Data from: Subtype diversity and reassortment potential for co-circulating avian influenza viruses at a diversity hot spot

1. Biological diversity has long been used to measure ecological health. While evidence exists from many ecosystems that declines in host biodiversity may lead to greater risk of disease emergence, the role of pathogen diversity in the emergence process remains poorly understood. Particularly, because a more diverse pool of pathogen types provides more ways in which evolutionary innovations may arise, we suggest that host–pathogen systems with high pathogen diversity are more prone to disease emergence than systems with relatively homogeneous pathogen communities. We call this prediction the diversity-emergence hypothesis. 2. To show how this hypothesis could be tested, we studied a system comprised of North American shorebirds and their associated low-pathogenicity avian influenza (LPAI) viruses. These viruses are important as a potential source of genetic innovations in influenza. A theoretical contribution of this study is an expression predicting the rate of viral subtype reassortment to be proportional to both prevalence and Simpson's Index, a formula that has been used traditionally to quantify biodiversity. We then estimated prevalence and subtype diversity in host species at Delaware Bay, a North American AIV hotspot, and used our model to extrapolate from these data. 3. We estimated that 4 to 39 virus subtypes circulated at Delaware Bay each year between 2000 and 2008, and that surveillance coverage (percentage of co-circulating subtypes collected) at Delaware Bay is only about 63·0%. Simpson's Index in the same period varied more than fourfold from 0·22 to 0·93. These measurements together with the model provide an indirect, model-based estimate of the reassortment rate. A proper test of the diversity-emergence hypothesis would require these results to be joined to independent and reliable estimates of reassortment, perhaps obtained through molecular surveillance. 4. These results suggest both that subtype diversity (and therefore reassortment) varies from year to year and that several subtypes contributing to reassortment are going undetected. The similarity between these results and more detailed studies of one host, ruddy turnstone (Arenaria interpres), further suggests that this species may be the primary host for influenza reassortment at Delaware Bay. 5. Biological diversity has long been quantified using Simpson's Index. Our model links this formula to a mechanistic account of reassortment in multipathogen systems in the form of subtype diversity at Delaware Bay, USA. As a theory of how pathogen diversity may influence the evolution of novel pathogens, this work is a contribution to the larger project of understanding the connections between biodiversity and disease.

1. 生物多样性（biological diversity）长期以来一直被用于衡量生态系统健康状况。尽管诸多生态系统的研究证据表明，宿主生物多样性下降可能提升疾病出现风险，但病原体多样性在疾病出现过程中的作用仍不甚明确。具体而言，由于病原体类型的多样化种群可为进化创新提供更多潜在路径，我们提出：相较于病原体群落相对均质的宿主-病原体系统，具备高病原体多样性的宿主-病原体系统更易发生疾病暴发。我们将这一预测命名为“多样性-出现假说（diversity-emergence hypothesis）”。
2. 为验证该假说的可行性，我们以北美鸻鹬类鸟类及其携带的低致病性禽流感（low-pathogenicity avian influenza, LPAI）病毒为研究系统开展研究。此类病毒作为流感病毒遗传创新的潜在来源，具有重要研究价值。本研究的一项理论贡献在于，推导出病毒亚型重配率与流行率及辛普森多样性指数（Simpson's Index）均呈正比的表达式——该指数传统上被用于量化生物多样性。随后，我们对北美禽流感病毒（avian influenza virus, AIV）热点区域特拉华湾（Delaware Bay）内宿主物种的病毒流行率与亚型多样性进行了估算，并基于上述数据利用所建模型开展外推分析。
3. 我们估算得出，2000年至2008年间，特拉华湾每年有4至39种病毒亚型循环传播，且该区域的监测覆盖率（即收集到的共循环亚型占比）仅约为63.0%。同期辛普森多样性指数的波动幅度超过四倍，介于0.22至0.93之间。上述测算结果结合所建模型，可实现基于模型的重配率间接估算。若要对“多样性-出现假说”开展严格验证，则需将本研究结果与通过分子监测获得的独立可靠的重配率估算值相结合。
4. 上述结果表明，病毒亚型多样性（进而影响重配事件）存在年度差异，且部分参与重配的亚型尚未被监测发现。本研究结果与针对单一宿主物种红颈滨鹬（Arenaria interpres）开展的更详细研究结果高度吻合，进一步表明红颈滨鹬可能是特拉华湾地区流感病毒重配的主要宿主。
5. 长期以来，辛普森多样性指数一直被用于量化生物多样性。我们所建模型将该公式与美国特拉华湾地区基于亚型多样性的多病原体系统重配机制分析相结合。本研究作为阐释病原体多样性如何影响新型病原体进化的理论成果，为探索生物多样性与疾病之间的关联这一宏观研究课题提供了重要支撑。