Mathematical modelling of COVID-19 incidence in~Moscow with an agent-based model
Diskretnyj analiz i issledovanie operacij, Tome 30 (2023) no. 2, pp. 15-47.

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The outbreak of the COVID-19 pandemic created an emergency situation in the public health system in Russia and in the world, which entailed the need to develop tools for predicting the progression of the pandemic and assessing the potential interventions. In the present day context, numerical simulation is actively used to solve such problems. The paper considers a COVID-19 agent-based megalopolis model. The model was developed in 2020 and was further refined in subsequent years. The capabilities of the model include the description of simultaneous spread of several virus strains and taking into account data on vaccination and population activity. The model parameters are calculated using statistical data on the daily number of newly diagnosed COVID-19 cases. The application of the model to describe the epidemiological situation in Moscow in 2021 and early 2022 was demonstrated. The capability for building predictions for 1–3 months was shown, taking into account the emergence of new SARS-CoV-2 variants, i. e. the Delta and Omicron strains. Tab. 3, illustr. 10, bibliogr. 64.
Keywords: COVID-19 pandemic, numerical simulation, agent-based model, COVID-19 epidemic development prediction, SARS-CoV-2 variants, Delta strain
Mots-clés : Omicron strain, vaccination.
@article{DA_2023_30_2_a1,
     author = {V. V. Vlasov and A. M. Deryabin and O. V. Zatsepin and G. D. Kaminskiy and E. V. Karamov and A. L. Karmanov and S. N. Lebedev and G. N. Rykovanov and A. V. Sokolov and N. A. Teplykh and A. S. Turgiyev and K. E. Khatuntsev},
     title = {Mathematical modelling of {COVID-19} incidence {in~Moscow} with an agent-based model},
     journal = {Diskretnyj analiz i issledovanie operacij},
     pages = {15--47},
     publisher = {mathdoc},
     volume = {30},
     number = {2},
     year = {2023},
     language = {ru},
     url = {http://geodesic.mathdoc.fr/item/DA_2023_30_2_a1/}
}
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V. V. Vlasov; A. M. Deryabin; O. V. Zatsepin; G. D. Kaminskiy; E. V. Karamov; A. L. Karmanov; S. N. Lebedev; G. N. Rykovanov; A. V. Sokolov; N. A. Teplykh; A. S. Turgiyev; K. E. Khatuntsev. Mathematical modelling of COVID-19 incidence in~Moscow with an agent-based model. Diskretnyj analiz i issledovanie operacij, Tome 30 (2023) no. 2, pp. 15-47. http://geodesic.mathdoc.fr/item/DA_2023_30_2_a1/

[1] V. A. Adarchenko, S. A. Baban, A. A. Bragin, et al., Simulation of the coronavirus epidemic with differential and statistical models, Prepr. 264, RFYaTs—VNIITF, Snezhinsk, 2020, 30 pp. (Russian)

[2] Bernoulli D., “Essai d'une nouvelle analyse de la mortalité causée par la petite vérole, et des advantages de l'inoculation pour la prévenir”, Histoire de l'Académie Royale des Sciences 1760, L'Imprimerie Royale, Paris, 1766, 1–45 (French)

[3] Farr W., “Progress of epidemics — Epidemic of small pox”, Second annual report of the Registrar-General of births, deaths, and marriages in England, W. Clowes and Sons, London, 1840, 91–98

[4] Brownlee J., “Statistical studies in immunity: The theory of an epidemic”, Proc. R. Soc. Edinb., 26:1 (1906), 484–521 | DOI

[5] Hamer W. H., “The Milroy lectures on epidemic disease in England — The evidence of variability and of persistency of type”, Lancet, 1:4307 (1906), 733–739

[6] Ross R., Report on the prevention of malaria in Mauritius, Waterlow and Sons, London, 1908, 202 pp.

