Back
 OJEpi  Vol.10 No.4 , November 2020
Real-Time COVID-19 Forecasting for Four States of India Using a Regression Transmission Model
Abstract: Introduction: More than a million people are reported to have been infected with COVID in India, since the beginning of the pandemic. However, the epidemic is not the same across the country. Though there are state-level variations rapidly changing disease dynamics and the response has created uncertainty towards appropriate use of models to project for the future. Method: This paper aims at using a validated semi-mechanistic stochastic model to generate short term forecasts. This analysis used data available at the respective state government bulletins for four states. The analysis used a simplified transmission model using Markov Chain Monte Carlo simulation with Metropolis-Hastings updating. Results: Two weeks were used to compare the results with the actual data. The forecasted results are well within the 25th and 75th percentile of the actual cases reported by the respective states. The results indicate a reliable method for a real-time short term forecasting of COVID-19 cases. The 1st week projected interquartile range and actual; reported cases for the state of Kerala, Tamil Nadu, Andhra Pradesh and Odisha were (1064 - 2532) 2234, (17,503 - 50,125) 27,214, (5225 - 11,003) 9563, (2559 - 4461) 3925, respectively. Similarly, the 2nd week projected interquartile range and actual; reported cases were (1055 - 7803) 4221, (18,298 - 73,952) 31,488, (4705 - 23,224) 13,357, (2701 - 9037) 4175 respectively. Conclusion: This real-time forecast can be used as an early warning tool for projecting the changes in the epidemic in the near future triggering proactive management steps.
Cite this paper: Choudhury, L. and Kumar, B. (2020) Real-Time COVID-19 Forecasting for Four States of India Using a Regression Transmission Model. Open Journal of Epidemiology, 10, 335-345. doi: 10.4236/ojepi.2020.104027.
References

[1]   Ministry of Health and Family Welfare. Government of India (2020) Update COVID-19 India, as on 4th June.

[2]   Press Information Bureau. Government of India (2020) Update on Novel Coronavirus: One Positive Case Reported in Kerala.
https://pib.gov.in/PressReleasePage.aspx?PRID=1601095

[3]   Abraham, P., et al. (2020) Laboratory Surveillance for SARS-CoV-2 in India: Performance of Testing & Descriptive Epidemiology of Detected COVID-19, January 22-April 30, 2020. Indian Journal of Medical Research, 151, 424-437.

[4]   Mandal, S., et al. (2020) Prudent Public Health Intervention Strategies to Control the Coronavirus Disease 2019 Transmission in India: A Mathematical Model-Based Approach. Indian Journal of Medical Research, 151, 190-199.
https://doi.org/10.4103/ijmr.IJMR_504_20

[5]   Ray, D., et al. (2020) Predictions and Role of Interventions for COVID-19 Outbreak in India: Crisis of Virus in India (COVIND).

[6]   Chatterjee, K., Chatterjee, K., Kumar, A. and Shankar, S. (2020) Healthcare Impact of COVID-19 Epidemic in India: A Stochastic Mathematical Model. Medical Journal Armed Forces India, 76, 147-155.
https://doi.org/10.1016/j.mjafi.2020.03.022

[7]   Patel, P., Athotra, A., Vaisakh, T., Dikid, T., Jain, S. and NCDC COVID Incident Management Team (2020) Impact of Nonpharmacological Interventions on COVID-19 Transmission Dynamics in India. Indian Journal of Public Health, 64, 142.
https://doi.org/10.4103/ijph.IJPH_510_20

[8]   Kucharski, A.J., et al. (2020) Early Dynamics of Transmission and Control of COVID-19: A Mathematical Modelling Study. The Lancet Infectious Diseases, 20, 553-558.
https://doi.org/10.1016/S1473-3099(20)30144-4

[9]   Aayog, N. (2019) Healthy States Progressive India: Report on the Ranks of States and Union Territories. Health Index.
http://social.niti.gov.in

[10]   Nishiura, H. (2011) Real-Time Forecasting of an Epidemic Using a Discrete Time Stochastic Model: A Case Study of Pandemic Influenza (H1N1-2009). BioMedical Engineering OnLine, 10, 15.
https://doi.org/10.1186/1475-925X-10-15

[11]   Kelly, J.D., et al. (2019) Real-Time Predictions of the 2018–2019 Ebola Virus Disease Outbreak in the Democratic Republic of the Congo Using Hawkes Point Process Models. Epidemics, 28, Article ID: 100354.
https://doi.org/10.1016/j.epidem.2019.100354

[12]   Akhmetzhanov, A.R., et al. (2018) Real Time Forecasting of Measles Using Generation-Dependent Mathematical Model in Japan, 2018. PLOS Currents.
https://doi.org/10.1371/currents.outbreaks.3cc277d133e2d6078912800748dbb492

[13]   Roosa, K., et al. (2020) Real-Time Forecasts of the COVID-19 Epidemic in China from February 5th to February 24th, 2020. Infectious Disease Modelling, 5, 256-263.
https://doi.org/10.1016/j.idm.2020.02.002

