Bayesian models for estimating the attack rate of epidemics

• Grant number: 19/21858-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: January 01, 2021
• End date: July 31, 2024
• Field of knowledge: Engineering - Electrical Engineering - Telecommunications
• Principal Investigator: Vitor Heloiz Nascimento
• Grantee: Carlos Augusto Prete Junior
• Host Institution: Escola Politécnica (EP). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 22/15985-1 - Leveraging genomic data to improve effective reproduction number estimates, BE.EP.DR

Abstract

Inferring the fraction of the population infected by an infeccious agent (attack rate) in real time is essential for monitoring emerging infectious diseases and predicting the trajectory of future epidemics. Estimating the attack rate is hindered by the high cost of mass testing, the delay in reporting test results in hospitalised patients, and the large proportion of non-reported asymptomatic or mild infections for diseases as COVID-19. Estimating the seroprevalence using blood donation samples is a low-cost alternative to infer the attack rate in real time. However, the reactivity of many assays wanes over time. This process is called seroreversion and leads to a decaying sensitivity, increasing the difficulty to obtain reliable seroprevalence estimates. In this project, we propose to develop a Bayesian model to obtain seroprevalence estimates accounting for seroreversion. We also intend to study the practical identifiability of these models, allowing users to compute the number of samples required for an acceptable uncertainty level. Finally, we propose to study the sensitivity of the estimated parameters to prior distributions. Since Bayesian models are employed in several areas and identifiability issues arise in several problemas, we expect the developed algorithms can be used in several applications. (AU)

Scientific publications

(9)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BUSS, LEWIS; PRETE, CARLOS A.; WHITTAKER, CHARLES; SALOMON, TASSILA; OIKAWA, MARCIO K.; PEREIRA, RAFAEL H. M.; MOURA, ISABEL C. G.; DELERINO, LUCAS; FRANCA, RAFAEL F. O.; MIYAJIMA, FABIO; et al. Predicting SARS-CoV-2 Variant Spread in a Completely Seropositive Population Using Semi-Quantitative Antibody Measurements in Blood Donors. VACCINES, v. 10, n. 9, p. 11-pg., 2022-09-01. (18/14389-0, 19/21858-0)

PRETE, CARLOS A., JR.; BUSS, LEWIS F.; WHITTAKER, CHARLES; SALOMON, TASSILA; OIKAWA, MARCIO K.; PEREIRA, RAFAEL H. M.; MOURA, ISABEL C. G.; DELERINO, LUCAS; BARRAL-NETTO, MANOEL; TAVARES, NATALIA M.; et al. SARS-CoV-2 antibody dynamics in blood donors and COVID-19 epidemiology in eight Brazilian state capitals: A serial cross-sectional study. eLIFE, v. 11, p. 53-pg., 2022-09-22. (18/14389-0, 19/21858-0)

FELIPE DE MELLO MARTINS; ALESSANDRA PINHEIRO VIDAL; JEEVAN GIDDALURU; BERNARDO MAIA DA SILVA; EVA K. LEE; PEIJUE ZHANG; LUCAS ESTEVES CARDOZO; CARLOS AUGUSTO PRETE JUNIOR; HELVES HUMBERTO DOMINGUES; ESTER CERDEIRA SABINO; et al. Temporal and spatial analysis of over 7,000 measles cases outbreak from 2018 to 2019 in the Brazilian Amazon. Einstein (São Paulo), v. 22, 2024-03-29. (19/21858-0)

PRETE JR, CARLOS A.; NASCIMENTO, VITOR H.; LOPES, CASSIO G.. Optimal Passive Source Localization for Acoustic Emissions. Entropy, v. 23, n. 12, DEC 2021. (19/21858-0, 18/12579-7)

PRETE, JR., CARLOS A.; BUSS, LEWIS F.; BUCCHERI, RENATA; ABRAHIM, CLAUDIA M. M.; SALOMON, TASSILA; CRISPIM, MYUKI A. E.; OIKAWA, MARCIO K.; GREBE, EDUARD; DA COSTA, ALLYSON G.; FRAIJI, NELSON A.; et al. einfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazi. BMC INFECTIOUS DISEASES, v. 22, n. 1, FEB 5 2022. (19/21858-0, 18/14389-0)

VERNAL, SEBASTIAN; NAHAS, ANDRESSA K.; NETO, FRANCISCO CHIARAVALLOTI; PRETE JUNIOR, CARLOS A.; CORTEZ, ANDRE L.; SABINO, ESTER CERDEIRA; LUNA, EXPEDITO JOSE DE ALBUQUERQUE. Geoclimatic, demographic and socioeconomic characteristics related to dengue outbreaks in Southeastern Brazil: an annual spatial and spatiotemporal risk model over a 12-year period. Revista do Instituto de Medicina Tropical de São Paulo, v. 63, 2021. (18/14389-0, 19/21858-0)

FARIA, NUNO R.; MELLAN, THOMAS A.; WHITTAKER, CHARLES; CLARO, INGRA M.; CANDIDO, DARLAN DA S.; MISHRA, SWAPNIL; CRISPIM, MYUKI A. E.; SALES, FLAVIA C.; HAWRYLUK, IWONA; MCCRONE, JOHN T.; et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, v. 372, n. 6544, p. 815+, MAY 21 2021. (20/04558-0, 19/21568-1, 19/21301-5, 18/14389-0, 17/13981-0, 20/04272-9, 18/25468-9, 16/18445-7, 19/21858-0, 18/17176-8, 19/12000-1, 19/07544-2, 18/12579-7, 19/24251-9)

LI, SABRINA L.; PEREIRA, RAFAEL H. M.; PRETE JR, CARLOS A.; ZAREBSKI, ALEXANDER E.; EMANUEL, LUCAS; ALVES, PEDRO J. H.; PEIXOTO, PEDRO S.; BRAGA, CARLOS K., V; DE SOUZA SANTOS, ANDREZA ARUSKA; DE SOUZA, WILLIAM M.; et al. Higher risk of death from COVID-19 in low-income and non-White populations of SAo Paulo, Brazil. BMJ GLOBAL HEALTH, v. 6, n. 4, p. 11-pg., 2021-04-01. (19/21858-0, 19/24251-9, 18/14389-0, 17/13981-0)

BRIZZI, ANDREA; WHITTAKER, CHARLES; SERVO, LUCIANA M. S.; HAWRYLUK, IWONA; PRETE JR, CARLOS A.; DE SOUZA, WILLIAM M.; AGUIAR, RENATO S.; ARAUJO, LEONARDO J. T.; BASTOS, LEONARDO S.; BLENKINSOP, ALEXANDRA; et al. Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals. Nature Medicine, v. 28, n. 7, p. 31-pg., 2022-05-10. (19/21858-0)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

PRETE JUNIOR, Carlos Augusto. Identification of stochastic non-linear dynamic systems for epidemic modelling.. 2024. Doctoral Thesis - Universidade de São Paulo (USP). Escola Politécnica (EP/BC) São Paulo.