[7] Kermack W. O., McKendrick A. G., “A contribution to the mathematical theory of epidemics”, Proc. R. Soc. Lond. Ser. A, 115:772 (1927), 700–721 | DOI

[8] R. M. Anderson and R. M. May, Infectious Diseases of Humans. Dynamics and Control, Oxford Univ. Press, Oxford, 1991

[9] Bhanot G., DeLisi C., Predictions for Europe for the COVID-19 pandemic from a SIR model, Prepr. Server Health Sci. medRxiv,, Cold Spring Harbor Lab, Oyster Bay, NY, 2020 (accessed Mar. 31, 2023) medrxiv.org/content/10.1101/2020.05.26.20114058

[10] V. L. Makarov, A. R. Bakhtizin, E. D. Sushko, and A. F. Ageeva, “Simulation the COVID-19 epidemic — advantages of an agent-based approach”, Ekon. Sots. Peremeny, Fakty Tend. Progn., 13:4 (2020), 58–73 (Russian)

[11] Noll N. B., Aksamentov I., Druelle V. et al., COVID-19 Scenarios: An interactive planning tool for COVID-19 outbreaks, Univ. Basel, Basel, 2020 (accessed Mar. 31, 2023) covid19-scenarios.org

[12] O. I. Krivorotko, S. I. Kabanikhin, N. Yu. Zyatkov, A. Yu. Prikhodko, N. M. Prokhoshin, and M. A. Shishlenin, “Mathematical modeling and forecasting of COVID-19 in Moscow and Novosibirsk region”, Num. Anal. Appl., 13:4 (2020), 332–348 | DOI | MR | Zbl

[13] M. A. Kondratyev, “Forecasting methods and models of disease spread”, Kompyut. Issled. Model., 5:5 (2013), 863–882 (Russian)

[14] N. T. J. Bailey, The Mathematical Approach to Biology and Medicine, John Wiley Sons, London, 1967

[15] Sirakoulis G. C., Karafyllidis I., Thanailakis A., “A cellular automaton model for the effects of population movement and vaccination on epidemic propagation”, Ecol. Model., 133:3 (2000), 209–223 | DOI

[16] Saramaki J., Kaski K., “Modelling development of epidemics with dynamic small-world networks”, J. Theor. Biology, 234:3 (2005), 413–421 | DOI | MR | Zbl

[17] Patel R., Longini I. M., Jr., Halloran M. E., “Finding optimal vaccination strategies for pandemic influenza using genetic algorithms”, J. Theor. Biology, 234:2 (2005), 201–212 | DOI | MR | Zbl

[18] Her. Rus. Acad. Sci., 86:3 (2016), 248–257 | DOI | DOI

[19] A. F. Ageeva, “Simulation of epidemics: Agent-based approach”, Model. Optim. Inf. Tekhnol., 8:3 (2020), 13 pp. (Russian)

[20] V. D. Perminov and M. A. Kornilina, “An individual-based model for simulation of an urban epidemic”, Mat. Model., 19:5 (2007), 116–127 (Russian) | Zbl

[21] Li J., Giabbanelli P., “Returning to a normal life via COVID-19 vaccines in the United States: A large-scale agent-based simulation study”, JMIR Med. Inform., 9:4 (2021), e27419, 19 pp. | DOI

[22] Nguyen L. K. N., Howick S., McLafferty D., Anderson G. H., Pravinkumar S. J., van der Meer R., Megiddo I., “Evaluating intervention strategies in controlling coronavirus disease 2019 (COVID-19) spread in care homes: An agent-based model”, Infect. Control Hosp. Epidemiol., 42:9 (2021), 1060–1070 | DOI

[23] Lorig F., Johansson E., Davidsson P., “Agent-based social simulation of the COVID-19 pandemic: A systematic review”, J. Artif. Soc. Soc. Simul., 24:3 (2021), 5, 26 pp. | DOI

[24] O. I. Krivorotko, S. I. Kabanikhin, M. I. Sosnovskaya, and D. V. Andornaya, “Sensitivity and identifiability analysis of COVID-19 pandemic models”, Vavilov. Zh. Genet. Sel., 25:1 (2021), 82–91 (Russian) | MR

[25] Mellacher P., “Endogenous viral mutations, evolutionary selection, and containment policy design”, J. Econ. Interact. Coord., 17 (2022), 801–825 | DOI

[26] Perez L., Dragicevic S., “An agent-based approach for modelling dynamics of contagious disease spread”, Int. J. Health Geogr., 8 (2009), 50, 17 pp. | DOI

[27] Frias-Martinez E., Williamson G., Frias-Martinez V., “An agent-based model of epidemic spread using human mobility and social network information”, 2011 IEEE Int. Conf. Privacy, Security, Risk and Trust; IEEE Int. Conf. Social Computing (Boston, MA, USA, Oct. 9–11, 2011), IEEE Comput. Soc., Los Alamitos, 2011, 49–56

