Structure in the variability of the basic reproductive number (R0) for Zika epidemics in the Pacific islands

eLife

Volumn 5, Issue NOVEMBER2016, 2016, Pages

  Champagne, Clara ^a,b   Salthouse, David Georges ^a   Paul, Richard ^c,d   Cao Lormeau, Van Mai ^e   Roche, Benjamin ^f   Cazelles, Bernard ^a,f  

^a ECOLE NORMALE SUPÉRIEURE   (France)

^b CREST   (France)

^c INSTITUT PASTEUR   (France)

^d CNRS   (France)

^e Institut Louis Malardé Pape'Ete   (France)

^f Sorbonne Universités   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASIC REPRODUCTION NUMBER; DISEASE SURVEILLANCE; DISEASE TRANSMISSION; GEOGRAPHIC DISTRIBUTION; HUMAN; INCUBATION TIME; INFECTION CONTROL; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; PACIFIC ISLANDS; POPULATION DENSITY; POPULATION SIZE; SEROPREVALENCE; STOCHASTIC MODEL; ZIKA FEVER; ZIKA VIRUS; EPIDEMIC; EPIDEMIOLOGICAL MONITORING; SEROEPIDEMIOLOGY; STATISTICAL MODEL;

BASIC REPRODUCTION NUMBER; EPIDEMICS; EPIDEMIOLOGICAL MONITORING; MODELS, STATISTICAL; PACIFIC ISLANDS; SEROEPIDEMIOLOGIC STUDIES; ZIKA VIRUS INFECTION;

EID: 85011019521     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.19874     Document Type: Article

References (60)

