## 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 occasionally 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/) \[metadata in French\].

* [SARS-CoV-2 (Covid-19) by the
  numbers](https://github.com/milo-lab/SARS-CoV-2/raw/master/versions/SARS-CoV-2_BTN.pdf)
  fact sheet (updated regularly).

* [MedCram series of medical
  lectures](https://www.youtube.com/user/MEDCRAMvideos/videos) with
  frequent updates on the epidemic.

## Country-specific links ##

* France

  * Epidemiological summary in France:
    [2020-03-15](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-15-mars-2020),
    [2020-03-24](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-24-mars-2020),
    [2020-04-02](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-2-avril-2020).

  * [Epidemiological monitoring data set](https://www.data.gouv.fr/fr/datasets/donnees-relatives-a-lepidemie-du-covid-19/)

  * [Covid-19 France cases situation](https://metabase.cedricguadalupe.com/public/dashboard/e771e5ed-45a0-40cd-b9c6-026c86a67117)

  * [Avis du conseil scientifique Covid-19](https://solidarites-sante.gouv.fr/actualites/presse/dossiers-de-presse/article/covid-19-_conseil-scientifique-covid-19)

* Italy

  * [Epidemiological monitoring data set](https://github.com/pcm-dpc/COVID-19/)

## Topical or time-specific links: ##

* [Immune responses in COVID-19 and potential vaccines: Lessons
  learned from SARS and MERS
  epidemic](http://apjai-journal.org/wp-content/uploads/2020/03/1.pdf),
  review article in Asian Pacific Journal of Allergy and Immunology
  (2020-03, vol. 38).

* [Estimating the number of infections and the impact of
  non-pharmaceutical interventions on Covid-19 in 11 European
  countries](https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-Europe-estimates-and-NPI-impact-30-03-2020.pdf)
  (2020-03-30) by the Imperial College Covid-19 Response Team.

* [Coronavirus: the key numbers we must find
  out](https://medium.com/@davidbessis/coronavirus-the-core-metrics-we-should-be-looking-at-2ca09a3dc4b1)
  (2020-03-26 Medium piece by David Bessis) emphasizes how little we
  know of the fatality ratio of Covid-19.

* [Perspectives on the Pandemic by Dr. John
  Ioannidis](https://www.youtube.com/watch?v=ZEr4rmjwd0g) (2020-03-25)
  cautions against making decisions without reliable data (e.g.,
  regarding fatality rate) (an extension of Dr. Ioannidis's 2020-03-17
  [“Fiasco in the making?” opinion
  piece](https://www.statnews.com/2020/03/17/a-fiasco-in-the-making-as-the-coronavirus-pandemic-takes-hold-we-are-making-decisions-without-reliable-data/)
  in *Stat News*).

* [Using a delay-adjusted case fatality ratio to estimate
  under-reporting](https://cmmid.github.io/topics/covid19/severity/global_cfr_estimates.html)
  (2020-03-22) by the Centre for Mathematical Modelling of Infectious
  Diseases.

* [The early phase of the COVID-19 outbreak in Lombardy,
  Italy](https://arxiv.org/abs/2003.09320) (2020-03-20 preprint),
  epidemiological characterization of the first 5830 lab-confirmed
  cases.

* [A thread about immunity by Nicholas
  A. Christakis](https://threadreaderapp.com/thread/1240689935557865472.html)
  (2020-03-20) explaining what we now know and don't know.

* [A thread about
  favipiravir](https://threadreaderapp.com/thread/1240261123712126978.html)
  (2020-03-18) as a possible treatment of Covid-19.

* [Global Covid-19 Case Fatality
  Rates](https://www.cebm.net/covid-19/global-covid-19-case-fatality-rates/)
  (2020-03-17, regularly updated), an estimation of CFR and IFR by the
  University of Oxford's Centre for Evidence-Based Medicine.

* [Aerosol and surface stability of SARS-CoV-2 as compared to
  SARS-CoV-1](https://www.nejm.org/doi/full/10.1056/NEJMc2004973)
  (Letter in NEJM, 2020-03-17).

* [Excess cases of Influenza like illnesses in France synchronous with
  Covid-19
  invasion](https://www.medrxiv.org/content/10.1101/2020.03.14.20035741v1)
  (2020-03-17 preprint), suggest larger circulation of SARS-CoV-2 in
  the French population than apparent from confirmed cases. ⁂ See also
  [this Twitter
  thread](https://twitter.com/FLAHAULT/status/1240337073531506690) for
  analogous observations in various countries.

* [Covid-19 ou la chronique d'une émergence
  annoncée](https://www.college-de-france.fr/site/actualites/Covid-19ChroniqueEmergenceAnnoncee.htm)
  (conference at the Collège de France, 2020-03-16, \[in French\]).

