (45.9%) and eastern (52.4%) Uganda. However, in the GPC alone, subtype D was the predominant subtype (39.1%). Of the 524 transmission clusters identified by Cluster Picker, all large clusters (≥5 individuals, n = 8) involved individuals from the GPC. In a multivariate analysis, clustering was strongly associated with being female (adjusted Odds Ratio, aOR = 1.28; 95% CI, 1.06–1.54), being >25 years (aOR = 1.52; 95% CI, 1.16–2.0) and being a resident in the GPC (aOR = 6.90; 95% CI, 5.22–9.21). Phylogeographic analysis showed significant viral dissemination (Bayes Factor test, BF > 3) from the GPC without significant viral introductions (BF < 3) into the GPC. The findings suggest localized HIV-1 transmission in the GPC. Intensifying geographically focused combination interventions in the GPC would contribute towards controlling HIV-1 infections.
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Affiliation(s)
- Deogratius Ssemwanga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
- Correspondence: ; Tel.: +256-(0)-417-704000
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Rebecca N. Nsubuga
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alfred Ssekagiri
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
| | - Anne Kapaata
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Maria Nannyonjo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Faridah Nassolo
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Alex Karabarinde
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Joseph Mugisha
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
| | - Janet Seeley
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, 15-17 Tavistock Place, London WC1H 9SH, UK
| | - Gonzalo Yebra
- The Roslin Institute, Royal (Dick) School of Veterinary Medicine, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK;
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK;
| | - Pontiano Kaleebu
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 256, Uganda; (N.B.); (R.N.N.); (A.K.); (M.N.); (F.N.); (A.K.); (J.M.); (J.S.); (P.K.)
- Department of General Virology, Uganda Virus Research Institute, Entebbe 256, Uganda;
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22
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Louca S. Phylogeographic Estimation and Simulation of Global Diffusive Dispersal. Syst Biol 2020; 70:340-359. [PMID: 32726450 DOI: 10.1093/sysbio/syaa061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 11/14/2022] Open
Abstract
The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example, for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2D plane; however, the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because spherical Brownian motion (SBM) differs from planar Brownian motion. No statistical method exists for estimating SBM diffusion coefficients from a given timetree and tip coordinates, and no method exists for simulating SBM along a given timetree. Here, I present new methods for simulating SBM along a given timetree, and for estimating SBM diffusivity from a given timetree and tip coordinates using a modification of Felsenstein's independent contrasts and maximum likelihood. My simulation and fitting methods can accommodate arbitrary time-dependent diffusivities and scale efficiently to trees with millions of tips, thus enabling new analyses even in cases where planar BM would be a sufficient approximation. I demonstrate these methods using a timetree of marine and terrestrial Cyanobacterial genomes, as well as timetrees of two globally circulating Influenza B clades. My methods are implemented in the R package "castor." [Independent contrasts; phylogenetic; random walk; simulation; spherical Brownian motion.].
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, USA.,Institute of Ecology and Evolution, University of Oregon, USA
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23
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Toxigenic Vibrio cholerae evolution and establishment of reservoirs in aquatic ecosystems. Proc Natl Acad Sci U S A 2020; 117:7897-7904. [PMID: 32229557 PMCID: PMC7149412 DOI: 10.1073/pnas.1918763117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well-recognized that Vibrio cholerae is also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in the persistence of the disease on the Indian subcontinent, an epidemiological view postulating that locally evolving environmental V. cholerae contributes to outbreaks outside Asia remains debated. The single-source introduction of toxigenic V. cholerae O1 in Haiti, one of the largest outbreaks occurring this century, with 812,586 suspected cases and 9,606 deaths reported through July 2018, provided a unique opportunity to evaluate the role of aquatic reservoirs and assess bacterial transmission dynamics across environmental boundaries. To this end, we investigated the phylogeography of both clinical and aquatic toxigenic V. cholerae O1 isolates and show robust evidence of the establishment of aquatic reservoirs as well as ongoing evolution of V. cholerae isolates from aquatic sites. Novel environmental lineages emerged from sequential population bottlenecks, carrying mutations potentially involved in adaptation to the aquatic ecosystem. Based on such empirical data, we developed a mixed-transmission dynamic model of V. cholerae, where aquatic reservoirs actively contribute to genetic diversification and epidemic emergence, which underscores the complexity of transmission pathways in epidemics and endemic settings and the need for long-term investments in cholera control at both human and environmental levels.
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Hong SL, Dellicour S, Vrancken B, Suchard MA, Pyne MT, Hillyard DR, Lemey P, Baele G. In Search of Covariates of HIV-1 Subtype B Spread in the United States-A Cautionary Tale of Large-Scale Bayesian Phylogeography. Viruses 2020; 12:v12020182. [PMID: 32033422 PMCID: PMC7077180 DOI: 10.3390/v12020182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Infections with HIV-1 group M subtype B viruses account for the majority of the HIV epidemic in the Western world. Phylogeographic studies have placed the introduction of subtype B in the United States in New York around 1970, where it grew into a major source of spread. Currently, it is estimated that over one million people are living with HIV in the US and that most are infected with subtype B variants. Here, we aim to identify the drivers of HIV-1 subtype B dispersal in the United States by analyzing a collection of 23,588 pol sequences, collected for drug resistance testing from 45 states during 2004-2011. To this end, we introduce a workflow to reduce this large collection of data to more computationally-manageable sample sizes and apply the BEAST framework to test which covariates associate with the spread of HIV-1 across state borders. Our results show that we are able to consistently identify certain predictors of spread under reasonable run times across datasets of up to 10,000 sequences. However, the general lack of phylogenetic structure and the high uncertainty associated with HIV trees make it difficult to interpret the epidemiological relevance of the drivers of spread we are able to identify. While the workflow we present here could be applied to other virus datasets of a similar scale, the characteristic star-like shape of HIV-1 phylogenies poses a serious obstacle to reconstructing a detailed evolutionary and spatial history for HIV-1 subtype B in the US.
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Affiliation(s)
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Correspondence:
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA;
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Michael T. Pyne
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA;
| | - David R. Hillyard
- Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA;
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (S.D.); (B.V.); (P.L.); (G.B.)
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25
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Impact of past climate warming on genomic diversity and demographic history of collared lemmings across the Eurasian Arctic. Proc Natl Acad Sci U S A 2020; 117:3026-3033. [PMID: 31988125 DOI: 10.1073/pnas.1913596117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Arctic climate was warmer than today at the last interglacial and the Holocene thermal optimum. To reveal the impact of past climate-warming events on the demographic history of an Arctic specialist, we examined both mitochondrial and nuclear genomic variation in the collared lemming (Dicrostonyx torquatus, Pallas), a keystone species in tundra communities, across its entire distribution in northern Eurasia. The ancestral phylogenetic position of the West Beringian group and divergence time estimates support the hypothesis of continental range contraction to a single refugial area located in West Beringia during high-magnitude warming of the last interglacial, followed by westward recolonization of northern Eurasia in the last glacial period. The West Beringian group harbors the highest mitogenome diversity and its inferred demography indicates a constantly large effective population size over the Late Pleistocene to Holocene. This suggests that northward forest expansion during recent warming of the Holocene thermal optimum did not affect the gene pool of the collared lemming in West Beringia but reduced genomic diversity and effective population size in all other regions of the Eurasian Arctic. Demographic inference from genomic diversity was corroborated by species distribution modeling showing reduction in species distribution during past climate warming. These conclusions are supported by recent paleoecological evidence suggesting smaller temperature increases and moderate northward forest advances in the extreme northeast of Eurasia during the Late Pleistocene-to-Holocene warming events. This study emphasizes the importance of West Beringia as a potential refugium for cold-adapted Arctic species under ongoing climate warming.
