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main.tex
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\documentclass{article}
% Packages used
\input{latex-head.tex}
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% Suppress the printing of the date
\date{}
\begin{document}
\title{Incident COVID-19 infections before Omicron in the \US}
% Authors and affiliations
\author[a]{Rachel Lobay\thanks{Corresponding author: Mailing and e-mail addresses as above. Telephone number: 1-604-822-0570.}}
\author[b]{Ajitesh Srivastava}
\author[c]{Ryan J.\ Tibshirani}
\author[d]{Daniel J.\ McDonald}
\affil[a]{Department of Statistics, The University of British Columbia, \par
Earth Sciences Building, 2207 Main Mall, Room 3182, \par Vancouver, BC, Canada, V6T 1Z4\\
\texttt{[email protected]}}
\affil[b]{Department of Computer and Electrical Engineering, University of Southern California, \par
EEB 226, 3740 McClintock Ave, \par
Los Angeles, CA, United States, 90089-2562\\
\texttt{[email protected]}}
\affil[c]{Department of Statistics, The University of California, Berkeley, \par
367 Evans Hall, \par
Berkeley, CA, United States, 94720-3860\\
\texttt{[email protected]}}
\affil[d]{Department of Statistics, The University of British Columbia, \par
Earth Sciences Building, 2207 Main Mall, Room 3182, \par Vancouver, BC, Canada, V6T 1Z4\\
\texttt{[email protected]}}
\maketitle
% Corresponding Author
%\textbf{Corresponding Author:} \\ Rachel Lobay. Mailing and e-mail addresses as above. Telephone number: 1-604-822-0570. \\
\newpage
\suppressfloats
\begin{abstract}
The timing and magnitude of COVID-19 infections are of interest to the public
and to public health, but these are challenging to ascertain due to the volume
of undetected asymptomatic cases and reporting delays. Accurate estimates of
COVID-19 infections based on finalized data can improve understanding of the
pandemic and provide more meaningful quantification of disease patterns and
burden. Therefore, we retrospectively estimate daily incident infections for
each \US state prior to Omicron. To this end, reported COVID-19 cases are
deconvolved to their likely date of infection onset using delay distributions
estimated from the CDC line list. Then, a novel serology-driven model is used to
scale these deconvolved cases to account for the unreported infections. The
resulting infection estimates incorporate variant-specific incubation periods,
reinfections, and waning antigenic immunity. They clearly demonstrate that
reported cases failed to reflect the full extent of disease burden in all
states. Most notably, infections were severely underreported during the Delta
wave, with an estimated reporting rate as low as 6.3\% in New Jersey, 7.3\% in
Maryland, and 8.4\% in Nevada. Moreover, in 44 states, fewer than 1/3 of
infections eventually appeared as case reports, and there were sustained periods
where surges in infections were virtually undetectable through reported cases.
This pattern was clearly illustrated by North and South Dakota during the spring
of 2021, as well as by several Northeastern states during the Delta wave of late
summer that year. While reported cases offered a convenient proxy of
disease burden, they failed to capture the full extent of infections and
severely underestimated the true disease burden. Our retrospective analysis
also estimates other important quantities for every state, including
variant-specific deconvolved cases, time-varying case ascertainment ratios, as
well as infection-hospitalization and infection-fatality ratios. \\
\noindent\textbf{Keywords:} COVID-19; SARS-CoV-2; Infections; Deconvolution; Time series; Seroprevalence; Antibody
\end{abstract}
\input{doc/intro.tex}
\input{doc/methods.tex}
\input{doc/results.tex}
\input{doc/discussion.tex}
\newpage
\section*{CRediT authorship contribution statement}
\textbf{Ryan J.\ Tibshirani:} Conceptualization, Methodology, Writing - Reviewing and editing.
\textbf{Daniel J.\ McDonald:} Conceptualization, Methodology, Software, Visualization, Writing - Reviewing and editing.
\textbf{Ajitesh Srivastava:} Methodology, Writing - Reviewing and editing.
\textbf{Rachel Lobay:} Methodology, Software, Visualization, Formal analysis, Writing - Original draft, Writing - Reviewing and editing.
%RL acquired the data, performed the
%statistical analysis, and wrote the initial draft of the paper. DJM, RT, and AS,
%reviewed and revised the paper. All authors were involved in significant
%discussion and development of the methodology.
\section*{Data availability}
The required materials and code for reproducing the figures and the numerical results are
available at
\href{https://github.com/cmu-delphi/latent-infections/}{https://github.com/cmu-delphi/latent-infections/}.
\section*{Funding}
This research did not receive any specific grant from funding agencies
in the public, commercial, or not-for-profit sectors.
\section*{Competing interests}
The authors declare no competing interests.
\section*{Acknowledgements}
We would like to thank members of the Delphi research group for valuable
feedback, and Change Healthcare and Optum/United Health Group for their
invaluable data partnership and collaboration.
We gratefully acknowledge all
data contributors, i.e., the Authors and their Originating laboratories
responsible for obtaining the specimens, and their Submitting laboratories for
generating the genetic sequence and metadata and sharing via the GISAID
Initiative \citep{elbe2017data}, on which this research is based.
% Required Gisaid acknowledgement
Any opinions, findings, and
conclusions or recommendations expressed in this material are
those of the authors and do not necessarily reflect the views of
the National Science Foundation and the Centers for Disease
Control and Prevention.
% NSF and CDC acknowledgement
DJM and RJT were supported by Centers for Disease Control and Prevention (CDC)
Grant No.\ 75D30123C15907. DJM and RL received support from the National
Sciences and Engineering Research Council of Canada and the University of
British Columbia. AS was supported by the Centers for Disease Control
and Prevention and the National Science Foundation under
Award No.\ 2223933 and 2333494.
\clearpage
%\bibliographystyle{apalike}
%\bibliographystyle{rss}
\bibliographystyle{elsarticle-harv}
\bibliography{bibliography.bib}
\end{document}