The evolution of epidemic influenza

Homologous recombination as an evolutionary force in the avian influenza A virus

Avian influenza A viruses (AIVs), including the H5N1, H9N2, and H7N7 subtypes, have been directly transmitted to humans, raising concerns over the possibility of a new influenza pandemic. To prevent a future avian influenza pandemic, it is very important to fully understand the molecular basis driving the change in AIV virulence and host tropism. Although virulent variants of other viruses have been generated by homologous recombination, the occurrence of homologous recombination within AIV segments is controversial and far from proven. This study reports three circulating H9N2 AIVs with similar mosaic PA genes descended from H9N2 and H5N1. Additionally, many homologous recombinants are also found deposited in GenBank. Recombination events can occur in PB2, PB1, PA, HA, and NP segments and between lineages of the same/different serotype. These results collectively demonstrate that intragenic recombination plays a role in driving the evolution of AIVs, potentially resulting in effects on AIV virulence and host tropism changes.

Surviving the bottleneck: transmission mutants and the evolution of microbial populations

The ability of microbial populations to increase fitness through fixation of mutants with an increased growth rate has been well described. In experimental studies, this is often the only way fitness can be increased. In natural settings, however, fitness can also be improved by increasing the ability of the microbe to transmit from one host to the next. For many pathogens, transmission includes a phase outside the host during which they need to survive before the chance of reinfecting a new host occurs. In such a situation, a reduced death rate during this phase will lead to improved fitness. Here, we compute the fixation probability of mutants that better survive the transmission bottleneck during the evolution of microbial populations. We derive analytical results that show that transmission mutants are often likely to occur and that their importance relative to growth mutants increases as the population decline during the transmission phase increases. We confirm our theoretical results with numerical simulations and suggest specific experiments that can be done to test our predictions.

Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States

To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006–2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006–2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.

This study is the first of its kind to reconstruct the spread of an epidemic of influenza A virus across a single country, in this case the United States. In contrast to a single viral lineage spreading across this country, a phylogenetic analysis of the whole-genome sequences of more than 300 influenza A viruses of the A/H1N1 and A/H3N2 subtypes sampled from the 2006–2007 epidemic season reveals that multiple phenotypically and antigenically distinct viral lineages of entered and co-circulated in the US during this time. Furthermore, the widespread co-circulation of multiple lineages, even in geographically remote localities, allowed for frequent reassortment between influenza A viruses of the same subtype. Through reassortment, a minor lineage of A/H3N2 viruses surprisingly re-acquired sensitivity to the adamantane class of antiviral drugs, and a new A/H1N1 antigenic variant emerged that later became globally dominant. In sum, these results highlight the complexity of the spread of influenza A virus in time and space, and highlight the need for intensified global surveillance involving whole-genome sequence data.

Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006)

Background

The underlying basis for the seasonality of influenza A viruses is still uncertain. Phylogenetic studies investigated this phenomenon but have lacked sequences from more subtropical and tropical regions, particularly from Southeast Asia.

Methodology/Principal Findings

281 complete hemagglutinin (HA) and neuraminidase (NA) sequences were obtained from influenza A(H3N2) viruses, collected over 10 years (1997–2006) from Hong Kong. These dated sequences were analyzed with influenza A(H3N2) vaccine strain sequences (Syd/5/97, Mos/10/99, Fuj/411/02, Cal/7/04) and 315 other publicly available dated sequences from elsewhere, worldwide. In addition, the NA sequence alignment was inspected for the presence of any naturally occurring, known, neuraminidase inhibitor (NAI) resistance-associated amino acid mutations (R292K and E119V). Before 2001, the Hong Kong HA and NA sequences clustered more closely with the older vaccine sequences (Syd/5/97, Mos/10/99) than did sequences from elsewhere. After 2001, this trend reversed with significant clusters containing HA and NA sequences from different locations, isolated at different times, suggesting that viral migration may account for much of the influenza A(H3N2) seasonality during this 10-year period. However, at least one example from Hong Kong was found suggesting that in some years, influenza A(H3N2) viruses may persist in the same location, perhaps continuing to circulate, sub-clinically, at low levels between seasons, to re-emerge in the influenza season the following year, relatively unchanged. None of these Hong Kong influenza A(H3N2) NA sequences contained any of the known NAI-resistance associated mutations.

Conclusions/Significance

The seasonality of influenza A(H3N2) may be largely due to global migration, with similar viruses appearing in different countries at different times. However, occasionally, some viruses may remain within a single location and continue to circulate within that population, to re-emerge during the next influenza season, with relatively little genetic change. Naturally occurring NAI resistance mutations were absent or, at least, very rare in this population.

A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus

We develop a model-based phylogenetic maximum likelihood test for evidence of preferential substitution toward a given residue at individual positions of a protein alignment--directional evolution of protein sequences (DEPS). DEPS can identify both the target residue and sites evolving toward it, help detect selective sweeps and frequency-dependent selection--scenarios that confound most existing tests for selection, and achieve good power and accuracy on simulated data. We applied DEPS to alignments representing different genomic regions of influenza A virus (IAV), sampled from avian hosts (H5N1 serotype) and human hosts (H3N2 serotype), and identified multiple directionally evolving sites in 5/8 genomic segments of H5N1 and H3N2 IAV. We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies and document known functional correlates, such as immune escape or host adaptation.

