EVOLUTION OF INFLUENZA A NUCLEOTIDE SEGMENTS THROUGH THE LENS OF DIFFERENT COMPLEXITY MEASURES

Evolution of influenza viruses is a highly complex process that is still poorly understood. Multiyear persistence of similar variants and accumulating evidences of existence of multigenic traits indicates that influenza viruses operate as integrated units and not only as sets of distinct genes. However, there is still no consensus on whether it is the case, and to what extent. One of the main problems is the lack of framework for analyzing and interpreting large body of available high dimensional genomic, clinical and epidemiological data. By reducing dimensionality of data we intend to show whether in addition to gene-centric selective pressure, the evolution of influenza RNA segments is also shaped by their mutual interactions. Therefore, we will analyze how different complexity/entropy measures (Shannon entropy, topological entropy and Lempel–Ziv complexity) can be used to study evolution of nucleotide segments of different influenza subtypes, while reducing data dimensionality. We show that, at the nucleotide level, multiyear clusters of genome-wide entropy/complexity correlations emerged during the H1N1 pandemic in 2009. Our data are the first empirical results that indirectly support the suggestion that a component of influenza evolutionary dynamics involves correlation between RNA segments. Of all used complexity/entropy measures, Shannon entropy shows the best correlation with epidemiological data.

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Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2012.0199 ◽

2013 ◽

Vol 368 (1614) ◽

pp. 20120199 ◽

Cited By ~ 30

Author(s):

Cécile Viboud ◽

Martha I. Nelson ◽

Yi Tan ◽

Edward C. Holmes

Keyword(s):

Influenza Virus ◽

Influenza A ◽

Large Scale ◽

Evolutionary Dynamics ◽

Spatial Scales ◽

Epidemiological Data ◽

Influenza Viruses ◽

Future Research ◽

Influenza A Viruses ◽

Molecular Studies

In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.

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Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution

10.1101/166082 ◽

2017 ◽

Author(s):

Jayna Raghwani ◽

Robin Thompson ◽

Katia Koelle

Keyword(s):

Adaptive Evolution ◽

Genetic Background ◽

Influenza A ◽

Seasonal Influenza ◽

Evolutionary Dynamics ◽

Gene Segment ◽

Influenza Viruses ◽

Neutral Evolution ◽

H3n2 Virus ◽

Genome Wide

ABSTRACTMost studies on seasonal influenza A/H3N2 virus adaptation have focused on the main antigenic gene, haemagglutinin. However, there is increasing evidence that the genome-wide genetic background of novel antigenic variants can influence these variants’ emergence probabilities and impact their patterns of dominance in the population. This suggests that non-antigenic genes may be important in shaping the viral evolutionary dynamics. To better understand the role of selection on non-antigenic genes in the adaptive evolution of seasonal influenza viruses, we here develop a simple population genetic model that considers a virus with one antigenic and one non-antigenic gene segment. By simulating this model under different regimes of selection and reassortment, we find that the empirical patterns of lineage turnover for the antigenic and non-antigenic gene segments are best captured when there is both limited viral coinfection and selection operating on both gene segments. In contrast, under a scenario of only neutral evolution in the non-antigenic gene segment, we see persistence of multiple lineages for long periods of time in that segment, which is not compatible with the observed molecular evolutionary patterns. Further, we find that reassortment, occurring in coinfected individuals, can increase the speed of viral adaptive evolution by primarily reducing selective interference and genetic linkage effects mediated by the non-antigenic gene segment. Together, these findings suggest that, for influenza, with 6 internal or non-antigenic gene segments, the evolutionary dynamics of novel antigenic variants are likely to be influenced by the genome-wide genetic background as a result of linked selection among both beneficial and deleterious mutations.

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The Dynamics of Influenza A H3N2 Defective Viral Genomes from a Human Challenge Study

10.1101/814673 ◽

2019 ◽

Cited By ~ 1

Author(s):

Michael A. Martin ◽

Drishti Kaul ◽

Gene S. Tan ◽

Christopher W. Woods ◽

Katia Koelle

Keyword(s):

