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

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 within-host virus diversity of infections in otherwise 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/H3N2 or A/H1N1pdm09 viruses between 2007 and 2009. For A/H1N1pdm09 infections during the 2009 pandemic, nonsynonymous changes were common early in infection but decreased or remained constant throughout infection. For A/H3N2 viruses, early infection was dominated by purifying selection. However, as the A/H3N2 infections progressed for longer-than-average duration (up to 2 weeks) in relatively young or influenza naive individuals, nonsynonymous variants increased in frequencies even though within-host virus titres decreased, leading to the maintenance of virus diversity via mutation-selection balance and provide important opportunities for within-host virus evolution.

Download Full-text

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.

Download Full-text

N-Glycolylneuraminic Acid in Animal Models for Human Influenza A Virus

Viruses ◽

10.3390/v13050815 ◽

2021 ◽

Vol 13 (5) ◽

pp. 815

Author(s):

Cindy M. Spruit ◽

Nikoloz Nemanichvili ◽

Masatoshi Okamatsu ◽

Hiromu Takematsu ◽

Geert-Jan Boons ◽

...

Keyword(s):

Sialic Acid ◽

Animal Models ◽

Influenza A ◽

Influenza Virus Infection ◽

Influenza Viruses ◽

Upper Respiratory Tract ◽

Human Influenza ◽

Influenza A Viruses ◽

Sialic Acid Content ◽

Acetylneuraminic Acid

The first step in influenza virus infection is the binding of hemagglutinin to sialic acid-containing glycans present on the cell surface. Over 50 different sialic acid modifications are known, of which N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) are the two main species. Animal models with α2,6 linked Neu5Ac in the upper respiratory tract, similar to humans, are preferred to enable and mimic infection with unadapted human influenza A viruses. Animal models that are currently most often used to study human influenza are mice and ferrets. Additionally, guinea pigs, cotton rats, Syrian hamsters, tree shrews, domestic swine, and non-human primates (macaques and marmosets) are discussed. The presence of NeuGc and the distribution of sialic acid linkages in the most commonly used models is summarized and experimentally determined. We also evaluated the role of Neu5Gc in infection using Neu5Gc binding viruses and cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH)-/- knockout mice, which lack Neu5Gc and concluded that Neu5Gc is unlikely to be a decoy receptor. This article provides a base for choosing an appropriate animal model. Although mice are one of the most favored models, they are hardly naturally susceptible to infection with human influenza viruses, possibly because they express mainly α2,3 linked sialic acids with both Neu5Ac and Neu5Gc modifications. We suggest using ferrets, which resemble humans closely in the sialic acid content, both in the linkages and the lack of Neu5Gc, lung organization, susceptibility, and disease pathogenesis.

Download Full-text

Improving pandemic influenza risk assessment

eLife ◽

10.7554/elife.03883 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 43

Author(s):

Colin A Russell ◽

Peter M Kasson ◽

Ruben O Donis ◽

Steven Riley ◽

John Dunbar ◽

...

Keyword(s):

Risk Assessment ◽

Pandemic Influenza ◽

Influenza A ◽

Sequence Data ◽

Virus Genome ◽

Influenza Viruses ◽

Influenza Surveillance ◽

Human Influenza ◽

Influenza A Viruses ◽

Virus Genotype

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

Download Full-text

Divergent Human-Origin Influenza Viruses Detected in Australian Swine Populations

Journal of Virology ◽

10.1128/jvi.00316-18 ◽

2018 ◽

Vol 92 (16) ◽

Cited By ~ 6

Author(s):

Frank Y. K. Wong ◽

Celeste Donato ◽

Yi-Mo Deng ◽

Don Teng ◽

Naomi Komadina ◽

...

