Using syndromic measures of mortality to capture the dynamics of COVID-19 in Java, Indonesia, in the context of vaccination rollout

Djaafara B.A., Whittaker C., Watson O.J., Verity R., Brazeau N.F., Widyastuti, Oktavia D., Adrian V., Salama N., Bhatia S., Nouvellet P., Sherrard-Smith E., Churcher T.S., Surendra H., Lina R.N., Ekawati L.L., Lestari K.D., Andrianto A., Thwaites G., Baird J.K., Ghani A.C., Elyazar I.R.F., Walker P.G.T.

MRC Centre for Global Infectious Disease Analysis and the Abdul Latif Jameel Institute for Disease and Emergency Analytics, School of Public Health, Imperial College London St Mary’s Campus, Norfolk Place, London, W2 1PG, United Kingdom; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia; Jakarta Provincial Department of Health, Jakarta, Indonesia; School of Life Sciences, University of Sussex, Brighton, United Kingdom; Centre for Tropical Medicine, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom


Abstract

Background: As in many countries, quantifying COVID-19 spread in Indonesia remains challenging due to testing limitations. In Java, non-pharmaceutical interventions (NPIs) were implemented throughout 2020. However, as a vaccination campaign launches, cases and deaths are rising across the island. Methods: We used modelling to explore the extent to which data on burials in Jakarta using strict COVID-19 protocols (C19P) provide additional insight into the transmissibility of the disease, epidemic trajectory, and the impact of NPIs. We assess how implementation of NPIs in early 2021 will shape the epidemic during the period of likely vaccine rollout. Results: C19P burial data in Jakarta suggest a death toll approximately 3.3 times higher than reported. Transmission estimates using these data suggest earlier, larger, and more sustained impact of NPIs. Measures to reduce sub-national spread, particularly during Ramadan, substantially mitigated spread to more vulnerable rural areas. Given current trajectory, daily cases and deaths are likely to increase in most regions as the vaccine is rolled out. Transmission may peak in early 2021 in Jakarta if current levels of control are maintained. However, relaxation of control measures is likely to lead to a subsequent resurgence in the absence of an effective vaccination campaign. Conclusions: Syndromic measures of mortality provide a more complete picture of COVID-19 severity upon which to base decision-making. The high potential impact of the vaccine in Java is attributable to reductions in transmission to date and dependent on these being maintained. Increases in control in the relatively short-term will likely yield large, synergistic increases in vaccine impact. © 2021, The Author(s).

COVID-19; Indonesia; Modelling; Non-pharmaceutical interventions; Surveillance; Vaccinations


Journal

BMC Medicine

Publisher: BioMed Central Ltd

Volume 19, Issue 1, Art No 146, Page – , Page Count


Journal Link: https://www.scopus.com/inward/record.uri?eid=2-s2.0-85108092039&doi=10.1186%2fs12916-021-02016-2&partnerID=40&md5=292defa6924e443a3a852f77324f6c9d

