Neutrality, Cross-Immunity and Subtype Dominance in Avian Influenza Viruses

<div><p>Avian influenza viruses (AIVs) are considered a threat for their potential to seed human influenza pandemics. Despite their acknowledged importance, there are significant unknowns regarding AIV transmission dynamics in their natural hosts, wild birds. Of particular interest is the difference in subtype dynamics between human and bird populations–in human populations, typically only two or three subtypes cocirculate, while avian populations are capable of simultaneously hosting a multitude of subtypes. One species in particular–ruddy turnstones (<i>Arenaria interpres</i>)–has been found to harbour a very wide range of AIV subtypes, which could make them a key player in the spread of new subtypes in wild bird populations. Very little is known about the mechanisms that drive subtype dynamics in this species, and here we address this gap in our knowledge. Taking advantage of two independent sources of data collected from ruddy turnstones in Delaware Bay, USA, we examine patterns of subtype diversity and dominance at this site. We compare these patterns to those produced by a stochastic, multi-strain transmission model to investigate possible mechanisms that are parsimonious with the observed subtype dynamics. We find, in agreement with earlier experimental work, that subtype differences are unnecessary to replicate the observed dynamics, and that neutrality alone is sufficient. We also evaluate the role of subtype cross-immunity and find that it is not necessary to generate patterns consistent with observations. This work offers new insights into the mechanisms behind subtype diversity and dominance in a species that has the potential to be a key player in AIV dynamics in wild bird populations.</p></div

Plots showing analyses of dominance and diversity patterns from datasets 1 and 2.

<p>The Simpson’s diversity index for the four subtypes of interest from both datasets is presented in (a). Absolute change in rank against rank ((b) and (c)), change in rank against rank ((d) and (e)) and rank-abundance curves ((f) and (g)) are presented for each dataset - panel letters given refer to datasets 1 and 2 respectively. Panels (h)-(k) show correlations in the data, with (h)-(i) showing any significant correlations between subtype presence/absence for the complete datasets, and (j)-(k) showing any correlations between prevalence levels for the 4 subtypes of interest.</p

The Cartesian distance between Barycentric coordinates for both the model and data, and their respective autocorrelations.

<p>Figures showing the Cartesian distance between Barycentric coordinates for both the data (a) and a model simulation using the best-fit parameter set (c). The autocorrelations for both of these are shown in figures (b) and (d) respectively. The 95% significance levels are not shown as their threshold is much larger than the calculated values.</p

Schematic of the model with two-subtypes depicted for illustration.

<p>Hosts are born susceptible to both subtypes () and their subsequent status with respect to both subtypes is tracked. Infection events are represented by solid arrows while loss of immunity is depicted by dotted arrows.</p

Prevalence plots of datasets 1 and 2.

<p>(a) A stacked bar chart of the approximate prevalence of HA subtypes. (b) The prevalence time series from both datasets for the four selected hemagglutinin (HA) subtypes. In both cases, the two datasets are separated by a gap on the x-axis. For dataset 1, a total of 4266 fecal or cloacal samples were collected over the time period 1985–2000 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088817#pone.0088817-Krauss1" target="_blank">[9]</a>; for dataset 2 the average annual sample size was 400.</p

Model predicted prevalence curves for all three hosts for a variety of different parameter sets.

<p>Panel (a) shows the prevalence curves for migratory ducks, resident ducks and ruddy turnstones for no cross-immunity and low transmission and consumption rates. Panel (b) shows the prevalence curves for all species for a cross-immunity rate of 0.5, with a higher transmission rate than in (a) and with a low consumption rate. Panel (c) shows the case with no cross-immunity, low transmission rate and an increased consumption rate (over (a) and (b)). Finally, panel (d) shows the prevalence curves when the cross-immunity rate is 0.5, transmission rate is low and consumption rate is greatly increased. In each panel, the histogram next to the ruddy turnstone (RUTU) prevalence curve is the histogram of the Simpson’s diversity index (SDI), as averaged over all simulations with the given parameter set. Simpson’s diversity index is calculated from a sample of the true prevalence, as calculated while the birds are present in Delaware Bay. See model description for more details on sampling. Note that “Mig” here stands for migrating ducks and “Res” denotes resident ducks.</p

