scholarly journals Evolutionary Dynamics and Global Diversity of Influenza A Virus

2015 ◽  
Vol 89 (21) ◽  
pp. 10993-11001 ◽  
Author(s):  
Daniel Rejmanek ◽  
Parviez R. Hosseini ◽  
Jonna A. K. Mazet ◽  
Peter Daszak ◽  
Tracey Goldstein
Keyword(s):  
East Asia ◽  
Influenza A Virus ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitution ◽  
Health Care Spending ◽  
Asian Countries ◽  
Substitution Rates ◽  
Country Level ◽  
Nucleotide Substitution Rates

ABSTRACTThe increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin (e.g., H5N1 and H7N9) in recent years underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 to 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socioeconomic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly in East Asia, than in Canada and the United States. Similarly, at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America. In contrast, the selection pressures (measured as ratios of nonsynonymous to synonymous evolutionary changes [dN/dSratios]) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort (i.e., total number of strains reported) and health care spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including a lack of sequences submitted from large portions of Africa and South America and a lack of geolocation information) and in broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world.IMPORTANCEIn recent years, an increasing number of influenza A virus (IAV) subtypes, including H5N1, H7N9, and H10N8, have been detected in humans. High fatality rates have led to an increased urgency to better understand where and how novel pathogenic influenza virus strains emerge. Our findings showed that mutational rates of 11 commonly encountered subtypes were higher in East Asian countries than in North America, suggesting that there may be a greater risk for the emergence of novel pathogenic strains in East Asia. In assessing the potential drivers of IAV subtype diversity, our analyses confirmed that reporting effort and health care spending were the best predictors of the observed subtype diversity at the country level. These findings underscore the need to increase sampling and reporting efforts for all subtypes in many undersampled countries throughout the world.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

Institutional Environment, Ownership, and Disclosure of Intangibles: Evidence from East Asia

2013 ◽  
Vol 13 (1) ◽  
pp. 33-59 ◽  
Author(s):  
Akmalia M. Ariff ◽  
Steven F. Cahan ◽  
David M. Emanuel
Keyword(s):  
East Asia ◽  
Institutional Environment ◽  
Value Relevance ◽  
East Asian ◽  
Balance Sheet ◽  
Asian Countries ◽  
Voluntary Disclosures ◽  
Country Level ◽  
Income Statement ◽  
Director Ownership

ABSTRACT This paper examines the value relevance of voluntary disclosures about intangibles in eight East Asian countries, and the effect of variation in company-level and country-level governance on the valuation of these disclosures. Using Easton and Sommers' (2003) deflated valuation approach in analyses involving 459 companies, we find that the voluntary disclosures are value relevant, over and above the numbers in the balance sheet and income statement. We also find that the value relevance of these disclosures is conditional on the level of director ownership and the strength of the institutional features of a country.

Plastome-Wide Nucleotide Substitution Rates Reveal Accelerated Rates in Papilionoideae and Correlations with Genome Features Across Legume Subfamilies

2017 ◽  
Vol 84 (4) ◽  
pp. 187-203 ◽  
Author(s):  
Erika N. Schwarz ◽  
Tracey A. Ruhlman ◽  
Mao-Lun Weng ◽  
Mohammad A. Khiyami ◽  
Jamal S. M. Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Substitution Rates ◽  
Genome Features ◽  
Nucleotide Substitution Rates

scholarly journals Influenza B viruses exhibit lower within-host diversity than influenza A viruses in human hosts

2019 ◽  
Author(s):  
Andrew L. Valesano ◽  
William J. Fitzsimmons ◽  
John T. McCrone ◽  
Joshua G. Petrie ◽  
Arnold S. Monto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Influenza A Virus ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Influenza Viruses ◽  
Influenza B Virus ◽  
Influenza B ◽  
Influenza A Viruses ◽  
Community Based ◽  
B Virus

