Literature and data sources

Databases

Introduction textbooks

  • “Modeling infectious diseases in humans and animals” by Keeling and Rohani (Princeton University Press)

  • “Epidemics - Models and Data using R” by Bjornstad (Springer)

General literature

Research literature and other sources

  • For estimates of the fractional change on R_e when certain non-pharmaceutical measures are taken:

    “The temporal association of introducing and lifting non-pharmaceutical interventions with the time-varying reproduction number (R) of SARS-CoV-2: a modelling study across 131 countries”, Li, Campbell, Kulkarni, Harpur, Nundy, Wang, Nair, Lancet Inf Dis, October 22, 2020. https://doi.org/10.1016/S1473-3099(20)30785-4

  • For Infection-Fatality ratios (IFR) as a function of age-group:

    Estimations of the overall IFR vary wildly, mainly due to the unknown ratio of reported positives over actual infections. But the age-dependency (relative) seems to be relatively well-measured.

    “Estimating the infection-fatality risk of SARS-CoV-2 in New York City during the spring 2020 pandemic wave: a model-based analysis”, Yang, Kandula, Huynh, Greene, Van Wye, Li, Tai Chan, McGibbon, Yeung, Olson, Fine, Shaman, Lancet Inf Dis, October 19, 2020. https://doi.org/10.1016/S1473-3099(20)30769-6

    “SARS-CoV-2 infection fatality risk in a nationwide seroepidemiological study”, Pastor-Barriuso, Perez-Gomez, Hernanc, Perez-Olmedad, Yottie, Oteod, Sanmarting, Leon-Gomeza, Fernandez- Garciab, Fernandez-Navarroa, Cruzh, Marting, Delgado-Sanza, Fernandez de Larreaa, Leon Paniaguae, Munoz-Montalvog, Blancog, Larrauri, Pollan, September 25, 2020, medRxiv https://doi.org/10.1101/2020.08.06.20169722

    Corona Podcast Christian Drosten, Folge 56 https://www.ndr.de/nachrichten/info/56-Coronavirus-Update-Das-Afrika-Raetsel,podcastcoronavirus242.html

  • For typical time until first symptoms appears (~ 5 to 7 days)

    “The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application”, Lauer, Grantz, Bi, Jones, Zheng, Meredith, Azman, Reich, Lessler, May 5, 2020, Annals of Internal Medicine, https://www.acpjournals.org/doi/10.7326/M20-0504

    “Incubation period of 2019 novel coronavirus (2019-nCoV) infections among travellers from Wuhan, China, 20-28 January 2020”, Backer, Klingenberg, Wallinga, February 28, 2020, Eurosurveillance Volume 25, Issue 5, 06/Feb/2020, https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.5.2000062

    “Estimation of incubation period distribution of COVID-19 using disease onset forward time: A novel cross-sectional and forward follow-up study”, Jing Qin, Chong You, Qiushi Lin, Taojun Hu, Shicheng Yu, Xiao-Hua Zhou, Sci Adv. 2020 Aug; 6(33): eabc1202, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7428324/

  • For typical generation time (~ 4 days)

    “Schätzung der aktuellen Entwicklung der SARS-CoV-2-Epidemie in Deutschland - Nowcasting”, Robert Koch Institut. https://www.rki.de/DE/Content/Infekt/EpidBull/Archiv/2020/17/Art_02.html

  • For typical delay between first symptoms and reported positive (~ 5 days)

    I could not find a clear statement about the mean delay between onset of symptoms and the reported positive test result. But from the RKI database this can be estimated. The Meldedatum column is the day of reported positive test. The Refdatum is (if the flag IstErkrankungsbeginn==1) the day of the onset of symptoms. The AnzahlFall is the number of cases reported. By making a histogram of the number of cases as a function of Meldedatum-Refdatum for delays between -10 days and +30 days I arrived at a mean of 5.3 days with a standard deviation of 4 days (2020-11-12). Only 1% of cases had a negative delay (negative means that the onset of symptoms occurred after the reported positive test).

  • For typical duration of ICU treatment (~ 10 days)

    “COVID-19 length of hospital stay: a systematic review and data synthesis”, Rees, Nightingale, Jafari, Waterlow, Clifford, Pearson, CMMID Working Group, Jombart, Procter and Knight, BMC Medicine (2020) 18:270 https://doi.org/10.1186/s12916-020-01726-3

    One can also estimate this from the DIVI data (Deutsche Interdisziplinäre Vereinigung für Intensiv- und Notfallmedizin), but I have not found the required information on the DIVI register (https://www.intensivregister.de/#/intensivregister). Instead, I extracted the data of October and November from the “Täglicher Lagebericht des RKI zur Coronavirus-Krankheit-2019” https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Situationsberichte/Gesamt.html One can compute from the data how many new patients are admitted each day, and how many treatments are ended each day. The latter should be reflecting the former, but delayed. The delay computed in this way varies between 5 days (mid-October) to 10 days (mid November).

  • General information about typical Covid-19 time scales in Germany:

    General information about Covid-19 from the RKI: https://www.rki.de/DE/Content/InfAZ/N/Neuartiges_Coronavirus/Steckbrief.html#doc13776792bodyText11