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## Main links, portals, etc.: ##
* Wikipedia articles [on the
outbreak](https://en.wikipedia.org/wiki/2019%E2%80%9320_coronavirus_outbreak),
[on the
virus](https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2)
and [on the disease it
causes](https://en.wikipedia.org/wiki/Coronavirus_disease_2019).
* [Daily situation
reports](https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports/)
and [general
updates](https://www.who.int/emergencies/diseases/novel-coronavirus-2019)
by the WHO.
* [Covid-19 global cases situation dashboard by John
Hopkins](https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6) (and [mobile version](https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/85320e2ea5424dfaaa75ae62e5c06e61)),
updated daily ([historical
data](https://github.com/CSSEGISandData/COVID-19)).
* [Covid-19 coronavirus section on
Worldometer](https://www.worldometers.info/coronavirus/).
* [Covid-19 page by Our World in
Data](https://ourworldindata.org/coronavirus).
* Epidemic data by Wolfram Data [for the
world](https://www.wolframcloud.com/obj/examples/COVID19World) and
[for China](https://www.wolframcloud.com/obj/examples/COVID19China).
* [Temporal variation in transmission during Covid-19
outbreak](https://cmmid.github.io/topics/covid19/current-patterns-transmission/global-time-varying-transmission.html)
by the Centre for Mathematical Modelling of Infectious Diseases,
updated daily with estimates on effective reproduction number in
various countries.
* [Phylogenetic tree of 2019-nCoV
strains](https://nextstrain.org/ncov) on Nextstrain ([data
source](https://github.com/nextstrain/ncov)).
* [Virus pathogen data portal on
2019-nCoV](https://www.viprbrc.org/brc/home.spg?decorator=corona_ncov).
* [CSV and JSON files with case counts per country, compiled
daily](https://www.data.gouv.fr/fr/datasets/coronavirus-covid19-evolution-par-pays-et-dans-le-monde-maj-quotidienne/) \[metadata in French\].
* [MedCram series of medical
lectures](https://www.youtube.com/user/MEDCRAMvideos/videos) with
daily updates on the epidemic.
## Topical or time-specific links: ##
* [How to contain an
epidemic](https://www.franceculture.fr/emissions/la-methode-scientifique/la-methode-scientifique-emission-du-vendredi-06-mars-2020),
radio broadcast on 2020-03-06 \[in French\] with infectiologist
Anne-Claude Crémieux and epidemiologist Arnaud Fontanet.
* [Persistence of coronaviruses on inanimate surfaces and their
inactivation with biocidal
agents](https://www.sciencedirect.com/science/article/pii/S0195670120300463),
published 2020-03 (not specific to SARS-CoV-2).
* [Twitter thread by Nicholas
A. Christakis](https://twitter.com/NAChristakis/status/1235204443362205699)
(on 2020-03-04) on the benefits of closing schools, based on a study
of the effects of the 1918 flu pandemic; key message: closing early
is important.
* [A paper on the origin and continuing evolution of
SARS-CoV-2](https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwaa036/5775463)
published on 2020-03-03 in the National Science Review, discussing
the coexistence of two types of strains, which they call ‘L’ (more
virulent) and ‘S’ (less virulent), the ‘L’ being more prevalent but
the ‘S’ becoming seemingly progressively more frequent because human
actions put more pressure against the more virulent strains. ⚔
[Beware](https://twitter.com/SciTania/status/1235283259510214656)
that the difference in virulence is inferred from propagation rates
rather than observed on clinical data, and the selective pressure
explanation is debatable.
* [Report on monitoring of persons exposed to patients with
Covid-19](https://www.cdc.gov/mmwr/volumes/69/wr/mm6909e1.htm)
published 2020-03-03 in CDC's Morbidity and Mortality Weekly Report:
key finding places symptomatic secondary attack rate at 0.45% among
close contacts and 10.5% among household members. ⚔ Here a [critical
look](https://twitter.com/AdamJKucharski/status/1235124770896826369)
at these figures by epidemiologist Adam Kucharski.
* [A discussion in *Science*
Magazine](https://www.sciencemag.org/news/2020/03/china-s-aggressive-measures-have-slowed-coronavirus-they-may-not-work-other-countries)
(2020-03-02; [Twitter
thread](https://twitter.com/kakape/status/1234603592407044096)) on
[the WHO
report](https://www.who.int/docs/default-source/coronaviruse/who-china-joint-mission-on-covid-19-final-report.pdf)
(released 2020-02-28) on the joint WHO-Chinese mission led by Bruce
Aylard to study the state of the epidemic in China; key message: the
measures taken by Chinese authorities to contain the epidemic
worked, but unclear what will happen in the long run or whether they
can be applied in other countries.
