omicron.bib

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   author = {Backer, Jantien A and Eggink, Dirk and Andeweg, Stijn P and Veldhuijzen, Irene K and van Maarseveen, Noortje and Vermaas, Klaas and Vlaemynck, Boris and Schepers, Raf and van den Hof, Susan and Reusken, Chantal BEM and Wallinga, Jacco},
   title = {{Shorter serial intervals in SARS-CoV-2 cases with Omicron BA.1 variant compared with Delta variant, the Netherlands, 13 to 26 December 2021}},
   journal = {Eurosurveillance},
   year = {2022},
   volume = {27},
   number = {6}, 
   pages = {2200042}
}

@article{he2020temporal,
  title={{Temporal dynamics in viral shedding and transmissibility of COVID-19}},
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  journal={Nature medicine},
  volume={26},
  number={5},
  pages={672--675},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{abbott2022test,
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  author={Abbott, Sam and Sherratt, Katharine and Gerstung, Moritz and Funk, Sebastian},
  year={2022},
  journal={medRxiv},
  url={\url{https://www.medrxiv.org/content/10.1101/2022.01.08.22268920v1}}
}

@article{park2021forward,
  title={Forward-looking serial intervals correctly link epidemic growth to reproduction numbers},
  author={Park, Sang Woo and Sun, Kaiyuan and Champredon, David and Li, Michael and Bolker, Benjamin M and Earn, David JD and Weitz, Joshua S and Grenfell, Bryan T and Dushoff, Jonathan},
  journal={Proceedings of the National Academy of Sciences},
  volume={118},
  number={2},
  year={2021},
  publisher={National Acad Sciences}
}

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@article{backer2020incubation,
  title={{Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China, 20--28 January 2020}},
  author={Backer, Jantien A and Klinkenberg, Don and Wallinga, Jacco},
  journal={Eurosurveillance},
  volume={25},
  number={5},
  pages={2000062},
  year={2020},
  publisher={European Centre for Disease Prevention and Control}
}

@article{park2020reconciling,
  title={{Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak}},
  author={Park, Sang Woo and Bolker, Benjamin M and Champredon, David and Earn, David JD and Li, Michael and Weitz, Joshua S and Grenfell, Bryan T and Dushoff, Jonathan},
  journal={Journal of the Royal Society Interface},
  volume={17},
  number={168},
  pages={20200144},
  year={2020},
  publisher={The Royal Society}
}

@article{sender2021unmitigated,
  title={The unmitigated profile of COVID-19 infectiousness},
  author={Sender, Ron and Bar-On, Yinon and Park, Sang Woo and Noor, Elad and Dushoff, Jonathan and Milo, Ron},
  journal={Elife},
  volume={11},
  pages={e79134},
  year={2022},
  publisher={eLife Sciences Publications Limited}
}

@article{park2022importance,
  title={{The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants}},
  author={Park, Sang Woo and Bolker, Benjamin M and Funk, Sebastian and Metcalf, C Jessica E and Weitz, Joshua S and Grenfell, Bryan T and Dushoff, Jonathan},
  journal={Journal of The Royal Society Interface},
  volume={19},
  number={191},
  pages={20220173},
  year={2022},
  publisher={The Royal Society}
}


@article{fraser2007estimating,
  title={Estimating individual and household reproduction numbers in an emerging epidemic},
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  journal={PloS one},
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}

@article{park2020inferring,
  title={Inferring generation-interval distributions from contact-tracing data},
  author={Park, Sang Woo and Champredon, David and Dushoff, Jonathan},
  journal={Journal of the Royal Society Interface},
  volume={17},
  number={167},
  pages={20190719},
  year={2020},
  publisher={The Royal Society}
}

@article{champredon2015intrinsic,
  title={Intrinsic and realized generation intervals in infectious-disease transmission},
  author={Champredon, David and Dushoff, Jonathan},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={282},
  number={1821},
  pages={20152026},
  year={2015},
  publisher={The Royal Society}
}