doi: 10.1186/s12916-021-02016-2

Issn: 17417015

Type: All Open Access, Gold, Green


References

(2020) WHO Coronavirus Disease (COVID-19) Dashboard, , https://covid19.who.int/, Accessed 3 Feb 2021; Rochmyaningsih, D., Indonesia finally reports two coronavirus cases. Scientists worry it has many more (2020) Science, , https://www.sciencemag.org/news/2020/03/indonesia-finally-reports-two-coronavirus-cases-scientists-worry-it-has-many-more.Accessed21Aug2020; De Salazar, P.M., Niehus, R., Taylor, A., Buckee, C.O.F., Lipsitch, M., Identifying locations with possible undetected imported severe acute respiratory syndrome coronavirus 2 cases by using importation predictions (2020) Emerg Infect Dis., 26 (7), pp. 1465-1469; (2020) COVID-19 Indonesia Situation Reports, , https://www.who.int/indonesia/news/novel-coronavirus/situation-reports; (2020) This year’s Idul Fitri Traffic Accidents Fall by 31 Percent, , https://www.thejakartapost.com/news/2020/06/09/this-years-idul-fitri-traffic-accidents-fall-by-31-percent.html, The Jakarta Post; Widianto, S., Indonesia’s capital to reimpose restrictions over coronavirus (2020) Reuters, , https://uk.reuters.com/article/health-coronavirus-indonesia-idINL4N2G62U5; (2021) Situation Update: Response to COVID-19 in Indonesia, , https://reliefweb.int/report/indonesia/situation-update-response-covid-19-indonesia-18-january-2021-enid, (As of 18 January 2021); Jiao, C., Aditya, A., Indonesia begins COVID-19 vacine rollout – and Jokowi is first to get jab (2021) Time, , https://time.com/5929160/indonesia-vaccine-rollout-jokowi/, Accessed 25 Jan 2021; (2021) Cabinet Secretariat of the Republic of Indonesia, , https://setkab.go.id/en/govt-to-kick-off-covid-19-vaccination-for-public-workers/, Accessed 29 Apr 2021; Watson, O.J., Alhaffar, M., Mehchy, Z., Whittaker, C., Akil, Z., Brazeau, N.F., Leveraging community mortality indicators to infer COVID-19 mortality and transmission dynamics in Damascus (2021) Syria. Nat Commun., 12, pp. 1-10. , https://doi.org/10.1038/s41467-021-22474-9; Burki, T., COVID-19 in Latin America (2020) Lancet Infect Dis., 20 (5), pp. 547-548; Spiegelhalter, D., Why has the UK done so badly on COVID-19? There are still no simple answers (2020) The Guardian, , https://www.theguardian.com/commentisfree/2020/aug/02/uk-covid-19-excess-deaths, Accessed 7 Sept 2020; Syakriah, A., An examination of Indonesia’s death toll: Could it be higher? (2020) The Jakarta Post, , https://www.thejakartapost.com/news/2020/04/28/an-examination-of-indonesias-death-toll-could-it-be-higher.html, Accessed 24 Nov 2020; (2020) Jakarta COVID-19 Data Monitoring, , https://corona.jakarta.go.id/id/data-pemantauan, Accessed 10 Dec 2020; Fasyankes, , http://sirs.yankes.kemkes.go.id/fo/, Accessed 11 Mar 2020; (2020) Ketahanan Kesehatan Dalam Menjalani Tatanan Hidup, , Baru. Jakarta; Chakraborty, S., Chakravarty, D., Discrete gamma distributions: properties and parameter estimations (2012) Commun Stat Theory Methods., 41 (18), pp. 3301-3324; Bi, Q., Wu, Y., Mei, S., Ye, C., Zou, X., Zhang, Z., Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: A retrospective cohort study (2020) Lancet Infect Dis, , https://doi.org/10.1016/S1473-3099(20)30287-5; Keeling, M.J., Danon, L., Vernon, M.C., House, T.A., Individual identity and movement networks for disease metapopulations (2010) Proc Natl Acad Sci U S A., 107 (19), pp. 8866-8870; Watson, O.J., Walker, P., Whittaker, C., Winskill, P., Charles, G., Squire: SEIR Transmission Model of COVID-19, , https://github.com/mrc-ide/squire; (2020) Global Flight Data Annual; Lauer, S.A., Grantz, K.H., Bi, Q., Jones, F.K., Zheng, Q., Meredith, H.R., Azman, A.S., Lessler, J., The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application (2020) Ann Intern Med., 172 (9), pp. 577-582; Walker, P.G.T., Whittaker, C., Watson, O.J., Baguelin, M., Winskill, P., Hamlet, A., The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries (2020) Science (80-), 369, p. eabc0035; ICNARC report on COVID-19 in critical care; (2020) Imperial College COVID-19 LMIC Reports, , https://mrc-ide.github.io/global-lmic-reports/, Version 5. MRC Centre for Global Infectious Disease Analysis, Imperial College London; Unwin, H.J.T., Mishra, S., Bradley, V.C., Gandy, A., Mellan, T.A., Coupland, H., (2020) State-level tracking of COVID-19 in the United States, , https://doi.org/10.1101/2020.07.13.20152355, medRxiv; Cori, A., Ferguson, N.M., Fraser, C., Cauchemez, S., A new