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Wikipedia articles on the outbreak, on the virus and on the disease it causes.
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Daily situation reports and general updates by the WHO.
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Covid-19 global cases situation dashboard by John Hopkins (and mobile version), updated daily (historical data).
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Epidemic data by Wolfram Data for the world and for China.
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Temporal variation in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak by the Centre for Mathematical Modelling of Infectious Diseases.
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Covid-19 epidemic forecasting by the Institute of Global Health, Faculty of Medicine, University of Geneva and the Swiss Data Science Center, ETH Zürich-EPFL.
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Covid-19 projections using Machine Learning created by Youyang Gu.
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Phylogenetic tree of 2019-nCoV strains on Nextstrain (data source).
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CSV and JSON files with case counts per country, compiled daily [metadata in French].
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SARS-CoV-2 (Covid-19) by the numbers fact sheet (updated regularly).
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COVID-19 Open Research Dataset (CORD-19) by Semantic Scholar.
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Bibliovid: veille scientifique sur Covid-19 [in French].
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MedCram series of medical lectures with frequent updates on the epidemic.
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France
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Epidemiological summary in France: 2020-03-15, 2020-03-24, 2020-04-02, 2020-04-09, 2020-04-16, 2020-04-23, 2020-04-30, 2020-05-07, 2020-05-14, 2020-05-21, 2020-05-29, 2020-06-04, 2020-06-11, 2020-06-18, 2020-06-25, 2020-07-02, 2020-07-09, 2020-07-16, 2020-07-23, 2020-07-30, 2020-08-06, 2020-08-13, 2020-08-20, 2020-08-27.
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Epidemiological monitoring data set: from emergency services and from hospitals.
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Géodes (graphical tool to display, compare and export epidemiological data sets and indicators).
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Italy
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Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China (Nature Communications, 2020-11-20). “We describe a city-wide SARS-CoV-2 nucleic acid screening programme between May 14 and June 1, 2020 in Wuhan. […] There were no positive tests amongst 1174 close contacts of asymptomatic cases.”
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Immunological memory to SARS-CoV-2 assessed for greater than six months after infection (2020-11-16 preprint). Twitter thread by last author summarizing results: “The upshot is that there is substantial immune memory after COVID-19.”
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Mobility network models of COVID-19 explain inequities and inform reopening (Nature, 2020-11-10). Attempts to use fine-grained mobility data derived from cell phone networks in 10 of the largest US metropolitan statistical areas to model the proportion of infections at various types of locations.
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High prevalence of pre-existing serological cross-reactivity against SARS-CoV-2 in sub-Sahara Africa (Int. J. Infect. Diseases, 2020-11-07). “Low SARS-CoV-2 infection and disease in SSA [Sub-Saharan Africa] appears to correlate with pre-pandemic serological cross-recognition of HCoVs [NL63 and 229E], which are substantially more prevalent in SSA than USA.”
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Evolution of Antibody Immunity to SARS-CoV-2 (2020-11-05 preprint). “The observation that memory B cell responses do not decay after 6.2 months, but instead continue to evolve, is strongly suggestive that individuals who are infected with SARS-CoV-2 could mount a rapid and effective response to the virus upon re-exposure.”
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Humoral Immune Response to SARS-CoV-2 in Iceland (NEJM, 2020-10-29). Conclusions: “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.”
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Robust neutralizing antibodies to SARS-CoV-2 infection persist for months (Science report, 2020-10-28). “We also show that titers are relatively stable for at least a period approximating 5 months and that anti-spike binding titers significantly correlate with neutralization of authentic SARS-CoV-2. Our data suggests that more than 90% of seroconverters make detectible neutralizing antibody responses. These titers remain relatively stable for several months after infection.”
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Virology, transmission, and pathogenesis of SARS-CoV-2 (British Medical Journal clinical update, 2020-10-23): an overview of what is currently known about SARS-CoV-2 transmission, pathology and immunity.