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26
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Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 2019; 15:e1007976. [PMID: 31809523 PMCID: PMC6897401 DOI: 10.1371/journal.ppat.1007976] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.
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27
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28
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De Scheerder MA, Vrancken B, Dellicour S, Schlub T, Lee E, Shao W, Rutsaert S, Verhofstede C, Kerre T, Malfait T, Hemelsoet D, Coppens M, Dhondt A, De Looze D, Vermassen F, Lemey P, Palmer S, Vandekerckhove L. HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs. Cell Host Microbe 2019; 26:347-358.e7. [PMID: 31471273 PMCID: PMC11021134 DOI: 10.1016/j.chom.2019.08.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/16/2019] [Accepted: 07/31/2019] [Indexed: 02/01/2023]
Abstract
Viral rebound upon stopping combined antiretroviral therapy poses a major barrier toward an HIV cure. Cellular and anatomical sources responsible for reinitiating viral replication remain a subject of ardent debate, despite extensive research efforts. To unravel the source of rebounding viruses, we conducted a large-scale HIV-STAR (HIV-1 sequencing before analytical treatment interruption to identify the anatomically relevant HIV reservoir) clinical trial. We collected samples from 11 participants and compared the genetic composition of (pro)viruses collected under treatment from different cellular and anatomical compartments with that of plasma viruses sampled during analytical treatment interruption. We found a remarkably heterogeneous source of viral rebound. In addition, irrespective of the compartment or cell subset, genetically identical viral expansions played a significant role in viral rebound. Our study suggests that although there does not seem to be a primary source for rebound HIV, cellular proliferation is an important driver of HIV persistence and should therefore be considered in future curative strategies.
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Affiliation(s)
- Marie-Angélique De Scheerder
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
| | - Bram Vrancken
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Simon Dellicour
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium; Spatial Epidemiology Laboratory (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Timothy Schlub
- University of Sydney, Faculty of Medicine and Health, Sydney School of Public Health, Sydney 2000, NSW, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Wei Shao
- Frederick National Laboratory for Cancer Research (FNLCR), Frederick, MD, USA
| | - Sofie Rutsaert
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Chris Verhofstede
- Aids Reference Laboratory, Ghent University Hospital, Ghent 9000, Belgium
| | - Tessa Kerre
- Department of Hematology, Ghent University Hospital, Ghent 9000, Belgium
| | - Thomas Malfait
- Department of Pulmonology, Ghent University Hospital, Ghent 9000, Belgium
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, Ghent 9000, Belgium
| | - Marc Coppens
- Department of Anesthesiology, Ghent University Hospital, Ghent 9000, Belgium
| | - Annemieke Dhondt
- Department of Nephrology, Ghent University Hospital, Ghent 9000, Belgium
| | - Danny De Looze
- Department of Gastro-Enterology, Ghent University Hospital, Ghent 9000, Belgium
| | - Frank Vermassen
- Department of Vascular Surgery, Ghent University Hospital, Ghent 9000, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Laboratory of Evolutionary and Computational Virology, Herestraat 49, Leuven 3000 Belgium
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney 2145, NSW, Australia
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of General Internal Medicine, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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29
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Phylogeography of Puumala orthohantavirus in Europe. Viruses 2019; 11:v11080679. [PMID: 31344894 PMCID: PMC6723369 DOI: 10.3390/v11080679] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Puumala virus is an RNA virus hosted by the bank vole (Myodes glareolus) and is today present in most European countries. Whilst it is generally accepted that hantaviruses have been tightly co-evolving with their hosts, Puumala virus (PUUV) evolutionary history is still controversial and so far has not been studied at the whole European level. This study attempts to reconstruct the phylogeographical spread of modern PUUV throughout Europe during the last postglacial period in the light of an upgraded dataset of complete PUUV small (S) segment sequences and by using most recent computational approaches. Taking advantage of the knowledge on the past migrations of its host, we identified at least three potential independent dispersal routes of PUUV during postglacial recolonization of Europe by the bank vole. From the Alpe-Adrian region (Balkan, Austria, and Hungary) to Western European countries (Germany, France, Belgium, and Netherland), and South Scandinavia. From the vicinity of Carpathian Mountains to the Baltic countries and to Poland, Russia, and Finland. The dissemination towards Denmark and North Scandinavia is more hypothetical and probably involved several independent streams from south and north Fennoscandia.
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30
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Evidence for both Intermittent and Persistent Compartmentalization of HIV-1 in the Female Genital Tract. J Virol 2019; 93:JVI.00311-19. [PMID: 30842323 DOI: 10.1128/jvi.00311-19] [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: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 12/26/2022] Open
Abstract
HIV-1 has been shown to evolve independently in different anatomical compartments, but studies in the female genital tract have been inconclusive. Here, we examined evidence of compartmentalization using HIV-1 subtype C envelope (Env) glycoprotein genes (gp160) obtained from matched cervicovaginal lavage (CVL) and plasma samples over 2 to 3 years of infection. HIV-1 gp160 amplification from CVL was achieved for only 4 of 18 acutely infected women, and this was associated with the presence of proinflammatory cytokines and/or measurable viremia in the CVL. Maximum likelihood trees and divergence analyses showed that all four individuals had monophyletic compartment-specific clusters of CVL- and/or plasma-derived gp160 sequences at all or some time points. However, two participants (CAP177 and CAP217) had CVL gp160 diversity patterns that differed from those in plasma and showed restricted viral flow from the CVL. Statistical tests of compartmentalization revealed evidence of persistent compartment-specific gp160 evolution in CAP177, while in CAP217 this was intermittent. Lastly, we identified several Env sites that distinguished viruses in these two compartments; for CAP177, amino acid differences arose largely through positive selection, while insertions/deletions were more common in CAP217. In both cases these differences contributed to substantial charge changes spread across the Env. Our data indicate that, in some women, HIV-1 populations within the genital tract can have Env genetic features that differ from those of viruses in plasma, which could impact the sensitivity of viruses in the genital tract to vaginal microbicides and vaccine-elicited antibodies.IMPORTANCE Most HIV-1 infections in sub-Saharan Africa are acquired heterosexually through the genital mucosa. Understanding the properties of viruses replicating in the female genital tract, and whether these properties differ from those of more commonly studied viruses replicating in the blood, is therefore important. Using longitudinal CVL and plasma-derived sequences from four HIV-1 subtype C-infected women, we found fewer viral migrations from the genital tract to plasma than in the opposite direction, suggesting a mucosal sieve effect from the genital tract to the blood compartment. Evidence for both persistent and intermittent compartmentalization between the genital tract and plasma viruses during chronic infection was detected in two of four individuals, perhaps explaining previously conflicting findings. In cases where compartmentalization occurred, comparison of CVL- and plasma-derived HIV sequences indicated that distinct features of viral populations in the CVL may affect the efficacy of microbicides and vaccines designed to provide mucosal immunity.
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31
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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: 228] [Impact Index Per Article: 38.0] [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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32
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Bui CM, Adam DC, Njoto E, Scotch M, MacIntyre CR. Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis. Emerg Microbes Infect 2018; 7:184. [PMID: 30459301 PMCID: PMC6246557 DOI: 10.1038/s41426-018-0185-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/08/2018] [Accepted: 09/20/2018] [Indexed: 11/08/2022]
Abstract
Avian influenza H5N1 subtype has caused a global public health concern due to its high pathogenicity in poultry and high case fatality rates in humans. The recently emerged H7N9 is a growing pandemic risk due to its sustained high rates of human infections, and recently acquired high pathogenicity in poultry. Here, we used Bayesian phylogeography on 265 H5N1 and 371 H7N9 haemagglutinin sequences isolated from humans, animals and the environment, to identify and compare migration patterns and factors predictive of H5N1 and H7N9 diffusion rates in China. H7N9 diffusion dynamics and predictor contributions differ from H5N1. Key determinants of spatial diffusion included: proximity between locations (for H5N1 and H7N9), and lower rural population densities (H5N1 only). For H7N9, additional predictors included low avian influenza vaccination rates, low percentage of nature reserves and high humidity levels. For both H5N1 and H7N9, we found viral migration rates from Guangdong to Guangxi and Guangdong to Hunan were highly supported transmission routes (Bayes Factor > 30). We show fundamental differences in wide-scale transmission dynamics between H5N1 and H7N9. Importantly, this indicates that avian influenza initiatives designed to control H5N1 may not be sufficient for controlling the H7N9 epidemic. We suggest control and prevention activities to specifically target poultry transportation networks between Central, Pan-Pearl River Delta and South-West regions.
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Affiliation(s)
- Chau M Bui
- University of New South Wales (UNSW), Sydney, NSW, Australia.
| | - Dillon C Adam
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Edwin Njoto
- University of New South Wales (UNSW), Sydney, NSW, Australia
| | - Matthew Scotch
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
| | - C Raina MacIntyre
- University of New South Wales (UNSW), Sydney, NSW, Australia
- Arizona State University (ASU), Tempe, AZ, USA
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33
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Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018; 4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.
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Affiliation(s)
- Simon Dellicour
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium.,Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12 50, av. FD Roosevelt, 1050 Bruxelles, Belgium
| | - Bram Vrancken
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Nídia S Trovão
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Denis Fargette
- Institut de Recherche pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), BP 64051 34394 Montpellier cedex 5, France
| | - Philippe Lemey
- Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Leuven, Belgium
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34
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Rasmussen DA, Wilkinson E, Vandormael A, Tanser F, Pillay D, Stadler T, de Oliveira T. Tracking external introductions of HIV using phylodynamics reveals a major source of infections in rural KwaZulu-Natal, South Africa. Virus Evol 2018; 4:vey037. [PMID: 30555720 PMCID: PMC6290119 DOI: 10.1093/ve/vey037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite increasing access to antiretrovirals, HIV incidence in rural KwaZulu-Natal remains among the highest ever reported in Africa. While many epidemiological factors have been invoked to explain such high incidence, widespread human mobility and viral movement suggest that transmission between communities may be a major source of new infections. High cross-community transmission rates call into question how effective increasing the coverage of antiretroviral therapy locally will be at preventing new infections, especially if many new cases arise from external introductions. To help address this question, we use a phylodynamic model to reconstruct epidemic dynamics and estimate the relative contribution of local transmission versus external introductions to overall incidence in KwaZulu-Natal from HIV-1 phylogenies. By comparing our results with population-based surveillance data, we show that we can reliably estimate incidence from viral phylogenies once viral movement in and out of the local population is accounted for. Our analysis reveals that early epidemic dynamics were largely driven by external introductions. More recently, we estimate that 35 per cent (95% confidence interval: 20-60%) of new infections arise from external introductions. These results highlight the growing need to consider larger-scale regional transmission dynamics when designing and testing prevention strategies.
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Affiliation(s)
- David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Alain Vandormael
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Frank Tanser
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Research Department of Infection & Population Health, University College London, UK
| | - Deenan Pillay
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, UK
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, USA
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Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun 2018; 9:2222. [PMID: 29884821 PMCID: PMC5993714 DOI: 10.1038/s41467-018-03763-2] [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: 11/06/2017] [Accepted: 03/12/2018] [Indexed: 01/25/2023] Open
Abstract
Genetic analyses have provided important insights into Ebola virus spread during the recent West African outbreak, but their implications for specific intervention scenarios remain unclear. Here, we address this issue using a collection of phylodynamic approaches. We show that long-distance dispersal events were not crucial for epidemic expansion and that preventing viral lineage movement to any given administrative area would, in most cases, have had little impact. However, major urban areas were critical in attracting and disseminating the virus: preventing viral lineage movement to all three capitals simultaneously would have contained epidemic size to one-third. We also show that announcements of border closures were followed by a significant but transient effect on international virus dispersal. By quantifying the hypothetical impact of different intervention strategies, as well as the impact of barriers on dispersal frequency, our study illustrates how phylodynamic analyses can help to address specific epidemiological and outbreak control questions. During the last Ebola virus outbreak in West Africa, a large amount of viral genomic data was obtained. Here, Dellicour et al. use phylodynamic approaches to assess effect of intervention strategies such as border closures.
