Lab Tracks
Four simultaneous applied labs will take place simultaneously, in two afternoon sessions. Participants should choose one of the labs, and follow the two sessions.
Each track will take place at different locations. Please see further informations about each location and institutions at the Venue page.
Epidemiological Surveillance Track
Emilio Ribas Institute and Epidemiological Surveillance Center of São Paulo
The visits of the surveillance component aim to present key institutions in the detection and response to public health emergencies in the state of São Paulo. We will start on Thursday 13th, with a visit to the Emilio Ribas Institute of Infectious Diseases, a tertiary specialized hospital. This is the hospital where suspected cases of infectious diseases are sent to be diagnosed and investigated. It is a centenary institution that comprises care, teaching, and research, holding an epidemiological surveillance unit. At this site, we will visit the emergency room, the ICU, the laboratory, and the surveillance units.
On Friday 14th, the same group will visit the Epidemiological Surveillance Center of the state of São Paulo, where the monitoring and rapid response to emergencies unit is located, and the Adolfo Lutz Institute, the state of São Paulo’s public health laboratory.
Public Policy Track
São Paulo`s City Government Innovation Laboratory and Public School on Public Administration
The public policy part of the workshop will introduce students to the challenges faced by the city government of Sao Paulo in confronting health emergencies using the COVID-19 pandemic as a case study. On both days, we will introduce indicators used to monitor policies and identify data sources commonly needed to evaluate policies. We will visit the (011).lab – São Paulo`s City Government Innovation Laboratory, where we will learn about the lab’s work to simulate and develop solutions to reduce transmission in the city’s subway and bus transportation network. We will also meet with the city government health secretariat to learn about management aspects of emergency preparedness, including how programs were planned and coordinated to address care delivery and epidemiological surveillance. As part of this visit, we will discuss the data systems used by the city government in health emergencies and the challenges surrounding integrating data systems to monitor trends effectively. On Day 2, we will meet with city managers to discuss budgeting and the city’s finances to understand how the metropolis allocated resources to respond to the health emergency.
“Case Study on the 011. Design Lab on Encouraging Preventive Behaviors against COVID-19 at Bus Terminals”
July 13, Thursday, 15h -16h.
Escola Municipal de Administração Pública de São Paulo (Rua Boa Vista, 280, 3º andar).
“Financing a Pandemic Response in the Metropolis: The Experience of Sao Paulo”
Meeting with Luis Felipe Vidal Arellano, Secretário de Fazenda Adjunto
July 14, Friday, 15h -16h
Modeling Track
School of Public Health of the University of São Paulo
The modeling lab part of the workshop will present the basics for understanding and using compartmental models (SIR and similar), and their applications in modeling disease transmission dynamics. Through a combination of theoretical explanations and hands-on exercises in Python, participants will explore the basic structure and key properties of compartmental models. The course will delve into the concepts of R0 and Rt, derived from these models, and their implications for epidemic dynamics. We will also discuss how to adapt compartmental models to make them more realistic, and how to evaluate and criticize proposed models for specific epidemic situations. Participants are not expected to have previous experience with Python, although basic notions of mathematics and programming will be useful. We aim to gather people of different backgrounds, enhancing their ability to contribute to epidemic research and response efforts.
Follow this link for syllabus and codes.
Virology Track
Institute of Tropical Medicine, Faculty of Medicine of the University of São Paulo
The virology part of the workshop will offer hands-on experience in developing a virus sequencing protocol based on integrating Oxford Nanopore MinION sequencing and performing bioinformatic analysis for public health purposes. This system was used by our teams to track different viral outbreaks including Zika, SARS-CoV-2, yellow fever, chikungunya, and most recently monkeypox, using optimized approaches that can now generate virus genomes in less than 24 hours. The first day of the practical course is dedicated to designing viral primer schemes for whole-genome sequencing and laboratory work using SARS-CoV-2 as an example. The second day focuses on computer-based data analysis comprising generation of consensus sequences and phylogenetic trees. Participants will gain skills in virus sequencing techniques and learn to process and analyze sequencing data using bioinformatic tools for potential outbreak investigations.