Keyword(s):

Influenza Virus ◽

Influenza A ◽

Swine Influenza ◽

Influenza Viruses ◽

Antigenic Drift ◽

Human Origin ◽

Human Influenza ◽

Influenza A Viruses ◽

Data Set ◽

Antigenic Properties

ABSTRACTGlobal swine populations infected with influenza A viruses pose a persistent pandemic risk. With the exception of a few countries, our understanding of the genetic diversity of swine influenza viruses is limited, hampering control measures and pandemic risk assessment. Here we report the genomic characteristics and evolutionary history of influenza A viruses isolated in Australia from 2012 to 2016 from two geographically isolated swine populations in the states of Queensland and Western Australia. Phylogenetic analysis with an expansive human and swine influenza virus data set comprising >40,000 sequences sampled globally revealed evidence of the pervasive introduction and long-term establishment of gene segments derived from several human influenza viruses of past seasons, including the H1N1/1977, H1N1/1995, H3N2/1968, and H3N2/2003, and the H1N1 2009 pandemic (H1N1pdm09) influenza A viruses, and a genotype that contained gene segments derived from the past three pandemics (1968, reemerged 1977, and 2009). Of the six human-derived gene lineages, only one, comprising two viruses isolated in Queensland during 2012, was closely related to swine viruses detected from other regions, indicating a previously undetected circulation of Australian swine lineages for approximately 3 to 44 years. Although the date of introduction of these lineages into Australian swine populations could not be accurately ascertained, we found evidence of sustained transmission of two lineages in swine from 2012 to 2016. The continued detection of human-origin influenza virus lineages in swine over several decades with little or unpredictable antigenic drift indicates that isolated swine populations can act as antigenic archives of human influenza viruses, raising the risk of reemergence in humans when sufficient susceptible populations arise.IMPORTANCEWe describe the evolutionary origins and antigenic properties of influenza A viruses isolated from two separate Australian swine populations from 2012 to 2016, showing that these viruses are distinct from each other and from those isolated from swine globally. Whole-genome sequencing of virus isolates revealed a high genotypic diversity that had been generated exclusively through the introduction and establishment of human influenza viruses that circulated in past seasons. We detected six reassortants with gene segments derived from human H1N1/H1N1pdm09 and various human H3N2 viruses that circulated during various periods since 1968. We also found that these swine viruses were not related to swine viruses collected elsewhere, indicating independent circulation. The detection of unique lineages and genotypes in Australia suggests that isolated swine populations that are sufficiently large can sustain influenza virus for extensive periods; we show direct evidence of a sustained transmission for at least 4 years between 2012 and 2016.

Download Full-text

The evolution of human influenza viruses

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2001.0999 ◽

2001 ◽

Vol 356 (1416) ◽

pp. 1861-1870 ◽

Cited By ~ 278

Author(s):

Alan J. Hay ◽

Victoria Gregory ◽

Alan R. Douglas ◽

Yi Pu Lin

Keyword(s):

Influenza A ◽

Influenza Viruses ◽

Antigenic Drift ◽

Influenza B ◽

Mixed Infections ◽

Human Influenza ◽

Influenza A Viruses ◽

Genetic Reassortment ◽

Influenza Ah1n1 ◽

Novel Influenza A

The evolution of influenza viruses results in (i) recurrent annual epidemics of disease that are caused by progressive antigenic drift of influenza A and B viruses due to the mutability of the RNA genome and (ii) infrequent but severe pandemics caused by the emergence of novel influenza A subtypes to which the population has little immunity. The latter characteristic is a consequence of the wide antigenic diversity and peculiar host range of influenza A viruses and the ability of their segmented RNA genomes to undergo frequent genetic reassortment (recombination) during mixed infections. Contrasting features of the evolution of recently circulating influenza AH1N1, AH3N2 and B viruses include the rapid drift of AH3N2 viruses as a single lineage, the slow replacement of successive antigenic variants of AH1N1 viruses and the co–circulation over some 25 years of antigenically and genetically distinct lineages of influenza B viruses. Constant monitoring of changes in the circulating viruses is important for maintaining the efficacy of influenza vaccines in combating disease.

Download Full-text

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.

Download Full-text

Stochastic processes dominate the within and between host evolution of influenza virus

10.1101/176362 ◽

2017 ◽

Cited By ~ 5

Author(s):

John T. McCrone ◽

Robert J. Woods ◽

Emily T. Martin ◽

Ryan E. Malosh ◽

Arnold S. Monto ◽

...