Genetic Drift ◽

Influenza A ◽

Evolutionary Dynamics ◽

De Novo ◽

Gene Segment ◽

Influenza Viruses ◽

Genomic Variation ◽

Wild Type Virus ◽

Single Nucleotide Variants ◽

Viral Genomes

AbstractThe rapid evolution of influenza is an important contributing factor to its high worldwide incidence. The emergence and spread of genetic point mutations has been thoroughly studied both within populations and within individual hosts. In addition, influenza viruses are also known to generate genomic variation during their replication in the form of defective viral genomes (DVGs). These DVGs are formed by internal deletions in at least one gene segment that render them incapable of replication without the presence of wild-type virus. DVGs have previously been identified in natural human infections and may be associated with less severe clinical outcomes. These studies have not been able to address how DVG populations evolve in vivo in individual infections due to their cross-sectional design. Here we present an analysis of DVGs present in samples from two longitudinal influenza A H3N2 human challenge studies. We observe the generation of DVGs in almost all subjects. Although the genetic composition of DVG populations was highly variable, identical DVGs were observed both between multiple samples within single hosts as well as between hosts. Most likely due to stochastic effects, we did not observe clear instances of selection for specific DVGs or for shorter DVGs over the course of infection. Furthermore, DVG presence was not found to be associated with peak viral titer or peak symptom scores. Our analyses highlight the diversity of DVG populations within a host over the course of infection and the apparent role that genetic drift plays in their population dynamics.ImportanceThe evolution of influenza virus, in terms of single nucleotide variants and the reassortment of gene segments, has been studied in detail. However, influenza is known to generate defective viral genomes (DVGs) during replication, and little is known about how these genomes evolve both within hosts and at the population level. Studies in animal models have indicated that prophylactically or therapeutically administered DVGs can impact patterns of disease progression. However, the formation of naturally-occurring DVGs, their evolutionary dynamics, and their contribution to disease severity in human hosts is not well understood. Here, we identify the formation of de novo DVGs in samples from human challenge studies throughout the course of infection. We analyze their evolutionary trajectories, revealing the important role of genetic drift in shaping DVG populations during acute infections with well-adapted viral strains.

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Cathepsin W Is Required for Escape of Influenza A Virus from Late Endosomes

mBio ◽

10.1128/mbio.00297-15 ◽

2015 ◽

Vol 6 (3) ◽

Cited By ~ 13

Author(s):

Thomas O. Edinger ◽

Marie O. Pohl ◽

Emilio Yángüez ◽

Silke Stertz

Keyword(s):

Influenza Virus ◽

Rna Interference ◽

Influenza A Virus ◽

Proteolytic Activity ◽

Influenza A ◽

Antiviral Drugs ◽

Influenza Viruses ◽

Late Endosomes ◽

Genome Wide ◽

Cathepsin W

ABSTRACT Human cathepsin W (CtsW) is a cysteine protease, which was identified in a genome-wide RNA interference (RNAi) screen to be required for influenza A virus (IAV) replication. In this study, we show that reducing the levels of expression of CtsW reduces viral titers for different subtypes of IAV, and we map the target step of CtsW requirement to viral entry. Using a set of small interfering RNAs (siRNAs) targeting CtsW, we demonstrate that knockdown of CtsW results in a decrease of IAV nucleoprotein accumulation in the nuclei of infected cells at 3 h postinfection. Assays specific for the individual stages of IAV entry further show that attachment, internalization, and early endosomal trafficking are not affected by CtsW knockdown. However, we detected impaired escape of viral particles from late endosomes in CtsW knockdown cells. Moreover, fusion analysis with a dual-labeled influenza virus revealed a significant reduction in fusion events, with no detectable impact on endosomal pH, suggesting that CtsW is required at the stage of viral fusion. The defect in IAV entry upon CtsW knockdown could be rescued by ectopic expression of wild-type CtsW but not by the expression of a catalytically inactive mutant of CtsW, suggesting that the proteolytic activity of CtsW is required for successful entry of IAV. Our results establish CtsW as an important host factor for entry of IAV into target cells and suggest that CtsW could be a promising target for the development of future antiviral drugs. IMPORTANCE Increasing levels of resistance of influenza viruses to available antiviral drugs have been observed. Development of novel treatment options is therefore of high priority. In parallel to the classical approach of targeting viral enzymes, a novel strategy is pursued: cell-dependent factors of the virus are identified with the aim of developing small-molecule inhibitors against a cellular target that the virus relies on. For influenza A virus, several genome-wide RNA interference (RNAi) screens revealed hundreds of potential cellular targets. However, we have only limited knowledge on how these factors support virus replication, which would be required for drug development. We have characterized cathepsin W, one of the candidate factors, and found that cathepsin W is required for escape of influenza virus from the late endosome. Importantly, this required the proteolytic activity of cathepsin W. We therefore suggest that cathepsin W could be a target for future host cell-directed antiviral therapies.

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The evolutionary dynamics of influenza A virus adaptation to mammalian hosts

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2012.0382 ◽

2013 ◽

Vol 368 (1614) ◽

pp. 20120382 ◽

Cited By ~ 27

Author(s):

S. Bhatt ◽

T. T. Lam ◽

S. J. Lycett ◽

A. J. Leigh Brown ◽

T. A. Bowden ◽

...