[28] Megiddo I., Colson A. R., Nandi A., Chatterjee S., Prinja S., Khera A., Laxminarayan R., “Analysis of the Universal Immunization Programme and introduction of a rotavirus vaccine in India with IndiaSim”, Vaccine, 32, Suppl. 1 (2014), A151–A161 | DOI

[29] Aleta A., Martín-Corral D., Pastore y Piontti A. et al., “Modelling the impact of testing, contact tracing and household quarantine on second waves of COVID-19”, Nat. Hum. Behav., 4:9 (2020), 964–971 | DOI

[30] Eubank S., Guclu H., Anil Kumar V. C., Marathe M. V., Srinivasan A., Toroczkai Z., Wang N., “Modelling disease outbreaks in realistic urban social networks”, Nature, 429:6988 (2004), 180–184 | DOI

[31] Hinch R., Probert W. J. M., Nurtay A. et al., “OpenABM-COVID-19—An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing”, PLOS Comput. Biol., 17:7 (2021), e1009146, 26 pp. | DOI

[32] Kerr C. C., Stuart R. M., Mistry D. et al., “Covasim: An agent-based model of COVID-19 dynamics and interventions”, PLOS Comput. Biol., 17:7 (2021), e1009149, 32 pp. | DOI

[33] Yrjölä J., Tuomisto J. T., Kolehmainen M., Bonsdorff J., Tikkanen T., REINA: Agent-based simulation model for COVID-19 spread in society and patient outcomes, Kausal, Helsinki, 2020 (accessed Mar. 31, 2023) github.com/kausaltech/reina-model

[34] G. N. Rykovanov, S. N. Lebedev, O. V. Zatsepin, et al., “Agent-based simulation of the COVID-19 epidemic in Russia”, Her. Rus. Acad. Sci., 92:4 (2022), 479–487 | DOI

[35] O. V. Zatsepin, A. A. Bragin, V. V. Vlasov, et al., “An agent-based model for the COVID-19 epidemic”, Zababakhin Scientific Readings, Proc. XV Int. Conf., Snezhinsk, Russia, Sept. 27 — Oct. 1 2021, Izd. RFYaTs—VNIITF, Snezhinsk, 2021, 230–231

[36] Grimm V., Railsback S. F., Individual-based modeling and ecology, Princeton Univ. Press, Princeton, 2005, 448 pp. | MR | Zbl

[37] Social and economic situation in Moscow, Federal State Statistics Service, M., 2021 (Russian) (accessed Mar. 31, 2023)

[38] Work and employment in Russia, Rosstat, M., 2019, 136 pp. (Russian) (accessed Mar. 31, 2023)

[39] Yandex Research—One day in the life of Moscow transport, Yandex, M., 2020 (Russian) (accessed Mar. 31, 2023)

[40] COVID-19: Community mobility reports, Google, Mountain View, CA, 2022 (accessed Mar. 31, 2023) google.com/covid19/mobility

[41] Cevik M., Kuppalli K., Kindrachuk J., Peiris M., “Virology, transmission, and pathogenesis of SARS-CoV-2”, BMJ, 371:8267 (2020), m3862, 6 pp. | DOI

[42] Aronna M. S., Guglielmi R., Moschen L. M., “A model for COVID-19 with isolation, quarantine and testing as control measures”, Epidemics, 34 (2021), 100437, 15 pp. | DOI

[43] Coronavirus COVID-19: Official information on the coronavirus in Russia, Natsionalnye Prioritety, M., 2023 (Russian) (accessed Mar. 31, 2023)

[44] N. V. Orlova, T. V. Gololobova, T. G. Suranova, M. N. Filatova, and S. Yu. Orlova, “Analysis of the dynamics of vaccination against coronavirus infection in Russia”, Med. Alf., 23 (2021), 8–12

[45] Sughayer M. A., Souan L., Abu Alhowr M. M. et al., “Comparison of the effectiveness and duration of anti-RBD SARS-CoV-2 IgG antibody response between different types of vaccines: Implications for vaccine strategies”, Vaccine, 40:20 (2022), 2841–2847 | DOI

[46] N. N. Kalitkin, Numerical Methods, Nauka, M., 1978 (Russian)