Histopathology lesions observed in wood ducks (<i>Aix sponsa</i>) that succumbed or survived after challenge with the highly pathogenic avian influenza virus A/whooper swan/Mongolia/244/05 (H5N1)^a.

a<p>Wood ducks were challenged via choanal cleft with a dose of 10⁴EID₅₀ of A/whooper swan/Mongolia/244/05 (H5N1) 21 days after experimental pre-exposure to different subtypes of low pathogenic avian influenza viruses.</p

Serological status, as determined by hemagglutination inhibition, of wood ducks (<i>Aix sponsa</i>) 21 days after experimental pre-exposure to low pathogenicity avian influenza (LPAI) viruses^a, and 10 days after challenge with the highly pathogenic avian influenza (HPAI) virus A/whooper swan/Mongolia/244/05 (H5N1)^b.

a<p>Birds were inoculated via choanal cleft with a dose of 10⁶EID₅₀ of different LPAI viruses. Serologic data of the naïve group were omitted due the 100% mortality observed in this group, and data of the A/mallard/Netherlands/2/05 (H5N2) group were omitted due to lack of seroconversion.</p>b<p>Birds were challenged via choanal cleft with a dose of 10⁴EID₅₀ of A/whooper swan/Mongolia/244/05 (H5N1), 21 days after experimental pre-exposure to different subtypes of LPAI viruses.</p>c<p>Samples with HI titer≥8 were considered positive.</p>d<p>HI using antigen against homosubtypic LPAI virus, either H1N1, H5N1, or H5N2.</p>e<p>HI using antigen against A/whooper swan/Mongolia/244/05 (H5N1).</p>f<p>Abbreviations: LPAIV-dpe = days after LPAI pre-exposure; HPAIV-dpc = days after H5N1 HPAI challenge; † = succumbed to HPAI H5N1 infection.</p

Serological status before and after the experimental low pathogenicity avian influenza (LPAI) virus exposure, virus isolation data, and mortality of wood ducks (<i>Aix sponsa</i>) experimentally inoculated^a with different subtypes of LPAI viruses and subsequently challenged with the highly pathogenic avian influenza (HPAI) virus A/whooper swan/Mongolia/244/05 (H5N1)^b.

a<p>Birds were pre-exposed via choanal cleft with a dose of 10⁶EID₅₀.</p>b<p>Birds were challenged via choanal cleft with a dose of 10⁴EID₅₀ 21 days after experimental pre-exposure to LPAI viruses.</p>c<p>Groups of wood ducks (n = 5) experimentally pre-exposed to different LPAI viruses.</p>d<p>The naïve group was not experimentally pre-exposed to LPAI virus.</p>e<p>Abbreviations: bELISA = blocking ELISA; HI = hemagglutination inhibition; MDT = mean death time (days); + = positive; − = negative; NA = non applicable.</p>f<p>bELISA result (number of birds). Twelve out of 25 birds had avian influenza nucleoprotein antibodies at the beginning of the trial, before experimental exposure to a LPAI virus.</p>g<p>Number of birds that had at least one cloacal and/or oropharyngeal swab that tested positive on virus isolation after avian influenza virus exposure/total number of birds.</p>h<p>HI using antigen against homosubtypic LPAI virus, either H5N2, H1N1, or H5N1. Serum samples were colleted 21 days after LPAI virus pre-exposure.</p

Immunohistochemical analysis for nucleoprotein of avian influenza virus of wood ducks (<i>Aix sponsa</i>) that succumbed to infection (n = 13) with the highly pathogenic avian influenza virus A/whooper swan/Mongolia/244/05 (H5N1)^a.

a<p>Wood ducks were challenged via choanal cleft with a dose of 10⁴EID₅₀ of A/whooper swan/Mongolia/244/05 (H5N1) 21 days after experimental pre-exposure to different subtypes of low pathogenic avian influenza viruses.</p>b<p>Numbers of immunohistochemically positive cells: + = few; ++ = moderate; +++ = numerous.</p><p>*Positive immunohistochemical staining associated or not with microscopic lesions.</p><p>**Positive immunohistochemical staining not associated with microscopic lesions.</p