REVIEWS The evolution of epidemic influenza Martha I. Nelson* and Edward C. Holmes*‡ Abstract | Recent developments in complete-genome sequencing, antigenic mapping and epidemiological modelling are greatly improving our knowledge of the evolution of human influenza virus at the epidemiological scale. In particular, recent studies have revealed a more complex relationship between antigenic evolution, natural selection and reassortment than previously realized. Despite these advances, there is much that remains to be understood about the epidemiology of influenza virus, particularly the processes that determine the virus’s strong seasonality. We argue that a complete understanding of the evolutionary biology of this important human pathogen will require a genomic view of genetic diversity, including the acquisition of polymorphism data from within individual hosts and from geographical regions, particularly the tropics, which have been poorly surveyed to date. Pandemic Influenza is one of the most important infectious diseases no onward transmission, as is currently the case with An epidemic that occurs over of humans. The annual mortality that is caused by influ- avian H5N1 influenza in humans; less frequently, they a large geographical area, enza in the United States alone is estimated at over 36,000 become established in new hosts, resulting in (irregular) including multiple countries. (REF. 1) (FIG. 1), whereas occasional global pandemics major human pandemics. can infect 20–40% of the population in a single year2. As Here we review our current understanding of the Epidemic The occurrence of more cases a notorious case in point, the pandemic of 1918–1919 evolutionary biology of human influenza A virus, show- than expected of an infectious caused possibly 20–50 million deaths on a global scale, ing how recent advances, particularly in comparative disease, in a defined making it the single most devastating disease outbreak genomics and epidemiology, have shed new light on geographical area over a in human history3. The recent uncertainty over whether this important pathogen. We focus on the patterns and defined time period. H5N1 avian influenza virus will adapt to human trans- processes of influenza virus evolution at the level of 4–7 Reassortment mission, and how its spread might be controlled , recurrent human epidemics, highlighting areas in which A form of recombination in highlight the threat that is posed by influenza and the future research might prove to be particularly profit- which two (or more) influenza need to understand its evolutionary dynamics. able. For details of the biology of avian influenza virus viruses, of the same or Influenza viruses are single-stranded, negative- and how it manifests as large-scale human outbreaks, different subtypes, co-infect a single cell and exchange RNA sense RNA viruses of the family Orthomyxoviridae see REFS 10–12. segments to form genetically that cause regular seasonal epidemics in humans, other novel viruses. mammalian species and birds. Three phylogenetically The determinants of influenza virus evolution and antigenically distinct viral types — A, B and C The phylodynamics of antigenic drift. Owing to the — circulate globally in human populations, although large amount of available sequence data, particularly type A viruses exhibit the greatest genetic diversity, from the HA1 domain of the HA protein, many studies *Center for Infectious Disease Dynamics, infect the widest range of host species and cause the have explored the evolutionary processes that shape the Department of Biology, vast majority of severe disease in humans, including genetic diversity of influenza A virus. Investigating The Pennsylvania State the great pandemics. The genome of influenza A virus the complex interplay between natural selection, University, University Park, (total length ~13 kb) is composed of eight segments that phylogeny and epidemiology is key to understanding Pennsylvania 16802, USA. can be exchanged through reassortment (FIG. 2). Wild influenza A virus evolution13,14. Because the human ‡Fogarty International Center, National Institutes of Health, waterfowl are the reservoir hosts for type A influenza immune response to viral infection is not completely cross- Bethesda, Maryland 20892, viruses, harbouring numerous antigenically distinct protective, natural selection favours amino-acid variants USA. subtypes (serotypes) of the two main viral antigens, of the HA and NA proteins that allow the virus to evade Correspondence to E.C.H. the haemagglutinin (HA) and neuraminidase (NA) sur- immunity, infect more hosts and proliferate15. This e-mail: [email protected] 8,9 doi:10.1038/nrg2053 face glycoproteins (16 HA and 9 NA subtypes) . These continual change in antigenic structure through time is 16 Published online avian viruses occasionally transmit to other species, in called antigenic drift . Although both the HA and NA 30 January 2007 which they either cause isolated outbreaks with little or proteins contain antigenic sites in which immune-driven 196 | MARCH 2007 | VOLUME 8 www.nature.com/reviews/genetics © 2007 Nature Publishing Group REVIEWS natural selection can occur, the HA1 domain of the HA 8.00 protein contains the highest concentration of epitopes 7.00 Deaths and, correspondingly, experiences the most intense Excess deaths positive selection pressure15,17–22. 