Homologous recombination is unlikely to play a major role in influenza B virus evolution

Influenza B viruses cause a significant amount of morbidity and mortality. The occurrence of homologous recombination in influenza viruses is controversial. To determine the extent of homologous recombination in influenza B viruses, recombination analyses of 2,650 sequences representing all eight segments of the influenza B viruses were carried out. Only four sequences were indentified as putative recombinants, which were verified using phylogenetic methods. However, the mosaics detected here were much likely to represent cases of laboratory-generated artificial recombinants. As in other myxoviruses, it is unlikely that homologous recombination plays a major role in influenza B virus evolution.

Influenza A virus neuraminidase limits viral superinfection

Enveloped viruses use multiple mechanisms to inhibit infection of a target cell by more than one virion. These mechanisms may be of particular importance for the evolution of segmented viruses, because superinfection exclusion may limit the frequency of reassortment of viral genes. Here, we show that cellular expression of influenza A virus neuraminidase (NA), but not hemagglutinin (HA) or the M2 proton pump, inhibits entry of HA-pseudotyped retroviruses. Cells infected with H1N1 or H3N2 influenza A virus were similarly refractory to HA-mediated infection and to superinfection with a second influenza A virus. Both HA-mediated entry and viral superinfection were rescued by the neuraminidase inhibitors oseltamivir carboxylate and zanamivir. These inhibitors also prevented the removal of alpha-2,3- and alpha-2,6-linked sialic acid observed in cells expressing NA or infected with influenza A viruses. Our data indicate that NA alone among viral proteins limits influenza A virus superinfection.

The evolution of norovirus, the "gastric flu"

The authors discuss the implications of a new study that presents compelling data to show that norovirus evolution is driven by immune selection pressure.

Evolution of pathogens in a man-made world

Human activities have resulted in substantial, large-scale environmental modifications, especially in the past century. Ecologists and evolutionary biologists are increasingly coming to realize that parasites and pathogens, like free-living organisms, evolve as the consequence of these anthropogenic changes. Although this area now commands the attention of a variety of researchers, a broad predictive framework is lacking, mainly because the links between human activities, the environment and parasite evolution are complex. From empirical and theoretical examples chosen in the literature, we give an overview of the ways in which humans can directly or indirectly influence the evolution of different traits in parasites (e.g. specificity, virulence, polymorphism). We discuss the role of direct and indirect factors as diverse as habitat fragmentation, pollution, biodiversity loss, climate change, introduction of species, use of vaccines and antibiotics, ageing of the population, etc. We also present challenging questions for further research. Understanding the links between anthropogenic changes and parasite evolution needs to become a cornerstone of public health planning, economic development and conservation biology.

The Widespread Evolutionary Significance of Viruses

In the last 30 years, the study of virus evolution has undergone a transformation. Originally concerned with disease and its emergence, virus evolution had not been well integrated into the general study of evolution. This chapter reviews the developments that have brought us to this new appreciation for the general significance of virus evolution to all life. We now know that viruses numerically dominate all habitats of life, especially the oceans. Theoretical developments in the 1970s regarding quasispecies, error rates, and error thresholds have yielded many practical insights into virus–host dynamics. The human diseases of HIV-1 and hepatitis C virus cannot be understood without this evolutionary framework. Yet recent developments with poliovirus demonstrate that viral fitness can be the result of a consortia, not one fittest type, a basic Darwinian concept in evolutionary biology. Darwinian principles do apply to viruses, such as with Fisher population genetics, but other features, such as reticulated and quasispecies-based evolution distinguish virus evolution from classical studies. The available phylogenetic tools have greatly aided our analysis of virus evolution, but these methods struggle to characterize the role of virus populations. Missing from many of these considerations has been the major role played by persisting viruses in stable virus evolution and disease emergence. In many cases, extreme stability is seen with persisting RNA viruses. Indeed, examples are known in which it is the persistently infected host that has better survival. We have also recently come to appreciate the vast diversity of phage (DNA viruses) of prokaryotes as a system that evolves by genetic exchanges across vast populations (Chapter 10). This has been proposed to be the “big bang” of biological evolution. In the large DNA viruses of aquatic microbes we see surprisingly large, complex and diverse viruses. With both prokaryotic and eukaryotic DNA viruses, recombination is the main engine of virus evolution, and virus host co-evolution is common, although not uniform. Viral emergence appears to be an unending phenomenon and we can currently witness a selective sweep by retroviruses that infect and become endogenized in koala bears.

