Science Forum: Viral factors in influenza pandemic risk assessment

Aquatic birds are the main reservoir of influenza A viruses in nature (Krauss and Webster, 2010). Influenza viruses from aquatic birds sporadically enter terrestrial bird and mammalian host populations and achieve sustained circulation in these new hosts (Vandegrift et al., 2010), sometimes after reassortment with influenza viruses already circulating in the new host (Webster et al., 1992). Adaptation of viruses from aquatic birds to mammals involves a change in tissue tropism from intestinal to respiratory epithelia (Hinshaw et al., 1979; Hénaux and Samuel, 2015).

Multiple influenza A subtypes—defined by the patterns of antibody recognition of two surface proteins, hemagglutinin (HA) and neuraminidase (NA)—circulate in avian species and swine at any given time. Among these, a number are known to cause sporadic zoonotic infections in humans (Peiris, 2009). More than one thousand human infections with avian influenza viruses were detected in the last decade, for example H5N1 and H7N9 (Qin et al., 2015) as well as swine influenza viruses, e.g. an H3N2 variant that spilled over into humans attending agricultural shows in the early 2010s, H3N2v (Jhung et al., 2013). In addition, zoonotic infections with other viruses from poultry or wild birds have occurred, including for example H7N7 (Fouchier et al., 2004), H10N8 (Wohlbold et al., 2015), H6N1 (Wei et al., 2013), H9N2 (Butt et al., 2005), and H5N6 (Yang et al., 2015); for more examples and a fuller discussion see (Short et al., 2015). The severity of zoonotic influenza A infections ranges from clinically inapparent (Gomaa et al., 2015; To et al., 2016) to fatal (de Jong et al., 2006; Gao et al., 2013).

Although secondary transmission can occur following some of these spillover events (Kucharski et al., 2014), only a very small proportion of them—four in the last hundred years, which seems to be close to the historical average (Patterson, 1986)—led to sustained person-to-person transmission with global spread (Box 1). There are 18 known HA types and 11 known NA types (Tong et al., 2013), which could theoretically be found in any combination. So far, sustained spread in humans has been limited to the H1N1, H2N2, and H3N2 subtypes (Kuiken et al., 2006), though it is possible that other subtypes circulated prior to 1918, the year of the first pandemic from which viruses are available for study (Worobey et al., 2014). Multiple virus–host interactions are necessary for replication and onward transmission; the differences in the genetic requirements to accomplish each of these interactions in humans versus other animals provide a barrier to sustained transmission following spillover (Russell et al., 2014).

Experiments in ferrets have been used to measure viral transmissibility via respiratory droplets (in this review we use this term to refer to any transmission through the air between ferrets that are not in direct or indirect physical contact). Droplet transmission in ferrets is a useful, albeit imperfect, correlate of the potential of influenza strains to transmit efficiently in human populations (Buhnerkempe et al., 2015). For this reason, some have argued that there is a general phenotype of 'transmissibility by respiratory droplets in mammals' such that experiments to select for such transmission in droplets in ferrets are important models of the process of adaptation to human transmission (Imai et al., 2012; Herfst et al., 2012). This view is not universally shared (Palese and Wang, 2012). Starting from an zoonotic highly pathogenic avian influenza isolate from a human case of infection (or a reassortant of the HA from a different zoonotic H5N1 highly pathogenic avian influenza isolate, with the other segments from the 2009 pandemic H1N1 strain), it was shown that certain specific traits that had been previously associated with mammalian host adaptation were required to achieve respiratory droplet transmission. These ferret-transmission phenotypes in turn were associated with certain genetic changes relative to the original avian viruses (Imai et al., 2012; Herfst et al., 2012; Linster et al., 2014). These specific changes occur both in HA and in polymerase-complex proteins.

The rationale for these experiments was that, because the ferret model recapitulates many features of human infection, changes identified in adaptation to ferret transmission would also be important for adaptation to sustained transmission in humans (Davis et al., 2014; Schultz-Cherry et al., 2014), though this can never be known with certainty (Palese and Wang, 2012). Notably, viruses isolated from humans who were infected by contact with birds show some of these changes (Russell et al., 2012; Bi et al., 2015), particularly the change at amino acid 627 of the PB2 gene (Jonges et al., 2014; Chen et al., 2014; Fonville et al., 2013), which often affects polymerase complex efficiency (see below). This indicates that even the first generation of human infection from nonhuman hosts can initiate a process of host adaptation. It also indicates that not all the human-adaptive changes must be in place in the avian reservoir to initiate this process. Some human infections, including some zoonotic cases (de Jong et al., 2006; Chen et al., 2014, 2006; Sha et al., 2016) and some cases early in a pandemic (Rogers and D'Souza, 1989; Connor et al., 1994; Stevens et al., 2006; Glaser et al., 2005; Pappas et al., 2010), involve viruses that are not yet fully human-adapted (see below and Tables 2–4). The interpretation of some of these isolates is complicated by uncertainty about whether they were passaged in hen’s eggs at some point in their history.

