Conjunction of factors triggering waves of seasonal influenza

  1. Ishanu Chattopadhyay
  2. Emre Kiciman
  3. Joshua W Elliott
  4. Jeffrey L Shaman
  5. Andrey Rzhetsky  Is a corresponding author
  1. University of Chicago, United States
  2. Microsoft Research, United States
  3. Columbia University, United States

Abstract

Using several longitudinal datasets describing putative factors affecting influenza incidence and clinical data on the disease and health status of over 150 million human subjects observed over a decade, we investigated the source and the mechanistic triggers of influenza epidemics. We conclude that the initiation of a pan-continental influenza wave emerges from the simultaneous realization of a complex set of conditions. The strongest predictor groups are as follows, ranked by importance: (1) the host population's socio- and ethno-demographic properties; (2) weather variables pertaining to specific humidity, temperature, and solar radiation; (3) the virus' antigenic drift over time; (4) the host populations land-based travel habits, and; (5) recent spatio-temporal dynamics, as reflected in the influenza wave auto-correlation. The models we infer are demonstrably predictive (area under the Receiver Operating Characteristic curve 80%) when tested with out-of-sample data, opening the door to the potential formulation of new population-level intervention and mitigation policies.

Article and author information

Author details

  1. Ishanu Chattopadhyay

    Computation Institute, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Emre Kiciman

    Computational Epidemiology and Social Sciences, Microsoft Research, Redmont, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Joshua W Elliott

    Computation Institute, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Jeffrey L Shaman

    Department of Environmental Health Sciences, Columbia University, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Andrey Rzhetsky

    Computation Institute, University of Chicago, Chicago, United States
    For correspondence
    arzhetsky@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6959-7405

Funding

Defense Sciences Office, DARPA (W911NF1410333)

  • Andrey Rzhetsky

National Institutes of Health (R01HL122712)

  • Andrey Rzhetsky

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2018, Chattopadhyay et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 3,483
    views
  • 485
    downloads
  • 39
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Ishanu Chattopadhyay
  2. Emre Kiciman
  3. Joshua W Elliott
  4. Jeffrey L Shaman
  5. Andrey Rzhetsky
(2018)
Conjunction of factors triggering waves of seasonal influenza
eLife 7:e30756.
https://doi.org/10.7554/eLife.30756

Share this article

https://doi.org/10.7554/eLife.30756

Further reading

    1. Epidemiology and Global Health
    Xiaoning Wang, Jinxiang Zhao ... Dong Liu
    Research Article

    Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar-sweetened beverages. Nevertheless, the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. We have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose, resembling the hyperangiogenic characteristics observed in proliferative diabetic retinopathy (PDR). Utilizing this model, we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels, especially intersegmental vessels (ISVs). The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells (ECs) into tip cells. Single-cell transcriptomic sequencing analysis of the ECs in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs, proliferating ECs, and a series of upregulated proangiogenic genes. Further analysis and experiments validated that reduced foxo1a mediated the excessive angiogenesis induced by monosaccharides via upregulating the expression of marcksl1a. This study has provided new evidence showing the negative effects of noncaloric monosaccharides on the vascular system and the underlying mechanisms.

    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease
    Amanda C Perofsky, John Huddleston ... Cécile Viboud
    Research Article

    Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997—2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity.