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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024; 15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
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Affiliation(s)
- Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ben Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tong Mu
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - R Alex Wiebe
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Fengyi Guo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nicola Lewis
- Animal and Plant Health Agency-Weybridge, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Department of Virology, Addlestone, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | | | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luojun Yang
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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2
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Li YQ, Ghafari M, Holbrook AJ, Boonen I, Amor N, Catalano S, Webster JP, Li YY, Li HT, Vergote V, Maes P, Chong YL, Laudisoit A, Baelo P, Ngoy S, Mbalitini SG, Gembu GC, Musaba AP, Goüy de Bellocq J, Leirs H, Verheyen E, Pybus OG, Katzourakis A, Alagaili AN, Gryseels S, Li YC, Suchard MA, Bletsa M, Lemey P. The evolutionary history of hepaciviruses. bioRxiv 2023:2023.06.30.547218. [PMID: 37425679 PMCID: PMC10327235 DOI: 10.1101/2023.06.30.547218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.
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Affiliation(s)
- YQ Li
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - M Ghafari
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AJ Holbrook
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - I Boonen
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - N Amor
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Catalano
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G61 1QH, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - JP Webster
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - YY Li
- College of Life Sciences, Linyi University, Linyi, 276000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - HT Li
- College of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - V Vergote
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - P Maes
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
| | - YL Chong
- Animal Resource Science and Management Group, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS), 94300, Malaysia
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, 999077, China
| | - A Laudisoit
- EcoHealth Alliance, New York, NY 10018, USA
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - P Baelo
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - S Ngoy
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - SG Mbalitini
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - GC Gembu
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Akawa P Musaba
- Faculty of Sciences, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - J Goüy de Bellocq
- Institute of Vertebrate Biology, The Czech Academy of Sciences, Květná 8, 603 65 Brno, Czech Republic
| | - H Leirs
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - E Verheyen
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - OG Pybus
- Department of Biology, University of Oxford, Oxford, OX1, UK
- Department of Pathobiology and Population Sciences, the Royal Veterinary College, University of London, Herts, AL9 7TA, UK
| | - A Katzourakis
- Department of Biology, University of Oxford, Oxford, OX1, UK
| | - AN Alagaili
- Laboratory of Biodiversity, Parasitology, and Ecology of Aquatic Ecosystems, Department of Biology - Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 2092, Tunisia
| | - S Gryseels
- Evolutionary Ecology group (EVECO), Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - YC Li
- Marine College, Shandong University (Weihai), Weihai, 264209, China
| | - MA Suchard
- Department of Biostatistics, University of California, Los Angeles, CA 90095, USA
| | - M Bletsa
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, 11527, Greece
| | - P Lemey
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Rega Institute, KU Leuven, Leuven, 3000, Belgium
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3
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Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. Cell 2021; 184:4939-4952.e15. [PMID: 34508652 PMCID: PMC8313480 DOI: 10.1016/j.cell.2021.07.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 12/12/2022]
Abstract
The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.
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Affiliation(s)
- Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Allison R Smither
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - John A Vanchiere
- Department of Pediatrics, Louisiana State University Health Sciences Center - Shreveport, Shreveport, LA 71130, USA
| | | | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Gytis Dudas
- Gothenburg Global Biodiversity Centre (GGBC), Gothenburg, Sweden
| | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maximilian Marshall
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Amy K Feehan
- Ochsner Clinic Foundation, New Orleans, Louisiana, USA
| | - Gilberto Sabino-Santos
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Centre for Virology Research, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP 14049900, Brazil
| | - Antoinette R Bell-Kareem
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manar Alkuzweny
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patricia Snarski
- Heart and Vascular Institute, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | | | - Rona S Scott
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Lilia I Melnik
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Raphaëlle Klitting
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michelle McGraw
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Arnaud C Drouin
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Physiology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Kaylynn J Genemaras
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Karissa Chao
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Bioinnovation Program, Tulane University, New Orleans, LA 70118, USA
| | - Sarah Topol
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Emily Spencer
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Laura Nicholson
- Scripps Research Translational Institute, La Jolla, CA 92037, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA; Rady Children's Hospital, San Diego, CA 92123, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | | | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada; Bluedot, Toronto, Canada; Department of Medicine, University of Toronto, Toronto, Canada
| | - Dahlene N Fusco
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA; Department of Medicine, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70114, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15219, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Belgium; Global Virology Network
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jeremy P Kamil
- Department of Microbiology and Immunology, Louisiana State University Health Science Center Shreveport, Shreveport, LA 71103, USA
| | - Robert F Garry
- Department of Microbiology and Immunology, School of Medicine, Tulane University, New Orleans, LA 70112, USA; Zalgen Labs LLC, Germantown, MD, USA
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Scripps Research Translational Institute, La Jolla, CA 92037, USA.