Certain types of countermeasures against an influenza pandemic are effective only against one lineage of viruses – for example, creating stockpiles or seed stocks of vaccines against a particular subtype, or culling poultry infected with that subtype. It is not currently feasible to invest in such countermeasures against all viruses circulating in avian or other reservoirs, or even against all those causing known zoonotic cases. Therefore, there would be value in an accurate system to assess the relative pandemic risks posed by each virus and prioritize them for the development of such strain-specific countermeasures, while directing fewer resources to strains of lower concern (Kaplan et al., 2016). This consideration has motivated calls for comprehensive analysis of all available data to assess the threat to public health posed by these strains. One response is the CDC’s Influenza Risk Assessment Tool (IRAT) (Trock et al., 2015), which incorporates elements including properties of the virus, field and epidemiological findings, and attributes of the human population to provide a framework to differentiate among novel influenza viruses thought to possess pandemic potential. Such risk assessments can help focus pandemic prevention and response efforts on the viruses thought to pose the highest risk of pandemic spread (Davis et al., 2014), in the most worrisome cases providing a rationale for costly measures such as poultry culling or vaccine seed stock development, or even stockpiling of large quantities of vaccine. A guiding question of this article is to examine the degree to which it is justified to rely on measurements and predictions of viral genetic and phenotypic traits in prioritizing responses to particular viral subtypes and within-subtype lineages.

There are several hurdles to evaluating the accuracy of such predictions (Russell et al., 2014). Factors limiting our ability to identify high-risk viruses and predict the risk they pose include:

• limited surveillance of nonhuman influenza viruses, such that high-risk viruses may not be detected and hence cannot be assessed (Butler, 2012). Limitations include both the number, geographic and species diversity of hosts sampled, and the difficulty in sampling all genetic variants present in a given infection (Poon et al., 2016; Varble et al., 2014);

• failure to fully characterize some viruses that are detected (Hoye et al., 2010);

• imperfect public health systems lacking capacity to detect zoonotic infections presenting in patients (Sanicas et al., 2014; Simonsen et al., 2013);

• epistasis and other complexities that prevent straightforward prediction of viral traits from genotype (Russell et al., 2014; Kryazhimskiy et al., 2011; Gong and Bloom, 2014; Bloom et al., 2010; Wu et al., 2016; Raman et al., 2014; Tharakaraman et al., 2013; Gong et al., 2013);

• technological limitations in molecular modeling and phenotypic assays that limit confidence in predicting and measuring viral traits (Russell, 2014);

• uncertainties about the taxonomic level at which risk predictions should be made (Box 2);

• practical, ethical and cost limitations of animal transmission experiments, as well as some exceptions to the correlation between human transmissibility and droplet transmissibility in nonhuman animal models (Buhnerkempe et al., 2015);

• lack of data on immediate animal precursors of viruses that caused previous pandemics;

• multiple scales at which viral strains compete and hence experience selection (i.e. replication within hosts, transmission between hosts). Evolutionary theory for such multi-scale selection is incomplete. Viral fitness components are rarely measured at both scales for the same strain and are imperfectly correlated across scales (Gog et al., 2015; Park et al., 2013; Beauchemin and Handel, 2011);

• the role of stochastic events in the ecology and evolution of influenza viruses during and after host-switching to humans (Gog et al., 2015; Lloyd-Smith et al., 2015), including the potential for transmission bottlenecks to either promote or inhibit emergence of human-adapted viruses (Varble et al., 2014; Moncla et al., 2016; Wilker et al., 2013; Zaraket et al., 2015).