@article{hart2022generation,
  title={{Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis}},
  author={Hart, William S and Miller, Elizabeth and Andrews, Nick J and Waight, Pauline and Maini, Philip K and Funk, Sebastian and Thompson, Robin N},
  journal={The Lancet Infectious Diseases},
  year={2022},
  publisher={Elsevier}
}

@article{ganyani2020estimating,
  title={{Estimating the generation interval for coronavirus disease (COVID-19) based on symptom onset data, March 2020}},
  author={Ganyani, Tapiwa and Kremer, Cecile and Chen, Dongxuan and Torneri, Andrea and Faes, Christel and Wallinga, Jacco and Hens, Niel},
  journal={Eurosurveillance},
  volume={25},
  number={17},
  pages={2000257},
  year={2020},
  publisher={European Centre for Disease Prevention and Control}
}

@article{zhao2021estimating,
  title={{Estimating the generation interval and inferring the latent period of COVID-19 from the contact tracing data}},
  author={Zhao, Shi and Tang, Biao and Musa, Salihu S and Ma, Shujuan and Zhang, Jiayue and Zeng, Minyan and Yun, Qingping and Guo, Wei and Zheng, Yixiang and Yang, Zuyao and others},
  journal={Epidemics},
  volume={36},
  pages={100482},
  year={2021},
  publisher={Elsevier}
}

@article{lehtinen2021relationship,
  title={On the relationship between serial interval, infectiousness profile and generation time},
  author={Lehtinen, Sonja and Ashcroft, Peter and Bonhoeffer, Sebastian},
  journal={Journal of the Royal Society Interface},
  volume={18},
  number={174},
  pages={20200756},
  year={2021},
  publisher={The Royal Society}
}

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  title={A note on generation times in epidemic models},
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  year={2019},
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}

@article{hay2021estimating,
  title={Estimating epidemiologic dynamics from cross-sectional viral load distributions},
  author={Hay, James A and Kennedy-Shaffer, Lee and Kanjilal, Sanjat and Lennon, Niall J and Gabriel, Stacey B and Lipsitch, Marc and Mina, Michael J},
  journal={Science},
  volume={373},
  number={6552},
  pages={eabh0635},
  year={2021},
  publisher={American Association for the Advancement of Science}
}

@article {hay2022viral,
article_type = {journal},
title = {{Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study}},
author = {Hay, James A and Kissler, Stephen M and Fauver, Joseph R and Mack, Christina and Tai, Caroline G and Samant, Radhika M and Connolly, Sarah and Anderson, Deverick J and Khullar, Gaurav and MacKay, Matthew and Patel, Miral and Kelly, Shannan and Manhertz, April and Eiter, Isaac and Salgado, Daisy and Baker, Tim and Howard, Ben and Dudley, Joel T and Mason, Christopher E and Nair, Manoj and Huang, Yaoxing and DiFiori, John and Ho, David D and Grubaugh, Nathan D and Grad, Yonatan H},
editor = {Rodriguez-Barraquer, Isabel and Ferguson, Neil M and Azman, Andrew},
volume = 11,
year = 2022,
month = {nov},
pub_date = {2022-11-16},
pages = {e81849},
citation = {eLife 2022;11:e81849},
doi = {10.7554/eLife.81849},
url = {https://doi.org/10.7554/eLife.81849},
abstract = {\textbf{Background:} The combined impact of immunity and SARS-CoV-2 variants on viral kinetics during infections has been unclear. \textbf{Methods:} We characterized 1,280 infections from the National Basketball Association occupational health cohort identified between June 2020 and January 2022 using serial RT-qPCR testing. Logistic regression and semi-mechanistic viral RNA kinetics models were used to quantify the effect of age, variant, symptom status, infection history, vaccination status and antibody titer to the founder SARS-CoV-2 strain on the duration of potential infectiousness and overall viral kinetics. The frequency of viral rebounds was quantified under multiple cycle threshold (Ct) value-based definitions. \textbf{Results:} Among individuals detected partway through their infection, 51.0\% (95\% credible interval [CrI]: 48.3–53.6\%) remained potentially infectious (Ct <30) 5 days post detection, with small differences across variants and vaccination status. Only seven viral rebounds (0.7\%; N=999) were observed, with rebound defined as 3+days with Ct <30 following an initial clearance of 3+days with Ct ≥30. High antibody titers against the founder SARS-CoV-2 strain predicted lower peak viral loads and shorter durations of infection. Among Omicron BA.1 infections, boosted individuals had lower pre-booster antibody titers and longer clearance times than non-boosted individuals. \textbf{Conclusions:} SARS-CoV-2 viral kinetics are partly determined by immunity and variant but dominated by individual-level variation. Since booster vaccination protects against infection, longer clearance times for BA.1-infected, boosted individuals may reflect a less effective immune response, more common in older individuals, that increases infection risk and reduces viral RNA clearance rate. The shifting landscape of viral kinetics underscores the need for continued monitoring to optimize isolation policies and to contextualize the health impacts of therapeutics and vaccines. \textbf{Funding:} Supported in part by CDC contract \#200-2016-91779, a sponsored research agreement to Yale University from the National Basketball Association contract \#21-003529, and the National Basketball Players Association.},
keywords = {SARS-CoV-2, COVID-19, viral kinetics, omicron, antibody, immunity},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}


