Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Amanda C. Perofsky; Chelsea L. Hansen; Roy Burstein; Shanda Boyle; Robin Prentice; Cooper Marshall; David Reinhart; Ben Capodanno; Melissa Truong; Kristen Schwabe-Fry; Kayla Kuchta; Brian Pfau; Zack Acker; Jover Lee; Thomas R. Sibley; Evan McDermot; Leslie Rodriguez-Salas; Jeremy Stone; Luis Gamboa; Peter D. Han; Amanda Adler; Alpana Waghmare; Michael L. Jackson; Michael Famulare; Jay Shendure; Trevor Bedford; Helen Y. Chu; Janet A. Englund; Lea M. Starita; Cécile Viboud

doi:10.1038/s41467-024-48528-2

Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

Amanda C. Perofsky^*, Chelsea L. Hansen, Roy Burstein, Shanda Boyle, Robin Prentice, Cooper Marshall, David Reinhart, Ben Capodanno, Melissa Truong, Kristen Schwabe-Fry, Kayla Kuchta, Brian Pfau, Zack Acker, Jover Lee, Thomas R. Sibley, Evan McDermot, Leslie Rodriguez-Salas, Jeremy Stone, Luis Gamboa, Peter D. HanAmanda Adler, Alpana Waghmare, Michael L. Jackson, Michael Famulare, Jay Shendure, Trevor Bedford, Helen Y. Chu, Janet A. Englund, Lea M. Starita, Cécile Viboud

^*Corresponding author for this work

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.

Original language	English
Article number	4164
Journal	Nature Communications
Volume	15
Number of pages	17
ISSN	2041-1723
DOIs	https://doi.org/10.1038/s41467-024-48528-2
Publication status	Published - 16 May 2024

Bibliographical note

Funding Information:
We thank the entire Seattle Flu Study (SFS) and Greater Seattle Coronavirus Assessment Network (SCAN) team for their hard work and dedication to these projects and the study participants for their participation in this research. We also thank Public Health \u2013 Seattle & King County for their contributions to the SCAN study and for providing samples collected at King County COVID-19 drive-through testing sites, the Tacoma-Pierce County Health Department for funding the collection and testing of SCAN respiratory specimens in Pierce County, and the Rapid Health Information Network (RHINO) program at the Washington Department of Health for providing syndromic surveillance data. We thank Dr. Jeff Duchin for helpful comments on the manuscript and the Division of International Epidemiology and Population Studies (DIEPS) of the Fogarty International Center and the Bedford Lab at Fred Hutch for useful discussions. This study used the high-performance computational resources of the Biowulf Linux cluster at the US National Institutes of Health ( http://biowulf.nih.gov ). Funding for the Seattle Flu Study and Greater Seattle Coronavirus Assessment Network (SCAN) was provided by Gates Ventures and the Howard Hughes Medical Institute. SCAN samples collected in Pierce County were funded by the Tacoma-Pierce County Health Department. ACP, CLH, SB, RP, CM, DR, BC, KSF, KK, BP, ZA, EM, LRS, JSt, LG, PDH, AW, JSh, TB, HYC, and LMS received third-party support from Gates Ventures through the Brotman Baty Institute during the conduct of the study. ACP, LMS, and TB are supported by CDC contract 75D30122C14368. RB and MF are employees of the Institute for Disease Modeling, a research group within and solely funded by the Bill and Melinda Gates Foundation. JSh and TB are supported by the Howard Hughes Medical Institute. CV is supported by the in-house research division of the Fogarty International Center, US National Institutes of Health. For samples collected through mechanisms other than SCAN, the funders had no role in any aspect of the study. Gates Ventures participated in the design of SCAN by providing input on the study screener and eligibility criteria but had no role in the conduct of SCAN, the collection, management, analysis, or interpretation of SCAN data, the preparation, review, or approval of this manuscript, or the decision to submit the manuscript for publication. No other funders were involved in any aspect of SCAN. Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US National Institutes of Health or the US government

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Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic yearsFinal published version, 7.78 MBLicence: CC BY