These difficulties are exacerbated by the fact that influenza pandemics are rare events, and that risk assessments are not yet made with enough quantitative precision to formally evaluate their practical application. Even perfect information about the viral determinants of pandemic risk might only be enough to distinguish between strains with a low risk of causing a pandemic (say, 0.1% per year) and those with an extremely low risk (say, less than 0.01% per year), with unpredictable ecological or evolutionary contingencies determining which of these low-probability events will actually occur. One such contingency is that an avian influenza virus could acquire one or more of the determinants of pandemic potential by reassorting with a human seasonal influenza virus.

With only one pandemic every few decades, the data set for testing the prediction of such rare events is inadequate, a problem that challenges predictions in many fields beyond infectious diseases (King and Zeng, 2001; Hansson, 2006). Evolutionary events in which a strain increases human-to-human transmissibility, but not enough to spark a pandemic, are extremely hard to observe, but if we could do so it would increase our ability to characterize the process of adaptation (Kucharski et al., 2015).

Despite these challenges, there has been tremendous interest and investment in making and using such predictions, and a number of new ideas to improve predictions are in various stages of development (Box 3). Building on the findings of a previous workshop (Russell et al., 2014), we considered in detail the present state of knowledge concerning three phenotypic traits: HA receptor binding specificity, and HA pH of activation, and polymerase complex activity, (Figure 1). These were chosen from a longer list of candidate traits (Table 1) because they span the viral life cycle (Figure 1) and their role in host adaptation has been extensively studied. All three are believed to be required for an influenza virus to cause a pandemic; consistent with this assumption, all three traits have been present to some degree in the earliest viruses isolated in pandemics since the 20th century, though some have been enhanced by subsequent evolution during seasonal transmission in humans. Moreover, for each of these three traits, viruses isolated from avian hosts typically do not show the mammalian-adapted phenotype, reflecting divergent selection pressures in the two classes of hosts (Tables 2, 3, and 4). All three traits changed in the adaptation of zoonotic H5 influenza viruses to droplet transmission in ferrets (Imai et al., 2012; Linster et al., 2014). We emphasize that each of these traits is quantitative, and that human-adaptation is not a threshold criterion but a continuum; in this review when we speak of human adaptation we mean a tendency to be better adapted to humans, rather than an absolute yes-or-no property.

Figure 1

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This review starts with a summary of our knowledge about the role of each of the three functional traits in conferring pandemic potential on a virus strain. Following these case studies, we draw some generalizations about the prospects of predicting pandemic risk from virus genotype or from assays of particular viral traits. For each trait we present a table showing the degree to which the sequence changes or phenotypic properties associated with avian or human adaptation are present in isolates from birds and humans, respectively. If the avian traits were always found in avian isolates and human traits always in human isolates, only the shaded cells on the main diagonal would be filled. In such a case, however, it is hard to see how viruses would ever make the jump from birds to humans, since so many traits would have to change simultaneously, and indeed the off-diagonal cells are not empty. Finding avian-adapted traits in viruses isolated from humans most often occurs in zoonotic cases, showing that not all human-adapted traits are required for the first human infection. In some cases there are also viruses isolated from humans after a pandemic starts that retain some degree of avian-like traits, and we discuss these in more detail in the text -- these represent the greatest challenge to use of genotypic or phenotypic information for pandemic prediction because they run the risk of false negatives. The other off-diagonal cell, which represents avian isolates with some human-like traits, simply shows that some circulation of viruses in birds is possible without the classical 'avian' phenotypes. How this happens is a phenomenon worthy of further study. We conclude with some recommendations for future research and for the practice of pandemic risk assessment.

There has been tremendous progress in understanding the traits involved in the adaptation of avian influenza viruses for efficient human-to-human transmission and the genetic and structural basis of each of these traits. While the ability to use virus sequence data to inform risk assessment of pandemic potential is improving, it remains essential to consider these data alongside other experimental and epidemiological data. For example, in 2013 there was a substantial increase in the number of human infections with A/H5N1 viruses in Cambodia. The increase in infections was cause for substantial concern by itself. Enhancing the level of concern was the finding that some of the viruses collected from infected humans contained previously identified genetic mutations suggestive of human adaptation (Davis et al., 2014). These findings led to extensive epidemiological and experimental investigations and then to the decision to produce a candidate vaccine virus from a virus representative of the 2013 Cambodian outbreaks.

