Covid 19

Epidemiological models

Authors	Publication date	Geographical region	Type	Description	Predictions
Chen et al	28.01.2020	Wuhan, China	SEIR (several species)	Model described virus transmission between bets (possible source), unknown host and human. For every species SEIR model is implemented. Simplified model with only human species is also considered.	The value of R0 was estimated of 2.30 from reservoir to person and 3.58 from person to person which means that the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population was 3.58.
Wu et al.	31.01.2020	Wuhan / China	SEIR	Model was created to reflect data obtained in Wuhan, then the model was extrapolated on China overall, taking into account cities connection with Wuhan and major routes of air and train transport	R0 for 2019-nCoV is 2.68, 75 815 individuals have been infected in Wuhan as of Jan 25, 2020. The epidemic doubling time was 6.4 days. Chongqing, Beijing, Shanghai, Guangzhou, and Shenzhen had imported 461, 113, 98, 111, and 80 infections from Wuhan, respectively. Epidemics are already growing exponentially in multiple major cities of China with a lag time behind the Wuhan of about 1–2 weeks. On the present trajectory, 2019-nCoV could be about to become a global epidemic in the absence of mitigation.To possibly succeed, substantial, even draconian measures that limit population mobility should be seriously and immediately considered in affected areas.
Danon et al.	14.02.2020	England and Whales	SEIR+Spatial	Authors used preexisted spatial metapopulation model to describe population movement between regions in England and Whales and standard SEIR model to describe Covid-19 spread in each particular region.	CoVID-19 outbreak will peak 126 to 147 days (~4 months) after the start of person-to-person transmission in England and Wales in the absence of controls, epidemic peak is predicted in June.
Westerhoff and Kolodkin	30.03.2020	Not specified	modified SEIR	Model distinguished between tested and non-testes subjects and takes into consideration adaptive government-induces social distancing policy	Strategies aiming for herd immunity are unacceptable and that a much stronger lockdown is required. Results suggest that the measures taken by many policy makers will be insufficient to quench the epidemic. Some Western policy makers engage in an adaptive lock down strategy but one of insufficient strength: model results suggest that their slowly increasing lock down strategy will not be effective. What is necessary is a strong lock down, which may then be softened as the number of infected individuals begins to decrease with time.
Tutu.ru	30.03.2020	Russian Federation	SIR + Spatial	Model uses dataset acquired by tutu.ru for movement statistics between nearly 170 000 Russian cities, villages and other inhabited localities. It investigates effects of restrictions on transition between cities on Covid19 spread. For each city simple SIR model is used.	Due to highly uneven population density (high in the western part and low in the eastern) it is possible to change epidemic timing by restricting movement between main transport hubs which will probably be economically justified in the future.
Chang et al.	02.04.2020	Australia	Agent-based	AceMod (The Australian Census-based Epidemic Model), containing 24 million agents, each of which represents individual with his own characteristics (gender, occupation, susceptibility) and social context. AceMod was previously developed and validated for simulations of pandemic influenza in Australia. Currently it was calibrated to describe covid-19 pandemic.	Effectiveness of school closures is limited, producing a two-week delay in epidemic peak, without a significant impact on the magnitude of the peak, in terms of incidence or prevalence. The temporal benefit of the two-week delay may be offset not only by logistical complications, but also by some increases in the fractions of both children and older adults during the period around the incidence peak. Social distancing (SD) strategy showed no benefit for lower levels of compliance (at 70% or less). Increasing a compliance level just by 10%,from 70% to 80%, may effectively control the spread of COVID-19 in Australia (during the suppression period).
Адарченко и др.	29.05.2020	Россия	SEIRD and Agent-based	Проведено моделирование развития эпидемии COVID-19 с целью предсказания ее параметров в зависимости от принимаемых мер противодействия: средней длительности эпидемии, наличия второго и/или последующих пиков заболеваемости, максимальной нагрузки на систему здравоохранения. Рассмотрено два подхода: детерминистский и статистический, которые используют методы теории нелинейных дифференциальных уравнений и «агентного» моделирования на основе метода Монте-Карло. Приводятся результаты моделирования развития эпидемии в Москве, Ухане и Нью-Йорке.	Учет асимптомных зараженных в детерменированной модели позволит показать, что расчеты модели принципиально не изменились, но максимумы пиков заражения стали меньше по сравнению с моделью без учета асимптомных в популяции. Полученные расчетные данные агентной модели показывают, что принимаемые властями ограничительные меры дают свой эффект, и в ряде регионов число заражений уже идет на спад. Однако это не означает, что после отмены карантинов эпидемия не может вспыхнуть вновь.
Westerhoff&Kolodkin	12.06.2020	The Netherlands	SEIR	Using standard systems biology methodologies a 14-compartment dynamic model was developed for the Coronavirus epidemic.	The model predicts that: (i) it will be impossible to limit lockdown intensity such that sufficient herd immunity develops for this epidemic to die down, (ii) the death toll from the SARS-CoV-2 virus decreases very strongly with increasing intensity of the lockdown, but (iii) the duration of the epidemic increases at first with that intensity and then decreases again, such that (iv) it may be best to begin with selecting a lockdown intensity beyond the intensity that leads to the maximum duration, (v) an intermittent lockdown strategy should also work and might be more acceptable socially and economically, (vi) an initially intensive but adaptive lockdown strategy should be most efficient, both in terms of its low number of casualties and shorter duration, (vii) such an adaptive lockdown strategy offers the advantage of being robust to unexpected imports of the virus, e.g. due to international travel, (viii) the eradication strategy may still be superior as it leads to even fewer deaths and a shorter period of economic downturn, but should have the adaptive strategy as backup in case of unexpected infection imports, (ix) earlier detection of infections is the most effective way in which the epidemic can be controlled, whilst waiting for vaccines..

