path: root/covid19-links.md

## 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.

* [Covid-19 projections using Machine
  Learning](https://covid19-projections.com/) created by Youyang Gu.

* [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),
    [2020-04-30](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-30-avril-2020),
    [2020-05-07](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-7-mai-2020),
    [2020-05-14](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-14-mai-2020),
    [2020-05-21](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-21-mai-2020),
    [2020-05-29](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-29-mai-2020),
    [2020-06-04](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-4-juin-2020),
    [2020-06-11](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-11-juin-2020),
    [2020-06-18](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-18-juin-2020),
    [2020-06-25](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-25-juin-2020),
    [2020-07-02](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-2-juillet-2020),
    [2020-07-09](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-9-juillet-2020),
    [2020-07-16](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-16-juillet-2020),
    [2020-07-23](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-23-juillet-2020),
    [2020-07-30](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-30-juillet-2020),
    [2020-08-06](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-6-aout-2020),
    [2020-08-13](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-13-aout-2020),
    [2020-08-20](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-20-aout-2020),
    [2020-08-27](https://www.santepubliquefrance.fr/maladies-et-traumatismes/maladies-et-infections-respiratoires/infection-a-coronavirus/documents/bulletin-national/covid-19-point-epidemiologique-du-27-aout-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: ##

* [Are we underestimating seroprevalence of
  SARS-CoV-2?](https://www.bmj.com/content/370/bmj.m3364) (*British
  Medical Journal* editorial, 2020-09-03).  Emphasizes the fact that
  SARS-CoV-2 seroprevalence studies show considerable variation and
  may underestimate true seroprevalence; and encourages testing for
  IgA antibodies.

* [Humoral Immune Response to SARS-CoV-2 in
  Iceland](https://www.nejm.org/doi/full/10.1056/NEJMoa2026116) (NEJM,
  2020-09-01).  Conclusion: “Our results indicate that antiviral
  antibodies against SARS-CoV-2 did not decline within 4 months after
  diagnosis.  We estimate that the risk of death from infection was
  0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland
  were not diagnosed by qPCR.”

* [Effect of Calcifediol Treatment and best Available Therapy versus
  best Available Therapy on Intensive Care Unit Admission and
  Mortality Among Patients Hospitalized for COVID-19: A Pilot
  Randomized Clinical
  study](https://www.sciencedirect.com/science/article/pii/S0960076020302764)
  (*J. Steroid Biochem. Molec. Biol.*, 2020-08-29).  Highlights: “ The
  vitamin D endocrine system may have a variety of actions on cells
  and tissues involved in COVID-19 progression.  Administration of
  calcifediol or 25-hydroxyvitamin D to hospitalized COVID-19 patients
  significantly reduced their need for Intensive Care United
  admission.  Calcifediol seems to be able to reduce severity of the
  disease.”

* [Feline coronavirus drug inhibits the main protease of SARS-CoV-2
  and blocks virus
  replication](https://www.nature.com/articles/s41467-020-18096-2)
  (*Nature*, 2020-08-27).  Lays the framework for the use of two
  dipeptide-based protease inhibitor (GC376 and GC373), found to be
  effective against Feline Enteric Coronavirus (FECoV), in human
  trials for the treatment of COVID-19.

* [Two metres or one: what is the evidence for physical distancing in
  covid-19?](https://www.bmj.com/content/370/bmj.m3223) (*British
  Medical Journal* analysis, 2020-08-25).  Argues that “current rules
  on safe physical distancing are based on outdated science; rules on
  distancing should reflect the multiple factors that affect risk,
  including ventilation, occupancy, and exposure time”, and proposes a
  table of low/medium/high risk configurations.

* [Progress report on the coronavirus
  pandemic](https://www.nature.com/articles/d41586-020-02414-1).
  (*Nature* editorial, 2020-08-19).

* [High prevalence of SARS-CoV-2 antibodies in care homes affected by
  COVID-19; a prospective cohort study in
  England](https://www.medrxiv.org/content/10.1101/2020.08.10.20171413v1)
  (2020-08-12 preprint).  Finds that older residents are able to mount
  the same antibody response and neutralizing antibodies against
  SARS-CoV-2 as the younger healthier staff, irrespective of gender or
  having symptoms.

