1
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Xu P, Liang S, Hahn A, Zhao V, Lo WT‘J, Haller BC, Sobkowiak B, Chitwood MH, Colijn C, Cohen T, Rhee KY, Messer PW, Wells MT, Clark AG, Kim J. e3SIM: epidemiological-ecological-evolutionary simulation framework for genomic epidemiology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601123. [PMID: 39005464 PMCID: PMC11244936 DOI: 10.1101/2024.06.29.601123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Infectious disease dynamics are driven by the complex interplay of epidemiological, ecological, and evolutionary processes. Accurately modeling these interactions is crucial for understanding pathogen spread and informing public health strategies. However, existing simulators often fail to capture the dynamic interplay between these processes, resulting in oversimplified models that do not fully reflect real-world complexities in which the pathogen's genetic evolution dynamically influences disease transmission. We introduce the epidemiological-ecological-evolutionary simulator (e3SIM), an open-source framework that concurrently models the transmission dynamics and molecular evolution of pathogens within a host population while integrating environmental factors. Using an agent-based, discrete-generation, forward-in-time approach, e3SIM incorporates compartmental models, host-population contact networks, and quantitative-trait models for pathogens. This integration allows for realistic simulations of disease spread and pathogen evolution. Key features include a modular and scalable design, flexibility in modeling various epidemiological and population-genetic complexities, incorporation of time-varying environmental factors, and a user-friendly graphical interface. We demonstrate e3SIM's capabilities through simulations of realistic outbreak scenarios with SARS-CoV-2 and Mycobacterium tuberculosis, illustrating its flexibility for studying the genomic epidemiology of diverse pathogen types.
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Affiliation(s)
- Peiyu Xu
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
| | - Shenni Liang
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Andrew Hahn
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Vivian Zhao
- Department of Computational Science, Cornell University, Ithaca, NY, USA
| | - Wai Tung ‘Jack’ Lo
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Benjamin C. Haller
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Melanie H. Chitwood
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Ted Cohen
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, New Haven, CT, USA
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Philipp W. Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, Ithaca, NY, USA
| | - Andrew G. Clark
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Jaehee Kim
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
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2
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Houben RMAC, Newton JR, van Maanen C, Waller AS, Sloet van Oldruitenborgh-Oosterbaan MM, Heesterbeek JAP. Untangling the stranglehold through mathematical modelling of Streptococcus equi subspecies equi transmission. Prev Vet Med 2024; 228:106230. [PMID: 38772119 DOI: 10.1016/j.prevetmed.2024.106230] [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: 12/17/2023] [Revised: 05/02/2024] [Accepted: 05/14/2024] [Indexed: 05/23/2024]
Abstract
Strangles, a disease caused by infection with Streptococccus equi subspecies equi (S. equi), is endemic worldwide and one of the most frequently diagnosed infectious diseases of horses. Recent work has improved our knowledge of key parameters of transmission dynamics, but important knowledge gaps remain. Our aim was to apply mathematical modelling of S. equi transmission dynamics to prioritise future research areas, and add precision to estimates of transmission parameters thereby improving understanding of S. equi epidemiology and quantifying the control effort required. A compartmental deterministic model was constructed. Parameter values were estimated from current literature wherever possible. We assessed the sensitivity of estimates for the basic reproduction number on the population scale to varying assumptions for the unknown or uncertain parameters of: (mean) duration of carriership (1∕γC), relative infectiousness of carriers (f), proportion of infections that result in carriership (p), and (mean) duration of immunity after natural infection (1∕γR). Available incidence and (sero-)prevalence data were compared to model outputs to improve point estimates and ranges for these currently unknown or uncertain transmission-related parameters. The required vaccination coverage of an ideal vaccine to prevent major outbreaks under a range of control scenarios was estimated, and compared available data on existing vaccines. The relative infectiousness of carriers (as compared to acutely ill horses) and the duration of carriership were identified as key knowledge gaps. Deterministic compartmental simulations, combined with seroprevalence data, suggest that 0.05
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Affiliation(s)
- R M A C Houben
- Department of Clinical Sciences, faculty of Veterinary medicine, Utrecht University, the Netherlands.
