Filters








3,771 Hits in 6.9 sec

Allele dynamics plots for the study of evolutionary dynamics in viral populations

Lars Steinbrück, Alice Carolyn McHardy
2010 Nucleic Acids Research  
We introduce 'allele dynamics plots' (AD plots) as a method for visualizing the evolutionary dynamics of a gene in a population.  ...  We analyze the method's merits with a detailed study of the evolutionary dynamics of seasonal influenza A viruses.  ...  Allele dynamics plots We describe AD plots for visualizing the evolutionary dynamics of a gene in a population and for identifying the alleles that are potentially under directional selection.  ... 
doi:10.1093/nar/gkq909 pmid:20959296 pmcid:PMC3017622 fatcat:xinsnynsmfgnhol3urtc2ajy5u

Fitness estimation for viral variants in the context of cellular coinfection [article]

Huisheng Zhu, Brent E Allman, Katia Koelle
2021 bioRxiv   pre-print
These findings underscore the importance of considering the process of cellular coinfection when studying within-host viral evolutionary dynamics.  ...  While methods have been developed to quantify the fitness effects of mutations using observed changes in allele frequencies over the course of a host's infection, none of the existing methods account for  ...  The effective viral population size N e for seasonal influenza A viruses has recently been version of the within-host evolutionary model presented in the previous section.  ... 
doi:10.1101/2021.04.26.441479 fatcat:von36z4w6ja2bg7hena7c6rtqq

Fitness Estimation for Viral Variants in the Context of Cellular Coinfection

Huisheng Zhu, Brent Allman, Katia Koelle
2021 Viruses  
These findings underscore the importance of considering the process of cellular coinfection when studying within-host viral evolutionary dynamics.  ...  While methods have been developed to quantify the fitness effects of mutations using observed changes in allele frequencies over the course of a host's infection, none of the existing methods account for  ...  Acknowledgments: We thank Thomas Friedrich and Katarina Braun at the University of Wisconsin for providing us with the measured allele frequencies of G778A that are plotted in Figure 2b of Wilker et  ... 
doi:10.3390/v13071216 pmid:34201862 pmcid:PMC8310006 fatcat:ipl2hz2qajgvbk7rjri2tqk5ei

Principles of dengue virus evolvability derived from genotype-fitness maps in human and mosquito cells [article]

Patrick T Dolan, Shuhei Taguwa, Mauricio Aguilar Rangel, Ashley Acevedo, Raul Andino, Judith Frydman
2020 bioRxiv   pre-print
We find DENV phenotypic adaptation is best described by the collective fitness contributions of all the alleles present in the population.  ...  of beneficial and deleterious mutations in shaping the fitness landscape driving host-specific paths of viral adaptation.  ...  ACKNOWLEDGEMENTS Research reported in this publication was supported by National Institutes of Health grants The copyright holder for this preprint (which was not peer-reviewed) is the .  ... 
doi:10.1101/2020.02.05.936195 fatcat:6dshyxwqhbagzaxs23cfuqy7fq

Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients

Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao, Mian Gan, Fang Li (+22 others)
2021 Genome Medicine  
We also compared the evolutionary dynamics of SARS-CoV-2 population in the respiratory tract (RT) and gastrointestinal tract (GIT).  ...  Our findings here illustrate the intra-host bottlenecks and evolutionary dynamics of SARS-CoV-2 in different anatomic sites and may provide new insights to understand the virus-host interactions of coronaviruses  ...  We thank the Guangdong Provincial Key Laboratory of Genome Read and Write and China National GeneBank at Shenzhen for providing sequencing service. We thank the patients who took part in this study.  ... 
doi:10.1186/s13073-021-00847-5 pmid:33618765 fatcat:xjimewicizhvxhs3payv6lju5e

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients [article]

Yanqun Wang, Daxi Wang, Lu Zhang, Wanying Sun, Zhaoyong Zhang, Weijun Chen, Airu Zhu, Yongbo Huang, Fei Xiao, Jinxiu Yao, Mian Gan, Fang Li (+24 others)
2020 bioRxiv   pre-print
However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown.  ...  Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events  ...  In contrast, viral populations in GIT showed a higher 202 9genetic diversity than those in RT, reflecting a larger effective viral population size in the GIT. .  ... 
doi:10.1101/2020.05.20.103549 fatcat:jztojjwmjfhlfn4mopnz5r2uqm

Predator-Prey Dynamics of Intra-Host Simian Immunodeficiency Virus Evolution Within the Untreated Host

Brittany Rife Magalis, Patrick Autissier, Kenneth C. Williams, Xinguang Chen, Cameron Browne, Marco Salemi
2021 Frontiers in Immunology  
The dynamic nature of the SIV population during disease progression in the SIV/macaque model of AIDS and the factors responsible for its behavior have not been documented, largely owing to the lack of  ...  In this study, we detail Bayesian coalescent inference of the changing collective intra-host viral effective population size (Ne) from various tissues over the course of infection and its relationship  ...  ACKNOWLEDGMENTS The authors acknowledge University of Florida Research Computing for providing computational resources and support that have contributed to the research results reported in this publication  ... 
doi:10.3389/fimmu.2021.709962 pmid:34691023 pmcid:PMC8527182 fatcat:qgpheu6ajrdqfaj7ztog6qvbhy