Cite this

Perofsky, A. C., Hansen, C. L., Burstein, R., Boyle, S., Prentice, R., Marshall, C., Reinhart, D., Capodanno, B., Truong, M., Schwabe-Fry, K., Kuchta, K., Pfau, B., Acker, Z., Lee, J., Sibley, T. R., McDermot, E., Rodriguez-Salas, L., Stone, J., Gamboa, L., ... Viboud, C. (2024). Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years. Nature Communications, 15, Article 4164. https://doi.org/10.1038/s41467-024-48528-2

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title = "Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years",

abstract = "Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.",

author = "Perofsky, {Amanda C.} and Hansen, {Chelsea L.} and Roy Burstein and Shanda Boyle and Robin Prentice and Cooper Marshall and David Reinhart and Ben Capodanno and Melissa Truong and Kristen Schwabe-Fry and Kayla Kuchta and Brian Pfau and Zack Acker and Jover Lee and Sibley, {Thomas R.} and Evan McDermot and Leslie Rodriguez-Salas and Jeremy Stone and Luis Gamboa and Han, {Peter D.} and Amanda Adler and Alpana Waghmare and Jackson, {Michael L.} and Michael Famulare and Jay Shendure and Trevor Bedford and Chu, {Helen Y.} and Englund, {Janet A.} and Starita, {Lea M.} and C{\'e}cile Viboud",

note = "Funding Information: We thank the entire Seattle Flu Study (SFS) and Greater Seattle Coronavirus Assessment Network (SCAN) team for their hard work and dedication to these projects and the study participants for their participation in this research. We also thank Public Health \u2013 Seattle & King County for their contributions to the SCAN study and for providing samples collected at King County COVID-19 drive-through testing sites, the Tacoma-Pierce County Health Department for funding the collection and testing of SCAN respiratory specimens in Pierce County, and the Rapid Health Information Network (RHINO) program at the Washington Department of Health for providing syndromic surveillance data. We thank Dr. Jeff Duchin for helpful comments on the manuscript and the Division of International Epidemiology and Population Studies (DIEPS) of the Fogarty International Center and the Bedford Lab at Fred Hutch for useful discussions. This study used the high-performance computational resources of the Biowulf Linux cluster at the US National Institutes of Health ( http://biowulf.nih.gov ). Funding for the Seattle Flu Study and Greater Seattle Coronavirus Assessment Network (SCAN) was provided by Gates Ventures and the Howard Hughes Medical Institute. SCAN samples collected in Pierce County were funded by the Tacoma-Pierce County Health Department. ACP, CLH, SB, RP, CM, DR, BC, KSF, KK, BP, ZA, EM, LRS, JSt, LG, PDH, AW, JSh, TB, HYC, and LMS received third-party support from Gates Ventures through the Brotman Baty Institute during the conduct of the study. ACP, LMS, and TB are supported by CDC contract 75D30122C14368. RB and MF are employees of the Institute for Disease Modeling, a research group within and solely funded by the Bill and Melinda Gates Foundation. JSh and TB are supported by the Howard Hughes Medical Institute. CV is supported by the in-house research division of the Fogarty International Center, US National Institutes of Health. For samples collected through mechanisms other than SCAN, the funders had no role in any aspect of the study. Gates Ventures participated in the design of SCAN by providing input on the study screener and eligibility criteria but had no role in the conduct of SCAN, the collection, management, analysis, or interpretation of SCAN data, the preparation, review, or approval of this manuscript, or the decision to submit the manuscript for publication. No other funders were involved in any aspect of SCAN. Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US National Institutes of Health or the US government",

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Perofsky, AC, Hansen, CL, Burstein, R, Boyle, S, Prentice, R, Marshall, C, Reinhart, D, Capodanno, B, Truong, M, Schwabe-Fry, K, Kuchta, K, Pfau, B, Acker, Z, Lee, J, Sibley, TR, McDermot, E, Rodriguez-Salas, L, Stone, J, Gamboa, L, Han, PD, Adler, A, Waghmare, A, Jackson, ML, Famulare, M, Shendure, J, Bedford, T, Chu, HY, Englund, JA, Starita, LM & Viboud, C 2024, 'Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years', Nature Communications, vol. 15, 4164. https://doi.org/10.1038/s41467-024-48528-2

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T1 - Impacts of human mobility on the citywide transmission dynamics of 18 respiratory viruses in pre- and post-COVID-19 pandemic years

AU - Perofsky, Amanda C.