Web apps for Covid-19 simulations and data

1. Covid-19 statistics and forecast developed by Biouml.Ru;

2. COVID-19 Scenario Analysis Tool (MRC Centre for Global Infectious Disease Analysis, Imperial College London);

3. MIT simulator of Covid-19;

4. A web application serves as a planning tool for COVID-19 outbreaks in communities across the world;

5. Los Alamos National Lab prediction;

6. University of Melburn prediction;

7. REINA (Realistic Epidemic Interaction Network Agent Model);

8. German Covid simulator;

9. Open Source QSP model describing SARS-CoV-2 virus and host cell life cycles, immune response and therapeutic treatments;

10. Sberindex;

11. Moscow map for coronavirus;

12. Web-based viewer for 3D visualization and analysis of the SARS-CoV-2 protein structures with respect to the CoV-2 mutational patterns;

13. These apps provide up-to-date visualizations of data tracking the global spread of Coronavirus Disease 2019 (COVID-19), easy access to the World Health Organization's daily situation reports on it and an overview of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic

Covid-19 statistics

1. JH Institute data;

2. UniOxford statistics and research;

3. Worldmeter;

4. Статистика по России;

Useful articles

1. Coronavirus research updates ;

2. A Global Effort to Define the Human Genetics f Protective Immunity to SARS-CoV-2 Infection;

3. https://science.sciencemag.org/content/368/6496/1274/tab-pdf A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2;

4. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses;

5. Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals;

6. A Novel Bat Coronavirus Closely Related to SARSCoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein;

7. Temporal dynamics in viral shedding and transmissibility of COVID-19;

8. Seroprevalence of SARS-CoV-2 in Hong Kong and in residents evacuated from Hubei province, China: a multicohort study;

9. Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections;

10. These Scenarios Show What a Second Wave of COVID-19 Could Look Like;

11. Herd Immunity: Understanding COVID-19;

12. The race for coronavirus vaccines: a graphical guide;

13. SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues;

14. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19;

15. Reducing transmission of SARS-CoV-2;

16. Epidemiological and Clinical Characteristics of COVID-19 in Adolescents and Young Adults;

17. Positive COVID-19 Test Doesn't Automatically Equate to Virulence;

18. Why herd immunity to COVID-19 is reached much earlier than thought;

19. A study on infectivity of asymptomatic SARS-CoV-2 carriers;

20. Why do some COVID-19 patients infect many others, whereas most don’t spread the virus at all?;

21. Calibration of individual-based models to epidemiological data: A systematic review

22. Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19.

23. Broad neutralization of SARS-related viruses by human monoclonal antibodies;

24. Antibody cocktail to SARS-CoV-2 spike protein prevents rapid mutational escape seen with individual antibodies;

25. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2

26. Natural History of Asymptomatic SARS-CoV-2 Infection

27. COVID-19: What proportion are asymptomatic?

28. Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections

29. Using influenza surveillance networks to estimate statespecific prevalence of SARS-CoV-2 in the United States

30. A mathematical model reveals the influence of population heterogeneity on herd immunity to SARS-CoV-2

31. Economic and social consequences of human mobility restrictions under COVID-19

32. Rapid Generation of Neutralizing Antibody Responses in COVID-19 Patients

33. Comparative replication and immune activation profiles of SARS-CoV-2 and SARS-CoV in human lungs: an ex vivo study with implications for the pathogenesis of COVID-19

34. Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion

35. Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing

36. A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates

37. Identifying airborne transmission as the dominant route for the spread of COVID-19

38. Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19

39. SARS-CoV-2 productively infects human gut enterocytes

40. Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

41. Critical Role of Type III Interferon in Controlling SARS-CoV-2 Infection in Human Intestinal Epithelial Cells

42. The challenges of modeling and forecasting the spread of COVID-19

43. Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study

44. SARS‐CoV‐2 coinfections: Could influenza and the common cold be beneficial?

45. The Pandemic’s Big Mystery: How Deadly Is the Coronavirus?

46. Estimating the burden of SARS-CoV-2 in France

47. Inferring change points in the spread of COVID-19 reveals the effectiveness of interventions

48. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells

49. Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

Lectures and talks

1. Ancha Baranova’s channel;

2. Происхождение нового коронавируса. Сергей Нетёсов;

3. Коронавирус: Новые данные. Лекция Сергея Нетёсова;

4. Справилась ли Россия с пандемией коронавируса? С. Нетесов;

5. Маргарита Романенко"Тот самый вирус: все что вы хотели знать о COVID19, но стеснялись спросить";