Russian version English version
Volume 15   Issue 2   Year 2020
Vlad A.I.1, Sannikova T.E.2, Romanyukha A.A.2

Transmission of Acute Respiratory Infections in a City: Agent-Based Approach

Mathematical Biology & Bioinformatics. 2020;15(2):338-356.

doi: 10.17537/2020.15.338.


  1. Uchaikin V.F., Nisevich N.I., Shamsheva O.V. Infektsionnye bolezni u detei (Infectious diseases in children): textbook. 2011 (in Russ.).
  2. Ostrye negrippoznye respiratornye infektsii (Acute non-influenza respiratory infections). Ed. G.I. Karpukhin. Saint Petersburg, 1996 (in Russ.).
  3. Kermack W.O., McKendrick A.G. A contribution to the mathematical theory of epidemics. Proceedings of the Royal Society of London. 1927;115(772):700-721. doi: 10.1098/rspa.1927.0118
  4. Liu W., Levin S.A., Iwasa Y. Influence of nonlinear incidence rates upon the behavior of SIRS epidemiological models. Journal of Mathematical Biology. 1986;23(2):187-204. doi: 10.1007/BF00276956
  5. Nucci M.C., Leach P.G.L. An integrable SIS model. Journal of Mathematical Analysis and Applications. 2004;290(2):506-518. doi: 10.1016/j.jmaa.2003.10.044
  6. Li M.Y., Graef J.R., Wang L., Karsai J. Global dynamics of a SEIR model with varying total population size. Mathematical Biosciences. 1999;160(2):191-213. doi: 10.1016/S0025-5564(99)00030-9
  7. Hethcote H.W. The Mathematics of Infectious Diseases. SIAM Review. 2000;42(4):599-653. doi: 10.1137/S0036144500371907
  8. Billari F. C., Prskawetz A. Agent-based computational demography: Using simulation to improve our understanding of demographic behaviour. Springer Science & Business Media, 2012.
  9. Perez L., Dragicevic S. An agent-based approach for modeling dynamics of contagious disease spread. International Journal of Health Geographics. 2009;8(1):50. doi: 10.1186/1476-072X-8-50
  10. El-Sayed A. M., Scarborough P., Seemann L., Galea S. Social network analysis and agent-based modeling in social epidemiology. Epidemiologic Perspectives & Innovations. 2012;9(1):1. doi: 10.1186/1742-5573-9-1
  11. Janssen M. A., Ostrom E. Empirically based, agent-based models. Ecology and Society. 2006;11(2). doi: 10.5751/ES-01861-110237
  12. Wang Z., Butner J. D., Kerketta R., Cristini V., Deisboeck T. S. Simulating cancer growth with multiscale agent-based modeling. In: Seminars in Cancer Biology. Academic Press, 2015;30:70. doi: 10.1016/j.semcancer.2014.04.001
  13. Bonabeau E. From classical models of morphogenesis to agent-based models of pattern formation. Artificial Life. 1997;3(3):191-211. doi: 10.1162/artl.1997.3.3.191
  14. Bauer A.L., Beauchemin C.A., Perelson A.S. Agent-based modeling of host-pathogen systems: The successes and challenges. Information Sciences. 2009;179(10):1379-1389. doi: 10.1016/j.ins.2008.11.012
  15. Frias-Martinez E., Williamson G., Frias-Martinez V. An Agent-Based Model of Epidemic Spread Using Human Mobility and Social Network Information. IEEE Conference on Social Computing. 2011. doi: 10.1109/PASSAT/SocialCom.2011.142
  16. Hunter E., Namee B.M., Kelleher J. An open-data-driven agent-based model to simulate infectious disease outbreaks. PLOS One. 2018;13(12):e0208775. doi: 10.1371/journal.pone.0208775