| | - J R Newton
- Equine Infectious Disease Surveillance (EIDS), Department of Veterinary Medicine, Cambridge, UK
| | | | - A S Waller
- Intervacc AB, Stockholm, Sweden; Department of Biomedical Science and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - J A P Heesterbeek
- Department of Population Health Sciences, faculty of Veterinary Medicine, Utrecht University, the Netherlands
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3
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Sun C, Fang R, Salemi M, Prosperi M, Rife Magalis B. DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction. PLoS Comput Biol 2024; 20:e1011351. [PMID: 38598563 PMCID: PMC11034642 DOI: 10.1371/journal.pcbi.1011351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 04/22/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations. Moreover, tree topology and the incorporation of population parameters (phylodynamics) can be useful in reconstructing the evolutionary dynamics of an epidemic across space and time among individuals. We now demonstrate the utility of phylodynamic trees for transmission modeling and forecasting, developing a phylogeny-based deep learning system, referred to as DeepDynaForecast. Our approach leverages a primal-dual graph learning structure with shortcut multi-layer aggregation, which is suited for the early identification and prediction of transmission dynamics in emerging high-risk groups. We demonstrate the accuracy of DeepDynaForecast using simulated outbreak data and the utility of the learned model using empirical, large-scale data from the human immunodeficiency virus epidemic in Florida between 2012 and 2020. Our framework is available as open-source software (MIT license) at github.com/lab-smile/DeepDynaForcast.
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Affiliation(s)
- Chaoyue Sun
- Department of Electrical and Computer Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
| | - Ruogu Fang
- Department of Electrical and Computer Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, United States of America
- Center for Cognitive Aging and Memory, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mattia Prosperi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Epidemiology, University of Florida, Gainesville, Florida, United States of America
| | - Brittany Rife Magalis
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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4
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Danesh G, Saulnier E, Gascuel O, Choisy M, Alizon S. TiPS
: Rapidly simulating trajectories and phylogenies from compartmental models. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gonché Danesh
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
| | - Emma Saulnier
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
| | | | - Marc Choisy
- Centre for Tropical Medicine and Global Health Nuffield Department of Medicine, University of Oxford Oxford UK
- Oxford University Clinical Research Unit Ho Chi Minh City Vietnam
| | - Samuel Alizon
- MIVEGEC, CNRS, IRD Université de Montpellier Montpellie France
- Center for Interdisciplinary Research in Biology (CIRB) College de France, CNRS, INSERM, Université PSL Paris France
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5
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Goldstein IH, Bayer D, Barilar I, Kizito B, Matsiri O, Modongo C, Zetola NM, Niemann S, Minin VM, Shin SS. Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission. PLoS Comput Biol 2022; 18:e1010696. [PMID: 36469509 DOI: 10.1371/journal.pcbi.1010696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Identifying host factors that influence infectious disease transmission is an important step toward developing interventions to reduce disease incidence. Recent advances in methods for reconstructing infectious disease transmission events using pathogen genomic and epidemiological data open the door for investigation of host factors that affect onward transmission. While most transmission reconstruction methods are designed to work with densely sampled outbreaks, these methods are making their way into surveillance studies, where the fraction of sampled cases with sequenced pathogens could be relatively low. Surveillance studies that use transmission event reconstruction then use the reconstructed events as response variables (i.e., infection source status of each sampled case) and use host characteristics as predictors (e.g., presence of HIV infection) in regression models. We use simulations to study estimation of the effect of a host factor on probability of being an infection source via this multi-step inferential procedure. Using TransPhylo-a widely-used method for Bayesian estimation of infectious disease transmission events-and logistic regression, we find that low sensitivity of identifying infection sources leads to dilution of the signal, biasing logistic regression coefficients toward zero. We show that increasing the proportion of sampled cases improves sensitivity and some, but not all properties of the logistic regression inference. Application of these approaches to real world data from a population-based TB study in Botswana fails to detect an association between HIV infection and probability of being a TB infection source. We conclude that application of a pipeline, where one first uses TransPhylo and sparsely sampled surveillance data to infer transmission events and then estimates effects of host characteristics on probabilities of these events, should be accompanied by a realistic simulation study to better understand biases stemming from imprecise transmission event inference.