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The effect of influenza vaccination on trained immunity: impact on COVID-19 (2020-10-16 preprint). Conclusion: “a quadrivalent inactivated influenza vaccine can induce trained immunity responses against SARS-CoV-2, which may result in relative protection against COVID-19. These data […] argue for a beneficial effect of influenza vaccination against influenza as well as COVID-19, and suggests its effective deployment in the 2020-2021 influenza season to protect against both infections.”
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Infection fatality rate of COVID-19 inferred from seroprevalence data (Bulletin of the WHO, 2020-10-14) by Dr. John Ioannidis. “The infection fatality rate of COVID-19 can vary substantially across different locations and this may reflect differences in population age structure and case-mix of infected and deceased patients and other factors. The inferred infection fatality rates tended to be much lower than estimates made earlier in the pandemic.”
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Less severe course of COVID-19 is associated with elevated levels of antibodies against seasonal human coronaviruses OC43 and HKU1 (HCoV OC43, HCoV HKU1) (2020-10-14 preprint). “Our results indicate that previous infections with seasonal coronaviruses might protect against a severe course of disease. This finding should be validated in other settings and could contribute to identify persons at risk before an infection.”
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Global perspective of COVID‐19 epidemiology for a full‐cycle pandemic (European Journal of Clinical Investigation, 2020-10-07). Provides a global perspective on the pandemic. Simulations are presented with a total of 1.58 to 8.76 million COVID-19 deaths over 5 years globally.
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Assessment of the risk of SARS-CoV-2 reinfection in an intense re-exposure setting (2020-09-28 preprint). Conclusions: “SARS-CoV-2 reinfection can occur but is a rare phenomenon suggestive of a strong protective immunity against reinfection that lasts for at least a few months post primary infection.”
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Covid-19: Do many people have pre-existing immunity? (British Medical Journal feature, 2020-09-17). “It seemed a truth universally acknowledged that the human population had no pre-existing immunity to SARS-CoV-2, but is that actually the case? Peter Doshi explores the emerging research on immunological responses.”
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COVID-19 and the Path to Immunity (JAMA Viewpoint, 2020-09-11). Summarizes various aspects of immune response to Covid-19 infection, and its durability.
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A Basic Review of the Preliminary Evidence That COVID-19 Risk and Severity Is Increased in Vitamin D Deficiency (Frontiers in Public Health, 2020-09-10). “Among the 47 original research studies summarized here, chart reviews found that serum vitamin D levels predicted COVID-19 mortality rates (16 studies) and linearly predicted COVID-19 illness severity (8 studies). […] Widely recommending 2,000 IU of vitamin D daily for all populations with limited ability to manufacture vitamin D from the sun has virtually no potential for harm and is reasonably likely to save many lives.”
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Use of “normal” risk to improve understanding of dangers of covid-19 (British Medical Journal analysis, 2020-09-09). Compares risk of dying by Covid-19 to “normal” (i.e., baseline mortality) risk for various age groups, suggesting that “being infected with SARS-CoV-2 contributes about a year's worth of extra risk of dying for those aged over 20” [a phrase which has been considerably misinterpreted].
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Immunological characteristics govern the changing severity of COVID-19 during the transition to endemicity (2020-09-05 preprint). “Our model recapitulates both the current severity of CoV-2 and the relatively benign nature of HCoVs; suggesting that once the endemic phase is reached, CoV-2 may be no more virulent than the common cold.”
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Are we underestimating seroprevalence of SARS-CoV-2? (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.
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Humoral Immune Response to SARS-CoV-2 in Iceland (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.”
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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 (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.”
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Inoculum at the time of SARS-CoV-2 exposure and risk of disease severity (J. Infect. Diseases, 2020-08). “We report three clusters of individuals that were potentially exposed to distinct inoculum in Madrid. […] Our data support that a greater viral inoculum at the time of SARS-CoV-2 exposure might determine a higher risk of severe COVID-19.”
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Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication (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.
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Two metres or one: what is the evidence for physical distancing in covid-19? (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.