* [Breadth of concomitant immune responses prior to patient recovery:
  a case report of non-severe
  COVID-19](https://www.nature.com/articles/s41591-020-0819-2) (Nature
  correspondence, 2020-03-16).

* [Forecasting short-term hospital needs in
  France](https://www.ea-reperes.com/wp-content/uploads/2020/03/PredictedFrenchHospitNeeds-EHESP-20200316.pdf) (2020-03-16).

* [Impact of non-pharmaceutical interventions to reduce Covid-19
  mortality and healthcare
  demand](https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf)
  (2020-03-16) by the Imperial College Covid-19 Response Team.

* [Substantial undocumented infection facilitates the rapid
  dissemination of novel coronavirus
  (SARS-CoV2)](https://science.sciencemag.org/content/early/2020/03/13/science.abb3221), published in *Science* (2020-03-16).

* [Reinfection could not occur in SARS-CoV-2 infected rhesus
  macaques](https://www.biorxiv.org/content/10.1101/2020.03.13.990226v1)
  (2020-03-14 preprint) assesses the immunity to SARS-CoV-2 from a
  first infection in the case of rhesus macaque monkeys.

* [Early epidemiological assessment of the transmission potential and
  virulence of Covid-19 in Wuhan City
  China](https://www.medrxiv.org/content/10.1101/2020.02.12.20022434v2)
  (2020-03-13 preprint) estimates that the proportion of infected
  people in Wǔhàn was far larger than estimated (and the fatality rate
  far lower than estimated).

* [Coronavirus: Why it's so deadly in
  Italy](https://medium.com/@andreasbackhausab/coronavirus-why-its-so-deadly-in-italy-c4200a15a7bf)
  (2020-03-13 Medium piece), emphasizes the role of demographics.

* [Estimates of the severity of COVID-19
  disease](https://www.medrxiv.org/content/10.1101/2020.03.09.20033357v1)
  (2020-03-13 preprint) puts the overall IFR at 0.7% and gives a
  breakdown per age group.

* [How will country-based mitigation measures influence the course of
  the Covid-19
  epidemic?](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2820%2930567-5/fulltext)
  (2020-03-09), a comment in The Lancet with a general discussion of
  the state of the epidemic and possible strategies.

* American Hospital Association's “Best Guess Epidemiology” has been
  [reported on
  Twitter](https://twitter.com/sethbannon/status/1236125593290276864)
  on 2020-03-07, estimating a disease burden of ~10× severe flu season
  (attack rate ~30–40%, of which 5% requiring hospitalization, 1–2%
  requiring ICU, 0.5% fatal).

* [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.

* [General information meeting about Covid-19 at the
  Sorbonne](https://www.youtube.com/watch?v=nWRKNKnt0ig) (2020-03-05).

* [Etimation of infection and case fatality ratios for Covid-19 using
  data from Diamond
  Princess](https://cmmid.github.io/topics/covid19/severity/diamond_cruise_cfr_estimates.html)
  by the Centre for Mathematical Modelling of Infectious Diseases,
  online 2020-03-05.

* [Serial interval of novel coronavirus (COVID-19)
  infections](https://www.ijidonline.com/article/S1201-9712(20)30119-3),
  published 2020-03-04, estimates the median serial interval at 4.0
  days.

* [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.

* [The species Severe acute respiratory syndrome-related coronavirus:
  classifying 2019-nCoV and naming it
  SARS-CoV-2](https://www.nature.com/articles/s41564-020-0695-z)
  (Nature Microbiology Consensus Statement, 2020-03-02).

* [SARS-Cov-2 and the lessons we have to learn from
  it](https://medium.com/@edwardnirenberg/sars-cov-2-and-the-lessons-we-have-to-learn-from-it-e2017fd5d3c),
  a well-written general summary by Edward Nirenberg (2020-03-02).
  Emphasis: “The real issue is what having this pandemic does to
  healthcare systems globally.”

* [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).

## More stuff ##

* [Links to Covid-19 related
  articles](https://www.reddit.com/r/Coronavirus/comments/feo68j/humanity_wins_our_fight_to_unlock_32544_covid19/fjpbaph/)
  unlocked after pressure on publishers.

## 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.

## My own explanatory threads on Twitter ##

* [Experiments on the influence of the social graph structure on
  attack rates of
  epidemics](https://threadreaderapp.com/thread/1241745979663155203.html)
  (2020-03-22).

* [Putting the Imperial College paper (by Ferguson &al) in
  perspective](https://threadreaderapp.com/thread/1240713126233899008.html)
  (2020-03-19).

* [On strategies ① (contain) and ② (mitigate) when dealing with an
  epidemic](https://threadreaderapp.com/thread/1237372990540713984.html)
  (2020-03-10).

* [On the final attack rate in the SIR epidemic
  model](https://threadreaderapp.com/thread/1236324650315059200.html)
  (2020-03-07).