1. Anderson RM, May RM. 1982. Directly transmitted infections diseases: control by vaccination. Science 215: 1053-1060. doi: 10.1126/science.7063839, PMID: 7063839
2. Andrieu C, Doucet A, Holenstein R. 2010. Particle Markov chain Monte Carlo methods. Journal of the Royal Statistical Society: Series B 72: 269-342. doi: 10.1111/j.1467-9868.2009.00736.x
3. Aubry M, Finke J, Teissier A, Roche C, Broult J, Paulous S, Desprès P, Cao-Lormeau VM, Musso D. 2015a. Seroprevalence of arboviruses among blood donors in French Polynesia, 2011-2013. International Journal of Infectious Diseases 41: 11-12. doi: 10.1016/j.ijid.2015.10.005, PMID: 26482390
4. Aubry M, Teissier A, Roche C, Teururai S, Desprès P, Mallet H, Merceron S, Huart M, Sicard S, Deparis X, Musso D, Cao-Lormeau V. 2015b. Serosurvey of Dengue, Zika and Other Mosquito-Borne Viruses in French Polynesia. Poster 765. Philadelphia, PA, USA: 64th Annual Meeting of the American Society of Tropical Medicine and Hygiene. Oct 25-29. http://www.abstractsonline.com/Plan/ViewAbstract.aspx?sKey=2e5199c4-aceb-4d61-8769-342586917c5a&cKey=74ffe328-3a83-4f28-84c6-5656971501c8&mKey=%7bAB652FDF-0111-45C7-A5E5-0BA9D4AF5E12%7d
5. Bearcroft WG. 1956. Zika virus infection experimentally induced in a human volunteer. Transactions of the Royal Society of Tropical Medicine and Hygiene 50: 442-448. doi: 10.1016/0035-9203(56)90090-6, PMID: 13380987
6. Blower SM, Dowlatabadi H. 1994. Sensitivity and uncertainty analysis of complex models of disease transmission: An HIV Model, as an Example. International Statistical Review/Revue Internationale de Statistique 62: 229-243. doi: 10.2307/1403510
7. Bowman LR, Runge-Ranzinger S, McCall PJ. 2014. Assessing the relationship between vector indices and dengue transmission: a systematic review of the evidence. PLoS Neglected Tropical Diseases 8: e2848. doi: 10.1371/journal.pntd.0002848, PMID: 24810901
8. Brady OJ, Johansson MA, Guerra CA, Bhatt S, Golding N, Pigott DM, Delatte H, Grech MG, Leisnham PT, Maciel-de-Freitas R, Styer LM, Smith DL, Scott TW, Gething PW, Hay SI. 2013. Modelling adult Aedes aegypti and Aedes albopictus survival at different temperatures in laboratory and field settings. Parasites & Vectors 6: 351. doi: 10.1186/1756-3305-6-351, PMID: 24330720
9. Brauer F, Castillo-Chavez C, Mubayi A, Towers S. 2016. Some models for epidemics of vector-transmitted diseases. Infectious Disease Modelling. doi: 10.1016/j.idm.2016.08.001
10. Bretó C, He D, Ionides EL, King AA. 2009. Time series analysis via mechanistic models. The Annals of Applied Statistics 3: 319-348. doi: 10.1214/08-AOAS201
11. Cao-Lormeau V-M, Blake A, Mons S, Lastère S, Roche C, Vanhomwegen J, Dub T, Baudouin L, Teissier A, Larre P, Vial A-L, Decam C, Choumet V, Halstead SK, Willison HJ, Musset L, Manuguerra J-C, Despres P, Fournier E, Mallet H-P, et al. 2016. Guillain-Barré Syndrome outbreak associated with Zika Virus infection in French Polynesia: a case-control study. The Lancet 387: 1531-1539. doi: 10.1016/S0140-6736(16)00562-6
12. Cao-Lormeau V-M, Roche C, Teissier A, Robin E, Berry A-L, Mallet H-P, Sall AA, Musso D. 2014. Zika Virus, French Polynesia, South Pacific, 2013. Emerging Infectious Diseases 20: 1084-1086. doi: 10.3201/eid2006. 140138
13. Carnell R. 2016. Package ‘lhs’. 0.14. http://cran.stat.auckland.ac.nz/web/packages/lhs/lhs.pdf
14. Cazelles B, Hales S. 2006. Infectious diseases, climate influences, and nonstationarity. PLoS Medicine 3: e328. doi: 10.1371/journal.pmed.0030328, PMID: 16903777
15. Chouin-Carneiro T, Vega-Rua A, Vazeille M, Yebakima A, Girod R, Goindin D, Dupont-Rouzeyrol M, Lourenço-de-Oliveira R, Failloux AB. 2016. Differential Susceptibilities of Aedes aegypti and Aedes albopictus from the Americas to Zika Virus. PLoS Neglected Tropical Diseases 10: e0004543. doi: 10.1371/journal.pntd.0004543, PMID: 26938868
