Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States

Stephen M. Kissler, Julia Gog, Cecile Viboud, V. Charu, Ottar N. Bjørnstad, Lone Simonsen, Bryan T. Grenfell

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populated, well-connected areas. For pandemic influenza, however, epidemiological data have not been available at a fine enough geographic resolution to test this assumption. Here, we make use of fine-scale influenza-like illness incidence data derived from electronic medical claims records gathered from 834 3-digit ZIP (postal) codes across the US to identify the key geographic establishment sites, or “hubs”, of the autumn wave of the 2009 A/H1N1pdm influenza pandemic in the United States. A mechanistic spatial transmission model is fit to epidemic onset times inferred from the data. Hubs are identified by tracing the most probable transmission routes back to a likely first establishment site. Four hubs are identified: two in the southeastern US, one in the central valley of California, and one in the midwestern US. According to the model, 75% of the 834 observed ZIP-level outbreaks in the US were seeded by these four hubs or their epidemiological descendants. Counter-intuitively, the pandemic hubs do not coincide with large and well-connected cities, indicating that factors beyond population density and travel volume are necessary to explain the establishment sites of the major autumn wave of the pandemic. Geographic regions are identified where infection can be statistically traced back to a hub, providing a testable prediction of the outbreak's phylogeography. Our method therefore provides an important way forward to reconcile spatial diffusion patterns inferred from epidemiological surveillance data and pathogen sequence data.
OriginalsprogEngelsk
TidsskriftEpidemics
Vol/bind26
Sider (fra-til)86-94
ISSN1755-4365
DOI
StatusUdgivet - 2019
Udgivet eksterntJa

Emneord

    Citer dette

    Kissler, S. M., Gog, J., Viboud, C., Charu, V., Bjørnstad, O. N., Simonsen, L., & Grenfell, B. T. (2019). Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States. Epidemics, 26, 86-94. https://doi.org/10.1016/j.epidem.2018.10.002
    Kissler, Stephen M. ; Gog, Julia ; Viboud, Cecile ; Charu, V. ; Bjørnstad, Ottar N. ; Simonsen, Lone ; Grenfell, Bryan T. / Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States. I: Epidemics. 2019 ; Bind 26. s. 86-94.
    @article{ce52c5f8eb52405cb4048bb4c3c6670e,
    title = "Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States",
    abstract = "A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populated, well-connected areas. For pandemic influenza, however, epidemiological data have not been available at a fine enough geographic resolution to test this assumption. Here, we make use of fine-scale influenza-like illness incidence data derived from electronic medical claims records gathered from 834 3-digit ZIP (postal) codes across the US to identify the key geographic establishment sites, or “hubs”, of the autumn wave of the 2009 A/H1N1pdm influenza pandemic in the United States. A mechanistic spatial transmission model is fit to epidemic onset times inferred from the data. Hubs are identified by tracing the most probable transmission routes back to a likely first establishment site. Four hubs are identified: two in the southeastern US, one in the central valley of California, and one in the midwestern US. According to the model, 75{\%} of the 834 observed ZIP-level outbreaks in the US were seeded by these four hubs or their epidemiological descendants. Counter-intuitively, the pandemic hubs do not coincide with large and well-connected cities, indicating that factors beyond population density and travel volume are necessary to explain the establishment sites of the major autumn wave of the pandemic. Geographic regions are identified where infection can be statistically traced back to a hub, providing a testable prediction of the outbreak's phylogeography. Our method therefore provides an important way forward to reconcile spatial diffusion patterns inferred from epidemiological surveillance data and pathogen sequence data.",
    keywords = "Pandemic influenza, transmission hubs, metapopulation, gravity model, Phylogeography",
    author = "Kissler, {Stephen M.} and Julia Gog and Cecile Viboud and V. Charu and Bj{\o}rnstad, {Ottar N.} and Lone Simonsen and Grenfell, {Bryan T.}",
    year = "2019",
    doi = "10.1016/j.epidem.2018.10.002",
    language = "English",
    volume = "26",
    pages = "86--94",
    journal = "Epidemics",
    issn = "1755-4365",
    publisher = "Elsevier BV",

    }

    Kissler, SM, Gog, J, Viboud, C, Charu, V, Bjørnstad, ON, Simonsen, L & Grenfell, BT 2019, 'Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States' Epidemics, bind 26, s. 86-94. https://doi.org/10.1016/j.epidem.2018.10.002

    Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States. / Kissler, Stephen M.; Gog, Julia; Viboud, Cecile; Charu, V.; Bjørnstad, Ottar N.; Simonsen, Lone; Grenfell, Bryan T.