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Affiliation(s)
- Simon Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Gytis Dudas
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, 98109, Seattle, WA, USA
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, United Kingdom
| | - Marc A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.,Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FL, UK.,Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium
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36
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Kinkar L, Laurimäe T, Acosta-Jamett G, Andresiuk V, Balkaya I, Casulli A, Gasser RB, van der Giessen J, González LM, Haag KL, Zait H, Irshadullah M, Jabbar A, Jenkins DJ, Kia EB, Manfredi MT, Mirhendi H, M'rad S, Rostami-Nejad M, Oudni-M'rad M, Pierangeli NB, Ponce-Gordo F, Rehbein S, Sharbatkhori M, Simsek S, Soriano SV, Sprong H, Šnábel V, Umhang G, Varcasia A, Saarma U. Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1. Int J Parasitol 2018; 48:729-742. [PMID: 29782829 DOI: 10.1016/j.ijpara.2018.03.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/05/2018] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
Echinococcus granulosus sensu stricto (s.s.) is the major cause of human cystic echinococcosis worldwide and is listed among the most severe parasitic diseases of humans. To date, numerous studies have investigated the genetic diversity and population structure of E. granulosus s.s. in various geographic regions. However, there has been no global study. Recently, using mitochondrial DNA, it was shown that E. granulosus s.s. G1 and G3 are distinct genotypes, but a larger dataset is required to confirm the distinction of these genotypes. The objectives of this study were to: (i) investigate the distinction of genotypes G1 and G3 using a large global dataset; and (ii) analyse the genetic diversity and phylogeography of genotype G1 on a global scale using near-complete mitogenome sequences. For this study, 222 globally distributed E. granulosus s.s. samples were used, of which 212 belonged to genotype G1 and 10 to G3. Using a total sequence length of 11,682 bp, we inferred phylogenetic networks for three datasets: E. granulosus s.s. (n = 222), G1 (n = 212) and human G1 samples (n = 41). In addition, the Bayesian phylogenetic and phylogeographic analyses were performed. The latter yielded several strongly supported diffusion routes of genotype G1 originating from Turkey, Tunisia and Argentina. We conclude that: (i) using a considerably larger dataset than employed previously, E. granulosus s.s. G1 and G3 are indeed distinct mitochondrial genotypes; (ii) the genetic diversity of E. granulosus s.s. G1 is high globally, with lower values in South America; and (iii) the complex phylogeographic patterns emerging from the phylogenetic and geographic analyses suggest that the current distribution of genotype G1 has been shaped by intensive animal trade.
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Affiliation(s)
- Liina Kinkar
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Teivi Laurimäe
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia
| | - Gerardo Acosta-Jamett
- Instituto de Medicina Preventiva Veterinaria y Programa de Investigación Aplicada en Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Vanessa Andresiuk
- Laboratorio de Zoonosis Parasitarias, FCEyN, UNMdP, Funes 3350, CP: 7600 Mar del Plata, Buenos Aires, Argentina
| | - Ibrahim Balkaya
- Department of Parasitology, Faculty of Veterinary Medicine, University of Atatürk, Erzurum, Turkey
| | - Adriano Casulli
- World Health Organization Collaborating Centre for the Epidemiology, Detection and Control of Cystic and Alveolar Echinococcosis, European Union Reference Laboratory for Parasites (EURLP), Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joke van der Giessen
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Luis Miguel González
- Parasitology Department, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Karen L Haag
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, Brazil
| | - Houria Zait
- Parasitology and Mycology Department, Mustapha University Hospital, 16000 Algiers, Algeria
| | - Malik Irshadullah
- Section of Parasitology, Department of Zoology, Aligarh Muslim University, Aligarh 202002, India
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - David J Jenkins
- School of Animal and Veterinary Sciences, Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia
| | - Eshrat Beigom Kia
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maria Teresa Manfredi
- Department of Veterinary Medicine, Università degli Studi di Milano, via Celoria 10, 20133 Milan, Italy
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Selim M'rad
- Laboratory of Medical and Molecular Parasitology-Mycology (LP3M), LR 12ES08. Faculty of Pharmacy, University of Monastir, 5000 Monastir, Tunisia
| | - Mohammad Rostami-Nejad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Myriam Oudni-M'rad
- Laboratory of Medical and Molecular Parasitology-Mycology (LP3M), LR 12ES08. Faculty of Pharmacy, University of Monastir, 5000 Monastir, Tunisia
| | - Nora Beatriz Pierangeli
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, Comahue National University, Buenos Aires 1400, 8300 Neuquén, Argentina
| | - Francisco Ponce-Gordo
- Department of Parasitology, Faculty of Pharmacy, Complutense University, Plaza Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Steffen Rehbein
- Merial GmbH, Kathrinenhof Research Center, Walchenseestr. 8-12, 83101 Rohrdorf, Germany
| | - Mitra Sharbatkhori
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sami Simsek
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, 23119 Elazig, Turkey
| | - Silvia Viviana Soriano
- Department of Microbiology and Parasitology, Faculty of Medical Sciences, Comahue National University, Buenos Aires 1400, 8300 Neuquén, Argentina
| | - Hein Sprong
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and Environment, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Viliam Šnábel
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Hlinkova 3, 040 01 Košice, Slovakia
| | - Gérald Umhang
- ANSES, Nancy Laboratory for Rabies and Wildlife, Wildlife Surveillance and Eco-epidemiology Unit, Malzéville 54220, France
| | - Antonio Varcasia
- Laboratory of Parasitology, Veterinary Teaching Hospital, Department of Veterinary Medicine, University of Sassari, Via Vienna, 2-07100 Sassari, Italy
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia.
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Dellicour S, Rose R, Faria NR, Vieira LFP, Bourhy H, Gilbert M, Lemey P, Pybus OG. Using Viral Gene Sequences to Compare and Explain the Heterogeneous Spatial Dynamics of Virus Epidemics. Mol Biol Evol 2017. [PMID: 28651357 DOI: 10.1093/molbev/msx176] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and to detect and compare the environmental factors that impact the velocity of viral spread in continuous spatial landscapes. We build on a recently developed statistical framework that uses spatially- and temporally-referenced phylogenies. We estimate several spatial statistics of virus spread, which reveal a higher diffusivity of RABV in domestic dogs compared with RABV in other mammals. This finding is explained by subsequent analyses of environmental heterogeneity, which indicate that factors relating to human geography play a significant role in RABV dispersion in domestic dogs. More generally, our results suggest that human-related factors are important worldwide in explaining RABV dispersion in terrestrial host species. Our study shows that phylogenetically informed viral movements can be used to elucidate the factors that impact virus dispersal, opening new opportunities for a better understanding of the impact of host species and environmental conditions on the spatial dynamics of rapidly evolving populations.
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Affiliation(s)
- Simon Dellicour
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | | | | | - Luiz Fernando Pereira Vieira
- Department of Laboratorial Diagnosis, Institute of Agricultural and Forest Defense of Espírito Santo (IDAF), Vitoria, Brazil
| | - Hervé Bourhy
- Institut Pasteur, Lyssavirus Dynamics and Host Adaptation Unit, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Marius Gilbert
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
| | - Philippe Lemey
- Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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38
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Troupin C, Picard-Meyer E, Dellicour S, Casademont I, Kergoat L, Lepelletier A, Dacheux L, Baele G, Monchâtre-Leroy E, Cliquet F, Lemey P, Bourhy H. Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus. Genome Biol Evol 2017; 9:3202-3213. [PMID: 29165566 PMCID: PMC5721339 DOI: 10.1093/gbe/evx236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/22/2022] Open
Abstract
The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on 80 newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution, and evolutionary time scale of these two subtypes in Europe. Our results suggest that the current lineage of EBLV-1 arose in Europe ∼600 years ago and the virus has evolved at an estimated average substitution rate of ∼4.19×10-5 subs/site/year, which is among the lowest recorded for RNA viruses. In parallel, we investigate the genetic structure of French serotine bats at both the nuclear and mitochondrial level and find that they constitute a single genetic cluster. Furthermore, Mantel tests based on interindividual distances reveal the absence of correlation between genetic distances estimated between viruses and between host individuals. Taken together, this indicates that the genetic diversity observed in our E. serotinus samples does not account for EBLV-1a and -1b segregation and dispersal in Europe.