[14]   Althaus, C.L. (2020) Real-Time Modeling and Projections of the COVID-19 Epidemic in Switzerland.
https://ispmbern.github.io/covid-19/swiss-epidemic-model

[15]   Hindustan Times (2020) Discrepancies in Covid Data Leave Haryana Health Authorities Baffled—Chandigarh.
https://www.hindustantimes.com/chandigarh/discrepancies-in-covid-data-leave-haryana-health-authorities-baffled/story-PExIZnMpk9WtgZioO5EACN.html

[16]   Government of Karnataka (2020) Home—COVID-19 Information Portal.
https://covid19.karnataka.gov.in/english

[17]   Health and Family Welfare Department (2020) Daily Bulletin—StopCoronaTN. Government of Tamil Nadu.
https://stopcorona.tn.gov.in/daily-bulletin/

[18]   Department of Health and Family Welfare (2020) COVID Dashboard. Government of Odisha.
https://health.odisha.gov.in/

[19]   Governmment of Andhra Pradesh (2020) COVID-19: Andhra Pradesh Department of Health, Medical, & Family Welfare.
http://hmfw.ap.gov.in/covid_19_dailybulletins.aspx

[20]   Asher, J. (2018) Forecasting Ebola with a Regression Transmission Model. Epidemics, 22, 50-55.
https://doi.org/10.1016/j.epidem.2017.02.009

[21]   Stephen, M. and Baum, G. (2020) COVID-19 Incubation Period: An Update. NEJM Journal Watch, 2020.
https://www.jwatch.org/na51083/2020/03/13/covid-19-incubation-period-update

[22]   Hindustan Times (2020) City to Breach 3k Covid-19 Cases Today as Health Department Clears Backlog of Samples—Gurugram—Hindustan Times.
https://www.hindustantimes.com/gurugram/city-to-breach-3k-cases-today-as-health-department-clears-backlog-of-samples/story-7elmD6dyh1iYmiI8npnGVI.html

[23]   Aderhold, A., Husmeier, D. and Grzegorczyk, M. (2017) Approximate Bayesian Inference in Semi-Mechanistic Models. Statistics and Computing, 27, 1003-1040.
https://doi.org/10.1007/s11222-016-9668-8

[24]   Funk, S., Camacho, A., Kucharski, A.J., Eggo, R.M. and Edmunds, W.J. (2018) Real-Time Forecasting of Infectious Disease Dynamics with a Stochastic Semi Mechanistic Model. Epidemics, 22, 56-61.
https://doi.org/10.1016/j.epidem.2016.11.003

[25]   Endo, A., van Leeuwen, E. and Baguelin, M. (2019) Introduction to Particle Markov-Chain Monte Carlo for Disease Dynamics Modellers. Epidemics, 29, Article ID: 100363.
https://doi.org/10.1016/j.epidem.2019.100363

[26]   Liu, F., Li, X. and Zhu, G. (2020) Using the Contact Network Model and Metropolis-Hastings Sampling to Reconstruct the COVID-19 Spread on the “Diamond Princess”. Science Bulletin, 65, 1297-1305.
https://doi.org/10.1016/j.scib.2020.04.043

[27]   Roberts, G.O., Gelman, A. and Gilks, W.R. (1997) Weak Convergence and Optimal Scaling of Random Walk Metropolis Algorithms. Annals of Applied Probability, 7, 110-120.
https://doi.org/10.1214/aoap/1034625254

[28]   Bédard, M. (2008) Optimal Acceptance Rates for Metropolis Algorithms: Moving beyond 0.234. Stochastic Processes and Their Applications, 118, 2198-2222.
https://doi.org/10.1016/j.spa.2007.12.005

[29]   R Core Team (2020) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing.
https://www.r-project.org

[30]   Wickham, H. (2009) ggplot2: Elegant Graphics for Data Analysis. In: ggplot2, Springer, New York, 1-7.
https://doi.org/10.1007/978-0-387-98141-3_1

[31]   Liu, Y., Gayle, A.A., Wilder-Smith, A. and Rocklöv, J. (2020) The Reproductive Number of COVID-19 Is Higher Compared to SARS Coronavirus. Journal of Travel Medicine, 27, taaa021.
https://doi.org/10.1093/jtm/taaa021

[32]   Viceconte, G. and Petrosillo, N. (2020) Covid-19 R0: Magic Number or Conundrum? Infectious Disease Reports, 12, 8516.
https://doi.org/10.4081/idr.2020.8516

[33]   Peirlinck, M., Linka, K., Sahli Costabal, F. and Kuhl, E. (2020) Outbreak Dynamics of COVID-19 in China and the United States. Biomechanics and Modeling in Mechanobiology, 1-15.
https://doi.org/10.1007/s10237-020-01332-5