Phylogenetic analysis reveals the global migration of seasonal influenza A viruses

The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus during the non-epidemic summer months. Herein, we take a step towards elucidating the seasonal emergence of influenza virus by determining the evolutionary relationship between populations of influenza A virus sampled from opposite hemispheres. We conducted a phylogenetic analysis of 487 complete genomes of human influenza A/H3N2 viruses collected between 1999 and 2005 from Australia and New Zealand in the southern hemisphere, and a representative sub-sample of viral genome sequences from 413 isolates collected in New York state, United States, representing the northern hemisphere. We show that even in areas as relatively geographically isolated as New Zealand's South Island and Western Australia, global viral migration contributes significantly to the seasonal emergence of influenza A epidemics, and that this migration has no clear directional pattern. These observations run counter to suggestions that local epidemics are triggered by the climate-driven reactivation of influenza viruses that remain latent within hosts between seasons or transmit at low efficiency between seasons. However, a complete understanding of the seasonal movements of influenza A virus will require greatly expanded global surveillance, particularly of tropical regions where the virus circulates year-round, and during non-epidemic periods in temperate climate areas.

The winter seasonality of influenza A virus in temperate climates is one of the most puzzling epidemiological patterns in infectious disease. To help resolve the issue of influenza seasonality, we studied, using viral genome sequence data, the patterns of global migration of influenza A virus, particularly between the northern and southern hemispheres. A phylogenetic analysis of approximately 900 complete genomes of the H3N2 subtype of human influenza A virus sampled from New Zealand and Australia (southern hemisphere), and New York state, United States (northern hemisphere), revealed that cross-hemisphere migration frequently occurs in both directions and involves multiple viral strains. Such global viral traffic therefore contributes significantly to the introduction of new influenza epidemics in both northern and southern hemispheres. These results also show that influenza A virus migrates afar during non-epidemic periods, rather than persisting locally at low levels during the influenza “off-season”. However, although this represents the largest and first bihemisphere study of its kind to our knowledge, the results highlight the need for sampling from tropical regions and during non-epidemic periods in temperate areas. Studies of this kind are critical to fully understand the geographical dispersal of influenza A virus and the role of climate in triggering seasonal epidemics.

Identification of a natural multi-recombinant of Newcastle disease virus

Newcastle disease (ND), caused by ND virus (NDV), is one of the most serious illnesses of birds, particularly chickens, and has been one of the major causes of economic losses in the poultry industry. Live vaccines are widely used to prevent chicken from NDV all over the world. Given the implications that recombination has for RNA virus evolution, it is clearly important to determine the extent to which recombination plays a role in NDV evolution. In this study, we performed the phylogenetic and recombination analysis on complete NDV genomes. A natural multi-recombinant cockatoo/Indonesia/14698/90 (AY562985) was identified. Its two minor parental-like strains might be from the NDV vaccine lineage and anhinga/U.S.(Fl)/44083/93 lineage, respectively. Our study suggests that recombination plays a role in NDV evolution. Especially, the study also suggests that live vaccines have capacity to play roles in shaping NDV evolution by homologous recombination with circulating virus.

Persistent infection and promiscuous recombination of multiple genotypes of an RNA virus within a single host generate extensive diversity

Recombination and reassortment of viral genomes are major processes contributing to the creation of new, emerging viruses. These processes are especially significant in long-term persistent infections where multiple viral genotypes co-replicate in a single host, generating abundant genotypic variants, some of which may possess novel host-colonizing and pathogenicity traits. In some plants, successive vegetative propagation of infected tissues and introduction of new genotypes of a virus by vector transmission allows for viral populations to increase in complexity for hundreds of years allowing co-replication and subsequent recombination of the multiple viral genotypes. Using a resequencing microarray, we examined a persistent infection by a Citrus tristeza virus (CTV) complex in citrus, a vegetatively propagated, globally important fruit crop, and found that the complex comprised three major and a number of minor genotypes. Subsequent deep sequencing analysis of the viral population confirmed the presence of the three major CTV genotypes and, in addition, revealed that the minor genotypes consisted of an extraordinarily large number of genetic variants generated by promiscuous recombination between the major genotypes. Further analysis provided evidence that some of the recombinants underwent subsequent divergence, further increasing the genotypic complexity. These data demonstrate that persistent infection of multiple viral genotypes within a host organism is sufficient to drive the large-scale production of viral genetic variants that may evolve into new and emerging viruses.

Exploring Variation in the d N /d S Ratio Among Sites and Lineages Using Mutational Mappings: Applications to the Influenza Virus

We use a likelihood-based method for mapping mutations on a phylogeny in a way that allows for both site-specific and lineage-specific variation in selection intensity. The method accounts for many of the potential sources of bias encountered in mapping of mutations on trees while still being computationally efficient. We apply the method to a previously published influenza data set to investigate hypotheses about changes in selection intensity in influenza strains. Influenza virus is sometimes propagated in chicken cells for several generations before sequencing, a process that has been hypothesized to induce mutations adapting the virus to the lab medium. Our analysis suggests that there are approximately twice as many replacement substitutions in lineages propagated in chicken eggs as in lineages that are not. Previous studies have attempted to predict which viral strains future epidemics may arise from using inferences regarding positive selection. The assumption is that future epidemics are more likely to arise from the strains in which positive selection on the so-called "trunk lineages" of the evolutionary tree is most pervasive. However, we find no difference in the strength of selection in the trunk lineages versus other evolutionary lineages. Our results suggest that it may be more difficult to use inferences regarding the strength of selection on mutations to make predictions regarding viral epidemics than previously thought.