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Affiliation(s)
- Cécile Troupin
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Evelyne Picard-Meyer
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Simon Dellicour
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Isabelle Casademont
- Unité de la Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
| | - Lauriane Kergoat
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Anthony Lepelletier
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Laurent Dacheux
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
| | - Guy Baele
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Elodie Monchâtre-Leroy
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Florence Cliquet
- Laboratory for Rabies and Wildlife ANSES, Nancy, OIE Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies, European Union Reference Laboratory for Rabies Serology, WHO Collaborating Centre for Research and Management on Zoonoses, Malzeville, France
| | - Philippe Lemey
- Institut Pasteur, Laboratory for Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute, KU Leuven – University of Leuven, Belgium
| | - Hervé Bourhy
- Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France
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Al-Qahtani AA, Baele G, Khalaf N, Suchard MA, Al-Anazi MR, Abdo AA, Sanai FM, Al-Ashgar HI, Khan MQ, Al-Ahdal MN, Lemey P, Vrancken B. The epidemic dynamics of hepatitis C virus subtypes 4a and 4d in Saudi Arabia. Sci Rep 2017; 7:44947. [PMID: 28322313 PMCID: PMC5359580 DOI: 10.1038/srep44947] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/15/2017] [Indexed: 02/06/2023] Open
Abstract
The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework. We also introduce a novel analytical method for an objective assessment of the migration intensity between locations. We find that international host mobility patterns dominate over within country spread in shaping the Saudi Arabia HCV4a epidemic, while this may be different for the HCV4d epidemic. This indicates that the subtypes 4a and 4d burden can be most effectively reduced by combining the prioritized screening and treatment of Egyptian immigrants with domestic prevention campaigns. Our results highlight that the joint investigation of evolutionary and epidemiological processes can provide valuable public health information, even in the absence of extensive metadata information.
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Affiliation(s)
- Ahmed A Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Guy Baele
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Nisreen Khalaf
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, USA
| | - Mashael R Al-Anazi
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Ayman A Abdo
- Section of Gastroenterology, Department of Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal M Sanai
- Gastroenterology Unit, Department of Medicine, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Hamad I Al-Ashgar
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed Q Khan
- Gastroenterology Unit, Department of Medicine, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia
| | - Mohammed N Al-Ahdal
- Department of Infection and Immunity, King Faisal Specialist Hospital &Research Center, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Alfaisal University School of Medicine, Riyadh, Saudi Arabia
| | - Philippe Lemey
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Bram Vrancken
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
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Chaillon A, Essat A, Frange P, Smith DM, Delaugerre C, Barin F, Ghosn J, Pialoux G, Robineau O, Rouzioux C, Goujard C, Meyer L, Chaix ML. Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies. Retrovirology 2017; 14:15. [PMID: 28222757 PMCID: PMC5322782 DOI: 10.1186/s12977-017-0339-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/07/2017] [Indexed: 11/10/2022] Open
Abstract
Background Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years. Results Sociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i.e. clusters of transmission, between HIV-1 sequences. Bayesian coalescent-based methods were used to examine the temporal and spatial dynamics of identified clusters from different regions in France. We also evaluated the use of network information to target prevention efforts. Participants were mostly Caucasian (85.9%) and men (86.7%) who reported sex with men (MSM, 71.4%). Overall, 387 individuals (28.5%) were involved in clusters: 156 patients (11.5%) in 78 dyads and 231 participants (17%) in 42 larger clusters (median size: 4, range 3–41). Compared to individuals with single PHI (n = 969), those in clusters were more frequently men (95.9 vs 83%, p < 0.01), MSM (85.8 vs 65.6%, p < 0.01) and infected with CRF02_AG (20.4 vs 13.4%, p < 0.01). Reconstruction of viral migrations across time suggests that Paris area was the major hub of dissemination of both subtype B and CRF02_AG epidemics. By targeting clustering individuals belonging to the identified active transmission network before 2010, 60 of the 143 onward transmissions could have been prevented. Conclusion These analyses support the hypothesis of a recent and rapid rise of CRF02_AG within the French HIV-1 epidemic among MSM. Combined with a short turnaround time for sample processing, targeting prevention efforts based on phylogenetic monitoring may be an efficient way to deliver prevention interventions but would require near real time targeted interventions on the identified index cases and their partners. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0339-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antoine Chaillon
- University of California, San Diego, 9500 Gilman Drive, Stein Clinical Research Building #325, La Jolla, CA, 92093-0697, USA.
| | - Asma Essat
- INSERM CESP U1018, University Paris Sud, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris (APHP), Le Kremlin-Bicêtre, France
| | - Pierre Frange
- EA7327, Université Paris Descartes, Paris, France.,Laboratoire de Microbiologie Clinique, Hôpital Necker - Enfants Malades, APHP, Paris, France
| | - Davey M Smith
- University of California, San Diego, 9500 Gilman Drive, Stein Clinical Research Building #325, La Jolla, CA, 92093-0697, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Constance Delaugerre
- INSERM U941, Laboratoire de Virologie, Université Paris Diderot, Hôpital Saint-Louis, AP-HP, CNR VIH associé Primo infection, Paris, France
| | - Francis Barin
- INSERM U966 and National Reference Center for HIV, CHU Bretonneau and Université François Rabelais, Tours, France
| | - Jade Ghosn
- EA7327, Université Paris Descartes, Paris, France.,UF de Thérapeutique en Immuno-Infectiologie, Hôpital Hôtel Dieu, APHP, Paris, France
| | - Gilles Pialoux
- Service des Maladies Infectieuses et Tropicales, Hôpital Tenon, APHP, Paris, France
| | - Olivier Robineau
- Service Universitaire des Maladies infectieuses et du Voyageur, Centre Hospitalier de Tourcoing, Tourcoing, France
| | | | - Cécile Goujard
- INSERM CESP U1018, University Paris Sud, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris (APHP), Le Kremlin-Bicêtre, France.,Service de Médecine interne et Immunologie clinique, Hôpital Bicêtre, APHP, Le Kremlin-Bicêtre, France
| | - Laurence Meyer
- INSERM CESP U1018, University Paris Sud, Hôpital Bicêtre, Assistance Publique-Hôpitaux de Paris (APHP), Le Kremlin-Bicêtre, France
| | - Marie-Laure Chaix
- INSERM U941, Laboratoire de Virologie, Université Paris Diderot, Hôpital Saint-Louis, AP-HP, CNR VIH associé Primo infection, Paris, France
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Franzo G, Tucciarone CM, Blanco A, Nofrarías M, Biarnés M, Cortey M, Majó N, Catelli E, Cecchinato M. Effect of different vaccination strategies on IBV QX population dynamics and clinical outbreaks. Vaccine 2016; 34:5670-5676. [PMID: 27670071 PMCID: PMC7173296 DOI: 10.1016/j.vaccine.2016.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/05/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022]
Abstract
Two large scale molecular epidemiology studies performed in Italy and Spain. The population dynamics trends differed between the two countries. Relevant association between changes in vaccination strategies and viral population. Strong association between viral population dynamics and outbreak frequency. Hill’s criteria for causation were accomplished.