Keyword(s):

Avian Influenza ◽

Adaptive Evolution ◽

Influenza A ◽

Evolutionary Dynamics ◽

Adaptive Dynamics ◽

Swine Influenza ◽

Influenza Viruses ◽

Viral Fitness ◽

Influenza A Viruses ◽

Entire Genome

Few questions on infectious disease are more important than understanding how and why avian influenza A viruses successfully emerge in mammalian populations, yet little is known about the rate and nature of the virus’ genetic adaptation in new hosts. Here, we measure, for the first time, the genomic rate of adaptive evolution of swine influenza viruses (SwIV) that originated in birds. By using a curated dataset of more than 24 000 human and swine influenza gene sequences, including 41 newly characterized genomes, we reconstructed the adaptive dynamics of three major SwIV lineages (Eurasian, EA; classical swine, CS; triple reassortant, TR). We found that, following the transfer of the EA lineage from birds to swine in the late 1970s, EA virus genes have undergone substantially faster adaptive evolution than those of the CS lineage, which had circulated among swine for decades. Further, the adaptation rates of the EA lineage antigenic haemagglutinin and neuraminidase genes were unexpectedly high and similar to those observed in human influenza A. We show that the successful establishment of avian influenza viruses in swine is associated with raised adaptive evolution across the entire genome for many years after zoonosis, reflecting the contribution of multiple mutations to the coordinated optimization of viral fitness in a new environment. This dynamics is replicated independently in the polymerase genes of the TR lineage, which established in swine following separate transmission from non-swine hosts.

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

10.1101/791038 ◽

2019 ◽

Cited By ~ 4

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.

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A29 Genetic heterogeneity of influenza A (H3N2) viruses in the United Kingdom, 2016–8

Virus Evolution ◽

10.1093/ve/vez002.028 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

M Galiano ◽

S Miah ◽

O Akinbami ◽

S Gonzalez Gonoggia ◽

J Ellis ◽

...

Keyword(s):

Amino Acid ◽

Genetic Heterogeneity ◽

Influenza A ◽

Evolutionary Dynamics ◽

Sequence Data ◽

Influenza Viruses ◽

Clinical Samples ◽

Gene Trees ◽

Emerging Viruses ◽

The Uk

Abstract For the last four influenza seasons in the UK, genetic characterization of seasonal influenza viruses has shifted from single hemagglutinin (HA) and neuraminidase (NA) genes to whole genome (WG) analysis, allowing for better insight into the evolutionary dynamics of this virus. Sequences (WG or HA/NA) were obtained from >900A (H3N2) viruses sampled in the UK during influenza seasons 2016/7 and 2017/8 and the inter-seasonal period. Viral RNA was extracted from clinical samples and amplified using a multi-segment RT-PCR. Amplicons were sequenced using Nextera library preparation for Illumina MiSeq sequencing. Sequence data ????were processed using BAM-SAM tools and PHE in-house scripts. Phylogenetic analysis of the HA gene indicates that they belong to genetic group 3C.2a, which has circulated since 2014. Season 2016/7 was characterized by the emergence of cluster 3C.2a.1; further genetic heterogeneity was seen with 6 new subclusters within 3C.2a and 3C.2a.1, with predominance of those characterized by amino acid changes N121K and S144K (3C.2a) and N121K, N171K, I406K, G484E (3C.2a.1). The NA genes clustered with a similar topology to the HA. Season 2017/8 was characterized by persistence of some clades from previous season with further diversification. Three of the 3C.2a clusters continued to circulate, with predominance of clade showing T131K, R142K, and R261Q (clade 3C.2a.2). The majority of HA sequences in 3C.2a1 fall into a new subcluster which has become predominant within this subgroup, with amino acid changes E62G, K92R, and T135K (3C.2a.1b). The topology of NA and internal gene trees showed evidence of reassortment events occurring at some point between the two seasons, with group 3C.2a2 acquiring NA and some internal genes from 3C.2a1 lineage viruses. The predominance of this group during 2017–8 might be due to fitness advantage related to the new genetic constellation. Emerging viruses from group 3C.3a also have acquired genes from lineage 3C.2a1, which could be the reason for their increased frequency to 20 per cent by the end of season 2017–8. Molecular epidemiology indicates emerging genetic diversity in A(H3N2) viruses during the period of study, leading to co-circulation of variants. The frequency of circulating HA genetic groups was quite variable, with rapidly changing patterns of predominance. Evidence of reassortment events was observed which could be responsible for the rise and predominance of some clades, and might predict the emergence of other variants.