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Progress report on the coronavirus pandemic. (Nature editorial, 2020-08-19).
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High prevalence of SARS-CoV-2 antibodies in care homes affected by COVID-19; a prospective cohort study in England (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.
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A country level analysis measuring the impact of government actions, country preparedness and socioeconomic factors on COVID-19 mortality and related health outcomes (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.”
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The impact of host resistance on cumulative mortality and the threshold of herd immunity for SARS-CoV-2 (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”.
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Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19 (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.”
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Syrian hamsters as a small animal model for SARS-CoV-2 infection and countermeasure development. “We assessed the replicative ability and pathogenesis of SARS-CoV-2 isolates in Syrian hamsters. SARS-CoV-2 isolates replicated efficiently in the lungs of hamsters, causing severe pathological lung lesions following intranasal infection. In addition, microcomputed tomographic imaging revealed severe lung injury that shared characteristics with SARS-CoV-2−infected human lung, including severe, bilateral, peripherally distributed, multilobular ground glass opacity, and regions of lung consolidation. SARS-CoV-2−infected hamsters mounted neutralizing antibody responses and were protected against subsequent rechallenge with SARS-CoV-2. […] Collectively, these findings demonstrate that this Syrian hamster model will be useful for understanding SARS-CoV-2 pathogenesis and testing vaccines and antiviral drugs.”
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Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion (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.”
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Systemic and mucosal antibody secretion specific to SARS-CoV-2 during mild versus severe COVID-19 (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.]
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Hydroxychloroquine or chloroquine with or without a macrolide for treatment of COVID-19: a multinational registry analysis (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.
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Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold (2020-05-12 preprint) suggests a lowering of herd immunity due to population heterogeneity.
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OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients (2020-05-07 preprint), a statistical analysis of 17M medical records to compute risk factors for death from Covid-19. ⚔ Twitter thread criticizing the analysis for possibility of “M bias”. Another such thread.
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The disease-induced herd immunity level for Covid-19 is substantially lower than the classical herd immunity level (2020-05-06 preprint) suggests a lowering of herd immunity due to population heterogeneity.
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The invisible pandemic (The Lancet correspondence, 2020-05-05). Johan Giesecke explains and argues the case for Sweden's strategy: “a lockdown might delay severe cases for a while, but once restrictions are eased, cases will reappear”.
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Immunology of COVID-19: current state of the science (2020-05-05, Cell Immunity), a review of the state of knowledge concerning innate and adaptive immune responses elicited by SARS-CoV-2 infection.
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Lockdown exit strategies and risk of a second epidemic peak: a stochastic agent-based model of SARS-CoV-2 epidemic in France (2020-05-05 preprint), a detailed model of the post-lockdown phase in France.
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What settings have been linked to SARS-CoV-2 transmission clusters? (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.
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Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China (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).”
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The race for coronavirus vaccines: a graphical guide (2020-04-28, Nature news feature), illustrating eight ways in which scientists hope to provide immunity to SARS-CoV-2.
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SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors (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.
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Cluster of COVID-19 in northern France: A retrospective closed cohort study (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%.
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Covid-19: one-month impact of the French lockdown on the epidemic burden (2020-04-22) modelling by EHESP team.
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The potential danger of suboptimal antibody responses in COVID-19 (2020-04-21, Nature Immunology) discusses antibody-dependent enhancement and how this impacts potential vaccine development.
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Estimating the burden of SARS-CoV-2 in France (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?]
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Persistence and efficiency of antibodies against SARS-CoV-2: the state of current knowledge (2020-04-20 [in French]).
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Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China (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%).
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Indoor transmission of SARS-CoV-2 (2020-04-07 preprint) confirms that sharing indoor place is the major Covid-19 infection risk, and analyses circumstances.
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Effectiveness of convalescent plasma therapy in severe COVID-19 patients (2020-04-06, PNAS) ⚔ Twitter thread discussing this.