The extreme variability and rapid evolution of Infectious bronchitis virus (IBV) has always represented the key challenge for its control because of the limited cross-protection among different strains. Several experimental trials have proven a broadening of the protection spectrum when animals are vaccinated with multiple genotypes. Nevertheless, the conditions of vaccine administration in field are so different that the generalization of experimental results is, at least, questionable. In the present study a large scale epidemiological-phylodynamic approach was used to reconstruct the demographic history of the major field genotype (i.e. the QX one) circulating in Italy and Spain. These two countries were selected because, even if they share a comparable epidemiological scenario, the implemented vaccination protocols did not vary in Spain while changed dramatically in Italy over the time period considered. One hundred and ninety-five Italian and 98 Spanish non-recombinant sequences of the hyper-variable region of the S1 gene obtained between 2012 and 2016 were analyzed using a serial coalescent-based approach to reconstruct viral population history over time. While the IBV QX population dynamics remained constant in Spain, a much more complex pattern was evidenced in Italy; both in terms of viral population size and clinical outbreak frequency. Remarkably, a strong association with changes in vaccination strategies was recognized. This allowed demonstrating, by accomplishing all Hill’s criteria for causation, the cause-effect relationship between the vaccine administration/withdrawal and the variation in viral population dynamics and, above all, IBV related outbreaks. Thus, a robust confirmation about the efficacy of IBV vaccination in field conditions was provided. Additionally, the history herein reported testifies the primary importance of rigorously planning not only the intervention strategies but also their monitoring and evaluation.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy.
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - Angela Blanco
- CESAC-Centre de Sanitat Avícola de Catalunya i Aragó, Ctra. Castellvell, s/n, 43206 Reus, Spain
| | - Miquel Nofrarías
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Mar Biarnés
- CESAC-Centre de Sanitat Avícola de Catalunya i Aragó, Ctra. Castellvell, s/n, 43206 Reus, Spain
| | - Marti Cortey
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Natàlia Majó
- Centre de Recerca en Sanitat Animal, CReSA, UAB-IRTA, Campus de la UAB, edifici CReSA, 08193 Bellaterra (Cerdanyola del Vallès), Barcelona, Spain; Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Elena Catelli
- Dipartimento di Scienze Mediche Veterinarie, Alma Mater Studiorum - Università di Bologna, Via Tolara di Sopra, 50, 40064 Ozzano dell'Emilia (BO), Italy
| | - Mattia Cecchinato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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Dibia IN, Sumiarto B, Susetya H, Putra AAG, Scott-Orr H, Mahardika GN. Phylogeography of the current rabies viruses in Indonesia. J Vet Sci 2016; 16:459-66. [PMID: 25643792 PMCID: PMC4701738 DOI: 10.4142/jvs.2015.16.4.459] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/23/2014] [Accepted: 12/30/2014] [Indexed: 12/25/2022] Open
Abstract
Rabies is a major fatal zoonotic disease in Indonesia. This study was conducted to determine the recent dynamics of rabies virus (RABV) in various areas and animal species throughout Indonesia. A total of 27 brain samples collected from rabid animals of various species in Bali, Sumatra, Kalimantan, Sulawesi, Java, and Flores in 2008 to 2010 were investigated. The cDNA of the nucleoprotein gene from each sample was generated and amplified by one-step reverse transcription-PCR, after which the products were sequenced and analyzed. The symmetric substitution model of a Bayesian stochastic search variable selection extension of the discrete phylogeographic model of the social network was applied in BEAST ver. 1.7.5 software. The spatial dispersal was visualized in Cartographica using Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. We demonstrated inter-island introduction and reintroduction, and dog was found to be the only source of infection of other animals. Ancestors of Indonesian RABVs originated in Java and its descendants were transmitted to Kalimantan, then further to Sumatra, Flores, and Bali. The Flores descendent was subsequently transmitted to Sulawesi and back to Kalimantan. The viruses found in various animal species were transmitted by the dog.
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Affiliation(s)
- I Nyoman Dibia
- Animal Disease Investigation Centre, Denpasar 80226, Indonesia.,Veterinary Science Post Graduate Program, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | - Bambang Sumiarto
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | - Heru Susetya
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Gajah Mada University, Yogyakarta 55281, Indonesia
| | | | - Helen Scott-Orr
- Faculty of Veterinary Science, University of Sydney, Camden 2570, Australia
| | - Gusti Ngurah Mahardika
- The Animal Biomedical and Molecular Biology Laboratory, Faculty of Veterinary Medicine, Udayana University, Denpasar 80226, Indonesia
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Tahsin T, Weissenbacher D, Rivera R, Beard R, Firago M, Wallstrom G, Scotch M, Gonzalez G. A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records. J Am Med Inform Assoc 2016; 23:934-41. [PMID: 26911818 PMCID: PMC4997033 DOI: 10.1093/jamia/ocv172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/22/2015] [Accepted: 10/22/2015] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases. MATERIALS AND METHODS We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus. RESULTS We found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. DISCUSSION Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction. CONCLUSION Our system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles.
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Affiliation(s)
- Tasnia Tahsin
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Davy Weissenbacher
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Robert Rivera
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Rachel Beard
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Mari Firago
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Garrick Wallstrom
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Matthew Scotch
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
| | - Graciela Gonzalez
- Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Scottsdale, AZ 85259, USA
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Reid MJC, Switzer WM, Schillaci MA, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Sandstrom PA, Brooks JI. Detailed phylogenetic analysis of primate T-lymphotropic virus type 1 (PTLV-1) sequences from orangutans (Pongo pygmaeus) reveals new insights into the evolutionary history of PTLV-1 in Asia. INFECTION GENETICS AND EVOLUTION 2016; 43:434-50. [PMID: 27245152 DOI: 10.1016/j.meegid.2016.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/28/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
While human T-lymphotropic virus type 1 (HTLV-1) originates from ancient cross-species transmission of simian T-lymphotropic virus type 1 (STLV-1) from infected nonhuman primates, much debate exists on whether the first HTLV-1 occurred in Africa, or in Asia during early human evolution and migration. This topic is complicated by a lack of representative Asian STLV-1 to infer PTLV-1 evolutionary histories. In this study we obtained new STLV-1 LTR and tax sequences from a wild-born Bornean orangutan (Pongo pygmaeus) and performed detailed phylogenetic analyses using both maximum likelihood and Bayesian inference of available Asian PTLV-1 and African STLV-1 sequences. Phylogenies, divergence dates and nucleotide substitution rates were co-inferred and compared using six different molecular clock calibrations in a Bayesian framework, including both archaeological and/or nucleotide substitution rate calibrations. We then combined our molecular results with paleobiogeographical and ecological data to infer the most likely evolutionary history of PTLV-1. Based on the preferred models our analyses robustly inferred an Asian source for PTLV-1 with cross-species transmission of STLV-1 likely from a macaque (Macaca sp.) to an orangutan about 37.9-48.9kya, and to humans between 20.3-25.5kya. An orangutan diversification of STLV-1 commenced approximately 6.4-7.3kya. Our analyses also inferred that HTLV-1 was first introduced into Australia ~3.1-3.7kya, corresponding to both genetic and archaeological changes occurring in Australia at that time. Finally, HTLV-1 appears in Melanesia at ~2.3-2.7kya corresponding to the migration of the Lapita peoples into the region. Our results also provide an important future reference for calibrating information essential for PTLV evolutionary timescale inference. Longer sequence data, or full genomes from a greater representation of Asian primates, including gibbons, leaf monkeys, and Sumatran orangutans are needed to fully elucidate these evolutionary dates and relationships using the model criteria suggested herein.
