Models of Viral Population Dynamics

2015 ◽  
pp. 277-302 ◽  
Author(s):  
Pranesh Padmanabhan ◽  
Narendra M. Dixit
Keyword(s):  
Population Dynamics ◽  
Viral Population

scholarly journals Introduction, Evolution, and Dissemination of Influenza A Viruses in Exhibition Swine in the United States during 2009 to 2013

2016 ◽  
Vol 90 (23) ◽  
pp. 10963-10971 ◽  
Author(s):  
Martha I. Nelson ◽  
Karla M. Stucker ◽  
Seth A. Schobel ◽  
Nídia S. Trovão ◽  
Suman R. Das ◽  
...  
Keyword(s):  
United States ◽  
Population Dynamics ◽  
Influenza A Virus ◽  
Influenza A ◽  
The United States ◽  
Viral Population ◽  
Influenza A Viruses ◽  
Swine Industry ◽  
Virus Diversity ◽  
Agricultural Fairs

ABSTRACT The swine-human interface created at agricultural fairs, along with the generation of and maintenance of influenza A virus diversity in exhibition swine, presents an ongoing threat to public health. Nucleotide sequences of influenza A virus isolates collected from exhibition swine in Ohio ( n = 262) and Indiana ( n = 103) during 2009 to 2013 were used to investigate viral evolution and movement within this niche sector of the swine industry. Phylogenetic and Bayesian analyses were employed to identify introductions of influenza A virus to exhibition swine and study viral population dynamics. In 2013 alone, we identified 10 independent introductions of influenza A virus into Ohio and/or Indiana exhibition swine. Frequently, viruses from the same introduction were identified at multiple fairs within the region, providing evidence of rapid and widespread viral movement within the exhibition swine populations of the two states. While pigs moving from fair to fair to fair is possible in some locations, the concurrent detection of nearly identical strains at several fairs indicates that a common viral source was more likely. Importantly, we detected an association between the high number of human variant H3N2 (H3N2v) virus infections in 2012 and the widespread circulation of influenza A viruses of the same genotype in exhibition swine in Ohio fairs sampled that year. The extent of viral diversity observed in exhibition swine and the rapidity with which it disseminated across long distances indicate that novel strains of influenza A virus will continue to emerge and spread within exhibition swine populations, presenting an ongoing threat to humans. IMPORTANCE Understanding the underlying population dynamics of influenza A viruses in commercial and exhibition swine is central to assessing the risk for human infections with variant viruses, including H3N2v. We used viral genomic sequences from isolates collected from exhibition swine during 2009 to 2013 to understand how the peak of H3N2v cases in 2012 relates to long-term trends in the population dynamics of pandemic viruses recently introduced into commercial and exhibition swine in the United States. The results of our spatial analysis underscore the key role of rapid viral dispersal in spreading multiple genetic lineages throughout a multistate network of agricultural fairs, providing opportunities for divergent lineages to coinfect, reassort, and generate new viral genotypes. The higher genetic diversity of genotypes cocirculating in exhibition swine since 2013 could facilitate the evolution of new reassortants, potentially with even greater ability to cause severe infections in humans or cause human-to-human transmission, highlighting the need for continued vigilance.

scholarly journals Molecular Evolution of Human Norovirus GII.2 Clusters

2021 ◽  
Vol 12 ◽  
Author(s):  
Xingguang Li ◽  
Haizhou Liu ◽  
Brittany Rife Magalis ◽  
Sergei L. Kosakovsky Pond ◽  
Erik M. Volz
Keyword(s):  
Population Dynamics ◽  
Selection Pressure ◽  
Evolutionary Rate ◽  
Winter Season ◽  
Viral Population ◽  
Evolutionary Adaptation ◽  
Effective Population ◽  
Human Norovirus ◽  
The Past ◽  
Norovirus Gii