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Baseline Characteristics and Outcomes of 1591 Patients Infected With SARS-CoV-2 Admitted to ICUs of the Lombardy Region, Italy (2020-04-06, JAMA).
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Respiratory virus shedding in exhaled breath and efficacy of face masks (Nature brief communication, 2020-04-03).
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“Coronavirus: Bad News Wrapped in Protein” infographic by the New York Times (2020-04-03), illustrating the proteins coded for by the SARS-CoV-2 genome and what function they (are thought to) have.
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Virological assessment of hospitalized patients with Covid-19 (2020-04-01, Nature), virological analysis of nine cases focusing on virus replication and shedding in the upper respiratory tract.
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Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic, review article in Asian Pacific Journal of Allergy and Immunology (2020-03, vol. 38).
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Estimating the number of infections and the impact of non-pharmaceutical interventions on Covid-19 in 11 European countries (2020-03-30) by the Imperial College Covid-19 Response Team.
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Coronavirus: the key numbers we must find out (2020-03-26 Medium piece by David Bessis) emphasizes how little we know of the fatality ratio of Covid-19.
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Perspectives on the Pandemic by Dr. John Ioannidis (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 in Stat News).
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Using a delay-adjusted case fatality ratio to estimate under-reporting (2020-03-22) by the Centre for Mathematical Modelling of Infectious Diseases.
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The early phase of the COVID-19 outbreak in Lombardy, Italy (2020-03-20 preprint), epidemiological characterization of the first 5830 lab-confirmed cases.
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A thread about immunity by Nicholas A. Christakis (2020-03-20) explaining what we now know and don't know.
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A thread about favipiravir (2020-03-18) as a possible treatment of Covid-19.
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The proximal origin of SARS-CoV-2 (Nature Medicine correspondence, 2020-03-17).
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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.
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Aerosol and surface stability of SARS-CoV-2 as compared to SARS-CoV-1 (Letter in NEJM, 2020-03-17).
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Excess cases of Influenza like illnesses in France synchronous with Covid-19 invasion (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 for analogous observations in various countries.
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Covid-19 ou la chronique d'une émergence annoncée (conference at the Collège de France, 2020-03-16, [in French]).
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Breadth of concomitant immune responses prior to patient recovery: a case report of non-severe COVID-19 (Nature correspondence, 2020-03-16).
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Forecasting short-term hospital needs in France (2020-03-16).
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Impact of non-pharmaceutical interventions to reduce Covid-19 mortality and healthcare demand (2020-03-16) by the Imperial College Covid-19 Response Team.
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Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2), published in Science (2020-03-16).
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Reinfection could not occur in SARS-CoV-2 infected rhesus macaques (2020-03-14 preprint) assesses the immunity to SARS-CoV-2 from a first infection in the case of rhesus macaque monkeys.
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The convalescent sera option for containing COVID-19 (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.
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Early epidemiological assessment of the transmission potential and virulence of Covid-19 in Wuhan City China (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).
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Coronavirus: Why it's so deadly in Italy (2020-03-13 Medium piece), emphasizes the role of demographics.
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Estimates of the severity of COVID-19 disease (2020-03-13 preprint) puts the overall IFR at 0.7% and gives a breakdown per age group.
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How will country-based mitigation measures influence the course of the Covid-19 epidemic? (2020-03-09), a comment in The Lancet with a general discussion of the state of the epidemic and possible strategies.
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American Hospital Association's “Best Guess Epidemiology” has been reported on Twitter 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).
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How to contain an epidemic, radio broadcast on 2020-03-06 [in French] with infectiologist Anne-Claude Crémieux and epidemiologist Arnaud Fontanet.
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General information meeting about Covid-19 at the Sorbonne (2020-03-05).
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Etimation of infection and case fatality ratios for Covid-19 using data from Diamond Princess by the Centre for Mathematical Modelling of Infectious Diseases, online 2020-03-05.
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Serial interval of novel coronavirus (COVID-19) infections, published 2020-03-04, estimates the median serial interval at 4.0 days.