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Affiliation(s)
- Michael J C Reid
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - William M Switzer
- Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA, USA 30329.
| | - Michael A Schillaci
- Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada.
| | - Manon Ragonnet-Cronin
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
| | - Isabelle Joanisse
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, Canada
| | - Kyna Caminiti
- Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada.
| | - Carl A Lowenberger
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
| | - Birute Mary F Galdikas
- Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA.
| | - Paul A Sandstrom
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada.
| | - James I Brooks
- National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, Canada.
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Dellicour S, Rose R, Pybus OG. Explaining the geographic spread of emerging epidemics: a framework for comparing viral phylogenies and environmental landscape data. BMC Bioinformatics 2016; 17:82. [PMID: 26864798 PMCID: PMC4750353 DOI: 10.1186/s12859-016-0924-x] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/28/2016] [Indexed: 11/22/2022] Open
Abstract
Background Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can indicate transmission linkages among infections that may not otherwise be evident. However, a remaining challenge is to develop an analytical framework that can test hypotheses about the effect of environmental variables on pathogen spatial spread. Recent phylogeographic approaches can reconstruct the history of virus dispersal from sampled viral genomes and infer the locations of ancestral infections. Such methods provide a unique source of spatio-temporal information, and are exploited here. Results We present and apply a new statistical framework that combines genomic and geographic data to test the impact of environmental variables on the mode and tempo of pathogen dispersal during emerging epidemics. First, the spatial history of an emerging pathogen is estimated using standard phylogeographic methods. The inferred dispersal path for each phylogenetic lineage is then assigned a “weight” using environmental data (e.g. altitude, land cover). Next, tests measure the association between each environmental variable and lineage movement. A randomisation procedure is used to assess statistical confidence and we validate this approach using simulated data. We apply our new framework to a set of gene sequences from an epidemic of rabies virus in North American raccoons. We test the impact of six different environmental variables on this epidemic and demonstrate that elevation is associated with a slower rabies spread in a natural population. Conclusion This study shows that it is possible to integrate genomic and environmental data in order to test hypotheses concerning the mode and tempo of virus dispersal during emerging epidemics. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0924-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simon Dellicour
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK. .,Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven, University of Leuven, Minderbroedersstaat 10, 3000, Leuven, Belgium.
| | - Rebecca Rose
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
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Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, Medstrand P, Albert J. HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries. Virus Evol 2016; 2:vew010. [PMID: 27774303 PMCID: PMC4989887 DOI: 10.1093/ve/vew010] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Increased knowledge about HIV-1 transmission dynamics in different transmission groups and geographical regions is fundamental for assessing and designing prevention efforts against HIV-1 spread. Since the first reported cases of HIV infection during the early 1980s, the HIV-1 epidemic in the Nordic countries has been dominated by HIV-1 subtype B and MSM transmission. HIV-1 pol sequences and clinical data of 51 per cent of all newly diagnosed HIV-1 infections in Sweden, Denmark, and Finland in the period 2000-2012 (N = 3,802) were analysed together with a large reference sequence dataset (N = 4,537) by trend analysis and phylogenetics. Analysis of the eight dominating subtypes and CRFs in the Nordic countries (A, B, C, D, G, CRF01_AE, CRF02_AG, and CRF06_cpx) showed that the subtype B proportion decreased while the CRF proportion increased over the study period. A majority (57 per cent) of the Nordic sequences formed transmission clusters, with evidence of mixing both geographically and between transmission groups. Detailed analyses showed multiple occasions of transmissions from MSM to heterosexuals and that active transmission clusters more often involved single than multiple Nordic countries. The strongest geographical link was between Denmark and Sweden. Finally, Denmark had a larger proportion of heterosexual domestic spread of HIV-1 subtype B (75 per cent) compared with Sweden (49 per cent) and Finland (57 per cent). We describe different HIV-1 transmission patterns between countries and transmission groups in a large geographical region. Our results may have implications for public health interventions in targeting HIV-1 transmission networks and identifying where to introduce such interventions.
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Affiliation(s)
- Joakim Esbjörnsson
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
| | - Mattias Mild
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Anne Audelin
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Helena Skar
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
| | - Louise Bruun Jørgensen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsi Liitsola
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Per Björkman
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Göran Bratt
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anders Sönnerborg
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Claus Nielsen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - SPREAD/ESAR Programme
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- REGA Institute, Katholieke Universiteit, Leuven, Belgium
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Technology, Linköping University, Campus Norrköping, Norrköping, Sweden
- Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
- Department of Clinical Science and Education, Venhälsan, Stockholm South General Hospital, Stockholm, Sweden
- Department of Infectious Diseases, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
- Division of Clinical Microbiology, Karolinska Institute, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Patrik Medstrand
- Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Jan Albert
- Department of Microbiology Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Othman I, Mirand A, Slama I, Mastouri M, Peigue-Lafeuille H, Aouni M, Bailly JL. Enterovirus Migration Patterns between France and Tunisia. PLoS One 2015; 10:e0145674. [PMID: 26709514 PMCID: PMC4692522 DOI: 10.1371/journal.pone.0145674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/06/2015] [Indexed: 02/03/2023] Open
Abstract
The enterovirus (EV) types echovirus (E-) 5, E-9, and E-18, and coxsackievirus (CV-) A9 are infrequently reported in human diseases and their epidemiologic features are poorly defined. Virus transmission patterns between countries have been estimated with phylogenetic data derived from the 1D/VP1 and 3CD gene sequences of a sample of 74 strains obtained in France (2000–2012) and Tunisia (2011–2013) and from the publicly available sequences. The EV types (E-5, E-9, and E-18) exhibited a lower worldwide genetic diversity (respective number of genogroups: 4, 5, and 3) in comparison to CV-A9 (n = 10). The phylogenetic trees estimated with both 1D/VP1 and 3CD sequence data showed variations in the number of co-circulating lineages over the last 20 years among the four EV types. Despite the low number of genogroups in E-18, the virus exhibited the highest number of recombinant 3CD lineages (n = 10) versus 4 (E-5) to 8 (E-9). The phylogenies provided evidence of multiple transportation events between France and Tunisia involving E-5, E-9, E-18, and CV-A9 strains. Virus spread events between France and 17 other countries in five continents had high probabilities of occurrence as those between Tunisia and two European countries other than France. All transportation events were supported by BF values > 10. Inferring the source of virus transmission from phylogenetic data may provide insights into the patterns of sporadic and epidemic diseases caused by EVs.