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4
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Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Dudas G, Snyder DJ, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem A, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh N, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG. Emergence of an early SARS-CoV-2 epidemic in the United States. medRxiv 2021. [PMID: 33564781 PMCID: PMC7872376 DOI: 10.1101/2021.02.05.21251235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The emergence of the early COVID-19 epidemic in the United States (U.S.) went largely undetected, due to a lack of adequate testing and mitigation efforts. The city of New Orleans, Louisiana experienced one of the earliest and fastest accelerating outbreaks, coinciding with the annual Mardi Gras festival, which went ahead without precautions. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large, crowded events may have accelerated early transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana initially had limited sequence diversity compared to other U.S. states, and that one successful introduction of SARS-CoV-2 led to almost all of the early SARS-CoV-2 transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras and that the festival dramatically accelerated transmission, eventually leading to secondary localized COVID-19 epidemics throughout the Southern U.S.. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate COVID-19 epidemics on a local and regional scale.
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5
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Membrebe JV, Baele G, Suchard MA, Lemey P. A63 Quantifying the dynamics of evolutionary rates through time. Virus Evol 2019. [PMCID: PMC6735781 DOI: 10.1093/ve/vez002.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The availability of evolutionary rate estimates in recent years led to the observation that they may depend on the time-scale on which they are measured. Specifically, RNA virus evolutionary rates are frequently estimated to be low towards the past and high towards the present. This time-dependent rate phenomenon (TDRP) has important implications for evolutionary studies as it could severely bias divergence time estimates. While recent studies are providing insights into the relationship between viral evolutionary rate and time, formal probabilistic models to draw inference under TDRP scenarios remain lacking. Here, we adopt epoch-modelling to develop a Bayesian model of discrete rate changes through time in an unknown evolutionary history and combine this with a log-linear parameterization of rates as a function of times in the past. We provide an implementation for nucleotide substitution rates as well as for nonsynonymous rates change in a codon substitution model. Using a foamy virus dataset for which internal node calibrations can be applied based on host-virus co-divergence, we estimate a significant decline in evolutionary rates as a function of time into the past for nucleotide substitutions as well as for non-synonymous substitutions in a codon model. We also estimate a deep evolutionary history for primate Lentiviruses by combining an HIV-1 group M node calibration and a biogeographic calibration for viruses in drill monkeys in the TDRP model. Our analyses lead to the conclusion that studies of evolutionary timescales require a reconsideration of substitution rates, in either codon and nucleotide substitution model, as a dynamic feature of molecular evolution.
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Affiliation(s)
- J V Membrebe
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - G Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - M A Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
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6
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Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S. Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak. Science 2019; 363:74-77. [PMID: 30606844 DOI: 10.1126/science.aau9343] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/12/2018] [Indexed: 12/15/2022]
Abstract
The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.