    I: Epidemics, Bind 26, 2019, s. 86-94.

    Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

    TY - JOUR

    T1 - Geographic Transmission Hubs of the 2009 Influenza Pandemic in the United States

    AU - Kissler, Stephen M.

    AU - Gog, Julia

    AU - Viboud, Cecile

    AU - Charu, V.

    AU - Bjørnstad, Ottar N.

    AU - Simonsen, Lone

    AU - Grenfell, Bryan T.

    PY - 2019

    Y1 - 2019

    N2 - A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populated, well-connected areas. For pandemic influenza, however, epidemiological data have not been available at a fine enough geographic resolution to test this assumption. Here, we make use of fine-scale influenza-like illness incidence data derived from electronic medical claims records gathered from 834 3-digit ZIP (postal) codes across the US to identify the key geographic establishment sites, or “hubs”, of the autumn wave of the 2009 A/H1N1pdm influenza pandemic in the United States. A mechanistic spatial transmission model is fit to epidemic onset times inferred from the data. Hubs are identified by tracing the most probable transmission routes back to a likely first establishment site. Four hubs are identified: two in the southeastern US, one in the central valley of California, and one in the midwestern US. According to the model, 75% of the 834 observed ZIP-level outbreaks in the US were seeded by these four hubs or their epidemiological descendants. Counter-intuitively, the pandemic hubs do not coincide with large and well-connected cities, indicating that factors beyond population density and travel volume are necessary to explain the establishment sites of the major autumn wave of the pandemic. Geographic regions are identified where infection can be statistically traced back to a hub, providing a testable prediction of the outbreak's phylogeography. Our method therefore provides an important way forward to reconcile spatial diffusion patterns inferred from epidemiological surveillance data and pathogen sequence data.

    AB - A key issue in infectious disease epidemiology is to identify and predict geographic sites of epidemic establishment that contribute to onward spread, especially in the context of invasion waves of emerging pathogens. Conventional wisdom suggests that these sites are likely to be in densely-populated, well-connected areas. For pandemic influenza, however, epidemiological data have not been available at a fine enough geographic resolution to test this assumption. Here, we make use of fine-scale influenza-like illness incidence data derived from electronic medical claims records gathered from 834 3-digit ZIP (postal) codes across the US to identify the key geographic establishment sites, or “hubs”, of the autumn wave of the 2009 A/H1N1pdm influenza pandemic in the United States. A mechanistic spatial transmission model is fit to epidemic onset times inferred from the data. Hubs are identified by tracing the most probable transmission routes back to a likely first establishment site. Four hubs are identified: two in the southeastern US, one in the central valley of California, and one in the midwestern US. According to the model, 75% of the 834 observed ZIP-level outbreaks in the US were seeded by these four hubs or their epidemiological descendants. Counter-intuitively, the pandemic hubs do not coincide with large and well-connected cities, indicating that factors beyond population density and travel volume are necessary to explain the establishment sites of the major autumn wave of the pandemic. Geographic regions are identified where infection can be statistically traced back to a hub, providing a testable prediction of the outbreak's phylogeography. Our method therefore provides an important way forward to reconcile spatial diffusion patterns inferred from epidemiological surveillance data and pathogen sequence data.

    KW - Pandemic influenza

    KW - transmission hubs

    KW - metapopulation

    KW - gravity model

    KW - Phylogeography

    U2 - 10.1016/j.epidem.2018.10.002

    DO - 10.1016/j.epidem.2018.10.002

    M3 - Journal article

    VL - 26

    SP - 86

    EP - 94

    JO - Epidemics

    JF - Epidemics

    SN - 1755-4365

    ER -