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Identification of genome-wide nucleotide sites associated with mammalian virulence in influenza A viruses

10.1101/416586 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yousong Peng ◽

Wenfei Zhu ◽

Zhaomin Feng ◽

Zhaozhong Zhu ◽

Zheng Zhang ◽

...

Keyword(s):

Influenza A ◽

Computational Analysis ◽

Acid Sites ◽

Influenza Viruses ◽

Virulence Determinants ◽

Influenza A Viruses ◽

Synonymous Mutations ◽

Genome Wide ◽

Viral Virulence ◽

Machine Learning Models

ABSTRACTMotivationThe virulence of influenza viruses is a complex multigenic trait. Previous studies about the virulence determinants of influenza viruses mainly focused on amino acid sites, ignoring the influence of nucleotide mutations.ResultsWe collected more than 200 viral strains from 21 subtypes of influenza A viruses with virulence in mammals and obtained over 100 mammalian virulence-related nucleotide sites across the genome by computational analysis. Interestingly, 50 of these nucleotide sites only experienced synonymous mutations. Further experiments showed that synonymous mutations in the top two of these nucleotide sites, i.e., PB1-2031 and PB1-633, enhanced the pathogenicity of the viruses in mice. Finally, machine-learning models with accepted accuracy for predicting mammalian virulence of influenza A viruses were built. Overall, this study highlighted the importance of nucleotide mutations, especially synonymous mutations in viral virulence, and provided rapid methods for evaluating the virulence of influenza A viruses. It could be helpful for early warning of newly emerging influenza A viruses.

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Within-host evolutionary dynamics of seasonal and pandemic human influenza A viruses in young children

eLife ◽

10.7554/elife.68917 ◽

2021 ◽

Vol 10 ◽

Author(s):

Alvin X Han ◽

Zandra C Felix Garza ◽

Matthijs RA Welkers ◽

René M Vigeveno ◽

Nhu Duong Tran ◽

...

Keyword(s):

Young Children ◽

Influenza A ◽

Evolutionary Dynamics ◽

De Novo ◽

Purifying Selection ◽

Influenza Viruses ◽

Human Influenza ◽

Influenza A Viruses ◽

Virus Diversity ◽

Host Evolution

The evolution of influenza viruses is fundamentally shaped by within-host processes. However, the within-host evolutionary dynamics of influenza viruses remain incompletely understood, in part because most studies have focused on infections in healthy adults based on single timepoint data. Here, we analysed the within-host evolution of 82 longitudinally-sampled individuals, mostly young children, infected with A/H1N1pdm09 or A/H3N2 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous minority variants were more prevalent than synonymous ones. For A/H3N2 viruses in young children, early infection was dominated by purifying selection. As these infections progressed, nonsynonymous variants typically increased in frequency even when within-host virus titres decreased. Unlike the short-lived infections of adults where de novo within-host variants are rare, longer infections in young children allow for the maintenance of virus diversity via mutation-selection balance creating potentially important opportunities for within-host virus evolution.

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A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.2763 ◽

2014 ◽

Vol 281 (1786) ◽

pp. 20132763 ◽

Cited By ~ 14

Author(s):

Andreas Wagner

Keyword(s):

Network Analysis ◽

Influenza A ◽

Evolutionary Dynamics ◽

Phylogenetic Analyses ◽

Influenza Viruses ◽

Spatial Proximity ◽

Evolutionary Constraints ◽

Single Nucleotide ◽

Time Resolved ◽

Organizational Patterns

Networks of evolving genotypes can be constructed from the worldwide time-resolved genotyping of pathogens like influenza viruses. Such genotype networks are graphs where neighbouring vertices (viral strains) differ in a single nucleotide or amino acid. A rich trove of network analysis methods can help understand the evolutionary dynamics reflected in the structure of these networks. Here, I analyse a genotype network comprising hundreds of influenza A (H3N2) haemagglutinin genes. The network is rife with cycles that reflect non-random parallel or convergent (homoplastic) evolution. These cycles also show patterns of sequence change characteristic for strong and local evolutionary constraints, positive selection and mutation-limited evolution. Such cycles would not be visible on a phylogenetic tree, illustrating that genotype network analysis can complement phylogenetic analyses. The network also shows a distinct modular or community structure that reflects temporal more than spatial proximity of viral strains, where lowly connected bridge strains connect different modules. These and other organizational patterns illustrate that genotype networks can help us study evolution in action at an unprecedented level of resolution.

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