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Affiliation(s)
- L E Kafetzopoulou
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S T Pullan
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven, Belgium
| | - M A Suchard
- Departments of Biomathematics, Biostatistics, and Human Genetics, University of California, Los Angeles, CA, USA
| | - D U Ehichioya
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - M Pahlmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - A Thielebein
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - J Hinzmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - L Oestereich
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - D M Wozniak
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - K Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - D Schachten
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - F Koenig
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - J Matjeschk
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lorenzen
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - S Lumley
- Public Health England, National Infection Service, Porton Down, UK
| | - Y Ighodalo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D I Adomeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - T Olokor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Omomoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Omiunu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Agbukor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Ebo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Aiyepada
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P Ebhodaghe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - B Osiemi
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhilomen
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Airende
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Esumeh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Muoebonam
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Giwa
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - A Ekanem
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Igenegbale
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Odigie
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Enigbe
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - J Oyakhilome
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E O Yerumoh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - I Odia
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Aire
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - M Okonofua
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - R Atafo
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - E Tobin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Asogun
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - N Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - P O Okokhere
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - M O Rafiu
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - K O Iraoyah
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | | | - P Akhideno
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - C Erameh
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - G Akpede
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | - E Isibor
- Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - D Naidoo
- World Health Organization, Geneva, Switzerland
| | - R Hewson
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.,Faculty of Clinical Sciences and International Public Health, Liverpool School of Tropical Medicine, Liverpool, UK
| | - J A Hiscox
- National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.,Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - R Vipond
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - M W Carroll
- Public Health England, National Infection Service, Porton Down, UK.,National Institute of Health Research (NIHR), Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - C Ihekweazu
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - P Formenty
- World Health Organization, Geneva, Switzerland
| | - S Okogbenin
- Irrua Specialist Teaching Hospital, Irrua, Nigeria.,Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Nigeria
| | | | - S Günther
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg, Germany
| | - S Duraffour
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,German Center for Infection Research (DZIF), partner site Hamburg, Germany
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7
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Fusaro A, Zecchin B, Vrancken B, Abolnik C, Ademun A, Akpeli Y, Alassane A, Awuni J, Couacy-Hymann E, Coulibaly M, Go-Maro E, Joannis T, Jumbo S, Minoungou G, Meseko C, Moutari S, Ndumu D, Twabela A, Wade A, Wiersma L, Zamperin G, Milani A, Lemey P, Monne I. Global origins of African highly pathogenic avian influenza H5Nx viruses and intracontinental spread. Int J Infect Dis 2019. [DOI: 10.1016/j.ijid.2018.11.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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8
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Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA, Kellam P, Cotten M, Lemey P, Nokes DJ. Erratum: Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains. Virus Evol 2018; 4:vey036. [PMID: 30464856 PMCID: PMC6240154 DOI: 10.1093/ve/vey036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[This corrects the article DOI: 10.1093/ve/vey027.][This corrects the article DOI: 10.1093/ve/vey027.].
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9
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Otieno JR, Kamau EM, Oketch JW, Ngoi JM, Gichuki AM, Binter Š, Otieno GP, Ngama M, Agoti CN, Cane PA, Kellam P, Cotten M, Lemey P, Nokes DJ. Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains. Virus Evol 2018; 4:vey027. [PMID: 30271623 PMCID: PMC6153471 DOI: 10.1093/ve/vey027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analysed 184 RSV-A whole-genome sequences (WGSs) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A circulation in this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identified signature amino acid substitutions between ON1 and GA2 viruses’ surface proteins (G and F), polymerase (L), and matrix M2-1 proteins, some of which were positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORFs) (G, F, L, N, and P) formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF also play a role in the adaptation of RSV to host populations, with the alternative possibility that some of the substitutions are neutral and provide no selective advantage. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies.
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Affiliation(s)
- J R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - E M Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - J W Oketch
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - J M Ngoi
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - A M Gichuki
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - Š Binter
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge,UK.,Kymab Ltd., Babraham Research Campus, Cambridge, UK
| | - G P Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - M Ngama
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya
| | - C N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya.,Department of Biomedical Sciences, Pwani University, Kilifi, Kenya
| | - P A Cane
- High Containment Microbiology, Public Health England, Salisbury, UK
| | - P Kellam
- Kymab Ltd., Babraham Research Campus, Cambridge, UK.,Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - M Cotten
- Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge,UK.,Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - P Lemey
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
| | - D J Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, P.O. Box 230, 80108 Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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10
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Faria NR, Kraemer MUG, Hill SC, Goes de Jesus J, Aguiar RS, Iani FCM, Xavier J, Quick J, du Plessis L, Dellicour S, Thézé J, Carvalho RDO, Baele G, Wu CH, Silveira PP, Arruda MB, Pereira MA, Pereira GC, Lourenço J, Obolski U, Abade L, Vasylyeva TI, Giovanetti M, Yi D, Weiss DJ, Wint GRW, Shearer FM, Funk S, Nikolay B, Fonseca V, Adelino TER, Oliveira MAA, Silva MVF, Sacchetto L, Figueiredo PO, Rezende IM, Mello EM, Said RFC, Santos DA, Ferraz ML, Brito MG, Santana LF, Menezes MT, Brindeiro RM, Tanuri A, Dos Santos FCP, Cunha MS, Nogueira JS, Rocco IM, da Costa AC, Komninakis SCV, Azevedo V, Chieppe AO, Araujo ESM, Mendonça MCL, Dos Santos CC, Dos Santos CD, Mares-Guia AM, Nogueira RMR, Sequeira PC, Abreu RG, Garcia MHO, Abreu AL, Okumoto O, Kroon EG, de Albuquerque CFC, Lewandowski K, Pullan ST, Carroll M, de Oliveira T, Sabino EC, Souza RP, Suchard MA, Lemey P, Trindade GS, Drumond BP, Filippis AMB, Loman NJ, Cauchemez S, Alcantara LCJ, Pybus OG. Genomic and epidemiological monitoring of yellow fever virus transmission potential. Science 2018; 361:894-899. [PMID: 30139911 PMCID: PMC6874500 DOI: 10.1126/science.aat7115] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/20/2018] [Indexed: 12/21/2022]
Abstract
The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.