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Affiliation(s)
- Isaac H Goldstein
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Damon Bayer
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Ivan Barilar
- German Center for Infection Research, Research Center Borstel, Borstel, Germany
| | | | | | | | - Nicola M Zetola
- Augusta University, Augusta, Georgia, United States of America
| | - Stefan Niemann
- German Center for Infection Research, Research Center Borstel, Borstel, Germany
| | - Volodymyr M Minin
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Sanghyuk S Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California, United States of America
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6
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Shchur V, Spirin V, Sirotkin D, Burovski E, De Maio N, Corbett-Detig R. VGsim: Scalable viral genealogy simulator for global pandemic. PLoS Comput Biol 2022; 18:e1010409. [PMID: 36001646 PMCID: PMC9447924 DOI: 10.1371/journal.pcbi.1010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 09/06/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
Accurate simulation of complex biological processes is an essential component of developing and validating new technologies and inference approaches. As an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from most regions in the world. More than 5.5 million viral sequences are publicly available as of November 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification of new variants with transmissibility and immunity evasion advantages. To our knowledge, there is no framework that is both efficient and flexible enough to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulator VGsim which addresses the problem of simulation genealogies under epidemiological models. The simulation process is split into two phases. During the forward run the algorithm generates a chain of population-level events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the population-level events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape. We develop a fast and flexible simulation software package VGsim for modeling epidemiological processes and generating genealogies of large pathogen samples. The software takes into account host population structure, pathogen evolution, host immunity and some other epidemiological aspects. The computational efficiency of the package allows to simulate genealogies of tens of millions of samples, which is important, e.g., for SARS-CoV-2 genome studies.
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Affiliation(s)
- Vladimir Shchur
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russia
- * E-mail:
| | - Vadim Spirin
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russia
| | - Dmitry Sirotkin
- International laboratory of statistical and computational genomics, HSE University, Moscow, Russia
| | | | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, California, United States of America
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7
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Marini S, Mavian C, Riva A, Prosperi M, Salemi M, Rife Magalis B. Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinformatics 2021; 38:856-860. [PMID: 34672334 PMCID: PMC8756195 DOI: 10.1093/bioinformatics/btab725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/10/2021] [Accepted: 10/18/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY TARDiS is a novel phylogenetic tool for optimal genetic subsampling. It optimizes both genetic diversity and temporal distribution through a genetic algorithm. AVAILABILITY AND IMPLEMENTATION TARDiS, along with example datasets and a user manual, is available at https://github.com/smarini/tardis-phylogenetics.