framework and software to estimate time-varying reproduction numbers during epidemics (2013) Am J Epidemiol., 178 (9), pp. 1505-1512; Cori, A., (2020) EpiEstim: A package to estimate time varying reproduction numbers from epidemic curves, , https://cran.r-project.org/package=EpiEstim, R package version 2.2-3; Google COVID-19 Community Mobility Reports, , https://www.google.com/covid19/mobility/, Accessed 22 Aug 2020; Djaafara, B.A., Whittaker, C., Watson, O.J., Verity, R., Brazeau, N.F., Oktavia, D., Quantifying the dynamics of COVID-19 burden and impact of interventions in Java (2020) Indonesia. Medrxiv., , https://doi.org/10.1101/2020.10.02.20198663; (2020), https://covid19.go.id/peta-sebaran, Satuan Tugas Penanganan COVID-19 (Indonesia COVID-19 Response Acceleration Task Force), Peta Sebaran, Accessed 3 Feb 2021; (2020) COVID-19 Di Indonesia @Kawalcovid19 Online Spreadsheet (Tab: Kasus per Provinsi), , kcov.id/daftarpositif; Ratcliffe, R., Cahya, G.H., COVID patients turned away as hospitals in Indonesia face collapse (2021) The Guardian, , https://www.theguardian.com/world/2021/jan/26/covid-patients-turned-away-as-hospitals-in-indonesia-face-collapse, Accessed 29 Jan 2021; Altmann, D.M., Douek, D.C., Boyton, R.J., What policy makers need to know about COVID-19 protective immunity (2020) Lancet., 395 (10236), pp. 1527-1529; Stephens, D.S., McElrath, M.J., COVID-19 and the Path to Immunity (2020) J Am Med Assoc., 324 (13), pp. 1279-1281; Britton, T., Ball, F., Trapman, P., A mathematical model reveals the influence of population heterogeneity on herd immunity to SARS-CoV-2 (2020) Science (80-), 369, pp. 846-849; Aschwanden, C., The false promise of herd immunity for COVID-19 (2020) Nature., 587 (7832), pp. 26-28; Flaxman, S., Mishra, S., Gandy, A., Unwin, H.J.T., Mellan, T.A., Coupland, H., Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe (2020) Nature., 584 (7820), pp. 257-261; Sabino, E.C., Buss, L.F., Carvalho, M.P.S., Prete, C.A., Jr., Crispim, M.A.E., Fraiji, N.A., Pereira, R.H.M., Faria, N.R., Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence (2021) Lancet., 397 (10273), pp. 452-455; Meldrum, A., Magome, M., (2021) South Africa Struggles with Post-Holiday Spike in COVID-19, , https://apnews.com/article/travel-south-africa-coronavirus-pandemic-holidays-africa-8a45947a6a4a1eeeb48102bb9d404206, Associated Press, Accessed 28 Jan 2021; Volz, E., Mishra, S., Chand, M., Barrett, J.C., Johnson, R., Geidelberg, L., Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England (2021) Nature, 593, pp. 266-269. , –,., https://doi.org/10.1038/s41586-021-03470-x; Buss, L.F., Prete, C.A., Abrahim, C.M.M., Mendrone, A., Salomon, T., de Almeida-Neto, C., Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic (2021) Science (80-), 371, pp. 288 LP-288292; Kim, J.H., Marks, F., Clemens, J.D., Looking beyond COVID-19 vaccine phase 3 trials (2021) Nat Med., 27 (2), pp. 205-211; Kupferschmidt, K., New mutations raise specter of ‘immune escape.’ (2021) Science (80-), 371, pp. 329 LP-329330; Davies, N.G., Abbott, S., Barnard, R.C., Jarvis, C.I., Kucharski, A.J., Munday, J.D., Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England (2021) Science (80-), 372, p. eabg3055; Faria, N.R., Mellan, T.A., Whittaker, C., Claro, I.S., Candidomishra, S., Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil (2021) Science, , (80-), eabh2644; (2021), https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/961042/S1095_NERVTAG_update_note_on_B.1.1.7_severity_20210211.pdf, NERVTAG: update note on B.1.1.7 severity, Accessed 16 Apr 2021; Widianto, S., (2021) Indonesia Says Identifies Two Cases of British COVID-19 Variant, , https://www.reuters.com/article/us-health-coronavirus-indonesia-idUSKBN2AU0SE, Reuters, Accessed 16 Apr 2021; Katriana, P.N., (2021) New COVID-19 variant B1525 identified in Batam of Riau Islands, , https://en.antaranews.com/news/172550/new-covid-19-variant-b1525-identified-in-batam-of-riau-islands, Antara News, Accessed 16 Apr 2021; (2021) Indonesia reports coronavirus case with “Eek” mutation: Reuters, , https://www.reuters.com/article/us-health-coronavirus-indonesia-mutation-idUSKBN2BT1FV, Reuters staff, Accessed 16 Apr 2021; Rochmyaningsih, D., Indonesia ramps up effort to spot elusive COVID variants (2021) Nikkei Asia, , https://asia.nikkei.com/Spotlight/Coronavirus/Indonesia-ramps-up-effort-to-spot-elusive-COVID-variants, Accessed 16 Apr 2021

Indexed by Scopus

Leave a Comment