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Affiliation(s)
- N R Faria
- Department of Zoology, University of Oxford, Oxford, UK.
| | - M U G Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- Computational Epidemiology Lab, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - S C Hill
- Department of Zoology, University of Oxford, Oxford, UK
| | - J Goes de Jesus
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R S Aguiar
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C M Iani
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - J Xavier
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - J Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - L du Plessis
- Department of Zoology, University of Oxford, Oxford, UK
| | - S Dellicour
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - J Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - R D O Carvalho
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - G Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - C-H Wu
- Department of Statistics, University of Oxford, Oxford, UK
| | - P P Silveira
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M B Arruda
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - M A Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - G C Pereira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - J Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
| | - U Obolski
- Department of Zoology, University of Oxford, Oxford, UK
| | - L Abade
- Department of Zoology, University of Oxford, Oxford, UK
- The Global Health Network, University of Oxford, Oxford, UK
| | - T I Vasylyeva
- Department of Zoology, University of Oxford, Oxford, UK
| | - M Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D Yi
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - D J Weiss
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - G R W Wint
- Department of Zoology, University of Oxford, Oxford, UK
| | - F M Shearer
- Malaria Atlas Project, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - S Funk
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - B Nikolay
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - V Fonseca
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - T E R Adelino
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M A A Oliveira
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - M V F Silva
- Laboratório Central de Saúde Pública, Instituto Octávio Magalhães, FUNED, Belo Horizonte, Minas Gerais, Brazil
| | - L Sacchetto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - P O Figueiredo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - I M Rezende
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - E M Mello
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - R F C Said
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D A Santos
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M L Ferraz
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M G Brito
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - L F Santana
- Secretaria de Estado de Saúde de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - M T Menezes
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - R M Brindeiro
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - A Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - F C P Dos Santos
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M S Cunha
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - J S Nogueira
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - I M Rocco
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - A C da Costa
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - S C V Komninakis
- Retrovirology Laboratory, Federal University of São Paulo, São Paulo, Brazil
- School of Medicine of ABC (FMABC), Clinical Immunology Laboratory, Santo André, São Paulo, Brazil
| | - V Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A O Chieppe
- Coordenação de Vigilância Epidemiológica do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - E S M Araujo
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - M C L Mendonça
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C C Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - C D Dos Santos
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - A M Mares-Guia
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R M R Nogueira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - P C Sequeira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - R G Abreu
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - M H O Garcia
- Departamento de Vigilância das Doenças Transmissíveis da Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília-DF, Brazil
| | - A L Abreu
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - O Okumoto
- Secretaria de Vigilância em Saúde, Coordenação Geral de Laboratórios de Saúde Pública, Ministério da Saúde, Brasília-DF, Brazil
| | - E G Kroon
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - C F C de Albuquerque
- Organização Pan - Americana da Saúde/Organização Mundial da Saúde - (OPAS/OMS), Brasília-DF, Brazil
| | - K Lewandowski
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - S T Pullan
- Public Health England, National Infections Service, Porton Down, Salisbury, UK
| | - M Carroll
- NIHR HPRU in Emerging and Zoonotic Infections, Public Health England, London, UK
| | - T de Oliveira
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- KwaZulu-Natal Research, Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - E C Sabino
- Instituto de Medicina Tropical e Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - R P Souza
- Núcleo de Doenças de Transmissão Vetorial, Instituto Adolfo Lutz, São Paulo, Brazil
| | - M A Suchard
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - P Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - G S Trindade
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - B P Drumond
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - A M B Filippis
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - N J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - S Cauchemez
- Mathematical Modelling of Infectious Diseases and Center of Bioinformatics, Institut Pasteur, Paris, France
- CNRS UMR2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - L C J Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil.
