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Modeling Epidemics, an Introduction University of Massachusetts Amherst ScholarWorks@UMass Amherst Science and Engineering Saturday Seminars STEM Education Institute 2020 Modeling Epidemics, An Introduction Shubha Tewari Follow this and additional works at: https://scholarworks.umass.edu/stem_satsem Part of the Epidemiology Commons, Immunology and Infectious Disease Commons, Influenza Virus Vaccines Commons, Science and Mathematics Education Commons, and the Teacher Education and Professional Development Commons Tewari, Shubha, "Modeling Epidemics, An Introduction" (2020). Science and Engineering Saturday Seminars. 49. Retrieved from https://scholarworks.umass.edu/stem_satsem/49 This Article is brought to you for free and open access by the STEM Education Institute at ScholarWorks@UMass Amherst. It has been accepted for inclusion in Science and Engineering Saturday Seminars by an authorized administrator of ScholarWorks@UMass Amherst. For more information, please contact [email protected]. 5/14/20 Modeling Epidemics: An Introduction Shubha Tewari Physics Department University of Massachusetts, Amherst 1 Outline of today’s session • Group discussion of videos watched – Mainly focus on 3Blue1Brown videos • Discussion of known facts about Covid-19/SARS-CoV-2 – Joint look at news articles and websites – Discussion of exponential growth • Introduction to SIR (Susceptible-Infected-Recovered) model • Excel demonstration of SIR model • Other models: SEIR, others • Modeling using python (time-permitting) 2 1 5/14/20 Useful Links • 3Blue1Brown is an excellent channel for explaining mathematical concepts: – Understanding exponential growth: https://www.youtube.com/watch?v=Kas0tIxDvrg – Epidemic modeling: https://www.youtube.com/watch?v=gxAaO2rsdIs • Prof. Nicholas Reich, UMass Amherst: https://reichlab.io/covid19-forecast-hub/ https://www.umass.edu/newsoffice/article/cdc-designates-umass-amherst-flu • From the NYT: Model forecasts: (April 22) https://www.nytimes.com/interactive/2020/04/22/upshot/coronavirus-models.html (May 12): https://www.nytimes.com/interactive/2020/05/12/upshot/coronavirus-models.html https://projects.fivethirtyeight.com/covid-forecasts/ Tracking cases: (US) https://www.nytimes.com/interactive/2020/us/coronavirus-us-cases.html (MA) https://www.mass.gov/info-details/covid-19-updates-and-information https://ourworldindata.org/covid-cases 3 4 2 5/14/20 5 At first look, it may appear India is doing much better than the US and the UK A closer look at the trends paints a more alarming picture for India 6 3 5/14/20 India Number of confirmed cases rising roughly linearly Doubling times: About 10-14 days 70747 cases (May 11) 7 What is exponential growth? See 3Blue1Brown: https://www.youtube.com/watch?v=Kas0tIxDvrg • Linear on a logarithmic scale – where does that come from? – Growth by a constant multiplicative, rather than additive factor (grains of rice story) �!"# = (1 + � ∗ �)�! �$:Number of cases E: number of contacts per case p: probability of infection from contact ! �!"# = 1 + � ∗ � �$ → exponential growth % What if � = 1 − ! ? → Get saturation of curve (logistic growth) %"#" 8 4 5/14/20 Why model? • Have some idea what to expect • Plan ahead – make social interventions in absence of medical ones – Compare effect of different non-pharmaceutical interventions • Get some intuition, based on existing and daily data, of how the disease is spreading 9 S-I-R Model Susceptible Infected Each individual is assigned to a compartment People move between Someone who is compartments as they Recovered susceptible can fall ill and get cured become infected and then recover Kermack & McKendrick 1927 10 5 5/14/20 S-I-R Model Susceptible Infected Susceptible individuals Someone who is need to come into susceptible can contact with infected become infected Recovered individuals to become and then recover infected (or be ‘removed’) 11 Discrete version of SIR model Sd+1 = Sd – b *Sd *I/N Id+1 = Id + b *Sd * I/N – g I Rd+1 = Rd + g I S0 = N – I0 I0 R0 = 0 S : susceptible I : infected R : recovered/removed 12 6 5/14/20 Full Mathematical model �� S(t): susceptible = −��� I(t) : infected �� R(t): recovered/removed !" = ��� − �� All vary with time t !# b: transmission rate �� g : recovery rate = �� �� S+I+R = 1 Initial conditions: S, I, R: scaled by total population R(0) = 0 I(0) = I0 S(0) = 1 – I0 13 How does the spread of disease change with time? • Basic Reproductive Ratio: R0 • In the SIR model, R0 = b/g • For Covid-19, R0 = 2 to 3 • After physical distancing measures introduced, R drops 14 7 5/14/20 SEIR Model �� = Λ − ��� − �� Susceptible �� �� = ��� − � + � � �� Exposed !" = �� − (� + �)� !# b : transmission rate !& g : recovery rate Infected = �� − �� !' L : birth rate µ : death rate a : (random) incubation period parameter Removed The exposed compartment 15 Covid-19: Serial Interval Serial interval: Time duration between a primary case-patient having symptom onset and a secondary case-patient having symptom onset 16 8 5/14/20 Examples of other models in current use S: susceptible E: exposed Ip: Infected, pre-symptomatic Ia: infected, asymptomatic Is : infected, severe Im : infected, mild H: hospitaliZed R: recovered D: dead Slides courtesy Prof. Gautam Menon, Also see: https://www.mordecailab.com Ashoka University, India 17 More complex epidemiological model The C’s represent the intensity of contacts Tuning C’s a non-pharmaceutical intervention Product of C’s and β determine R Reduced R: A lockdown Reduce C’s: Testing-quarantining Slides courtesy Prof. Gautam Menon, Ashoka University, India 18 9 5/14/20 Other useful links • Models – Wikipedia: • https://en.wikipedia.org/wiki/Compartmental_models_in_epidemiology – MIDAS network of infectous disease modeling: • https://midasnetwork.us/covid-19/ • Further reading – CDC: • https://www.cdc.gov/coronavirus/2019-nCoV/index.html – From The Atlantic: • https://www.theatlantic.com/health/archive/2020/04/pandemic-confusing-uncertainty/610819 – On mutations: • https://www.nytimes.com/interactive/2020/04/30/science/coronavirus-mutations.html 19 10.
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