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Affiliation(s)
- Simone Marini
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA,Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA,Department of Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville, FL 32611, USA
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8
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Giovanetti M, Cella E, Benedetti F, Rife Magalis B, Fonseca V, Fabris S, Campisi G, Ciccozzi A, Angeletti S, Borsetti A, Tambone V, Sagnelli C, Pascarella S, Riva A, Ceccarelli G, Marcello A, Azarian T, Wilkinson E, de Oliveira T, Alcantara LCJ, Cauda R, Caruso A, Dean NE, Browne C, Lourenco J, Salemi M, Zella D, Ciccozzi M. SARS-CoV-2 shifting transmission dynamics and hidden reservoirs potentially limit efficacy of public health interventions in Italy. Commun Biol 2021; 4:489. [PMID: 33883675 PMCID: PMC8060392 DOI: 10.1038/s42003-021-02025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/03/2021] [Indexed: 01/08/2023] Open
Abstract
We investigated SARS-CoV-2 transmission dynamics in Italy, one of the countries hit hardest by the pandemic, using phylodynamic analysis of viral genetic and epidemiological data. We observed the co-circulation of multiple SARS-CoV-2 lineages over time, which were linked to multiple importations and characterized by large transmission clusters concomitant with a high number of infections. Subsequent implementation of a three-phase nationwide lockdown strategy greatly reduced infection numbers and hospitalizations. Yet we present evidence of sustained viral spread among sporadic clusters acting as "hidden reservoirs" during summer 2020. Mathematical modelling shows that increased mobility among residents eventually catalyzed the coalescence of such clusters, thus driving up the number of infections and initiating a new epidemic wave. Our results suggest that the efficacy of public health interventions is, ultimately, limited by the size and structure of epidemic reservoirs, which may warrant prioritization during vaccine deployment.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Brittany Rife Magalis
- Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, ICB, 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, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
| | - Silvia Fabris
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Giovanni Campisi
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Alessandra Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | | | | | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli", University of Rome "La Sapienza", Rome, Italy
| | - Alberto Riva
- ICBR, University of Florida, Gainesville, FL, USA
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Policlinico Umberto I Università 'Sapienza', Rome, Italy
| | - Alessandro Marcello
- Laboratory of Molecular Virology, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roberto Cauda
- Department Infectious Diseases, - Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, Section of Microbiology, University of Brescia, Brescia, Italy
| | - Natalie E Dean
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Cameron Browne
- Department of Mathematics, University of Lafayette, Lafayette, LA, USA
| | - Jose Lourenco
- Department of Zoology, University of Oxford, Oxford, UK
| | - Marco Salemi
- Emerging Pathogens Institute & Department of Pathology, College of Medicine, University of Florida, Gainesville, FL, USA.
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy.
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9
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Aubry F, Jacobs S, Darmuzey M, Lequime S, Delang L, Fontaine A, Jupatanakul N, Miot EF, Dabo S, Manet C, Montagutelli X, Baidaliuk A, Gámbaro F, Simon-Lorière E, Gilsoul M, Romero-Vivas CM, Cao-Lormeau VM, Jarman RG, Diagne CT, Faye O, Faye O, Sall AA, Neyts J, Nguyen L, Kaptein SJF, Lambrechts L. Recent African strains of Zika virus display higher transmissibility and fetal pathogenicity than Asian strains. Nat Commun 2021; 12:916. [PMID: 33568638 PMCID: PMC7876148 DOI: 10.1038/s41467-021-21199-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/16/2021] [Indexed: 11/09/2022] Open
Abstract
The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towards higher transmissibility and pathogenicity of the African ZIKV lineage. Whether this apparent paradox reflects the use of relatively old African ZIKV strains in most laboratory studies is unclear. Here, we experimentally compare seven low-passage ZIKV strains representing the recently circulating viral genetic diversity. We find that recent African ZIKV strains display higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice than their Asian counterparts. We emphasize the high epidemic potential of African ZIKV strains and suggest that they could more easily go unnoticed by public health surveillance systems than Asian strains due to their propensity to cause fetal loss rather than birth defects. Here, the authors compare seven low passage Zika virus (ZIKV) strains representing the recently circulating viral genetic diversity of African and Asian strains and find that African ZIKV strains have higher transmissibility in mosquitoes and higher lethality in both adult and fetal mice.