  17. Merler S., Ajelli M., Fumanelli L., Gomes M.F., Piontti A.P., Rossi L., Chao D.L., Longini I.M. Jr., Halloran M.E., Vespignani A. Spatio-temporal spread of the Ebola 2014 outbreak in Liberia and the effectiveness of non-pharmaceutical interventions: a computational modelling analysis. The Lancet Infectious Diseases. 2015;15(2):204-211. doi: 10.1016/S1473-3099(14)71074-6
  18. Kim Y., Ryu H., Lee S. Agent-Based Modeling for Super-Spreading Events: A Case Study of MERS-CoV Transmission Dynamics in the Republic of Korea. International Journal of Environmental Research and Public Health. 2018;15(11). Article No. 2369. doi: 10.3390/ijerph15112369
  19. Hackl J., Dubernet T. Epidemic Spreading in Urban Areas Using Agent-Based Transportation Models. Future Internet. 2019;11(4):92. doi: 10.3390/fi11040092
  20. Macal C., North M. Introductory tutorial: Agent-based modeling and simulation. In: Proceedings of the Winter Simulation Conferenc IEEE. 2014:6-20. doi: 10.1109/WSC.2014.7019874
  21. Romanyukha A.A., Sannikova T.E., Drynov I.D. The origin of acute respiratory epidemics. Herald of the Russian Academy of Sciences. 2011;81(1):31-34. doi: 10.1134/S1019331611010114
  22. Hydrometcenter of Russia. Ezhemesiachnye i ezhesutochnye srednie mnogoletnie znacheniia (normy) temperatury vozdukha dlia Moskvy (Monthly and daily average long-term values (norms) of air temperature for Moscow). (accessed 15 March 2020).
  23. Karpova L.S., Volik K.M., Smorodintseva E.A., Stolyarova T.P., Popovtseva N.M., Stolyarov K.A. Different Etiologies on other ARVI in Children and Adults in 2014 to 2016. Epidemiology and Vaccinal Prevention. 2018;17(6):35-47 (in Russ.). doi: 10.31631/2073-3046-2018-17-35-47
  24. Seo Y.B., Song J.Y., Choi M.J., Kim I.S., Yang T.U., Hong K.-W., Cheong H.J., Kim W.J. Etiology and Clinical Outcomes of Acute Respiratory Virus Infection in Hospitalized Adults. Infect. Chemother. 2014;46(2):67-76. doi: 10.3947/ic.2014.46.2.67
  25. Lessler J., Reich N.G., Brookmeyer R., Perl T.M., Nelson K.E., Cummings D.A.T. Incubation periods of acute respiratory viral infections: a systematic review. The Lancet Infectious Diseases. 2009;9(5):291-300. doi: 10.1016/S1473-3099(09)70069-6
  26. Esposito S., Daleno C., Baldanti F., Scala A., Campanini G., Taroni F., Fossali E., Pelucchi C., Principi N.N. Viral shedding in children infected by pandemic A/H1N1/2009 influenza virus. Virology Journal. 2011;8(1):349. doi: 10.1186/1743-422X-8-349
  27. Carrat F., Vergu E., Ferguson N.M., Lemaitre M., Cauchemez S., Leach S., Valleron A.-J. Time Lines of Infection and Disease in Human Influenza: A Review of Volunteer Challenge Studies. American Journal of Epidemiology. 2008;167(7):775-785. doi: 10.1093/aje/kwm375
  28. Jane M., Vidal M.J., Soldevila N., Romero A., Martinez A., Torner N., Godoy P., Launes C., Rius C., Marcos M.A.A., Dominguez A. Epidemiological and clinical characteristics of children hospitalized due to influenza A and B in the south of Europe, 2010-2016. Scientific Reports. 2019;9(1):12853. doi: 10.1038/s41598-019-49273-z
  29. Zlateva K.T., de Vries J.J.C., Coenjaerts F.E.J., van Loon A.M., Verheij T., Little P., Butler C.C., Goossens H., Ieven M., Claas E.C.J. Prolonged shedding of rhinovirus and re-infection in adults with respiratory tract illness. European Respiratory Journal. 2014;44(1):169-177. doi: 10.1183/09031936.00172113