While predictions of virus phenotypes from sequence data can be informative, they are not infallible, for several reasons, notably the large number of sites involved in determining such traits (Raman et al., 2014; Russell, 2014; Cauldwell et al., 2014; Mehle and Doudna, 2009; Mänz et al., 2012; Herfst et al., 2010), the important role of epistasis (dependence of a mutation’s effect on the genetic background in which it appears) in determining these traits (Russell et al., 2014; Kryazhimskiy et al., 2011; Gong and Bloom, 2014; Bloom et al., 2010; Wu et al., 2016; Raman et al., 2014; Tharakaraman et al., 2013; Gong et al., 2013), and the consequent imperfections in our ability to map single sequence polymorphisms to a trait value. For example, the hallmark HA amino acid residues 190, 226 and 228 are important to human adaptation, but “human-adapting” mutations at these residues do not always change receptor-binding specificity; it depends on the genetic background. Similarly, amino acid residues 627 and 701 of the PB2 protein are often involved in human adaptation, but both carried the “avian-adapted” residue in the 2009 H1N1 pandemic strain. When these changes were introduced individually or together in the laboratory, the resulting polymerase showed greater activity in a minigenome assay, but replication was unchanged or attenuated in vitro, in mice, and in ferrets (Herfst et al., 2010; Jagger et al., 2010). After the pandemic strain was identified and its anomalous residues at these sites noted, other sites within PB2 were identified and found to be responsible for human adaptation (Mehle and Doudna, 2009; Yamada et al., 2010).

Based on the evidence to date, it seems clear that all three of the traits considered in this review, and possibly others in Table 1, must be simultaneously present at least to some degree for a strain to cause a pandemic. Yet with only a few instances of pandemic strains emerging per century, it should not be surprising that a new pandemic strain would violate an apparent rule of human adaptation that applied perfectly to previous pandemic strains, as in the case of the PB2 residues associated with human adaptation in 2009, or as in the case of activation pH of HA in early 2009 isolates (Russier et al., 2016), which had a value outside the range previously seen in human influenza viruses. It is unclear whether the list of sites and phenotypic traits associated with human adaptation is nearly complete or will continue to grow as we experience additional pandemics. At least for the traits of receptor binding (Childs et al., 2009) (Table 2) and acid stability (Russier et al., 2016) (Table 3), full human adaptation may not be required to initiate a pandemic in a virus that is otherwise well-adapted for humans. Thus, whether or not the list of traits required for pandemic is now complete, our understanding of where the threshold lies for being sufficiently human-adapted continues to change.

There are three complementary approaches to address these limitations: improving genetic prediction of biological traits, improving assays of these traits, and improving animal models of human transmission; all approaches are currently progressing in parallel (Holder et al., 2011; Simon et al., 2011). The first approach aims to further refine our understanding of sequence-to-trait relationships by continued studies of diverse, naturally or artificially produced mutations and their effects on the traits of interest. Such research could use all of the approaches described above and higher-throughput assays that could be developed with improved technology, for example as described in Box 3. This will include generating mutations not found in known strains in nature to probe for those that could be involved in human adaptation in the future (Hanson et al., 2015; Thyagarajan and Bloom, 2014). The goal would be to identify classes of functionally equivalent substitutions, sufficient individually or in defined combinations to confer a trait of interest when introduced into a defined, avian-adapted genetic background. Use of in vitro approaches with noninfectious viruses or viral components, or infectious viruses containing surface proteins to which there was already population-wide immunity would reduce the possible biosafety and biosecurity risks of such studies (Lipsitch and Inglesby, 2014).

The second approach is to develop and improve the throughput and accuracy of biochemical and cell-biological assays of these traits, so that virus isolates can be characterized phenotypically in a routine manner, reducing reliance on sequence-based predictions. It seems feasible to develop high-throughput versions of many of the assays described in this review for each of the three traits discussed, which could then be routinely run on surveillance isolates to contribute to risk prediction. For none of these three traits is there a single gold standard assay, and different assays may provide different estimates of risk.