BackgroundThe human norovirus GII.2 outbreak during the 2016–2017 winter season was of unprecedented scale and geographic distribution.MethodsWe analyzed 519 complete VP1 gene sequences of the human norovirus GII.2 genotype sampled during the 2016–2017 winter season, as well as prior (dating back to 1976) from 7 countries. Phylodynamic analyses of these sequences were performed using maximum likelihood and Bayesian statistical frameworks in order to estimate viral evolutionary and population dynamics associated with the outbreak.ResultsOur results revealed an increase in the genetic diversity of human norovirus GII.2 during the recent Asian outbreak and diversification was characterized by at least eight distinct clusters. Bayesian estimation of viral population dynamics revealed a highly fluctuating effective population size, increasing in frequency during the past 15 years.ConclusionDespite an increasing viral diversity, we found no evidence of an elevated evolutionary rate or significant selection pressure in human norovirus GII.2, indicating viral evolutionary adaptation was not responsible for the volatility of or spread of the virus during this time.

scholarly journals Viral population dynamics and virulence thresholds

2012 ◽  
Vol 15 (4) ◽  
pp. 525-530 ◽  
Author(s):  
Karen Z Lancaster ◽  
Julie K Pfeiffer
Keyword(s):  
Population Dynamics ◽  
Viral Population

scholarly journals Rapid dissemination and monopolization of viral populations in mice revealed using a panel of barcoded viruses

2019 ◽  
Author(s):  
Broc T. McCune ◽  
Matthew R. Lanahan ◽  
Benjamin R. tenOever ◽  
Julie K. Pfeiffer
Keyword(s):  
Population Dynamics ◽  
Gastrointestinal Tract ◽  
Enteric Virus ◽  
Population Diversity ◽  
Viral Population ◽  
Post Inoculation ◽  
Systemic Dissemination ◽  
Mouse Tissues ◽  
Oral Inoculation ◽  
Rapid Dissemination

AbstractThe gastrointestinal tract presents a formidable barrier for pathogens to initiate infection. Despite this barrier, enteroviruses, including coxsackievirus B3 (CVB3), successfully penetrate the intestine to initiate infection and spread systemically prior to shedding in stool. However, the effect of the gastrointestinal barrier on CVB3 population dynamics is relatively unexplored, nor are the selective pressures acting on CVB3 in the intestine well-characterized. To examine viral population dynamics in orally infected mice, we produced over one hundred CVB3 viruses harboring unique nine nucleotide “barcodes.” Using this collection of barcoded viruses, we found diverse viral populations throughout each mouse within the first day post-infection, but by 48 hours the viral populations were dominated by less than three barcoded viruses in intestinal and extra-intestinal tissues. Using light-sensitive viruses to track replication status, we found diverse viruses had replicated prior to loss of diversity. Sequencing whole viral genomes from samples later in infection did not reveal detectable viral adaptations. Surprisingly, orally inoculated CVB3 was detectable in pancreas and liver as soon as 20 minutes post inoculation, indicating rapid systemic dissemination. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues. These results underscore a complex dynamic between dissemination and clearance for an enteric virus.ImportanceEnteric viruses initiate infection in the gastrointestinal tract but can disseminate to systemic sites. However, the dynamics of viral dissemination are unclear. In this study, we created a library of 135 barcoded coxsackieviruses to examine viral population diversity across time and space following oral inoculation of mice. Overall, we found that the broad population of viruses disseminates early, followed by monopolization of mouse tissues with three or fewer pool members at later time points. Interestingly, we detected virus in systemic tissues such as pancreas and liver just 20 minutes post-oral inoculation. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues.

scholarly journals Encapsidation of Staufen-2 Enhances Infectivity of HIV-1

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2459
Author(s):  
Kannan Balakrishnan ◽  
Ananda Jaguva Vasudevan ◽  
Krishnaveni Mohareer ◽  
Tom Luedde ◽  
Carsten Münk ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Host Factors ◽  
Viral Population ◽  
Antiviral Protein ◽  
Viral Propagation ◽  
Human Immuno Deficiency Virus ◽  
Nucleocytoplasmic Export ◽  
Hiv 1