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - O G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
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11
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Vinken L, Fransen K, Pineda-Peña AC, Alexiev I, Balotta C, Debaisieux L, Devaux C, García Ribas S, Gomes P, Incardona F, Kaiser R, Ruelle J, Sayan M, Paraschiv S, Paredes R, Peeters M, Sonnerborg A, Vancutsem E, Van den Wijngaert S, Van Ranst M, Verhofstede C, Vandamme AM, Lemey P, Van Laethem K. A21 HIV-1 sub-subtype F1 outbreak among MSM in Belgium. Virus Evol 2017; 3:vew036.020. [PMID: 28845274 PMCID: PMC5565986 DOI: 10.1093/ve/vew036.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Affiliation(s)
- L Vinken
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - K Fransen
- Department of Clinical Sciences, Aids Reference laboratory, Institute of Tropical Medicine, Antwerp, Belgium
| | - A C Pineda-Peña
- Global Health and Tropical Medicine-GHTM, Institute for Hygiene and Tropical Medicine, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - I Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - C Balotta
- 'L. Sacco' Hospital, Infectious Diseases and Immunopathology Section, Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - L Debaisieux
- AIDS Reference Laboratory, Université Libre de Bruxelles, Hopital Erasme, Brussels, Belgium
| | - C Devaux
- Department of Infection and Immunity, Laboratory of Retrovirology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - S García Ribas
- Department of Clinical Sciences, Aids Reference laboratory, Institute of Tropical Medicine, Antwerp, Belgium
| | - P Gomes
- HEM - Centro Hospitalar de Lisboa Ocidental, SPC, LMCBM, Lisbon, Portugal
| | | | - R Kaiser
- University of Cologne, Institute of Virology, Cologne, Germany
| | - J Ruelle
- Unit of Medical Microbiology (MBLG), Université Catholique de Louvain, Institute of Experimental and Clinical Research (IREC), Brussels, Belgium
| | - M Sayan
- Clinical Laboratory, Kocaeli University, Izmit, Kocaeli, Turkey
| | - S Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases 'Matei Bals', Bucharest, Romania
| | - R Paredes
- Universitat Autònoma de Barcelona, IrsiCaixa AIDS Research Institute, Badalona, Catalonia, Spain
| | - M Peeters
- Institut de Recherche pour le Développement, INSERM U1175, and University of Montpellier, Unité Mixte Internationale 233, Montpellier, France
| | - A Sonnerborg
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - E Vancutsem
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - S Van den Wijngaert
- Department of Microbiology, Saint-Pierre University Hospital, Brussels, Belgium
| | - M Van Ranst
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - C Verhofstede
- Department of Clinical Chemistry, Microbiology and Immunology, AIDS Reference Laboratory, Ghent University, Ghent, Belgium
| | - A-M Vandamme
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - P Lemey
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
| | - K Van Laethem
- KU Leuven - University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
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12
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Mather A, Reid S, Maskell D, Parkhill J, Fookes M, Harris S, Brown D, Coia J, Mulvey M, Gilmour M, Petrovska L, de Pinna E, Kuroda M, Akiba M, Izumiya H, Connor T, Suchard M, Lemey P, Mellor D, Haydon D, Thomson N. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science 2013; 341:1514-7. [PMID: 24030491 PMCID: PMC4012302 DOI: 10.1126/science.1240578] [Citation(s) in RCA: 233] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.
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Affiliation(s)
- A.E. Mather
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - S.W.J. Reid
- Royal Veterinary College, North Mymms, Hatfield, UK
| | - D.J. Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - J. Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M.C. Fookes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - S.R. Harris
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - D.J. Brown
- Scottish Salmonella Shigella and Clostridium difficile Reference Laboratory, Stobhill Hospital, Glasgow, UK
| | - J.E. Coia
- Scottish Salmonella Shigella and Clostridium difficile Reference Laboratory, Stobhill Hospital, Glasgow, UK
| | - M.R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - M.W. Gilmour
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - L. Petrovska
- Animal Health and Veterinary Laboratories Agency, Weybridge, UK
| | - E. de Pinna
- Gastrointestinal Bacteria Reference Unit, Public Health England, Colindale, London, UK
| | - M. Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - M. Akiba
- Bacterial and Parasitic Disease Research Division, National Institute of Animal Health, Ibaraki, Japan
| | - H. Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - T.R. Connor
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M.A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, and Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, USA
| | - P. Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - D.J. Mellor
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - D.T. Haydon
- Boyd Orr Centre for Population and Ecosystem Health, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - N.R. Thomson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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13
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Baele G, Lemey P. Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency. Bioinformatics 2013; 29:1970-9. [DOI: 10.1093/bioinformatics/btt340] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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14
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Abstract
Recently, we proposed a new classification for 'subgenotype A' of hepatitis B virus (HBV), in which the novel 'quasi-subgenotype A3' group comprising HBV 'subgenotype A3', 'tentative A4', and A5 was introduced. Newly 'Tentative subgenotype A7' strains from Cameroon were introduced by Hubschen et al. However, our meticulous phylogenetic analysis demonstrated that these isolates should also be classified into 'quasi-subgenotype A3'. Such misclassification can be avoided by following established principles for HBV subgenotyping. Moreover, their close evolutionary relationship with A3 highlights our hypothesis that geographical origin may be an important factor in further classification of HBV subgenotypes.