The third approach is to improve animal models to more precisely study phenotypes that are important for human adaptation, and to clarify whether the notion of 'mammalian adaptation' is in fact a valid category. Ferrets are the closest known model for human transmission (see Box 4). Respiratory-droplet transmission studies in ferrets, and potentially in other animal models, have shown a remarkably strong correlation with human transmissibility of influenza A strains (Buhnerkempe et al., 2015). While these assays are not perfectly predictive, they may be the most reliable way at present to assess the transmission potential of a virus in human populations. Here a partial counterexample to their overall strong predictive value is H7N9 avian influenza isolates from human zoonotic cases. These viruses transmit in ferrets, albeit less efficiently than human seasonal strains, yet human-to-human transmission has been extremely rare in the hundreds of human zoonotic cases caused by H7N9 (Buhnerkempe et al., 2015). A challenge is the expense and practical challenge of using large enough numbers of ferrets (Buhnerkempe et al., 2015; Belser et al., 2013; Nishiura et al., 2013) to assess transmissibility; this will remain a technique of limited throughput for the foreseeable future. Nonetheless, the value of ferret testing for risk assessment can be enhanced in at least two ways: first, by standardizing the conditions for ferret transmission experiments, so these can be more confidently compared between laboratories; and second, by continuing to combine ferret studies with studies of viral traits and sequence/structural studies to further identify correlates of transmissibility in ferrets.

Box 4

Ferret model: validity and limitations in pandemic risk assessment.

The use of small mammalian models in influenza virus pathogenesis and transmission has proven invaluable for the study of these complex, polygenic traits. The ferret model is particularly valuable, as ferrets are highly susceptible to most influenza A viruses without the need for prior host adaptation. However, even this gold-standard model is not a true substitute for humans. Below, we summarize the benefits, drawbacks, and alternatives to the ferret model for the study of influenza.

Validity. Influenza is a respiratory pathogen in humans, and employing mammalian models that possess comparable lung physiology permits a greater extrapolation of results from the laboratory. Importantly, the linkage types and distribution of sialic acids throughout the ferret respiratory tract are generally comparable to humans (Jayaraman et al., 2012; Jia et al., 2014): like humans, ferrets express the sialic acid ​N-acetylneuraminic acid (​Neu5Ac), but not the sialic acid ​N-glycolylneuraminic acid (​Neu5Gc), on respiratory epithelia. As a result, ferrets are uniquely suited for the study of influenza viruses compared with other small mammalian models which express Neu5Gc (Ng et al., 2014). Furthermore, human and avian influenza viruses exhibit comparable binding to upper and lower respiratory tract tissues in ferrets and humans (van Riel et al., 2006; Shinya et al., 2006).

Secondly, ferrets infected with influenza viruses demonstrate numerous clinical signs and symptoms of infection associated with human disease. Ferrets infected with human influenza viruses often exhibit transient weight loss, transient fever, and sneezing, whereas infection with selected HPAI viruses in this species can lead to pronounced weight loss, sustained fever, lethargy, dyspnea, and neurological complications (Belser et al., 2009). Thus, ferrets represent a preclinical model to assess the ability of novel vaccine and antiviral treatments to mitigate influenza virus. As ferrets are a suitable model for the coincident study of pathogenesis and transmission, this model allows for a greater understanding of virus-host interactions and the interplay between both of these parameters.

Finally, the ferret model can yield valuable insights about the potential human-to-human transmissibility of influenza viruses – the critical determinant of pandemic risk. A recent meta-analysis showed that estimates of transmissibility derived from ferret respiratory droplet transmission studies could explain 66% of measured variation in human transmissibility, for influenza subtypes that have been detected in humans (Buhnerkempe et al., 2015). Furthermore, there is a strong statistical relationship between the attack rates measured in particular ferret experiments and the probability that the influenza strain in question is capable of sustained transmission among humans: if two-thirds or more of contact ferrets become infected via respiratory droplets, then the strain is likely to have pandemic potential (see figure). However, extrapolation of this relationship to novel strains is inherently risky, and variable outcomes observed for H7N9 influenza transmission in ferrets highlight the potential for false alarms. Further analysis of ferret transmission experiments, ideally in concert with molecular and virological research, could raise their sensitivity and specificity for identifying pandemic threats.

Limitations. There is no ‘perfect’ small mammalian model for influenza. A longstanding challenge of the ferret model has been limited availability of ferret-specific commercial reagents compared with other models, though recent sequencing of the ferret genome should improve this situation (Peng et al., 2014). Ethical considerations, and the size and cost of ferrets, necessitate generally small sample sizes in ferret experiments, limiting statistical power (Belser et al., 2013). Like other vertebrate models, the ferret is not appropriate for high-throughput screens, so research in the ferret model is most potent when complemented with in vitro and computational approaches. Finally, ferrets are not well suited to model the multiple influenza exposures over several years that may be experienced by humans and may mold their immune responses in ways that affect the infection risk with subsequent viruses (Andrews et al., 2015). Studies of first influenza infection in ferrets may thus overestimate infection and/or transmission risk relative to that in populations with a history of prior infection with related viruses (Belser et al., 2016).