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Affiliation(s)
- Fabien Aubry
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Sofie Jacobs
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Maïlis Darmuzey
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Sebastian Lequime
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium.,Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Leen Delang
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France.,IRD, SSA, AP-HM, UMR Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Aix Marseille University, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Natapong Jupatanakul
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Elliott F Miot
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Stéphanie Dabo
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France
| | - Caroline Manet
- Mouse Genetics Laboratory, Institut Pasteur, Paris, France
| | | | - Artem Baidaliuk
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.,Evolutionary Genomics of RNA Viruses Group, Institut Pasteur, Paris, France
| | - Fabiana Gámbaro
- Evolutionary Genomics of RNA Viruses Group, Institut Pasteur, Paris, France
| | | | - Maxime Gilsoul
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Claudia M Romero-Vivas
- Laboratorio de Enfermedades Tropicales, Departamento de Medicina, Fundación Universidad del Norte, Barranquilla, Colombia
| | | | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Cheikh T Diagne
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Ousmane Faye
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Amadou A Sall
- Arbovirus and Viral Hemorrhagic Fevers Unit, Institut Pasteur Dakar, Dakar, Senegal
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium
| | - Laurent Nguyen
- GIGA-Stem Cells/GIGA-Neurosciences, Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), C.H.U. Sart Tilman, University of Liège, Liège, Belgium
| | - Suzanne J F Kaptein
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Leuven, Belgium.
| | - Louis Lambrechts
- Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris, France.
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Lequime S, Dehecq JS, Matheus S, de Laval F, Almeras L, Briolant S, Fontaine A. Modeling intra-mosquito dynamics of Zika virus and its dose-dependence confirms the low epidemic potential of Aedes albopictus. PLoS Pathog 2020; 16:e1009068. [PMID: 33382858 PMCID: PMC7774846 DOI: 10.1371/journal.ppat.1009068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/14/2020] [Indexed: 01/01/2023] Open
Abstract
Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered until the end of 2019, when several autochthonous transmissions of the virus vectored by Ae. albopictus occurred in France. Aside from these few locally acquired ZIKV infections, most territories colonized by Ae. albopictus have been spared so far. The risk level of ZIKV emergence in these areas remains however an open question. To assess Ae. albopictus' vector potential for ZIKV and identify key virus outbreak predictors, we built a complete framework using the complementary combination of (i) dose-dependent experimental Ae. albopictus exposure to ZIKV followed by time-dependent assessment of infection and systemic infection rates, (ii) modeling of intra-human ZIKV viremia dynamics, and (iii) in silico epidemiological simulations using an Agent-Based Model. The highest risk of transmission occurred during the pre-symptomatic stage of the disease, at the peak of viremia. At this dose, mosquito infection probability was estimated to be 20%, and 21 days were required to reach the median systemic infection rates. Mosquito population origin, either temperate or tropical, had no impact on infection rates or intra-host virus dynamic. Despite these unfavorable characteristics for transmission, Ae. albopictus was still able to trigger and yield large outbreaks in a simulated environment in the presence of sufficiently high mosquito biting rates. Our results reveal a low but existing epidemic potential of Ae. albopictus for ZIKV, that might explain the absence of large scale ZIKV epidemics so far in territories occupied only by Ae. albopictus. They nevertheless support active surveillance and eradication programs in these territories to maintain the risk of emergence to a low level.
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Affiliation(s)
- Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Jean-Sébastien Dehecq
- French Ministry of Health, Agence Régionale de Santé de La Réunion, Vector control Unit, La Reunion Island, Saint-Denis, France
| | - Séverine Matheus
- Laboratory of Virology, National Reference Center for Arboviruses, Institut Pasteur, Guyane Française, Cayenne, France
- Environment and infections risks unit, Institut Pasteur, Paris, France
| | - Franck de Laval
- SSA, Service de Santé des Armées, CESPA, Centre d’épidémiologie et de santé publique des armées, Marseille, France
- Aix Marseille Univ, INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l’Information Médicale, Marseille, France
| | - Lionel Almeras
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sébastien Briolant
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Albin Fontaine
- Unité Parasitologie et Entomologie, Département Microbiologie et maladies infectieuses, Institut de Recherche Biomédicale des Armées (IRBA), Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, UMR Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
- IHU Méditerranée Infection, Marseille, France
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