[47] “The report by Anna Popova, the head of the Rospotrebnadzor, at the meeting with Putin”, Izvestiya, 2020, Apr. 28 (Russian) (accessed Mar. 31, 2023)

[48] “Coronavirus antibodies found in almost 20% of New Yorkers”, Life, 2020, May 3 (Russian) (accessed Mar. 31, 2023)

[49] Research of population immunity to the new coronavirus infection in Muscovites, June 11, Mosgorzdrav, 2020 (Russian) (accessed Mar. 31, 2023)

[50] Tracking SARS-CoV-2 variants, World Health Organ, Geneva, 2023 (accessed Mar. 31, 2023) who.int/en/activities/tracking-SARS-CoV-2-variants

[51] Tsueng G., Mullen J. L., Alkuzweny M. et al., “Outbreak.info Research Library: A standardized, searchable platform to discover and explore COVID-19 resources”, Nat. Methods, 20 (2023), 536–540 (accessed Mar. 31, 2023) outbreak.info | DOI

[52] Variants of the Virus, Centers for Disease Control and Prevention, Atlanta, GA, 2023 (accessed Mar. 31, 2023) cdc.gov/coronavirus/2019-ncov/variants/index.html

[53] Hodcroft E., CoVariants: Per country. Overview of variants in countries, Univ. Bern, Bern, 2023 (accessed Mar. 31, 2023) covariants.org/per-country

[54] Gushchin V. A., Dolzhikova I. V., Shchetinin A. M. et al., “Neutralizing activity of sera from Sputnik V-vaccinated people against variants of concern (VOC: B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.617.3) and Moscow endemic SARS-CoV-2 variants”, Vaccines, 9:7 (2021), 779, 12 pp. | DOI

[55] Naaber P., Tserel L., Kangro K. et al., “Dynamics of antibody response to BNT162b2 vaccine after six months: A longitudinal prospective study”, Lancet Reg. Health Eur., 10 (2021), 100208, 9 pp. | DOI

[56] Jordan S. C., Shin B.-H., Gadsden T.-A. M. et al., “T cell immune responses to SARS-CoV-2 and variants of concern (Alpha and Delta) in infected and vaccinated individuals”, Cell. Mol. Immunol., 18:11 (2021), 2554–2556 | DOI | MR

[57] Cherednik I., “Modeling the waves of Covid-19”, Acta Biotheoretica, 70:1 (2021), 8, 36 pp. | DOI

[58] Campbell F., Archer B., Laurenson-Schafer H. et al., “Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021”, Eurosurveillance, 26:24 (2021), 5, 6 pp. | DOI | Zbl

[59] Dagpunar J., Interim estimates of increased transmissibility, growth rate, and reproduction number of the Covid-19 B.1.617.2 variant of concern in the United Kingdom, Prepr. Server Health Sci. medRxiv, Cold Spring Harbor Lab, Oyster Bay, NY, 2021 (accessed Mar. 31, 2023) medrxiv.org/content/10.1101/2021.06.03.21258293

[60] Mallapaty S., “COVID vaccines cut the risk of transmitting Delta—but not for long”, Nature. News, 2021, Oct. 5 (accessed Mar. 31, 2023) nature.com/articles/d41586-021-02689-y

[61] Kim D., Jo J., Lim J.-S., Ryu S., Serial interval and basic reproduction number of SARS-CoV-2 Omicron variant in South Korea, Prepr. Server Health Sci. medRxiv, , Cold Spring Harbor Lab., Oyster Bay, NY, 2021 (accessed Mar. 31, 2023) medrxiv.org/content/10.1101/2021.12.25.21268301

[62] Hansen P. R., “Relative contagiousness of emerging virus variants: An analysis of the Alpha, Delta, and Omicron SARS-CoV-2 variants”, Econom. J., 25:3 (2021), 739–761 | DOI

[63] Gonzalez Lopez Ledesma M. M., Sanchez L., Ojeda D. S. et al., “Longitudinal study after Sputnik V vaccination shows durable SARS-CoV-2 neutralizing antibodies and reduced viral variant escape to neutralization over time”, mBio, 31:1 (2022), e03442-21, 9 pp.

[64] Corrao G., Franchi M., Cereda D. et al., “Persistence of protection against SARS-CoV-2 clinical outcomes up to 9 months since vaccine completion: A retrospective observational analysis in Lombardy, Italy”, Lancet Infect. Dis., 22:5 (2022), 649–656 | DOI