Background:Phylodynamics,the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations,was originally defined in the context of rapidly evolving viruses and used...Background:Phylodynamics,the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations,was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics.The concept of phylodynamics has evolved since the early 21^(st)century,extending its reach to slower-evolving pathogens,including bacteria and fungi,and to the identification of influential factors in disease spread and pathogen population dynamics.Results:The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework.These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins,evolutionary history,and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus(HIV),Zika,and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus.Conclusions:Capitalizing on an extensive review of the literature,we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments,highlighting the advancements in phylodynamics,as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.展开更多
Background: Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS)have been documented worldwide and more than a third of those cases have died. While the greatest number ofc...Background: Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS)have been documented worldwide and more than a third of those cases have died. While the greatest number ofcases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republic of Korea showedthat a pandemic is a possibility that cannot be ignored. Due to the deficit of knowledge in transmissionmethodology, targeted treatment and possible vaccines, understanding this virus should be a priority. Our aim wasto combine epidemiological data from literature with genetic information from viruses sequenced around theworld to present a phylodynamic picture of MERS spread molecular level to global scale.Methods: We performed a qualitative meta-analysis of all laboratory confirmed cases worldwide to date based onliterature, with emphasis on international transmission and healthcare associated infections. In parallel, we usedpublicly available MERS-CoV genomes from GenBank to create a phylogeographic tree, detailing geospatial timelineof viral evolution.Results: Several healthcare associated outbreaks starting with the retrospectively identified hospital outbreak inJordan to the most recent outbreak in Riyadh, Saudi Arabia have occurred. MERS has also crossed many oceans,entering multiple nations in eight waves between 2012 and 2015. In this paper, the spatiotemporal history of MERScases, as documented epidemiologically, was examined by Bayesian phylogenetic analysis. Distribution ofsequences into geographic clusters and interleaving of MERS-CoV sequences from camels among those isolatedfrom humans indicated that multiple zoonotic introductions occurred in endemic nations. We also report asummary of basic reproduction numbers for MERS-CoV in humans and camels.Conclusion: Together, these analyses can help us identify factors associated with viral evolution and spread as wellas establish efficacy of infection control measures. The results are especially pertinent to countries without currentMERS-CoV endemic, since their unfamiliarity makes them particularly susceptible to uncontrollable spread of a virusthat may be imported by travelers.展开更多
文摘Background:Phylodynamics,the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations,was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics.The concept of phylodynamics has evolved since the early 21^(st)century,extending its reach to slower-evolving pathogens,including bacteria and fungi,and to the identification of influential factors in disease spread and pathogen population dynamics.Results:The phylodynamic approach has now become a fundamental building block for the development of comparative phylogenetic tools capable of incorporating epidemiological surveillance data with molecular sequences into a single statistical framework.These innovative tools have greatly enhanced scientific investigations of the temporal and geographical origins,evolutionary history,and ecological risk factors associated with the growth and spread of viruses such as human immunodeficiency virus(HIV),Zika,and dengue and bacteria such as Methicillin-resistant Staphylococcus aureus.Conclusions:Capitalizing on an extensive review of the literature,we discuss the evolution of the field of infectious disease epidemiology and recent accomplishments,highlighting the advancements in phylodynamics,as well as the challenges and limitations currently facing researchers studying emerging pathogen epidemics across the globe.
基金supported by the Virogenesis projectfunding from the European Union’s Horizon 2020 research and innovation program under grant agreement No.634650.
文摘Background: Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS)have been documented worldwide and more than a third of those cases have died. While the greatest number ofcases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republic of Korea showedthat a pandemic is a possibility that cannot be ignored. Due to the deficit of knowledge in transmissionmethodology, targeted treatment and possible vaccines, understanding this virus should be a priority. Our aim wasto combine epidemiological data from literature with genetic information from viruses sequenced around theworld to present a phylodynamic picture of MERS spread molecular level to global scale.Methods: We performed a qualitative meta-analysis of all laboratory confirmed cases worldwide to date based onliterature, with emphasis on international transmission and healthcare associated infections. In parallel, we usedpublicly available MERS-CoV genomes from GenBank to create a phylogeographic tree, detailing geospatial timelineof viral evolution.Results: Several healthcare associated outbreaks starting with the retrospectively identified hospital outbreak inJordan to the most recent outbreak in Riyadh, Saudi Arabia have occurred. MERS has also crossed many oceans,entering multiple nations in eight waves between 2012 and 2015. In this paper, the spatiotemporal history of MERScases, as documented epidemiologically, was examined by Bayesian phylogenetic analysis. Distribution ofsequences into geographic clusters and interleaving of MERS-CoV sequences from camels among those isolatedfrom humans indicated that multiple zoonotic introductions occurred in endemic nations. We also report asummary of basic reproduction numbers for MERS-CoV in humans and camels.Conclusion: Together, these analyses can help us identify factors associated with viral evolution and spread as wellas establish efficacy of infection control measures. The results are especially pertinent to countries without currentMERS-CoV endemic, since their unfamiliarity makes them particularly susceptible to uncontrollable spread of a virusthat may be imported by travelers.