Staufen, the RNA-binding family of proteins, affects various steps in the Human Immuno-Deficiency Virus (HIV-1) replication cycle. While our previous study established Staufen-2–HIV-1 Rev interaction and its role in augmenting nucleocytoplasmic export of RRE-containing viral RNA, viral incorporation of Staufen-2 and its effect on viral propagation were unknown. Here, we report that Staufen-2 interacts with HIV-1 Gag and is incorporated into virions and that encapsidated Staufen-2 boosted viral infectivity. Further, Staufen-2 gets co-packaged into virions, possibly by interacting with host factors Staufen-1 or antiviral protein APOBEC3G, which resulted in different outcomes on the infectivity of Staufen-2-encapsidated virions. These observations suggest that encapsidated host factors influence viral population dynamics and infectivity. With the explicit identification of the incorporation of Staufen proteins into HIV-1 and other retroviruses, such as Simian Immunodeficiency Virus (SIV), we propose that packaging of RNA binding proteins, such as Staufen, in budding virions of retroviruses is probably a general phenomenon that can drive or impact the viral population dynamics, infectivity, and evolution.

scholarly journals A multiple-site-specific heteroduplex tracking assay as a tool for the study of viral population dynamics

2001 ◽  
Vol 98 (1) ◽  
pp. 176-181 ◽  
Author(s):  
W. Resch ◽  
N. Parkin ◽  
E. L. Stuelke ◽  
T. Watkins ◽  
R. Swanstrom
Keyword(s):  
Population Dynamics ◽  
Viral Population ◽  
Multiple Site ◽  
Site Specific

scholarly journals Rapid Dissemination and Monopolization of Viral Populations in Mice Revealed Using a Panel of Barcoded Viruses

2019 ◽  
Vol 94 (2) ◽  
Author(s):  
Broc T. McCune ◽  
Matthew R. Lanahan ◽  
Benjamin R. tenOever ◽  
Julie K. Pfeiffer
Keyword(s):  
Population Dynamics ◽  
Gastrointestinal Tract ◽  
Enteric Virus ◽  
Population Diversity ◽  
Viral Population ◽  
Viral Genomes ◽  
Systemic Dissemination ◽  
Mouse Tissues ◽  
Oral Inoculation ◽  
Rapid Dissemination

ABSTRACT The gastrointestinal tract presents a formidable barrier for pathogens to initiate infection. Despite this barrier, enteroviruses, including coxsackievirus B3 (CVB3), successfully penetrate the intestine to initiate infection and spread systemically prior to shedding in stool. However, the effect of the gastrointestinal barrier on CVB3 population dynamics is relatively unexplored, and the selective pressures acting on CVB3 in the intestine are not well characterized. To examine viral population dynamics in orally infected mice, we produced over 100 CVB3 clones harboring nine unique nucleotide “barcodes.” Using this collection of barcoded viruses, we found diverse viral populations throughout each mouse within the first day postinfection, but by 48 h the viral populations were dominated by fewer than three barcoded viruses in intestinal and extraintestinal tissues. Using light-sensitive viruses to track replication status, we found that diverse viruses had replicated prior to loss of diversity. Sequencing whole viral genomes from samples later in infection did not reveal detectable viral adaptations. Surprisingly, orally inoculated CVB3 was detectable in pancreas and liver as soon as 20 min postinoculation, indicating rapid systemic dissemination. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues. These results underscore a complex dynamic between dissemination and clearance for an enteric virus. IMPORTANCE Enteric viruses initiate infection in the gastrointestinal tract but can disseminate to systemic sites. However, the dynamics of viral dissemination are unclear. In this study, we created a library of 135 barcoded coxsackieviruses to examine viral population diversity across time and space following oral inoculation of mice. Overall, we found that the broad population of viruses disseminates early, followed by monopolization of mouse tissues with three or fewer pool members at later time points. Interestingly, we detected virus in systemic tissues such as pancreas and liver just 20 min after oral inoculation. These results suggest rapid dissemination of diverse viral populations, followed by a major restriction in population diversity and monopolization in all examined tissues.

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