6.00 At the phylogenetic scale, the continual selective 5.00 turnover of amino-acid variants is thought to produce 4.00 the distinctive ‘cactus-like’ phylogenetic tree of the HA1 domain from A/H3N2 subtype viruses13,15,17. A single 3.00 main trunk lineage depicts the pathway of advantageous 2.00 mutations that have been fixed by natural selection 1.00 through time, from past to present, whereas short side / 100,000 rate death P&I Monthly branches that stem from this trunk represent those 0.00 isolates that die out because they were insufficiently antigenically distinct to evade immunity. The apparent Jan-59 Jan-61 Jan-63 Jan-65 Jan-67 Jan-69 Jan-71 Jan-73 Jan-75 Jan-77 Jan-79 Jan-81 Jan-83 Jan-85 Jan-87 Jan-89 Jan-91 Jan-93 Jan-95 Jan-97 Jan-99 Jan-01 regularity of this phylogenetic pattern has generated much Figure 1 | The periodicity of pneumonia and influenza interest, because of the potential to predict the future mortality and excess mortality rates. Monthly course of viral evolution and, in doing so, aid vaccine pneumonia and influenza (P&I) death rates and excess death rates (above the baseline mortality due to other strain selection23. Likewise, there is still considerable respiratory pathogens) in the United States from 1959 to debate over what aspects of influenza epidemiology so 2001 are shown (see the web site for the US National strongly favour the survival of a single HA1 trunk lineage Center for Health Statistics). Peaks occur during the in human A/H3N2 viruses, whereas multiple lineages winter in northern latitudes at ~2–5 year intervals, seem to co-circulate more frequently within populations usually during H3N2-dominant seasons, since the 1968 of equine H3N8 (REF. 24), human H1N113 and influenza pandemic. See REF. 81 for more details. viruses types B25,26 and C27 (in which the equivalent Haemagglutinin haemagglutininesterase protein is termed HEF). An influenza virus surface Although antigenic changes in the haemagglutinin increased frequency of non-synonymous substitutions, glycoprotein, denoted HA, protein are clearly important determinants of viral fit- which reflects the continual fixation of (advantageous) which is responsible for viral binding and entry into host ness, the ‘progressive’ model of influenza A evolution, as amino-acid replacements (BOX 1). Similarly, many of the epithelial cells. Sixteen HA typified by the cactus-like phylogeny, was formed on the mutations that fall on the side branches of the HA1 tree serotypes are present in basis of studies that largely focused on HA1 in isolation, are likely to be deleterious, and will not achieve fixation animal species. considered relatively few sequences from individual time even in the absence of immune selection. However, it is Neuraminidase points and geographical locations, and often targeted important to note that because the computational tools An influenza virus surface strains with unusual antigenic properties in the inter- that measure the extent of positive selection are inher- glycoprotein, denoted NA, ests of vaccine design. Indeed, the antigenic evolution ently conservative, and quantify the successive fixation which is involved in the of HA1 seems to be more clustered than continuous28. of non-synonymous mutations at specific amino- budding (release) of new Moreover, the recent explosion of large-scale genome acid sites, adaptive evolution is likely to occur more virions from infected cells. Nine NA serotypes are sequence data from H3N2 viruses has shown that the frequently than is usually detected (BOX 1). In the future, 32 present in animal species. evolutionary pattern that is observed in the HA1 domain methods that account for the rate of amino-acid fixation does not always apply to the rest of the viral genome29,30. (as opposed to simply considering the total number of Antigenic drift In contrast to the restricted number of lineages that can fixation events) might offer more analytical power. The continual evasion of host immunity by the gradual be observed at any time point in HA1, whole-genome Although antigenic drift is undoubtedly an important accumulation of mutations phylogenies show the coexistence of multiple viral aspect