AbstractInfluenza B virus undergoes seasonal antigenic drift more slowly than influenza A, but the reasons for this difference are unclear. While the evolutionary dynamics of influenza viruses play out globally, they are fundamentally driven by mutation, reassortment, drift, and selection within individual hosts. These processes have recently been described for influenza A virus, but little is known about the evolutionary dynamics of influenza B virus (IBV) at the level of individual infections and transmission events. Here we define the within-host evolutionary dynamics of influenza B virus by sequencing virus populations from naturally-infected individuals enrolled in a prospective, community-based cohort over 8176 person-seasons of observation. Through analysis of high depth-of-coverage sequencing data from samples from 91 individuals with influenza B, we find that influenza B virus accumulates lower genetic diversity than previously observed for influenza A virus during acute infections. Consistent with studies of influenza A viruses, the within-host evolution of influenza B viruses is characterized by purifying selection and the general absence of widespread positive selection of within-host variants. Analysis of shared genetic diversity across 15 sequence-validated transmission pairs suggests that IBV experiences a tight transmission bottleneck similar to that of influenza A virus. These patterns of local-scale evolution are consistent with influenza B virus’ slower global evolutionary rate.ImportanceThe evolution of influenza virus is a significant public health problem and necessitates the annual evaluation of influenza vaccine formulation to keep pace with viral escape from herd immunity. Influenza B virus is a serious health concern for children, in particular, yet remains understudied compared to influenza A virus. Influenza B virus evolves more slowly than influenza A, but the factors underlying this are not completely understood. We studied how the within-host diversity of influenza B virus relates to its global evolution by sequencing viruses from a community-based cohort. We found that influenza B virus populations have lower within-host genetic diversity than influenza A virus and experience a tight genetic bottleneck during transmission. Our work provides insights into the varying dynamics of influenza viruses in human infection.

scholarly journals Nucleotide substitution rates of diatom plastid encoded protein genes are correlated with genome architecture

2019 ◽  
Author(s):  
Mengjie Yu ◽  
Tracey A Ruhlman ◽  
Nahid H Hajrah ◽  
Mohammad A Khiyami ◽  
Mumdooh J Sabir ◽  
...  
Keyword(s):  
Nucleotide Substitution ◽  
Terrestrial Ecosystems ◽  
Rate Heterogeneity ◽  
Substitution Rates ◽  
Protein Coding ◽  
Plastid Genomes ◽  
Rate Acceleration ◽  
Functional Classes ◽  
Nucleotide Substitution Rates ◽  
Positive Correlations

Diatoms are the largest group of heterokont algae with more than 100,000 species. They are photosynthetic, unicellular eukaryotes that contribute ~ 45% of global primary production and inhabit marine, aquatic and terrestrial ecosystems. Despite their ubiquity and environmental significance very few diatom plastid genomes (plastomes) have been sequenced and studied. This study explored the pattern of diatom plastid nucleotide substitution rates across the entire suite of plastome protein-coding genes for 40 taxa representing the major clades. Substitution rate acceleration was lineage specific with the highest rates in the araphid 2 taxon Astrosyne radiata and radial 2 taxon Proboscia sp. Rate heterogeneity was also evident in different functional classes of genes. Similar to land plants, proteins genes involved in photosynthetic metabolism have substantially lower rates than those involved in transcription and translation. Significant positive correlations were identified between rates and measures of genomic rearrangement, but not plastome size. This work advances the current understanding of diatom plastomes and provides a foundation for future studies of their evolution.

scholarly journals Dinucleotide evolutionary dynamics in influenza A virus

2019 ◽  
Vol 5 (2) ◽  
Author(s):  
Haogao Gu ◽  
Rebecca L Y Fan ◽  
Di Wang ◽  
Leo L M Poon
Keyword(s):  
Influenza Virus ◽  
Codon Usage ◽  
Influenza A Virus ◽  
Codon Usage Bias ◽  
Influenza A ◽  
Evolutionary Dynamics ◽  
Synonymous Codon ◽  
Amino Acid Sequences ◽  
In Vivo Models

Abstract Significant biases of dinucleotide composition in many RNA viruses including influenza A virus have been reported in recent years. Previous studies have showed that a codon-usage-altered influenza mutant with elevated CpG usage is attenuated in mammalian in vitro and in vivo models. However, the relationship between dinucleotide preference and codon usage bias is not entirely clear and changes in dinucleotide usage of influenza virus during evolution at segment level are yet to be investigated. In this study, a Monte Carlo type method was applied to identify under-represented or over-represented dinucleotide motifs, among different segments and different groups, in influenza viral sequences. After excluding the potential biases caused by codon usage and amino acid sequences, CpG and UpA were found under-represented in all viral segments from all groups, whereas UpG and CpA were found over-represented. We further explored the temporal changes of usage of these dinucleotides. Our analyses revealed significant decrease of CpG frequency in Segments 1, 3, 4, and 5 in seasonal H1 virus after its re-emergence in humans in 1977. Such temporal variations were mainly contributed by the dinucleotide changes at the codon positions 3-1 and 2-3 where silent mutations played a major role. The depletions of CpG and UpA through silent mutations consequently led to over-representations of UpG and CpA. We also found that dinucleotide preference directly results in significant synonymous codon usage bias. Our study helps to provide details on understanding the evolutionary history of influenza virus and selection pressures that shape the virus genome.

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