  30. Peltola V., Waris M., Kainulainen L., Kero J., Ruuskanen O. Virus shedding after human rhinovirus infection in children, adults and patients with hypogammaglobulinaemia. Clinical Microbiology and Infection. 2013;19(7):E322-E327. doi: 10.1111/1469-0691.12193
  31. Hall C.B., Walsh E.E., Long C.E., Schnabel K.C. Immunity to and frequency of reinfection with respiratory syncytial virus. The Journal of Infectious Diseases. 1991;163(4):693-698. doi: 10.1093/infdis/163.4.693
  32. Abels S., Nadal D., Stroehle A., Bossart W. Reliable Detection of Respiratory Syncytial Virus Infection in Children for Adequate Hospital Infection Control Management. Journal of Clinical Microbiology. 2001;39(1):3135-3139. doi: 10.1128/JCM.39.9.3135-3139.2001
  33. DeVincenzo J.P., Wilkinson T., Vaishnaw A., Cehelsky J., Meyers R., Nochur S., Harrison L., Meeking P., Mann A., Moane E., Oxford J., Pareek R., Moore R., Walsh E., Studholme R., Dorsett P., Alvarez R., Lambkin-Williams R. Viral Load Drives Disease in Humans Experimentally Infected with Respiratory Syncytial Virus. American Journal of Respiratory and Critical Care Medicine. 2010;182(10):1305-1314. doi: 10.1164/rccm.201002-0221OC
  34. Haque E., Banik U., Monwar T., Anthony L., Adhikary A.K. Worldwide increased prevalence of human adenovirus type 3 (HAdV-3) respiratory infections is well correlated with heterogeneous hypervariable regions (HVRs) of hexon. PLOS One. 2018;13(3):e0194516. doi: 10.1371/journal.pone.0194516
  35. La Rosa A.M., Champlin R.E., Mirza N., Gajewski J., Giralt S., Rolston K.V., Raad I., Jacobson K., Kontoyiannis D., Elting L., Whimbey E. Adenovirus Infections in Adult Recipients of Blood and Marrow Transplants. Clinical Infectious Diseases. 2001;32(6):871-876. doi: 10.1086/319352
  36. Sieg S., Muro-Cacho C., Robertson S., Huang Y., Kaplan D. Infection and immunoregulation of T lymphocytes by parainfluenza virus type 3. PNAS. 1994;91(14):6293-6297. doi: 10.1073/pnas.91.14.6293
  37. Oxford Textbook of Medicine: Infection. Eds. Warrell D., Cox T.M., Firth J., Torok E. Oxford University Press, 2012.
  38. Monto A.S., Lim S.K. The Tecumseh Study of Respiratory Illness. VI. Frequency of and relationship between outbreaks of coronavirus infection. The Journal of Infectious Diseases. 1974;129(3):271-276. doi: 10.1093/infdis/129.3.271
  39. Feikin D.R., Fu W., Park D.E., Shi Q., Higdon M.M., Baggett H.C., Brooks W.A., Deloria Knoll M., Hammitt L.L., Howie S.R.C., et al. Is Higher Viral Load in the Upper Respiratory Tract Associated With Severe Pneumonia? Findings From the PERCH Study. Clinical Infectious Diseases. 2017;64(3):S337-S346. doi: 10.1093/cid/cix148
  40. Viboud C., Boelle P.Y., Cauchemez S., Lavenu A., Valleron A.J., Flahault A., Carrat F. Risk factors of influenza transmission in households. British Journal of General Practice. 2004;54(506):684-689. doi: 10.1016/j.ics.2004.01.013
  41. Bayram R.O., Ozdemir H., Emsen A., Dagi H.T., Artac H. Reference ranges for serum immunoglobulin (IgG, IgA, and IgM) and IgG subclass levels in healthy children. Turkish Journal of Medical Sciences. 2019;49(2):497-505. doi: 10.3906/sag-1807-282
  42. Jafarzadeh A., Sadeghi M., Karam G.A., Vazirinejad R. Salivary IgA and IgE levels in healthy subjects: relation to age and gender. Brazilian Oral Research. 2010;24(1):21-27. doi: 10.1590/S1806-83242010000100004