Keyword(s):

Influenza Virus ◽

Stochastic Processes ◽

Influenza A ◽

Evolutionary Dynamics ◽

Sequence Data ◽

Influenza A Viruses ◽

Effective Population ◽

The Individual ◽

Host Evolution

AbstractThe global evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define the dynamics of influenza A virus populations in human hosts through next generation sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected over 5 seasons from individuals in a prospective community-based cohort, they are broadly representative of natural human infections with seasonal viruses. We used viral sequence data from 35 serially sampled individuals to estimate a within host effective population size of 30-70 and an in vivo mutation rate of 4x10−5 per nucleotide per cellular infectious cycle. These estimates are consistent across several models and robust to the models' underlying assumptions. We also identified 43 epidemiologically linked and genetically validated transmission pairs. Maximum likelihood optimization of multiple transmission models estimates an effective transmission bottleneck of 1-2 distinct genomes. Our data suggest that positive selection of novel viral variants is inefficient at the level of the individual host and that genetic drift and other stochastic processes dominate the within and between host evolution of influenza A viruses.

Download Full-text

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.

Download Full-text

Caspase-Dependent N-Terminal Cleavage of Influenza Virus Nucleocapsid Protein in Infected Cells

Journal of Virology ◽

10.1128/jvi.73.12.10158-10163.1999 ◽

1999 ◽

Vol 73 (12) ◽

pp. 10158-10163 ◽

Cited By ~ 72

Author(s):

O. P. Zhirnov ◽

T. E. Konakova ◽

W. Garten ◽

H.-D. Klenk

Keyword(s):

Nucleocapsid Protein ◽

Influenza A ◽

Influenza Viruses ◽

Influenza B Virus ◽

Influenza B ◽

Cleavage Sites ◽

Human Influenza ◽

Influenza A Viruses ◽

N Terminus ◽

Infected Cells

ABSTRACT The nucleocapsid protein (NP) (56 kDa) of human influenza A viruses is cleaved in infected cells into a 53-kDa form. Likewise, influenza B virus NP (64 kDa) is cleaved into a 55-kDa protein with a 62-kDa intermediate (O. P. Zhirnov and A. G. Bukrinskaya, Virology 109:174–179, 1981). We show now that an antibody specific for the N terminus of influenza A virus NP reacted with the uncleaved 56-kDa form but not with the truncated NP53 form, indicating the removal of a 3-kDa peptide from the N terminus. Amino acid sequencing revealed the cleavage sites ETD16*G for A/Aichi/68 NP and sites DID7*G and EAD61*V for B/Hong Kong/72 NP. With D at position −1, acidic amino acids at position −3, and aliphatic ones at positions −2 and +1, the NP cleavage sites show a recognition motif typical for caspases, key enzymes of apoptosis. These caspase cleavage sites demonstrated evolutionary stability and were retained in NPs of all human influenza A and B viruses. NP of avian influenza viruses, which is not cleaved in infected cells, contains G instead of D at position 16. Oligopeptide DEVD derivatives, specific caspase inhibitors, were shown to prevent the intracellular cleavage of NP. All three events, the NP cleavage, the increase of caspase activity, and the development of apoptosis, coincide in cells infected with human influenza A and B viruses. The data suggest that intracellular cleavage of NP is exerted by host caspases and is associated with the development of apoptosis at the late stages of infection.

Download Full-text

Incorporating demographic stochasticity into multi-strain epidemic models: application to influenza A

Journal of The Royal Society Interface ◽

10.1098/rsif.2008.0467 ◽

2009 ◽

Vol 6 (40) ◽

pp. 989-996 ◽

Cited By ~ 20

Author(s):

Pavlo Minayev ◽

Neil Ferguson

Keyword(s):

Influenza A ◽

Simulation Models ◽

Influenza Viruses ◽

Infection Prevalence ◽

Human Influenza ◽

Influenza A Viruses ◽

Demographic Stochasticity ◽

Transient Strain ◽

Strain Diversity ◽

Transmission Parameters

We develop mathematical models of the transmission and evolution of multi-strain pathogens that incorporate strain extinction and the stochastic generation of new strains via mutation. The dynamics resulting from these models is then examined with the applied aim of understanding the mechanisms underpinning the evolution and dynamics of rapidly mutating pathogens, such as human influenza viruses. Our approach, while analytically relatively simple, gives results that are qualitatively similar to those obtained from much more complex individually based simulation models. We examine strain dynamics as a function of cross-immunity and key transmission parameters, and show that introducing strain extinction and modelling mutation as a stochastic process significantly changes the model dynamics, leading to lower strain diversity, reduced infection prevalence and shorter strain lifetimes. Finally, we incorporate transient strain-transcending immunity in the model and demonstrate that it reduces strain diversity further, giving patterns of sequential strain replacement similar to that seen in human influenza A viruses.

Download Full-text