Ethics approval and consent to participate: The study was approved by the University of Washington Institutional Review Board and the Centers for Disease Control and Prevention relied on that review and approval. All participants provided informed consent and/or assent. All methods were carried out in accordance with relevant guidelines and regulations
Consent for Publication: Not applicable.
Availability of data and materials: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. All consensus genomes were publicly deposited to the Global Initiative on Sharing All Influenza Data (GISAID; gisaid.org21) database immediately after data generation. The GISAID accession numbers for SARS-CoV-2 positive samples utilized in this analysis are listed here:
GISAID name
|
GISAID Accession
|
B/Washington/E8/2019
|
EPI_ISL_16209231
|
B/Washington/E7/2019
|
EPI_ISL_16173925
|
B/Washington/E6/2019
|
EPI_ISL_16173551
|
B/Washington/E5/2019
|
EPI_ISL_16173550
|
B/Washington/E4/2019
|
EPI_ISL_16173548
|
B/Washington/E3/2019
|
EPI_ISL_16173547
|
B/Washington/E2/2019
|
EPI_ISL_16173546
|
B/Washington/E1/2019
|
EPI_ISL_16173543
|
B/Washington/C1/2020
|
EPI_ISL_16173541
|
B/Washington/O1/2020
|
EPI_ISL_16173540
|
B/Washington/O3/2019
|
EPI_ISL_16173539
|
B/Washington/O2/2019
|
EPI_ISL_16173538
|
B/Washington/O1/2019
|
EPI_ISL_16173536
|
B/Washington/D1/2019
|
EPI_ISL_16173535
|
B/Washington/L2/2020
|
EPI_ISL_16173534
|
B/Washington/L1/2020
|
EPI_ISL_16173533
|
A/Washington/L4/2020
|
EPI_ISL_16171529
|
A/Washington/L3/2020
|
EPI_ISL_16171527
|
A/Washington/L2/2020
|
EPI_ISL_16171526
|
A/Washington/L1/2020
|
EPI_ISL_16171525
|
A/Washington/D2/2020
|
EPI_ISL_16169725
|
A/Washington/D1/2020
|
EPI_ISL_16169724
|
A/Washington/F1/2020
|
EPI_ISL_16120168
|
Competing interests: Dr. Chu reported consulting with Ellume, Pfizer, The Bill and Melinda Gates Foundation, Glaxo Smith Kline, and Merck. She has received research funding from Gates Ventures, Sanofi Pasteur, and support and reagents from Ellume and Cepheid outside of the submitted work. Dr. Englund reported consulting with Sanofi Pasteur, AstraZeneca, and Meissa Vaccines, and has received research funding from AstraZeneca, GlaxoSmithKline, Merck, and Pfizer outside the submitted work.
Funding: The first year of this study was part of the Seattle Flu Study, funded by Gates Ventures. Gates Ventures was not involved in the design of the study, does not have any ownership over the management and conduct of the study, the data, or the rights to publish. This work was supported by the Centers for Disease Control and Prevention [Contract number: 75D30120C09190]. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention or its various funders.
Authors’ contributions:
Conceived of study: Anne Emanuels, Jessica Heimonen, Constance Ogokeh, Melissa A. Rolfes, James P. Hughes, Timothy M. Uyeki, Lea M. Starita, Janet A. Englund, Helen Y. Chu
Designed study tools for data collection or analysis: Jessica Heimonen, Jessica O'Hanlon, Anne Emanuels, Amanda M. Casto, Christian Frazar, Peter D. Han, Constance Ogokeh, Melissa A. Rolfes, Timothy M. Uyeki, Lea M. Starita, Janet A. Englund, Helen Y. Chu
Collected data or supervised data collection: Anne Emanuels, Jessica Heimonen, Jessica O'Hanlon, Anne Emanuels, Peter D. Han, Lea M. Starita, Janet A. Englund, Helen Y. Chu
Analyzed data or supervised analysis: Anne Emanuels, Amanda M. Casto, Julia H. Rogers, Erin Chung, Constance Ogokeh, Melissa A. Rolfes, James P. Hughes, Helen Y. Chu
Wrote manuscript: Anne Emanuels, Amanda M. Casto
Edited manuscript: Constance Ogokeh, Melissa A. Rolfes, Julia H. Rogers, Erin Chung, Eric J. Chow, James P. Hughes, Janet A. Englund, Helen Y. Chu
Acknowledgements: We would like to thank all the household members who volunteered their time, effort, and dedication to this study. This study was supported by the Seattle Flu Study (SFS) team, with the full list of SFS investigators listed below. REDCap at ITHS is supported by the National Center for Advancing Translational Sciences of the National Institutes of Health under Award Number UL1 TR002319. This work was supported in part by the National Institutes of Health (grant T32HD007233 to EC).
- Seattle Flu Study Principal Investigators – Helen Y. Chu, Michael Boeckh, Janet A. Englund, Michael Famulare, Barry R. Lutz, Deborah A. Nickerson, Mark J. Rieder, Lea M. Starita, Matthew Thompson, Jay Shendure, and Trevor Bedford.
- Seattle Flu Study Co-Investigators – Amanda Adler, Elisabeth Brandstetter, Roy Burstein, Shari Cho, Anne Emanuels, Chris D. Frazar, Rachel E. Geyer, Peter D. Han, James Hadfield, Jessica Heimonen, Michael L. Jackson, Anahita Kiavand, Ashley E. Kim, Louise E. Kimball, Jack Henry Kotnik, Kirsten Lacombe, Jennifer K. Logue, Victoria Lyon, Denise J. McCulloch, Jessica O'Hanlon, Matthew Richardson, Julia H. Rogers, Thomas R. Sibley, Monica L. Zigman Suchsland, Melissa Truong, Caitlin R. Wolf, and Weizhi Zhong.