@article{pearson2021bounding,
  title={{Bounding the levels of transmissibility \& immune evasion of the Omicron variant in South Africa}},
  author={Pearson, Carl AB and Silal, Sheetal P and Li, Michael WZ and Dushoff, Jonathan and Bolker, Benjamin M and Abbott, Sam and van Schalkwyk, Cari and Davies, Nicholas G and Barnard, Rosanna C and Edmunds, W John and others},
  journal={MedRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{kraemer2021monitoring,
  title={{Monitoring key epidemiological parameters of SARS-CoV-2 transmission}},
  author={Kraemer, Moritz UG and Pybus, Oliver G and Fraser, Christophe and Cauchemez, Simon and Rambaut, Andrew and Cowling, Benjamin J},
  journal={Nature medicine},
  volume={27},
  number={11},
  pages={1854--1855},
  year={2021},
  publisher={Nature Publishing Group}
}

@article{park2020time,
  title={{The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak}},
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  volume={31},
  pages={100392},
  year={2020},
  publisher={Elsevier}
}

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  title={Reconstructing influenza incidence by deconvolution of daily mortality time series},
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@article{song2022serial,
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  journal={Emerging Infectious Diseases},
  volume={28},
  number={3},
  pages={756},
  year={2022},
  publisher={Centers for Disease Control and Prevention}
}

@article{jansen2021investigation,
  title={{Investigation of a Sars-Cov-2 B.1.1.529 (Omicron) variant cluster—--Nebraska, November--December 2021}},
  author={Jansen, Lauren and Tegomoh, Bryan and Lange, Kate and Showalter, Kimberly and Figliomeni, Jon and Abdalhamid, Baha and Iwen, Peter C and Fauver, Joseph and Buss, Bryan and Donahue, Matthew},
  journal={Morbidity and Mortality Weekly Report},
  volume={70},
  number={5152},
  pages={1782},
  year={2021},
  publisher={Centers for Disease Control and Prevention}
}

@article{brandal2021outbreak,
  title={{Outbreak caused by the SARS-CoV-2 Omicron variant in Norway, November to December 2021}},
  author={Brandal, Lin T and MacDonald, Emily and Veneti, Lamprini and Ravlo, Tine and Lange, Heidi and Naseer, Umaer and Feruglio, Siri and Bragstad, Karoline and Hungnes, Olav and {\O}deskaug, Liz E and others},
  journal={Eurosurveillance},
  volume={26},
  number={50},
  pages={2101147},
  year={2021},
  publisher={European Centre for Disease Prevention and Control}
}

@article{ferretti2020quantifying,
  title={{Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing}},
  author={Ferretti, Luca and Wymant, Chris and Kendall, Michelle and Zhao, Lele and Nurtay, Anel and Abeler-D{\"o}rner, Lucie and Parker, Michael and Bonsall, David and Fraser, Christophe},
  journal={Science},
  volume={368},
  number={6491},
  pages={eabb6936},
  year={2020},
  publisher={American Association for the Advancement of Science}
}