Mapping the Evolutionary Potential of RNA Viruses

Patrick T. Dolan, Zachary J. Whitfield, Raul Andino
2018 Cell Host and Microbe  
We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.  ...  New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution.  ...  Acknowledgments The authors thank Dr. Edward Holmes and Dr. Jesse Bloom for helpful comments on this manuscript. This work is in part supported by NIH (R01 AI36178 and P01  ... 
doi:10.1016/j.chom.2018.03.012 pmid:29649440 pmcid:PMC5908228 fatcat:ehu7hkibfrhk7iniselppnb3ea

The feedback between selection and demography shapes genomic diversity during coevolution

Cas Retel, Vienna Kowallik, Weini Huang, Benjamin Werner, Sven Künzel, Lutz Becks, Philine G. D. Feulner
2019 Science Advances  
In the host, population expansion enabled rapid generation of genetic diversity in accordance with neutral processes.  ...  This study demonstrates that molecular evolution during species interactions is shaped by both eco-evolutionary feedback dynamics and interspecific differences in how genetic diversity is generated and  ...  Acknowledgments: We are grateful to the sequencing team at the MPI in Plön for assistance and to G. Bartolomucci for help with the collection of the phenotypic data.  ... 
doi:10.1126/sciadv.aax0530 pmid:31616788 pmcid:PMC6774728 fatcat:ebtrtt5epreinfkwmsfjnywmwm

On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

Nicholas Renzette, Susanne P. Pfeifer, Sebastian Matuszewski, Timothy F. Kowalik, Jeffrey D. Jensen, Jae U. Jung
2016 Journal of Virology  
These results thus represent a major shift in the current view of observed viral variation.  ...  For example, in human cytomegalovirus, the nucleotide diversity estimates are 10-fold higher for interhost data, while the number of segregating (i.e., polymorphic) sites is 6-fold lower.  ...  ACKNOWLEDGMENTS We thank Kristen Irwin for careful readings of the manuscript.  ... 
doi:10.1128/jvi.01976-16 pmid:27974561 pmcid:PMC5309957 fatcat:z2bflamky5cwxbgfkrublldqo4

Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses [article]

Thorsten Ralf Klingen, Susanne Reimering, Jens Loers, Kyra Mooren, Frank Klawonn, Thomas Krey, Guelsah Gabriel, Alice McHardy
2017 bioRxiv   pre-print
Using SD plots, we studied the past genome-wide adaptation of the 2009 pandemic H1N1 influenza A (pH1N1) and seasonal H3N2 influenza A (sH3N2) viruses.  ...  Here we describe a computational method named Sweep Dynamics (SD) plots.  ...  SD plots analyze the evolutionary dynamics of alleles, representing individual amino acid changes within the viral population.  ... 
doi:10.1101/110528 fatcat:smy6suo3pvg4nfojh2etgowese

Invited Commentary: Evaluating Vaccination Programs Using Genetic Sequence Data

M. E. Halloran, E. C. Holmes
2009 American Journal of Epidemiology  
Because of the potential use of these methods in future vaccination studies, the authors discuss the utility of these methods and the data requirements needed for them to be convincing.  ...  are to be commended for attempting to use the coalescent analysis of viral sequence data to evaluate a hepatitis B vaccination program.  ...  ACKNOWLEDGMENTS Conflict of interest: none declared.  ... 
doi:10.1093/aje/kwp366 pmid:19910381 pmcid:PMC2800275 fatcat:ajclubx4mzcnpcez3k6p5qoo3m

Single-Virion Sequencing Of Lamivudine Treated HBV Populations Reveal Population Evolution Dynamics And Demographic History [article]

Yuan O Zhu, Pauline PK Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F Burkholder (+1 others)
2017 bioRxiv   pre-print
Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies.  ...  To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key.  ...  Acknowledgements We thank Wendy Soon, Gary Chen and the entire Next Generation Sequencing Platform team at the Genome Institute of Singapore for their support and expertise.  ... 
doi:10.1101/129023 fatcat:i2kxc2biujd45b2aoorkpdlw24

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history

Yuan O. Zhu, Pauline P. K. Aw, Paola Florez de Sessions, Shuzhen Hong, Lee Xian See, Lewis Z. Hong, Andreas Wilm, Chen Hao Li, Stephane Hue, Seng Gee Lim, Niranjan Nagarajan, William F. Burkholder (+1 others)
2017 BMC Genomics  
Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies.  ...  To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key.  ...  Acknowledgements We thank Wendy Soon, Gary Chen and the entire Next Generation Sequencing Platform team at the Genome Institute of Singapore for their support and expertise.  ... 
doi:10.1186/s12864-017-4217-1 pmid:29078745 pmcid:PMC5660452 fatcat:hnrealfxcff6bo7ttlnrsiu264

Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses

Thorsten R. Klingen, Susanne Reimering, Jens Loers, Kyra Mooren, Frank Klawonn, Thomas Krey, Gülsah Gabriel, Alice C. McHardy
2018 Scientific Reports  
The negative-sense RNA genome consists of eight segments that encode for 14 viral proteins 4 .  ...  Currently, the viral subtypes sH3N2 and pH1N1 are circulating in the human population. The H3N2 virus was introduced into the human population in 1968 and is endemic ever since.  ...  The Heinrich Pette Institute, Leibniz Institute for Experimental Virology, is supported by the Free and Hanseatic City of Hamburg and the Federal Ministry of Health.  ... 
doi:10.1038/s41598-017-18791-z pmid:29321538 pmcid:PMC5762865 fatcat:zi63v2xqcng4jjpeprgvjpjz6y
« Previous Showing results 1 — 15 out of 3,771 results