Alternatives. The ferret is but one of several well-characterized mammalian models for influenza virus. Mice are widely used in the field as they offer a greater availability of commercially available species-specific reagents, permit studies with greater statistical power due to larger sample sizes, and offer the advantage of transgenic animals. However, not all human influenza viruses replicate well in mice without prior adaptation due to a predominance of avian-like receptors in the murine respiratory tract; also mice do not display clinical signs and symptoms of influenza that mimic humans, and are not a reliable model for virus transmission studies. The guinea pig is another model, and offers several comparable advantages to ferrets, including generally similar lung physiology to humans and potential for transmission studies. Experiments in guinea pigs are often less expensive than in ferrets, because of lower husbandry costs and reduced drug costs when dosing is based on body weight (Lowen and Palese, 2007). However, guinea pigs do not exhibit clinical signs and symptoms of infection similar to humans, and do not exhibit severe disease following infection with HPAI or pandemic influenza viruses, limiting their utility for viral pathogenesis studies.

Box 4-figure 1

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https://doi.org/10.7554/eLife.18491.011

While the biological properties of a virus certainly play a large role in determining the pandemic risk posed by a strain, it is possible that even a virus perfectly adapted for human-to-human transmission might fail to transmit extensively, due to ecological factors, chance, or both. Initiation of a pandemic requires not only a well-adapted virus but ecological opportunity to spill over into humans (perhaps multiple times if the first introduction is not “successful” [Mills et al., 2006]), as well as a human population that is immunologically susceptible and sufficiently connected to establish ongoing transmission (Box 5). Additional complexity arises from the fact that selection pressures for within-host proliferation and competition may diverge from those needed for efficient transmission (Park et al., 2013). Genetic bottlenecks at the time of transmission (Poon et al., 2016; Varble et al., 2014; Zaraket et al., 2015) may further enhance the role of chance, as a highly adaptive variant arising in a host may not get transmitted in a particular event. However, selective bottlenecks, which have been observed in experimental transmission of H5N1 and avian-like H1N1 viruses in ferrets, could lower the barrier to emergence of human-adapted viruses (Moncla et al., 2016; Wilker et al., 2013). Both ecological and host factors are considered in the CDC’s IRAT (Trock et al., 2015).

Box 5

Role of seroepidemiology in pandemic risk assessment.

Pandemic threat assessment can also be enhanced by immunological surveys of human populations in geographical area where strains of concern are known to be circulating (Van Kerkhove et al., 2011). Serological surveys can help to estimate the frequency of spillover infections from non-human to human hosts and also to assess the degree of cross reactivity arising from endemic human strains that share recent genomic ancestors with non-human strains of concern (Figure for Box 4).

Attempts have been made to use serological surveys to estimate the rate of spillover infections to humans for recent strains of concern (Wang et al., 2012; Van Kerkhove et al., 2012). Sometimes blood samples are obtained from the general population (Chao et al., 2011) and other times only high risk individuals are tested. Inherent measurement error and cross-reactivity between human and non-human strains make the measurement of low rates of incidence problematic (Van Kerkhove et al., 2012). Confidence that serologic responses truly reflect zoonotic transmission, rather than cross-reactivity with antibodies generated in response to human influenza infection, may be enhanced by comparison of high-risk persons to those without known exposure to zoonotic sources (Huang et al., 2015; Gomaa et al., 2015). Although there is evidence of exposure of poultry workers to H5N1 influenza viruses in China, rates are much lower than for other endemic non-human influenza viruses(Kim et al., 2011), such as H9N2 (Blair et al., 2013). More recent studies of exposure of high risk workers to the H7N9 lineage suggest even higher rates of exposure to this new strain than has been observed in similar studies of H5N1 or H9N2 (Wang et al., 2014).

Even when rates of spillover can be estimated accurately, the use of such information in pandemic threat assessment is not obvious. Clearly, the first detected presence of human infections for a given strain is of concern because the degree of transmissibility among humans is unknown. Should the emergent strain fail to achieve sustained transmission, it is not immediately clear how best to use further information on the frequency of human spillover infections. For example, should we interpret high sustained levels of human spillover as evidence of increased risk because of the number of human infections, or as evidence of decreasing risk because of the number of times the strain has failed to achieve sustained transmission?