@article{ferretti2020timing,
  title={{The timing of COVID-19 transmission}},
  author={Ferretti, Luca and Ledda, Alice and Wymant, Chris and Zhao, Lele and Ledda, Virginia and Abeler-D{\"o}rner, Lucie and Kendall, Michelle and Nurtay, Anel and Cheng, Hao-Yuan and Ng, Ta-Chou and others},
  year={2020},
  journal={medRxiv},
  url={\url{https://www.medrxiv.org/content/10.1101/2020.09.04.20188516v2}}
}

@article{kremer2022observed,
  title={{Serial Intervals for SARS-CoV-2 Omicron and Delta Variants, Belgium, November 19--December 31, 2021}},
  author={Kremer, C{\'e}cile and Braeye, Toon and Proesmans, Kristiaan and Andr{\'e}, Emmanuel and Torneri, Andrea and Hens, Niel},
  journal={Emerging Infectious Diseases},
  volume={28},
  number={8},
  pages={1699},
  year={2022},
  publisher={Centers for Disease Control and Prevention}
}


@article{selby2022generation,
  title={{Estimating generation time of Omicron}},
  author={Selby, Alex},
  year={2022},
  url={\url{http://sonorouschocolate.com/covid19/index.php?title=Estimating_Generation_Time_Of_Omicron}}
}

@Article{ito2022estimating,
title = {{Estimating relative generation times and reproduction numbers of Omicron BA.1 and BA.2 with respect to Delta variant in Denmark}},
journal = {Mathematical Biosciences and Engineering},
volume = {19},
number = {9},
pages = {9005-9017},
year = {2022},
issn = {1551-0018},
doi = {10.3934/mbe.2022418},
url = {https://www.aimspress.com/article/doi/10.3934/mbe.2022418},
author = {Kimihito Ito and Chayada Piantham and Hiroshi Nishiura},
keywords = {SARS-CoV-2, Omicron-BA.1, Omicron-BA.2, relative generation time, relative reproduction number},
}


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@article{netherlandslockdown,
  title={{Slowing the spread of the Omicron variant: lockdown in the Netherlands}},
  author={{Government of the Netherlands}},
  year={2021},
  note={\url{https://www.government.nl/latest/news/2021/12/18/slowing-the-spread-of-the-omicron-variant-lockdown-in-the-netherlands}}
}

@article{netherlandsrelax,
  title={{Shops, gyms and hairdressers to reopen on Saturday 15 January}},
  author={{Government of the Netherlands}},
  year={2021},
  note={\url{https://www.government.nl/topics/coronavirus-covid-19/news/2022/01/14/shops-gyms-and-hairdressers-to-reopen-on-saturday-15-january}}
}

@article{netherlandsopen,
  title={{Nearly all locations can be open until 22:00}},
  author={{Government of the Netherlands}},
  year={2021},
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}

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@article{kissler2021viral,
author = {Kissler, Stephen M. and Fauver, Joseph R. and Mack, Christina and Tai, Caroline G. and Breban, Mallery I. and Watkins, Anne E. and Samant, Radhika M. and Anderson, Deverick J. and Metti, Jessica and Khullar, Gaurav and Baits, Rachel and MacKay, Matthew and Salgado, Daisy and Baker, Tim and Dudley, Joel T. and Mason, Christopher E. and Ho, David D. and Grubaugh, Nathan D. and Grad, Yonatan H.},
title = {Viral Dynamics of {SARS-CoV-2} Variants in Vaccinated and Unvaccinated Persons},
journal = {New England Journal of Medicine},
volume = {385},
number = {26},
pages = {2489-2491},
year = {2021},
doi = {10.1056/NEJMc2102507},
    note ={PMID: 34941024},

URL = { 
        https://doi.org/10.1056/NEJMc2102507
    
},
eprint = { 
        https://doi.org/10.1056/NEJMc2102507
    
}

}

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  title={The intrinsic rate of increase and the overlap of successive generations in a population of guillemots (\textit{Uria aalge} {Pont}.)},
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  title={Age, stages, and the role of generation time in matrix models},
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@article{bienvenu2015new,
  title={A new approach to the generation time in matrix population models},
  author={Bienvenu, Fran{\c{c}}ois and Legendre, St{\'e}phane},
  journal={The American Naturalist},
  volume={185},
  number={6},
  pages={834--843},
  year={2015},
  publisher={University of Chicago Press Chicago, IL}
}