16. CHSP. 2014. Surveillance de la dengue et du zika en Polynésie franç aise, données actualisées au 28 mars 2014. Centre d’hygiène et de salubritépublique. http://www.hygiene-publique.gov.pf/IMG/pdf/bulletin_dengue_28-03-14.pdf
17. DASS. 2014. Situation sanitaire en Nouvelle Calédonie. Les arboviroses: Dengue, Chikungunya, Zika. Direction des Affaires Sanitaires et Sociales de Nouvelle Calédonie. http://www.dass.gouv.nc/portal/page/portal/dass/librairie/fichiers/32142267.PDF
18. Daudens E, Lastere S, Hirschauer C, Cao-Lormeau V-M, Louette R, Roche C, Chee Ayee A, Goffard N, Vrousos E, Renou L, Wiegandt A. 2009. Épidémiologie de la dengue et stratégies de lutte en Polynésie franç aise, 2006-2008. Numéro thématique. Polynésie franç aise: une situation particuliè re. Bulletin Epidémiologique Hebdomadaire, N°48-49-50: 499-503.
19. Diekmann O, Heesterbeek JAP, Roberts MG. 2010. The construction of next-generation matrices for compartmental epidemic models. Journal of the Royal Society Interface 7: 873-885. doi: 10.1098/rsif.2009.0386
20. Dietz K. 1993. The estimation of the basic reproduction number for infectious diseases. Statistical Methods in Medical Research 2: 23-41. doi: 10.1177/096228029300200103, PMID: 8261248
21. Doucet A, Freitas N, Gordon N. 2001. Sequential Monte Carlo Methods in Practice. New York: Springer. doi: 10. 1007/978-1-4757-3437-9
22. Doucet A, Johansen AM. 2011. A tutorial on particle filtering and smoothing: fifteen years later.
23. Duffy MR, Chen TH, Hancock WT, Powers AM, Kool JL, Lanciotti RS, Pretrick M, Marfel M, Holzbauer S, Dubray C, Guillaumot L, Griggs A, Bel M, Lambert AJ, Laven J, Kosoy O, Panella A, Biggerstaff BJ, Fischer M, Hayes EB. 2009. Zika virus outbreak on yap island, Federated States of Micronesia. New England Journal of Medicine 360: 2536-2543. doi: 10.1056/NEJMoa0805715, PMID: 19516034
24. Dupont-Rouzeyrol M, O’Connor O, Calvez E, Daurès M, John M, Grangeon JP, Gourinat AC. 2015. Co-infection with Zika and dengue viruses in 2 patients, New Caledonia, 2014. Emerging Infectious Diseases 21: 381-382. doi: 10.3201/eid2102.141553, PMID: 25625687
25. Dureau J, Ballesteros S, Bogich T. 2013 SSM: Inference for time series analysis with State Space Models. https://github.com/JDureau/ssm/blob/master/doc/doc.pdf.
26. Favier C, Degallier N, Rosa-Freitas MG, Boulanger JP, Costa Lima JR, Luitgards-Moura JF, Menkès CE, Mondet B, Oliveira C, Weimann ET, Tsouris P. 2006. Early determination of the reproductive number for vector-borne diseases: the case of dengue in Brazil. Tropical Medicine and International Health 11: 332-340. doi: 10.1111/j. 1365-3156.2006.01560.x, PMID: 16553913
27. Funk S, Kucharski AJ, Camacho A, Eggo RM, Yakob L, Edmunds WJ. 2016. Comparative analysis of dengue and Zika outbreaks reveals differences by setting and virus. bioRxiv. doi: 10.1101/043265
28. Gao D, Lou Y, He D, Porco TC, Kuang Y, Chowell G, Ruan S. 2016. Prevention and Control of Zika as a Mosquito-Borne and Sexually Transmitted Disease: A Mathematical Modeling Analysis. Scientific Reports 6: 28070. doi: 10.1038/srep28070, PMID: 27312324
29. Halstead SB. 2008. Dengue virus-mosquito interactions. Annual Review of Entomology 53: 273-291. doi: 10. 1146/annurev.ento.53.103106.093326, PMID: 17803458
30. Harrington LC, Fleisher A, Ruiz-Moreno D, Vermeylen F, Wa CV, Poulson RL, Edman JD, Clark JM, Jones JW, Kitthawee S, Scott TW. 2014. Heterogeneous feeding patterns of the dengue vector, Aedes aegypti, on individual human hosts in rural Thailand. PLoS Neglected Tropical Diseases 8: e3048. doi: 10.1371/journal.pntd. 0003048, PMID: 25102306
31. Hayes EB. 2009. Zika Virus outside Africa. Emerging Infectious Diseases 15: 1347-1350. doi: 10.3201/eid1509. 090442, PMID: 19788800