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Affiliation(s)
- Ines Othman
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia
- University of Carthage, Faculty of Sciences of Bizerte, Tunisia
| | - Audrey Mirand
- Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Enterovirus–Parechovirus, Clermont-Ferrand, France
| | - Ichrak Slama
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia
- University of Carthage, Faculty of Sciences of Bizerte, Tunisia
| | - Maha Mastouri
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia
- Fattouma Bourguiba University Hospital, Laboratory of Microbiology, Monastir, Tunisia
| | - Hélène Peigue-Lafeuille
- Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Service de Virologie, Centre National de Référence des Enterovirus–Parechovirus, Clermont-Ferrand, France
| | - Mahjoub Aouni
- University of Monastir, Faculty of Pharmacy, LR99-ES27, Monastir, Tunisia
| | - Jean-Luc Bailly
- Université d’Auvergne, EPIE, EA 4843, Clermont-Ferrand, France
- * E-mail:
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Famulare M, Hu H. Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria. Int Health 2015; 7:130-8. [PMID: 25733563 PMCID: PMC4379986 DOI: 10.1093/inthealth/ihv012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background Phylogeography improves our understanding of spatial epidemiology. However, application to practical problems requires choices among computational tools to balance statistical rigor, computational complexity, sensitivity to sampling strategy and interpretability. Methods We introduce a fast, heuristic algorithm to reconstruct partially-observed transmission networks (POTN) that combines features of phylogenetic and transmission tree approaches. We compare the transmission network generated by POTN with existing algorithms (BEAST and SeqTrack), and discuss the benefits and challenges of phylogeographic analysis on examples of epidemic and endemic diseases: Ebola virus, H1N1 pandemic influenza and polio. Results For the 2014 Sierra Leone Ebola virus outbreak and the 2009 H1N1 outbreak, all three methods provide similarly plausible transmission histories but differ in detail. For polio in northern Nigeria, we discuss performance trade-offs between the POTN and discrete phylogeography in BEAST and conclude that spatial history reconstruction is limited by under-sampling. Conclusions POTN is complementary to available tools on densely-sampled data, fails gracefully on under-sampled data and is scalable to accommodate larger datasets. We provide further evidence for the utility of phylogeography for understanding transmission networks of rapidly evolving epidemics. We propose simple heuristic criteria to identify how sampling rates and disease dynamics interact to determine fundamental limitations of phylogeographic inference.
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Affiliation(s)
| | - Hao Hu
- Institute for Disease Modeling, Bellevue, WA 98005, USA
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49
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Trovão NS, Suchard MA, Baele G, Gilbert M, Lemey P. Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1. Mol Biol Evol 2015; 32:3264-75. [PMID: 26341298 DOI: 10.1093/molbev/msv185] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Since its first isolation in 1996 in Guangdong, China, the highly pathogenic avian influenza virus (HPAIV) H5N1 has circulated in avian hosts for almost two decades and spread to more than 60 countries worldwide. The role of different avian hosts and the domestic-wild bird interface has been critical in shaping the complex HPAIV H5N1 disease ecology, but remains difficult to ascertain. To shed light on the large-scale H5N1 transmission patterns and disentangle the contributions of different avian hosts on the tempo and mode of HPAIV H5N1 dispersal, we apply Bayesian evolutionary inference techniques to comprehensive sets of hemagglutinin and neuraminidase gene sequences sampled between 1996 and 2011 throughout Asia and Russia. Our analyses demonstrate that the large-scale H5N1 transmission dynamics are structured according to different avian flyways, and that the incursion of the Central Asian flyway specifically was driven by Anatidae hosts coinciding with rapid rate of spread and an epidemic wavefront acceleration. This also resulted in long-distance dispersal that is likely to be explained by wild bird migration. We identify a significant degree of asymmetry in the large-scale transmission dynamics between Anatidae and Phasianidae, with the latter largely representing poultry as an evolutionary sink. A joint analysis of host dynamics and continuous spatial diffusion demonstrates that the rate of viral dispersal and host diffusivity is significantly higher for Anatidae compared with Phasianidae. These findings complement risk modeling studies and satellite tracking of wild birds in demonstrating a continental-scale structuring into areas of H5N1 persistence that are connected through migratory waterfowl.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marc A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
| | - Marius Gilbert
- Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium Fonds National de la Recherche Scientifique, Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium
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Pfeiffer DU, Stevens KB. Spatial and temporal epidemiological analysis in the Big Data era. Prev Vet Med 2015; 122:213-20. [PMID: 26092722 PMCID: PMC7114113 DOI: 10.1016/j.prevetmed.2015.05.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/27/2015] [Accepted: 05/31/2015] [Indexed: 10/27/2022]
Abstract
Concurrent with global economic development in the last 50 years, the opportunities for the spread of existing diseases and emergence of new infectious pathogens, have increased substantially. The activities associated with the enormously intensified global connectivity have resulted in large amounts of data being generated, which in turn provides opportunities for generating knowledge that will allow more effective management of animal and human health risks. This so-called Big Data has, more recently, been accompanied by the Internet of Things which highlights the increasing presence of a wide range of sensors, interconnected via the Internet. Analysis of this data needs to exploit its complexity, accommodate variation in data quality and should take advantage of its spatial and temporal dimensions, where available. Apart from the development of hardware technologies and networking/communication infrastructure, it is necessary to develop appropriate data management tools that make this data accessible for analysis. This includes relational databases, geographical information systems and most recently, cloud-based data storage such as Hadoop distributed file systems. While the development in analytical methodologies has not quite caught up with the data deluge, important advances have been made in a number of areas, including spatial and temporal data analysis where the spectrum of analytical methods ranges from visualisation and exploratory analysis, to modelling. While there used to be a primary focus on statistical science in terms of methodological development for data analysis, the newly emerged discipline of data science is a reflection of the challenges presented by the need to integrate diverse data sources and exploit them using novel data- and knowledge-driven modelling methods while simultaneously recognising the value of quantitative as well as qualitative analytical approaches. Machine learning regression methods, which are more robust and can handle large datasets faster than classical regression approaches, are now also used to analyse spatial and spatio-temporal data. Multi-criteria decision analysis methods have gained greater acceptance, due in part, to the need to increasingly combine data from diverse sources including published scientific information and expert opinion in an attempt to fill important knowledge gaps. The opportunities for more effective prevention, detection and control of animal health threats arising from these developments are immense, but not without risks given the different types, and much higher frequency, of biases associated with these data.
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Affiliation(s)
- Dirk U Pfeiffer
- Veterinary Epidemiology, Economics & Public Health Group, Department of Production & Population Health, Royal Veterinary College, London, UK.
| | - Kim B Stevens
- Veterinary Epidemiology, Economics & Public Health Group, Department of Production & Population Health, Royal Veterinary College, London, UK
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