## 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 the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak](https://epiforecasts.io/covid/posts/global/) by the Centre for Mathematical Modelling of Infectious Diseases. * [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). * [COVID-19 Open Research Dataset (CORD-19)](https://pages.semanticscholar.org/coronavirus-research) by Semantic Scholar. * [Bibliovid: veille scientifique sur Covid-19](https://bibliovid.org/) \[in French\]. * [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), [2020-04-09](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-9-avril-2020), [2020-04-16](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-16-avril-2020), [2020-04-23](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-23-avril-2020). * Epidemiological monitoring data set: [from emergency services](https://www.data.gouv.fr/fr/datasets/donnees-des-urgences-hospitalieres-et-de-sos-medecins-relatives-a-lepidemie-de-covid-19/) and [from hospitals](https://www.data.gouv.fr/fr/datasets/donnees-hospitalieres-relatives-a-lepidemie-de-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: ## * [Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold](https://www.medrxiv.org/content/10.1101/2020.04.27.20081893v2) (2020-05-12 preprint) suggests a lowering of herd immunity due to population heterogeneity. * [OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients](https://www.medrxiv.org/content/10.1101/2020.05.06.20092999v1) (2020-05-07 preprint), a statistical analysis of 17M medical records to compute risk factors for death from Covid-19. ⚔ [Twitter thread](https://twitter.com/EpiEllie/status/1258607277357006849) criticizing the analysis for possibility of “M bias”. [Another such thread](https://twitter.com/bristimtom/status/1259458854020165632). * [The disease-induced herd immunity level for Covid-19 is substantially lower than the classical herd immunity level](https://arxiv.org/abs/2005.03085) (2020-05-06 preprint) suggests a lowering of herd immunity due to population heterogeneity. * [Immunology of COVID-19: current state of the science](https://www.cell.com/immunity/fulltext/S1074-7613%2820%2930183-7) (2020-05-05, *Cell Immunity*), a review of the state of knowledge concerning innate and adaptive immune responses elicited by SARS-CoV-2 infection. * [Lockdown exit strategies and risk of a second epidemic peak: a stochastic agent-based model of SARS-CoV-2 epidemic in France](https://www.medrxiv.org/content/10.1101/2020.04.30.20086264v1) (2020-05-05 preprint), a detailed model of the post-lockdown phase in France. * [Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China](https://science.sciencemag.org/content/early/2020/04/28/science.abb8001) (2020-04-29, Science report). From the abstract: “Daily contacts were reduced 7–8-fold during the COVID-19 social distancing period, with most interactions restricted to the household. We find that children 0–14 years are less susceptible to SARS-CoV-2 infection than adults 15–64 years of age (odd ratio 0.34, 95%CI 0.24–0.49), while in contrast, individuals over 65 years are more susceptible to infection (odd ratio 1.47, 95%CI: 1.12–1.92).” * [The race for coronavirus vaccines: a graphical guide](https://www.nature.com/articles/d41586-020-01221-y) (2020-04-28, Nature news feature), illustrating eight ways in which scientists hope to provide immunity to SARS-CoV-2. * [SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors](https://www.medrxiv.org/content/10.1101/2020.04.21.20068858v1) (2020-04-24) by the Institut Pasteur. Studies the levels of anti-SARS-CoV-2 antibodies in hospitalized patients versus pauci-symptomatic individuals versus blood donors. * [Cluster of COVID-19 in northern France: A retrospective closed cohort study](https://www.medrxiv.org/content/10.1101/2020.04.18.20071134v1) (2020-04-23) by the Institut Pasteur. Analyses the results of antibody detection tests on blood samples from a cluster connected to the high school of Crépy-en-Valois, finding an attack rate of 26%. * [Covid-19: one-month impact of the French lockdown on the epidemic burden](https://www.ea-reperes.com/wp-content/uploads/2020/04/ImpactConfinement-EHESP-20200322v1.pdf) (2020-04-22) modelling by EHESP team. * [The potential danger of suboptimal antibody responses in COVID-19](https://www.nature.com/articles/s41577-020-0321-6) (2020-04-21, Nature Immunology) discusses antibody-dependent enhancement and how this impacts potential vaccine development. * [Estimating the burden of SARS-CoV-2 in France](https://hal-pasteur.archives-ouvertes.fr/pasteur-02548181) (2020-04-21) by the Institut Pasteur. Among conclusions, finds that lockdown reduced the reproductive number from 3.3 to 0.5, and that 5.7% of the population will have been infected by May 11. *\[Move this to the country-specific section?\]* * [Persistence and efficiency of antibodies against SARS-CoV-2: the state of current knowledge](https://www.vidal.fr/actualites/24770/persistance_et_efficacite_des_anticorps_neutralisants_contre_le_sars_cov_2_etat_des_connaissances_et_lecons_des_autres_coronavirus_humains/) (2020-04-20 \[in French\]). * [Indoor transmission of SARS-CoV-2](https://www.medrxiv.org/content/10.1101/2020.04.04.20053058v1) (2020-04-07 preprint) confirms that sharing indoor place is the major Covid-19 infection risk, and analyses circumstances. * [Effectiveness of convalescent plasma therapy in severe COVID-19 patients](https://www.pnas.org/content/early/2020/04/02/2004168117) (2020-04-06, PNAS) ⚔ [Twitter thread discussing this](https://twitter.com/DrEricDing/status/1248059832038502402). * [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). * [Respiratory virus shedding in exhaled breath and efficacy of face masks](https://www.nature.com/articles/s41591-020-0843-2) (Nature brief communication, 2020-04-03). * [“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. * [Virological assessment of hospitalized patients with Covid-19](https://www.nature.com/articles/s41586-020-2196-x) (2020-04-01, *Nature*), virological analysis of nine cases focusing on virus replication and shedding in the upper respiratory tract. * [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. * [The proximal origin of SARS-CoV-2](https://www.nature.com/articles/s41591-020-0820-9) (Nature Medicine correspondence, 2020-03-17). * [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. * [The convalescent sera option for containing COVID-19](https://www.jci.org/articles/view/138003) (Journal of Clinical Investigation, 2020-03-13) argues that human convalescent serum is an option for prevention and treatment of COVID-19 disease that could be rapidly available when there are sufficient numbers of people who have recovered. * [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. * (Reproduction numbers of infectious disease models)[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002118/] comments on the definition of R₀ in various models. * Wikipedia page about [compartmental models in epidemiology](https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology) such as the SIR model. * [Epidemiological parameter review and comparative dynamics of various human respiratory infections](https://www.medrxiv.org/content/10.1101/2020.02.04.20020404v1). * [Contacts in context: large-scale setting-specific social mixing matrices from the BBC *Pandemic* project](https://www.medrxiv.org/content/10.1101/2020.02.16.20023754v2) evaluating social mixing data. ## My own explanatory threads on Twitter ## * [On evidence or lack of evidence that Covid-19 infections confer immunity](https://threadreaderapp.com/thread/1254069215264419841.html) and [an epidemiological estimation of the order of magnitude of immunity conferred by HCoVs](https://threadreaderapp.com/thread/1254105660440092674.html) (2020-04-25). * [Why the variance of infectious contacts received matters more than the variance of infectious contacts made](https://threadreaderapp.com/thread/1252581933835575297.html) (2020-04-21). * [Problems with the definition of “herd immunity”](https://threadreaderapp.com/thread/1250817310526525440.html) (2020-04-16). * [The problem with using models to predict the future](https://threadreaderapp.com/thread/1249738327143501824.html) (2020-04-13). * [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).