AU - Hansen, Chelsea L.

AU - Burstein, Roy

AU - Boyle, Shanda

AU - Prentice, Robin

AU - Marshall, Cooper

AU - Reinhart, David

AU - Capodanno, Ben

AU - Truong, Melissa

AU - Schwabe-Fry, Kristen

AU - Kuchta, Kayla

AU - Pfau, Brian

AU - Acker, Zack

AU - Lee, Jover

AU - Sibley, Thomas R.

AU - McDermot, Evan

AU - Rodriguez-Salas, Leslie

AU - Stone, Jeremy

AU - Gamboa, Luis

AU - Han, Peter D.

AU - Adler, Amanda

AU - Waghmare, Alpana

AU - Jackson, Michael L.

AU - Famulare, Michael

AU - Shendure, Jay

AU - Bedford, Trevor

AU - Chu, Helen Y.

AU - Englund, Janet A.

AU - Starita, Lea M.

AU - Viboud, Cécile

N1 - Funding Information: We thank the entire Seattle Flu Study (SFS) and Greater Seattle Coronavirus Assessment Network (SCAN) team for their hard work and dedication to these projects and the study participants for their participation in this research. We also thank Public Health \u2013 Seattle & King County for their contributions to the SCAN study and for providing samples collected at King County COVID-19 drive-through testing sites, the Tacoma-Pierce County Health Department for funding the collection and testing of SCAN respiratory specimens in Pierce County, and the Rapid Health Information Network (RHINO) program at the Washington Department of Health for providing syndromic surveillance data. We thank Dr. Jeff Duchin for helpful comments on the manuscript and the Division of International Epidemiology and Population Studies (DIEPS) of the Fogarty International Center and the Bedford Lab at Fred Hutch for useful discussions. This study used the high-performance computational resources of the Biowulf Linux cluster at the US National Institutes of Health ( http://biowulf.nih.gov ). Funding for the Seattle Flu Study and Greater Seattle Coronavirus Assessment Network (SCAN) was provided by Gates Ventures and the Howard Hughes Medical Institute. SCAN samples collected in Pierce County were funded by the Tacoma-Pierce County Health Department. ACP, CLH, SB, RP, CM, DR, BC, KSF, KK, BP, ZA, EM, LRS, JSt, LG, PDH, AW, JSh, TB, HYC, and LMS received third-party support from Gates Ventures through the Brotman Baty Institute during the conduct of the study. ACP, LMS, and TB are supported by CDC contract 75D30122C14368. RB and MF are employees of the Institute for Disease Modeling, a research group within and solely funded by the Bill and Melinda Gates Foundation. JSh and TB are supported by the Howard Hughes Medical Institute. CV is supported by the in-house research division of the Fogarty International Center, US National Institutes of Health. For samples collected through mechanisms other than SCAN, the funders had no role in any aspect of the study. Gates Ventures participated in the design of SCAN by providing input on the study screener and eligibility criteria but had no role in the conduct of SCAN, the collection, management, analysis, or interpretation of SCAN data, the preparation, review, or approval of this manuscript, or the decision to submit the manuscript for publication. No other funders were involved in any aspect of SCAN. Disclaimer: The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US National Institutes of Health or the US government

PY - 2024/5/16

Y1 - 2024/5/16

N2 - Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.

AB - Many studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the effects of population mobility on the transmission of 17 endemic viruses and SARS-CoV-2 in Seattle over a 4-year period, 2018-2022. Before 2020, visits to schools and daycares, within-city mixing, and visitor inflow preceded or coincided with seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of COVID-19 stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagging and negatively correlated with SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger, longer-lasting relationships with mobility than SARS-CoV-2. Overall, mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change and at the beginning of epidemic waves.

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DO - 10.1038/s41467-024-48528-2

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AN - SCOPUS:85193522024

SN - 2041-1723

VL - 15

JO - Nature Communications

JF - Nature Communications

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ER -