## 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: ## * [Baseline Characteristics and Outcomes of 1591 Patients Infected With SARS-CoV-2 Admitted to ICUs of the Lombardy Region, Italy](https://jamanetwork.com/journals/jama/fullarticle/2764365) (2020-04-06, JAMA). * [“Coronavirus: Bad News Wrapped in Protein” infographic by the New York Times](https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html) (2020-04-03), illustrating the proteins coded for by the SARS-CoV-2 genome and what function they (are thought to) have. * [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).