32. Imai N, Dorigatti I, Cauchemez S, Ferguson NM. 2015. Estimating dengue transmission intensity from sero- prevalence surveys in multiple countries. PLoS Neglected Tropical Diseases 9: e0003719. doi: 10.1371/journal. pntd.0003719, PMID: 25881272
33. Insee. 2012. Populations légales au recensement de la population 2012 De Polynésie franç aise: Institut National de la Statistique et des Etudes Economiques. https://www.insee.fr/fr/statistiques/2122859.
34. Insee. 2014. Populations légales au recensement de la population 2014 de Nouvelle-Calédonie: Institut National de la Statistique et des Etudes Economiques. https://www.insee.fr/fr/statistiques/2122859.
35. Kucharski AJ, Funk S, Eggo RM, Mallet HP, Edmunds WJ, Nilles EJ. 2016. Transmission Dynamics of Zika Virus in Island Populations: A Modelling Analysis of the 2013-14 French Polynesia Outbreak. PLoS Neglected Tropical Diseases 10: e0004726. doi: 10.1371/journal.pntd.0004726, PMID: 27186984
36. Laneri K, Bhadra A, Ionides EL, Bouma M, Dhiman RC, Yadav RS, Pascual M. 2010. Forcing versus feedback: epidemic malaria and monsoon rains in northwest India. PLoS Computational Biology 6: e1000898. doi: 10. 1371/journal.pcbi.1000898, PMID: 20824122
37. Ledermann JP, Guillaumot L, Yug L, Saweyog SC, Tided M, Machieng P, Pretrick M, Marfel M, Griggs A, Bel M, Duffy MR, Hancock WT, Ho-Chen T, Powers AM. 2014. Aedes hensilli as a potential vector of Chikungunya and Zika Viruses. PLoS Neglected Tropical Diseases 8: e3188. doi: 10.1371/journal.pntd.0003188, PMID: 25299181
38. Lessler J, Ott CT, Carcelen AC, Konikoff JM, Williamson J, Bi Q, Kucirka LM, Cummings DA, Reich NG, Chaisson LH. 2016. Times to key events in Zika Virus infection and implications for blood donation: a systematic review. Bulletin of the World Health Organization 94: 841-849. doi: 10.2471/BLT.16.174540, PMID: 27821887
39. Liu-Helmersson J, Stenlund H, Wilder-Smith A, Rocklöv J. 2014. Vectorial capacity of Aedes aegypti: effects of temperature and implications for global dengue epidemic potential. PLoS One 9: e89783. doi: 10.1371/journal. pone.0089783, PMID: 24603439
40. Lloyd AL. 2001. Destabilization of epidemic models with the inclusion of realistic distributions of infectious periods. Proceedings of the Royal Society B: Biological Sciences 268: 985-993. doi: 10.1098/rspb.2001.1599
41. Mallet H-P, Vial A, Musso D. 2015. Bilan de l’épidémie a` virus Zika en Polynésie franç aise. Bulletin d’Informations Sanitaires Epidemiologiques Et Statistiques 13 http://www.hygiene-publique.gov.pf/IMG/pdf/no13_-_mai_ 2015_-_zika.pdf.
42. Massad E, Burattini MN, Coutinho FA, Lopez LF. 2003. Dengue and the risk of urban yellow fever reintroduction in São Paulo State, Brazil. Revista de Saúde Pública 37: 477-484. doi: 10.1590/S0034-89102003000400013, PMID: 12937709
43. Metcalf CJE, Farrar J, Cutts FT, Basta NE, Graham AL, Lessler J, Ferguson NM, Burke DS, Grenfell BT. 2016. Use of serological surveys to generate key insights into the changing global landscape of infectious disease. The Lancet 388: 728-730. doi: 10.1016/S0140-6736(16)30164-7
44. Musso D, Gubler DJ. 2016. Zika virus. Clinical Microbiology Reviews 29: 487-524. doi: 10.1128/CMR.00072-15, PMID: 27029595
45. Nishiura H, Kinoshita R, Mizumoto K, Yasuda Y, Nah K. 2016a. Transmission potential of Zika Virus infection in the South Pacific. International Journal of Infectious Diseases 45: 95-97. doi: 10.1016/j.ijid.2016.02.017, PMID: 26923081
46. Nishiura H, Mizumoto K, Villamil-Gómez WE, Rodríguez-Morales AJ. 2016b. Preliminary estimation of the basic reproduction number of zika virus infection during Colombia epidemic, 2015-2016. Travel Medicine and Infectious Disease 14: 274-276. doi: 10.1016/j.tmaid.2016.03.016, PMID: 27060613