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Persistence of coronaviruses on inanimate surfaces and their inactivation with biocidal agents, published 2020-03 (not specific to SARS-CoV-2).
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Twitter thread by Nicholas A. Christakis (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.
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A paper on the origin and continuing evolution of SARS-CoV-2 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 that the difference in virulence is inferred from propagation rates rather than observed on clinical data, and the selective pressure explanation is debatable.
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Report on monitoring of persons exposed to patients with Covid-19 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 at these figures by epidemiologist Adam Kucharski.
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The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 (Nature Microbiology Consensus Statement, 2020-03-02).
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SARS-Cov-2 and the lessons we have to learn from it, 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.”
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A discussion in Science Magazine (2020-03-02; Twitter thread) on the WHO report (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.
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A fairly detailed FAQ video [index of questions at 1′10″] uploaded on 2020-03-03 by Inés Dawson. [TODO: write some kind of summary here.]
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Simulation of the effect of extra hand-washing 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.
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Two hour-long live interviews [in French] by Brut: Arnaud Fontanet (epidemiologist at the Institut Pasteur) on 2020-02-26, and Éric Caumes (head of the department of infectious diseases at the Pitié hospital in Paris) on 2020-02-28. [I didn't have time to watch.]
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Twitter Q&A thread by virologist Ian M. Mackay on 2020-02-28; discusses, inter alia, reinfection (here, here and here; seems to think false recovery is more likely than reinfection), attack rate (thinks 70% is probably overestimated), virus lifetime, fatality rate in Italy (probably seems high because of observation bias) and more.
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A discussion of seasonality of SARS-CoV-2 by epidemiologist Marc Lipsitch [date≤2020-02-26]; summary: despite seasonality of related viruses, it probably won't go away on its own in the summer.
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A primer for the general public on virus mutation [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.
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Interview of Éric Caumes (head of the department of infectious diseases at the Pitié hospital in Paris) 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.
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Thread by epidemiologist Marc Lipsitch on 2020-02-23 (Twitter link), 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).
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What we have learnt as of 2020-02-20, MOOC by epidemiologist Arnaud Fontanet for the Institut Pasteur; summarizes main information as of this date. [TODO: write better summary here.]
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Thread by epidemiologist Marc Lipsitch on 2020-02-14 (Twitter link), 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.
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Epidemiological characteristics report published in China CDC Weekly [mirror] detailing breakdown of cases and statistics up to 2020-02-11 (72 314 cases).
- Links to Covid-19 related articles unlocked after pressure on publishers.
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Definition of morbidity frequency measures and mortality frequency measures 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.
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(Reproduction numbers of infectious disease models)[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002118/] comments on the definition of R₀ in various models.
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Wikipedia page about compartmental models in epidemiology such as the SIR model.
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Epidemiological parameter review and comparative dynamics of various human respiratory infections.
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Contacts in context: large-scale setting-specific social mixing matrices from the BBC Pandemic project evaluating social mixing data.
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A note concerning herd immunity (unconditional versus conditional on other measures) (2020-11-05).
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A caution regarding how effective reproduction numbers are computed (2020-10-25).
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Computation of attack rate in function of variance (dispersion) in graph models + more mathematical details (2020-05-08).
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On evidence or lack of evidence that Covid-19 infections confer immunity and an epidemiological estimation of the order of magnitude of immunity conferred by HCoVs (2020-04-25).
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Why the variance of infectious contacts received matters more than the variance of infectious contacts made (2020-04-21).
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Problems with the definition of “herd immunity” (2020-04-16).
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The problem with using models to predict the future (2020-04-13).
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Experiments on the influence of the social graph structure on attack rates of epidemics (2020-03-22).
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Putting the Imperial College paper (by Ferguson &al) in perspective (2020-03-19).
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On strategies ① (contain) and ② (mitigate) when dealing with an epidemic (2020-03-10).
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On the final attack rate in the SIR epidemic model (2020-03-07).