  43. Axtell R.L. Zipf distribution of U.S. firm sizes. Science. 2001;293(5536):1818-1820. doi: 10.1126/science.1062081
  44. Barabasi A.L., Albert R. Emergence of scaling in random networks. Science. 1999;286(5439):509-512. doi: 10.1126/science.286.5439.509
  45. Ali H., Sadegh N., Behrouz M.-B., Qiang Q. ROLL: Fast In-Memory Generation of Gigantic Scale-free Networks. SIGMOD '16: Proceedings of the 2016 International Conference on Management of Data. 2016:1829-1842. doi: 10.1145/2882903.2882964
  46. Popova A.Yu., Ezhlova E.B., Melnikova A.A., Miheev V.N., Ryzhikov A.B., Ilicheva T.N., Domkina A.M., Mikheeva I.V., Saltykova T.S., Saltykova T.S. The Impact Annual Immunization against Flu on Morbidity of Flu in the Russian Federation. Epidemiology and Vaccinal Prevention. 2016;15(1):48-55. doi: 10.31631/2073-3046-2016-15-1-48-55
  47. Leung N.H.L., Xu C., Ip D.K.M., Cowling B.J. The fraction of influenza virus infections that are asymptomatic: a systematic review and meta-analysis. Epidemiology. 2015;26(6):862-872. doi: 10.1097/EDE.0000000000000340
  48. Galanti M., Birger R., Ud-Dean M., Filip I., Morita H., Comito D., Anthony S., Freyer G.A., Ibrahim S., Lane B., Matienzo N., Ligon C., Rabadan R., Shittu A., Tagne E., Shaman J. Rates of asymptomatic respiratory virus infection across age groups. Epidemiology and Infection. 2019;147(e176):1-6. doi: 10.1017/S0950268819000505
  49. Ip D.K.M., Lau L.L.H., Leung N.H.L., Fang V.J., Chan K.-H., Chu D.K.W., Leung G.M., Peiris J.S.M., Uyeki T.M., Cowling B.J. Viral Shedding and Transmission Potential of Asymptomatic and Paucisymptomatic Influenza Virus Infections in the Community. Clinical Infectious Diseases. 2017;64(6):736-742. doi: 10.1093/cid/ciw841
  50. Moreira L.P., Watanabe A.S.A., Camargo C.N., Melchior T.B., Granato C., Bellei N. Respiratory syncytial virus evaluation among asymptomatic and symptomatic subjects in a university hospital in Sao Paulo, Brazil, in the period of 2009-2013. Influenza and Other Respiratory Viruses. 2018;12(3):326-330. doi: 10.1111/irv.12518
  51. Elveback L.R., Fox J.P., Ackerman E., Langworthy A., Boyd M., Gatewood L. An influenza simulation model for immunization studies. American Journal of Epidemiology. 1976;103(2):152-165. doi: 10.1093/oxfordjournals.aje.a112213
  52. Tsang T.K., Cowling B.J., Fang V.J., Chan K.-H., Ip D.K.M., Leung G.M., Peiris J.S.M., Cauchemez S. Influenza A Virus Shedding and Infectivity in Households. The Journal of Infectious Diseases. 2015;212(9):1420-14280. doi: 10.1093/infdis/jiv225
  53. Valle S.Y.D., Hyman J.M., Hethcote H.W., Eubank S.G. Mixing patterns between age groups in social networks. Social Networks. 2007;29(4):539-554. doi: 10.1016/j.socnet.2007.04.005
  54. Eccles R. An Explanation for the Seasonality of Acute Upper Respiratory Tract Viral Infections. Acta Otolaryngol. 2002;122(2):183-191. doi: 10.1080/00016480252814207
  55. Eccles R. An Explanation for the Seasonality of Acute Upper Respiratory Tract Viral Infections. Acta Otolaryngol. 2002;122(2):183-191. doi: 10.1080/00016480252814207
Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2020.15.338
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)


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