47. Pandey A, Mubayi A, Medlock J. 2013. Comparing vector-host and SIR models for dengue transmission. Mathematical Biosciences 246: 252-259. doi: 10.1016/j.mbs.2013.10.007, PMID: 24427785
48. Petersen LR, Jamieson DJ, Powers AM, Honein MA. 2016. Zika virus. The New England Journal of Medicine 374: 1552-1563. doi: 10.1056/NEJMra1602113, PMID: 27028561
49. Pujol G, Iooss B, Janon A. 2016. Package ‘sensitivity’. https://cran.r-project.org/web/packages/sensitivity/sensitivity.pdf
50. Reiner RC, Perkins TA, Barker CM, Niu T, Chaves LF, Ellis AM, George DB, Le Menach A, Pulliam JRC, Bisanzio D, Buckee C, Chiyaka C, Cummings DAT, Garcia AJ, Gatton ML, Gething PW, Hartley DM, Johnston G, Klein EY, Michael E, et al. 2013. A systematic review of mathematical models of mosquito-borne pathogen transmission: 1970-2010. Journal of The Royal Society Interface 10: 20120921 doi: 10.1098/rsif.2012.0921
51. Roberts GO, Rosenthal JS. 2009. Examples of adaptive MCMC. Journal of Computational and Graphical Statistics 18: 349-367. doi: 10.1198/jcgs.2009.06134
52. Roy M, Bouma MJ, Ionides EL, Dhiman RC, Pascual M. 2013. The potential elimination of Plasmodium vivax malaria by relapse treatment: insights from a transmission model and surveillance data from NW India. PLoS Neglected Tropical Diseases 7: e1979. doi: 10.1371/journal.pntd.0001979, PMID: 23326611
53. Schuler-Faccini L, Ribeiro EM, Feitosa IML, Horovitz DDG, Cavalcanti DP, Pessoa A, Doriqui MJR, Neri JI, Neto Joao Monteiro de Pina, Wanderley HYC, Cernach M, El-Husny AS, Pone MVS, Serao CLC, Sanseverino MTV, Neto J, Neto JM, Brazilian Medical Genetics Society-Zika Embryopathy Task Force. 2015. Possible Association Between Zika Virus Infection and Microcephaly - Brazil, 2015. MMWR. Morbidity and Mortality Weekly Report 65: 59-62. doi: 10.15585/mmwr.mm6503e2
54. Smith DL, Perkins TA, Reiner RC, Barker CM, Niu T, Chaves LF, Ellis AM, George DB, Le Menach A, Pulliam JR, Bisanzio D, Buckee C, Chiyaka C, Cummings DA, Garcia AJ, Gatton ML, Gething PW, Hartley DM, Johnston G, Klein EY, et al. 2014. Recasting the theory of mosquito-borne pathogen transmission dynamics and control. Transactions of the Royal Society of Tropical Medicine and Hygiene 108: 185-197. doi: 10.1093/trstmh/tru026, PMID: 24591453
55. Telle O, Vaguet A, Yadav NK, Lefebvre B, Cebeillac A, Nagpal BN, Daudé E, Paul RE. 2016. The spread of dengue in an endemic urban milieu-The Case of Delhi, India. PLoS One 11: e0146539. doi: 10.1371/journal. pone.0146539, PMID: 26808518
56. Thompson RN, Gilligan CA, Cunniffe NJ. 2016. Detecting presymptomatic infection is necessary to forecast major epidemics in the earliest stages of infectious disease outbreaks. PLOS Computational Biology 12: e1004836. doi: 10.1371/journal.pcbi.1004836, PMID: 27046030
57. Towers S, Brauer F, Castillo-Chavez C, Falconar AK. I, Mubayi A, Romero-Vivas CME. 2016. Estimation of the reproduction number of the 2015 zika virus outbreak in Barranquilla, Colombia, and a first estimate of the relative role of sexual transmission. arXiv. https://arxiv.org/abs/1606.01422.
58. van den Driessche P, Watmough J. 2002. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Mathematical Biosciences 180: 29-48. doi: 10.1016/S0025-5564 (02)00108-6, PMID: 12387915
59. Wang L, Valderramos SG, Wu A, Ouyang S, Li C, Brasil P, Bonaldo M, Coates T, Nielsen-Saines K, Jiang T, Aliyari R, Cheng G. 2016. From mosquitos to humans: Genetic Evolution of Zika Virus. Cell Host & Microbe 19: 561-565. doi: 10.1016/j.chom.2016.04.006, PMID: 27091703
60. World Health Organisation. 2016. WHO statement on the first meeting of the International Health Regulations (2005) (IHR 2005) Emergency Committee on Zika virus and observed increase in neurological disorders and neonatal malformations. http://www.who.int/mediacentre/news/statements/2016/1st-emergency-committee- zika/en/