@article {hart2021,
article_type = {journal},
title = {{High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing}},
author = {Hart, William S and Maini, Philip K and Thompson, Robin N},
editor = {Flegg, Jennifer and Franco, Eduardo and Kao, Rowland Raymond and Lee, Elizabeth},
volume = 10,
year = 2021,
month = {apr},
pub_date = {2021-04-26},
pages = {e65534},
citation = {eLife 2021;10:e65534},
doi = {10.7554/eLife.65534},
url = {https://doi.org/10.7554/eLife.65534},
abstract = {\textbf{Background:} Understanding changes in infectiousness during SARS-COV-2 infections is critical to assess the effectiveness of public health measures such as contact tracing. \textbf{Methods:} Here, we develop a novel mechanistic approach to infer the infectiousness profile of SARS-COV-2-infected individuals using data from known infector–infectee pairs. We compare estimates of key epidemiological quantities generated using our mechanistic method with analogous estimates generated using previous approaches. \textbf{Results:} The mechanistic method provides an improved fit to data from SARS-CoV-2 infector–infectee pairs compared to commonly used approaches. Our best-fitting model indicates a high proportion of presymptomatic transmissions, with many transmissions occurring shortly before the infector develops symptoms. \textbf{Conclusions:} High infectiousness immediately prior to symptom onset highlights the importance of continued contact tracing until effective vaccines have been distributed widely, even if contacts from a short time window before symptom onset alone are traced. \textbf{Funding:} Engineering and Physical Sciences Research Council (EPSRC).},
keywords = {COVID-19, contact tracing, infectiousness profile, generation time, presymptomatic transmission, mathematical modelling},
journal = {eLife},
issn = {2050-084X},
publisher = {eLife Sciences Publications, Ltd},
}

@article{jonasson2022unifying,
  title={A unifying framework for estimating generation time in age-structured populations: implications for phylogenetics and conservation biology},
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  journal={The American Naturalist},
  volume={200},
  number={1},
  pages={48--62},
  year={2022},
  publisher={The University of Chicago Press Chicago, IL}
}

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  title={{The mathematical demography of the California Condor population}},
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@article{giaimo2023generation,
  title={Generation time in stage-structured populations under fluctuating environments},
  author={Giaimo, Stefano and Traulsen, Arne},
  journal={The American Naturalist},
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  number={3},
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  year={2023},
  publisher={The University of Chicago Press Chicago, IL}
}

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  year={2009},
  publisher={Wiley Online Library}
}

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  title={Generation time, net reproductive rate, and growth in stage-age-structured populations},
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@article{allen2022comparative,
  title={{Comparative transmission of SARS-CoV-2 Omicron (B. 1.1. 529) and Delta (B. 1.617. 2) variants and the impact of vaccination: national cohort study, England}},
  author={Allen, Hester and Tessier, Elise and Turner, Charlie and Anderson, Charlotte and Blomquist, Paula and Simons, David and L{\o}chen, Alessandra and Jarvis, Christopher I and Groves, Natalie and Capelastegui, Fernando and others},
  journal={Epidemiology \& Infection},
  pages={1--20},
  year={2022},
  publisher={Cambridge University Press}
}

@article{del2022secondary,
  title={{Secondary attack rate, transmission and incubation periods, and serial interval of SARS-CoV-2 Omicron variant, Spain}},
  author={Del {\'A}guila-Mej{\'\i}a, Javier and Wallmann, Reinhard and Calvo-Montes, Jorge and Rodr{\'\i}guez-Lozano, Jes{\'u}s and Valle-Madrazo, Trinidad and Aginagalde-Llorente, Adrian},
  journal={Emerging Infectious Diseases},
  volume={28},
  number={6},
  pages={1224},
  year={2022},
  publisher={Centers for Disease Control and Prevention}
}