* [A country level analysis measuring the impact of government
  actions, country preparedness and socioeconomic factors on COVID-19
  mortality and related health
  outcomes](https://www.thelancet.com/journals/eclinm/article/PIIS2589-5370%2820$2930208-X/fulltext)
  (2020-07-21, *EClinicalMedicine*).  A country level exploratory
  analysis to assess the impact of timing and type of national health
  policy/actions undertaken towards COVID-19 mortality and related
  health outcomes.  Sample finding: “Rapid border closures, full
  lockdowns, and wide-spread testing were not associated with COVID-19
  mortality per million people.”

* [The impact of host resistance on cumulative mortality and the
  threshold of herd immunity for
  SARS-CoV-2](https://www.medrxiv.org/content/10.1101/2020.07.15.20154294v1)
  (2020-07-16 preprint).  Key finding: “\[Herd immunity threshold\]
  may be greatly reduced if a fraction of the population is unable to
  transmit the virus due to innate resistance or cross-protection from
  exposure to seasonal coronaviruses”.

* [Robust T cell immunity in convalescent individuals with
  asymptomatic or mild
  COVID-19](https://www.biorxiv.org/content/10.1101/2020.06.29.174888v1)
  (2020-06-29 preprint).  Key finding: “Our collective dataset shows
  that SARS-CoV-2 elicits robust memory T cell responses akin to those
  observed in the context of successful vaccines, suggesting that
  natural exposure or infection may prevent recurrent episodes of
  severe COVID-19 also in seronegative individuals.”

* [Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune
  Response without
  Seroconversion](https://www.medrxiv.org/content/10.1101/2020.06.21.20132449v1)
  (2020-06-20 preprint).  Conclusion: “Exposure to SARS-CoV-2 can
  induce virus-specific T cell responses without seroconversion.  T
  cell responses may be more sensitive indicators of SARS-Co-V-2
  exposure than antibodies.  Our results indicate that epidemiological
  data relying only on the detection of SARS-CoV-2 antibodies may lead
  to a substantial underestimation of prior exposure to the virus.”

* [Systemic and mucosal antibody secretion specific to SARS-CoV-2
  during mild versus severe
  COVID-19](https://www.biorxiv.org/content/10.1101/2020.05.21.108308v1)
  (2020-05-23 preprint).  Main conclusion: “Data show that systemic
  IgA and IgG production against SARS-CoV-2 develops mainly in severe
  COVID-19, with very high IgA levels seen in patients with severe
  ARDS, whereas mild disease may be associated with transient serum
  titers of SARS-CoV-2-specific antibodies but stimulate mucosal
  SARS-CoV-2-specific IgA secretion.  The findings suggest four grades
  of antibody responses dependent on COVID-19 severity.”

\[Note that around the end of May I stopped maintaining this list.
Still adding a few papers later, but it's definitely less complete
than it used to be.\]

* [Hydroxychloroquine or chloroquine with or without a macrolide for
  treatment of COVID-19: a multinational registry
  analysis](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2820%2931180-6)
  (2020-05-22, *The Lancet*).  Key finding: were unable to confirm a
  benefit of hydroxychloroquine or chloroquine, when used alone or
  with a macrolide, on in-hospital outcomes for COVID-19.  Each of
  these drug regimens was associated with decreased in-hospital
  survival and an increased frequency of ventricular arrhythmias when
  used for treatment of COVID-19.

* [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.

* [What settings have been linked to SARS-CoV-2 transmission
  clusters?](https://wellcomeopenresearch.org/articles/5-83)
  (2020-05-01, open peer review) identifies possible places linked to
  clusters of Covid-19 cases.  Key finding: many examples of
  SARS-CoV-2 clusters linked to a wide range of mostly indoor
  settings: few reports came from schools, many from households, and
  an increasing number were reported in hospitals and elderly care
  settings across Europe.

* [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 \[in French\]).

* [Estimating the overdispersion in COVID-19 transmission using
  outbreak sizes outside
  China](https://wellcomeopenresearch.org/articles/5-67) (2020-04-09,
  open peer review) attempts to estimate variance in COVID-19
  transmission rates by modeling secondary transmission rates as a
  negative-binomial distribution with mean R₀ in the 2–3 consensus
  range and estimating the overdispersion parameter.  Key finding: the
  overdispersion parameter k of a negative-binomial distribution was
  estimated to be around 0.1, suggesting that 80% of secondary
  transmissions may have been caused by a small fraction of infectious
  individuals (~10%).

* [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).