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Affiliation(s)
- M R Pourkarim
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
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15
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Verbeeck J, Kwanten L, D’Heygere F, Beguin A, Michiels S, Desombere I, Leroux-Roels G, Lemey P, Nevens F, Ranst M. HCV genotype distribution in Flanders and Brussels (Belgium): unravelling the spread of an uncommon HCV genotype 5a cluster. Eur J Clin Microbiol Infect Dis 2010; 29:1427-34. [DOI: 10.1007/s10096-010-1021-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 07/26/2010] [Indexed: 12/15/2022]
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16
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Pourkarim M, Verbeeck J, Rahman M, Amini-Bavil-Olyaee S, Forier A, Lemey P, Maes P. OP3-8 Evolutionary analysis of Hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium. J Clin Virol 2009. [DOI: 10.1016/s1386-6532(09)70054-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Ross RS, Verbeeck J, Viazov S, Lemey P, Van Ranst M, Roggendorf M. Evidence for a complex mosaic genome pattern in a full-length hepatitis C virus sequence. Evol Bioinform Online 2008; 4:249-54. [PMID: 19204822 PMCID: PMC2614189 DOI: 10.4137/ebo.s1038] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The genome of the hepatitis C virus (HCV) exhibits a high genetic variability. This remarkable heterogeneity is mainly attributed to the gradual accumulation of mutational changes, whereas the contribution of recombination events to the evolution of HCV remains controversial so far. While performing phylogenetic analyses including a large number of sequences deposited in the GenBank, we encountered a full-length HCV sequence (AY651061) that showed evidence for inter-subtype recombination and was, therefore, subjected to a detailed analysis of its molecular structure. The obtained results indicated that AY651061 does not represent a "simple" HCV 1c isolate, but a complex 1a/1c mosaic genome, showing five putative breakpoints in the core to NS3 regions. To our knowledge, this is the first report on a mosaic HCV full-length sequence with multiple breakpoints. The molecular structure of AY651061 is reminiscent of complex homologous recombinant variants occurring among other members of the flaviviridae family, e.g. GB virus C, dengue virus, and Japanese encephalitis virus. Our finding of a mosaic HCV sequence may have important implications for many fields of current HCV research which merit careful consideration.
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Affiliation(s)
- R S Ross
- Institute of Virology, National Reference Centre for HCV, Essen University Hospital, University of Duisburg-Essen, Essen, Germany.
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18
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Abstract
We employed recently developed statistical methods to explore the epidemic behaviour of hepatitis C subtype 1a and subtype 3a among injecting drug users (IDUs) in Flanders, Belgium, using new gene sequence data sampled among two geographically distinct populations of IDUs. First the extent of hepatitis C transmission across regions/countries was studied through calculation of association indices. It was shown that viral exchange had occurred between both populations in Flanders as well as across international borders. Furthermore, evidence was found suggestive of subtypes 1a and 3a predominantly circulating in subpopulations of Flemish IDUs, exhibiting different degrees of travelling/migration behaviour. Secondly, through coalescent-based analysis the viral epidemic history of the hepatitis C subtype 1a and 3a epidemics was inferred. Evidence was found for different dynamic forces driving both epidemics. Moreover, results suggested that the hepatitis C subtype 3a epidemic has reached a steady state, while the hepatitis C 1a epidemic has not, which therefore might become the predominant subtype among IDUs.
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Affiliation(s)
- C Matheï
- Department of General Practice, Katholieke Universiteit Leuven, Leuven, Belgium.