Cross reactivity between non-human and human influenza strains has implications beyond the measurement of spillover infections. Often levels of cross reactivity in humans may indicate some degree of reduced population susceptibility (Worobey et al., 2014). All else equal, such evidence of lower population susceptibility should reduce our level of concern about a pandemic threat from a particular virus, because even if it gains efficient human-to-human transmissibility, its effective reproductive number and the proportion of the population at risk will be less than for a virus to which there is no cross-reaction in the population. For example, older individuals are thought to have been far less susceptible to pandemic H1N1 than were younger individuals, because they had previously been exposed to similar strains early in life (Yu et al., 2008). The low average age of infection with a swine variant form of H3N2 (H3N2v) in North America (Jhung et al., 2013) is likely driven by reduced susceptibility in adults because of early exposure to similar strains. Such immunological overlaps are likely to be a general feature of influenza emergence because human strains frequently emerge into swine populations (Nelson et al., 2015).

Data on reduced human susceptibility due to cross-reactivity must be synthesized with other data used for threat assessment. In some cases, the aging of the part of the population with prior exposure to a closely related strain could be the most important known factor increasing the risk of an emergence event. Mechanistic models could be used to estimate the degree of increased risk of emergence due to the aging of partially immune cohorts.

Box 5-figure 1

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https://doi.org/10.7554/eLife.18491.013

Evolutionary factors also play a role in pandemic risk evaluations. Even with excellent surveillance, we may never isolate exactly the virus that is destined to cause a pandemic from an animal reservoir or a zoonotic human case; rather, we may isolate its evolutionary precursor. Understanding the potential of a strain to produce pandemic-capable progeny is yet a further scientific challenge. Perhaps the most startling finding of the gain-of-transmissibility experiments with H5N1 avian influenza viruses was that so few mutations were required to convert a strain circulating in birds to mammalian transmission. This concern was reinforced by a finding that many of these mutations, including combinations of some of them, were already present in strains isolated during surveillance (Russell et al., 2012). The interpretation of the latter finding, however, is complicated by the problem of epistasis: the effect of these mutations in the genetic background of field strains may or may not be the same as in the strain studied in the laboratory.

It seems clear that a pandemic risk assessment informed by genetic sequence data is better than one uninformed by such sequence data, but the thought experiment of considering the 2009 swine-origin virus, had it been seen prior to initiating the pandemic, shows that such efforts may fail to identify the risk posed by strains that subsequently cause a pandemic. According to the knowledge at the time, early human isolates of 2009 (and presumably their swine precursors) would have had an HA intermediate between human and avian adaptation in terms of receptor binding. They had an activation pH outside the range previously seen in human viruses and more typical of avian viruses. Moreover, these viruses lacked the amino acid residues then thought to confer human adaptation for the polymerase complex. We must imagine that had this strain been detected in swine surveillance prior to the pandemic emergence, genetic as well as phenotypic considerations would have marked it as low risk, creating a false-negative risk assessment. Given that this virus did in fact create a pandemic, it is evident that failure of a nonhuman influenza virus to fully meet the three criteria discussed in this review does not disqualify it from posing a significant risk of a pandemic.

Whether false positive predictions of high pandemic risk are also possible is more difficult to determine, because even a strain that is truly high risk may fail to cause a pandemic for any number of reasons; thus it is challenging to prove that an assessment of high risk for a particular strain was erroneous. From a decision-making perspective, a false positive is perhaps less worrisome than a false negative, as a false positive may motivate expenditure on prevention measures directed at a strain that would not have caused a pandemic, while a false negative may lead to a failure to respond to a strain that would.

As we seek to improve our understanding of genetic and phenotypic bases of efficient human transmission of influenza viruses, there are multiple possible approaches. One approach that has received considerable attention recently is to perform gain-of-transmissibility studies in highly pathogenic avian viruses; this has been controversial because of concerns about the unusual biosafety and biosecurity risks entailed in such studies (for contrasting perspectives on these risks, see the exchange in 2014–5 between Lipsitch and Inglesby, and Fouchier [Lipsitch and Inglesby, 2014, 2015; Fouchier, 2015]).