[34]   Song, R., et al. (2020) Clinical and Epidemiological Features of COVID-19 Family Clusters in Beijing, China. Journal of Infection, 81, E26-E30.
https://doi.org/10.1016/j.jinf.2020.04.018

[35]   Ganyani, T., et al. (2020) Estimating the Generation Interval for Coronavirus Disease (COVID-19) Based on Symptom Onset Data, March 2020. Eurosurveillance, 25, Article ID: 2000257.
https://doi.org/10.2807/1560-7917.ES.2020.25.17.2000257

[36]   Boldog, P., Tekeli, T., Vizi, Z., Dénes, A., Bartha, F.A. and Röst, G. (2020) Risk Assessment of Novel Coronavirus COVID-19 Outbreaks Outside China. Journal of Clinical Medicine, 9, 571.
https://doi.org/10.3390/jcm9020571

[37]   Indian Institute for Population Sciences (IIPS) and ICF (2017) National Family Health Survey (NFHS-4), 2015-16: India. Int. Inst. Popul. Sci. ICF, 1-192.

[38]   Roda, W.C., Varughese, M.B., Han, D. and Li, M.Y. (2020) Why Is It Difficult to Accurately Predict the COVID-19 Epidemic? Infectious Disease Modelling, 5, 271-281.
https://doi.org/10.1016/j.idm.2020.03.001

[39]   Telangana Coronavirus News: Highest Positivity, Slow Recoveries, Low Testing: Telangana’s Worsening Covid-19 Stats. The Economic Times.
https://economictimes.indiatimes.com/news/politics-and-nation/highest-positivity-slow-recoveries-low-testing-telanganas-worsening-covid-19-stats/articleshow/76755301.cms

[40]   Covid Testing Numbers in Karnataka Down Sharply and So Are Fresh Cases. The Economic Times.
https://economictimes.indiatimes.com/news/politics-and-nation/covid-testing-numbers-in-karnataka-down-sharply-and-so-are-fresh-cases/articleshow/76333982.cms

[41]   Tsang, T.K., et al. (2020) Effect of Changing Case Definitions for COVID-19 on the Epidemic Curve and Transmission Parameters in Mainland China: A Modelling Study. The Lancet Public Health, 5, e289-e296.
https://doi.org/10.1016/S2468-2667(20)30089-X

[42]   Anderson, R.M., Hollingsworth, T.D., Baggaley, R.F., Maddren, R. and Vegvari, C. (2020) COVID-19 Spread in the UK: The End of the Beginning? The Lancet.
https://doi.org/10.1016/S0140-6736(20)31689-5

[43]   ECDC (2020) Rapid Risk Assessment: Resurgence of Reported Cases of COVID 19 in the EU/EEA, the UK and EU Candidate and Potential Candidate Countries. Risk Assessment.
https://www.ecdc.europa.eu/en/publications-data/rapid-risk-assessment-resurgence-reported-cases-covid-19#copy-to-clipboard

[44]   Shah, K., Awasthi, A., Modi, B., Kundarpur, R. and Saxena, D. (2020) Unfolding Trends of COVID-19 Transmission in India: Critical Review of Available Mathematical Models. Indian Journal of Community Health, 32, 206-214.
https://www.iapsmupuk.org/journal/index.php/IJCH/article/view/1460/991

[45]   Holmdahl, I. and Buckee, C. (2020) Wrong But Useful—What Covid-19 Epidemiologic Models Can and Cannot Tell Us. The New England Journal of Medicine, 383, 303-305.
https://doi.org/10.1056/NEJMp2016822

[46]   Delamater, P.L., Street, E.J., Leslie, T.F., Yang, Y.T. and Jacobsen, K.H. (2019) Complexity of the Basic Reproduction Number (R0). Emerging Infectious Diseases, 25, 1-4.
https://doi.org/10.3201/eid2501.171901

[47]   Bhaskar, A., Ponnuraja, C., Srinivasan, R. and Padmanaban, S. (2020) Distribution and Growth Rate of COVID-19 Outbreak in Tamil Nadu: A Log-Linear Regression Approach. Indian Journal of Public Health, 64, 188.
https://doi.org/10.4103/ijph.IJPH_502_20

[48]   Tiwari, S., Kumar, S. and Guleria, K. (2020) Outbreak Trends of Coronavirus (COVID-19) in India: A Prediction. Disaster Medicine and Public Health Preparedness.
https://doi.org/10.1017/dmp.2020.115

[49]   Tomar, A. and Gupta, N. (2020) Prediction for the Spread of COVID-19 in India and Effectiveness of Preventive Measures. Science of the Total Environment, 728, Article ID: 138762.
https://doi.org/10.1016/j.scitotenv.2020.138762

[50]   National Institute of Medical Statistics and National AIDS Control Organisation (2012) Technical Report India: HIV Estimates-2012. New Delhi.

[51]   COVID-19 Forecasts: Cumulative Deaths CDC.
https://www.cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html

 
 
Top