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19
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Deforche K, Camacho R, Van Laethem K, Lemey P, Rambaut A, Moreau Y, Vandamme AM. Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. ACTA ACUST UNITED AC 2007; 24:34-41. [PMID: 18024973 DOI: 10.1093/bioinformatics/btm540] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION HIV-1 antiviral resistance is a major cause of antiviral treatment failure. The in vivo fitness landscape experienced by the virus in presence of treatment could in principle be used to determine both the susceptibility of the virus to the treatment and the genetic barrier to resistance. We propose a method to estimate this fitness landscape from cross-sectional clinical genetic sequence data of different subtypes, by reverse engineering the required selective pressure for HIV-1 sequences obtained from treatment naive patients, to evolve towards sequences obtained from treated patients. The method was evaluated for recovering 10 random fictive selective pressures in simulation experiments, and for modeling the selective pressure under treatment with the protease inhibitor nelfinavir. RESULTS The estimated fitness function under nelfinavir treatment considered fitness contributions of 114 mutations at 48 sites. Estimated fitness correlated significantly with the in vitro resistance phenotype in 519 matched genotype-phenotype pairs (R(2) = 0.47 (0.41 - 0.54)) and variation in predicted evolution under nelfinavir selective pressure correlated significantly with observed in vivo evolution during nelfinavir treatment for 39 mutations (with FDR = 0.05). AVAILABILITY The software is available on request from the authors, and data sets are available from http://jose.med.kuleuven.be/~kdforc0/nfv-fitness-data/.
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Affiliation(s)
- K Deforche
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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20
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Mikhail M, Wang B, Lemey P, Beckholdt B, Vandamme AM, Gill MJ, Saksena NK. Full-length HIV type 1 genome analysis showing evidence for HIV type 1 transmission from a nonprogressor to two recipients who progressed to AIDS. AIDS Res Hum Retroviruses 2005; 21:575-9. [PMID: 15989463 DOI: 10.1089/aid.2005.21.575] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epidemiologically-linked HIV-1 transmission cohorts serve as excellent models to study HIV disease progression. The actual relationship between viral variability and HIV disease outcome can be extrapolated only through such rare epidemiologically linked HIV-1-infected cohorts. We present here a cohort of three patients with the source termed donor A (a nonprogressor) and two recipients B and C. Both recipients acquired HIV through blood transfusion from donor A and have progressed to AIDS. By analyzing 15 near full-length HIV- 1 genomes (8.7 kb each genome) from longitudinally collected peripheral blood cell samples (four time points for patient A, four for patient B, and seven from patient C), we were able to demonstrate transmission of HIV from donor A and epidemiologic linkage among members A, B, and C after 10 years of HIV infection. These analyses are novel in demonstrating that HIV-1-infected nonprogressing individuals bear the potential to transmit HIV-1 variants and that HIV variants, which led to a benign disease in a nonprogressor donor, were able to cause disease in other individuals. Overall, these studies highlight the utility of full genome sequencing in establishing epidemiologic linkage in a chronically infected HIV cohort after 10 years of initial infection.
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Affiliation(s)
- Meriet Mikhail
- Retroviral Genetics Laboratory, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, The University of Sydney, Westmead NSW 2145, Sydney, Australia
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21
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Hens K, Lemey P, Macours N, Francis C, Huybrechts R. Cyclorraphan yolk proteins and lepidopteran minor yolk proteins originate from two unrelated lipase families. Insect Mol Biol 2004; 13:615-623. [PMID: 15606810 DOI: 10.1111/j.0962-1075.2004.00520.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Vitellogenins, cyclorraphan yolk proteins and lepidopteran minor yolk proteins are three classes of female-specific proteins that serve as an embryonic nutritional store. Similarity to vertebrate lipid-binding proteins was established for vitellogenins and yolk proteins, vitellogenins being related to apolipoprotein B and yolk proteins to lipases. Recently, similarity between yolk proteins and minor yolk proteins was reported and it was suggested that yolk proteins are more related to minor yolk proteins than to vertebrate lipases. In this study, we cloned five additional yolk proteins from the grey fleshfly Neobellieria bullata, formerly known as Sarcophaga bullata. We used this sequence data, combined with sequence data retrieved from the NCBI protein database to evaluate the yolk protein-lipase and the yolk protein-minor yolk protein relationship. We found no similarity between yolk proteins and minor yolk proteins, but we showed that yolk proteins are related to a family of lipases containing vertebrate hepatic and pancreatic lipases while minor yolk proteins are related to a family of lipases containing vertebrate gastric and lingual lipases. The fact that three different classes of yolk storage proteins show similarity to three different classes of vertebrate lipid-binding proteins strongly suggests that this lipid-binding feature is important for insect yolk storage proteins.