There are alternative approaches to ferret gain-of-transmission experiments in highly pathogenic avian influenza viruses, though disagreement remains about the level of evidence such alternatives provide. One alternative is to perform similar experiments starting from avian viruses that are not highly pathogenic in mammals, and/or are related to currently circulating human seasonal viruses, so that immunity would already be present in the population. Such experiments can provide the same degree of causal rigor as gain-of-function in highly pathogenic avian viruses with novel surface antigens and can elucidate general principles of mammalian adaptation, but they cannot confirm that the same changes would be observed in other strains that are not used in the experiment. A recent report shows a related way forward: the recreation of the steps of mammalian adaptation using viruses whose HA and NA are already circulating in humans (Lakdawala et al., 2015). Such loss+gain-of-transmissibility experiments reconstruct the properties of naturally occurring seasonal human strains, from laboratory-generated, avian-adapted (or at least human-deadapted) precursors. Reconstructing such seasonal strains should pose a risk similar to that of working with the seasonal strains themselves, less than that of a novel subtype. A 2011 report employed a similar strategy, demonstrating the importance of HA activation pH in mouse adaptation by selection experiments on a live attenuated H5N1 vaccine strain lacking the NS1 gene (Krenn et al., 2011). More recently, a 2009 H1N1 pandemic virus was modified to express a mutation that increased pH of HA activation, then selected in ferrets for droplet transmission, and it was found that a second site mutation partially restored the lower pH of activation of the selected virus (Russier et al., 2016). One limitation of de-adaptation strategies is that the acquisition of transmissibility is perhaps most likely to evolve by reversion of the de-adaptation changes. As with all gain-of-function and loss-of-function studies, epistatic effects of other loci in the genetic background of the viruses used in such studies set limits to the generalizability of such experiments. Another kind of alternative is simple characterization of ferret transmissibility of naturally occurring highly pathogenic strains without selection for airborne transmission. This approach can provide correlative evidence for the importance of genetic differences but cannot prove the mechanistic role of any particular change.

Even if strain-based assessment methods were much better, surveillance would be a key rate-limiting step for pandemic risk assessment to direct countermeasure development. If a virus about to cause a pandemic is not found in surveillance it cannot be assessed. The fact that we have yet to identify a pandemic strain in nonhuman hosts or in human spillover cases before the pandemic starts indicates there is much work to be done. Although surveillance has expanded since the 2009 pandemic, it has not been designed to optimize the chances of detecting a pandemic strain before it becomes pandemic; indeed, how to do so is not clear at present. Some possible considerations would be to maximize the diversity of isolates collected, to preferentially sample strains that are known to cause human infections, and to feed back information from risk assessments to inform choice of sampling. Rapid sequencing and phenotypic characterization of strains and dissemination of this information, along with interpretations of the risk profiles implied, is also important to maximizing the value of surveillance. Further thought should be given to the possibility of using high-throughput sequencing as a screen for which viruses should be subjected to phenotypic testing, which for the moment is typically more costly, slower, and lower-throughput than sequencing. More deliberate approaches to the design of surveillance systems would also depend on answering the question addressed in Box 2: how different must a virus be from previously characterized viruses to merit separate evaluation of its pandemic risk? The uncertainties noted above about the phenotypic characteristics of viruses isolated from previous pandemics (which may have been present in the primary isolate or may have arisen during egg passage in the laboratory) underline the need for careful attention to passage histories of surveillance isolates to avoid altering their genotype and phenotype post-isolation (Bush et al., 2000). Expanding and rationalizing surveillance in this way would require overcoming political, logistical and financial constraints that vary between countries and regions.

Even with all of the foregoing suggestions in place, it may be improbable that we can reliably identify the 'needle in the haystack' that is the next pandemic influenza strain. Ultimately, the goal is not risk assessment for its own sake, but preparedness and early response to pandemic threats. In other areas where security is at stake, it has been argued that making and improving predictions should be accompanied by a systematic effort to design responses that will not fail even if the predictions are wrong (Danzig, 2011). In the influenza context, the value of some countermeasures is strongly reliant on our ability to identify truly high-risk prepandemic threats: notably, preparation of seed vaccine stocks for candidate pandemic strains, stockpiling of subtype-specific vaccines, and culling of poultry infected with such strains. Other types of countermeasures, ranging from strengthening local public health departments to stockpiling antivirals or ventilators to developing faster processes for vaccine manufacture to universal vaccines that should be effective against any influenza A strain, should provide benefits whether or not we have advance notice of the strain causing the next pandemic. A comprehensive assessment of priorities to prevent or mitigate the next influenza pandemic should consider the balance between improving our risk assessment capacity and developing responses robust to the possibility that we will once again be caught by surprise.

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