* [A fairly detailed FAQ
video](https://www.youtube.com/watch?v=oA8XYSftmtQ) \[[index of
questions at
1′10″](https://www.youtube.com/watch?v=oA8XYSftmtQ#t=1m10s)\]
uploaded on 2020-03-03 by [Inés
Dawson](https://twitter.com/InesLauraDawson). *\[TODO: write some
kind of summary here.\]*
* [Simulation of the effect of extra
hand-washing](https://twitter.com/FryRsquared/status/1234491912775782400)
on the spread of an epidemic (a simulation performed in 2018,
retweeted on 2020-03-02); key message: it really has an impact, not
just on the speed of progression but also on the final attack rate.
* Two hour-long live interviews \[in French\] by Brut: [Arnaud
Fontanet (epidemiologist at the Institut
Pasteur)](https://www.youtube.com/watch?v=vs2oyLSlo0Q) on
2020-02-26, and [Éric Caumes (head of the department of infectious
diseases at the Pitié hospital in
Paris)](https://www.youtube.com/watch?v=L5thFsjoHok) on 2020-02-28.
*\[I didn't have time to watch.\]*
* [Twitter Q&A
thread](https://twitter.com/MackayIM/status/1233509962292375559) by
virologist [Ian M. Mackay](https://virologydownunder.com/) on
2020-02-28; discusses, inter alia, reinfection
([here](https://twitter.com/MackayIM/status/1233512522168356864),
[here](https://twitter.com/MackayIM/status/1233512323358363654) and
[here](https://twitter.com/MackayIM/status/1233511497017561090);
seems to think false recovery is more likely than reinfection),
[attack
rate](https://twitter.com/MackayIM/status/1233511899083530240)
(thinks 70% is probably overestimated), [virus
lifetime](https://twitter.com/MackayIM/status/1233522944137187329),
[fatality rate in
Italy](https://twitter.com/MackayIM/status/1233521001578803200)
(probably seems high because of observation bias) and more.
* [A discussion of seasonality of SARS-CoV-2 by epidemiologist Marc
Lipsitch](https://docs.google.com/document/d/17mWPx-HTE1F2RKkbJlt4VkSYaznUiJgt21nuvmu51Kc)
\[date≤2020-02-26\]; summary: despite seasonality of related
viruses, it probably won't go away on its own in the summer.
* [A primer for the general public on virus
mutation](https://ccdd.hsph.harvard.edu/mutation-adaptation-and-virus-genomes-a-primer-for-the-public/)
\[date≤2020-02-26\]; main message is that we don't know much about
mutations of this particular virus, but mutations aren't
particularly scary in and of themselves.
* [Interview of Éric Caumes (head of the department of infectious
diseases at the Pitié hospital in
Paris)](https://www.jim.fr/e-docs/covid_19_la_riposte_est_elle_plus_redoutable_que_le_virus__181852/document_jim_tube.phtml)
on 2020-02-25 \[in French\], discussing various issues
(contagiousness, attack rate, fatality rate, mutation rate, etc.);
main message seems to be that we are overreacting.
* [Thread by epidemiologist Marc
Lipsitch](https://threadreaderapp.com/thread/1231425805898657795.html)
on 2020-02-23 ([Twitter
link](https://twitter.com/mlipsitch/status/1231425805898657795)),
discussing the possibility and effectiveness of (temporary vs
long-term) countermeasures (case-based containment vs lockdowns,
etc.); expresses skepticism as to effectiveness of Chinese lockdowns
(and reliability of reported figures).
* [What we have learnt as of 2020-02-20, MOOC by epidemiologist Arnaud
Fontanet for the Institut
Pasteur](https://www.youtube.com/watch?v=4l_NxT9XJHk); summarizes
main information as of this date. *\[TODO: write better summary
here.\]*
* [Thread by epidemiologist Marc
Lipsitch](https://threadreaderapp.com/thread/1228373884027592704.html)
on 2020-02-14 ([Twitter
link](https://twitter.com/mlipsitch/status/1228373884027592704)),
discussing attack rate (=cumulated infection rate) r and the
estimation that 40%≲r≲70% “in a situation without effective
controls” based on comparison with similar epidemics.
* [Epidemiological characteristics report published in *China CDC
Weekly*](http://weekly.chinacdc.cn/fileCCDCW/journal/article/ccdcw/newcreate/COVID-19.pdf)
\[[mirror](https://github.com/cmrivers/ncov/blob/master/COVID-19.pdf)\]
detailing breakdown of cases and statistics up to 2020-02-11 (72 314
cases).
## Not Covid-19 specific but still relevant ##
* Definition of [morbidity frequency
measures](https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section2.html)
and [mortality frequency
measures](https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section3.html)
from (online version of) the CDC's book *Principles of Epidemiology
in Public Health Practice*: explains definitions of “attack rate”,
“secondary attack rate”, “case-fatality rate”, etc.
* Wikipedia page about [compartmental models in
epidemiology](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology)
such as the SIR model.
|