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Affiliation(s)
- K Hens
- Department of Biology, Catholic University of Leuven, Leuven, Belgium.
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22
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Paraskevis D, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM. SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics 2004; 21:1274-5. [PMID: 15546940 DOI: 10.1093/bioinformatics/bti139] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.
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Affiliation(s)
- D Paraskevis
- Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
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23
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Paraskevis D, Lemey P, Salemi M, Suchard M, Van De Peer Y, Vandamme AM. Analysis of the evolutionary relationships of HIV-1 and SIVcpz sequences using bayesian inference: implications for the origin of HIV-1. Mol Biol Evol 2003; 20:1986-96. [PMID: 12949143 DOI: 10.1093/molbev/msg207] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The most plausible origin of HIV-1 group M is an SIV lineage currently represented by SIVcpz isolated from the chimpanzee subspecies Pan troglodytes troglodytes. The origin of HIV-1 group O is less clear. Putative recombination between any of the HIV-1 and SIVcpz sequences was tested using bootscanning and Bayesian-scanning plots, as well as a new method using a Bayesian multiple change-point (BMCP) model to infer parental sequences and crossing-over points. We found that in the case of highly divergent sequences, such as HIV-1/SIVcpz, Bayesian scanning and BMCP methods are more appropriate than bootscanning analysis to investigate spatial phylogenetic variation, including estimating the boundaries of the regions with discordant evolutionary relationships and the levels of support of the phylogenetic clusters under study. According to the Bayesian scanning plots and BMCP method, there was strong evidence for discordant phylogenetic clustering throughout the genome: (1) HIV-1 group O clustered with SIVcpzANT/TAN in middle pol, and partial vif/env; (2) SIVcpzGab1 clustered with SIVcpzANT/TAN in 3'pol/vif, and middle env; (3) HIV-1 group O grouped with SIVcpzCamUS and SIVcpzGab1 in p17/p24; (4) HIV-1 group M was more closely related to SIVcpzCamUS in 3'gag/pol and in middle pol, whereas in partial gp120 group M clustered with group O. Conditionally independent phylogenetic analysis inferred by maximum likelihood (ML) and Bayesian methods further confirmed these findings. The discordant phylogenetic relationships between the HIV-1/SIVcpz sequences may have been caused by ancient recombination events, but they are also due, at least in part, to altered rates of evolution between parental SIVcpz lineages.
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Affiliation(s)
- D Paraskevis
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
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24
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Rector A, Lemey P, Laffut W, Keyaerts E, Struyf F, Wollants E, Vermeire S, Rutgeerts P, Van Ranst M. Mannan-binding lectin (MBL) gene polymorphisms in ulcerative colitis and Crohn's disease. Genes Immun 2001; 2:323-8. [PMID: 11607788 DOI: 10.1038/sj.gene.6363784] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2001] [Revised: 06/06/2001] [Accepted: 07/02/2001] [Indexed: 12/20/2022]
Abstract
The inflammatory bowel diseases (IBD), Crohn's disease (CD), and ulcerative colitis (UC), are complex multifactorial traits involving both environmental and genetic factors. Mannan-binding lectin (MBL) plays an important role in non-specific immunity and complement activation. Point mutations in codons 52, 54 and 57 of exon 1 of the MBL gene are associated with decreased MBL plasma concentrations and increased susceptibility to various infectious diseases. If these MBL mutations could lead to susceptibility to putative IBD-etiological microbial agents, or could temper the complement-mediated mucosal damage in IBD, MBL could function as the link between certain microbial, immunological and genetic factors in IBD. In this study, we investigated the presence of the codon 52, 54 and 57 mutations of the MBL gene in 431 unrelated IBD patients, 112 affected and 141 unaffected first-degree relatives, and 308 healthy control individuals. In the group of sporadic IBD patients (n = 340), the frequency of the investigated MBL variants was significantly lower in UC patients when compared with CD patients (P = 0.01) and with controls (P = 0.02). These results suggest that MBL mutations which decrease the formation of functional MBL could protect against the clinical development of sporadic UC, but not of CD. This could be explained by the differential T-helper response in both diseases.
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Affiliation(s)
- A Rector
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, Leuven, Belgium
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