Welcome Room: Floor 4, 4205

Introductory lecture - Stochastic epidemic models: the homogeneous case

• Tom Britton (Stockholm University)

Room: Floor 4, 4205

Introductory lecture - Stochastic epidemic models: introducing heterogeneities

• Lorenzo Pellis (University of Manchester)

Room: Floor 4, 4205

Introductory lecture - Role of epidemic models in public health policy support

• Mirjam Kretzschmar (University Medical Center Utrecht)

Room: Floor 4, 4205

Introductory lecture - Statistical inference for epidemic models

• Daniela De Angelis

Room: Floor 4, 4205

Research lecture - Mitigation of Superspreader driven epidemics - Chair: Prof Tom Britton, Stockholm University

• Kim Sneppen (Copenhagen University)

Room: Floor 4, 4205

Research lecture - Modeling spatial transmission of infectious diseases - Chair: Prof Tom Britton, Stockholm University

• Sen Pei (Columbia University)

Room: Floor 4, 4205

Research lecture - Time-since-infection models for contact tracing and waning immunity - Chair: Prof Daniela De Angelis, University of Cambridge

• Francesca Scarabel (University of Leeds)

Room: Floor 4, 4205

Research lecture - Jointly modelling epidemics and the economy, with an application to COVID-19 - Chair: Prof Daniela De Angelis, University of Cambridge

• Otilia Boldea (Tilburg University)

Room: Floor 4, 4205

Research lecture - From Pandemic to endemic: the interplay of immunity, viral evolution, and seasonality -Chair: Prof Lorenzo Pellis, University of Manchester

• Richard Neher (University of Basel)

Room: Floor 4, 4205

Research lecture - Overdispersed allele frequency fluctuations illuminate disease transmission networks in an ongoing pandemic - Chair: Prof Lorenzo Pellis, University of Manchester

• Oskar Hallatschek (University of Leipzig)

Room: Floor 4, 4205

ONLINE Research lecture - Antigenic evolution and evolutionary consequences of vaccination against SARS CoV-2 - Chair: Prof Lorenzo Pellis, University of Manchester

• Igor Rouzine

Room: Room 5

Research lecture - Investigating COVID-19 dynamics with agent-based models - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht

• Francesco Di Ruscio (Norwegian Institute of Public Health)

Room: Floor 4, 4205

Research lecture - Estimating the incidence and prevalence of hepatitis C virus among at-risk groups in Norway to monitor progress towards elimination - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht

• Jørgen Eriksson Midtbø (Norwegian Institute of Public Health)

Room: Floor 4, 4205

Research lecture - Modelling the importance of population behaviour and seasonality on SARS-CoV-2 spread using Google community mobility reports and weather data - Chair: Prof Mirjam Kretzschmar, University Medical Center Utrecht

• Hilde Kjelgaard Brustad (University of Oslo)

Room: Floor 4, 4205

Discussion - Inference and identifiability in infectious disease models

• Daniela De Angelis
• Otilia Boldea
• Sen Pei

Room: Albano 3: 6228 - Mega (22 seats)

Discussion - Multiscale (within-and-between host) and multi-strain models

• Lorenzo Pellis
• Francesca Scarabel

Room: Albano 3: 6228 - Mega (22 seats)

Research seminar - Rate of evolution and fitness landscape of SARS-CoV-2

• Richard Neher

Room: Albano 3: 6228 - Mega (22 seats)

Research seminar - Gradual waning of immunity in SIRS models - Chair: Dr Jørgen Eriksson Midtbø, FHI

• Mohamed El Khalifi (Stockholm University)

Room: Floor 4, 4205

Research seminar -Application of network science in the infectious disease research - Chair: Dr Jørgen Eriksson Midtbø, FHI

• Veronika Halász (Heidelberg University)

Room: Floor 4, 4205

Research seminar -Model-based evaluation of post-pandemic vaccination strategies to reduce COVID-19 in patients with chronic diseases - Chair: Dr Jørgen Eriksson Midtbø, FHI

• Ilse Westerhof (University Medical Center Utrecht)

Room: Floor 4, 4205

Social activity: Vasa Museum Room: Albano 3: 6228 - Mega (22 seats)

Research seminar - Models of pathogens interaction - Chair: Prof Pejman Rohani, University of Georgia

• Lulla Opatowski (Institut Pasteur)

Room: Floor 4, 4205

Research seminar - Development of trait-based models for understanding and approximating pathogen spillover systems - Chair: Prof Pejman Rohani, University of Georgia

• Marina Treskova (Heidelberg University)

Research seminar - Estimating transmission trees while allowing for multiple introductions, applied to SARS-CoV-2 in Dutch mink farms - Chair: Prof Pejman Rohani, University of Georgia

• Bastiaan Van der Roest (University Medical Center Utrecht)

Social activity: Skansen Museum Room: Albano 3: 6228 - Mega (22 seats)

Research seminar - Inferring the ecological and evolutionary determinants of pathogen re-emergence - Chair: Prof Joacim Rocklöv, Heidelberg University

• Pejman Rohani (University of Georgia)

Room: Floor 4, 4205

Research seminar - Impact of human behavior on ITNs control strategies to prevent the spread of vector borne diseases - Chair: Prof Joacim Rocklöv, Heidelberg University

• Manalebish Debalike Asfaw (Addis Ababa University)

Room: Floor 4, 4205

Research seminar - Challenges in modeling complex multi-host infectious diseases: West Nile virus spread and its dependence on climatic conditions - Chair: Prof Joacim Rocklöv, Heidelberg University

• Julian Heidecke (Heildelberg University)

Room: Floor 4, 4205

Research seminar - Epidemic models with manual and digital contact tracing - Chair: Prof Joacim Rocklöv, Heidelberg University

• Dongni Zhang (Stockholm University)

Room: Floor 4, 4205

Research seminar - Inclusion of environmental drivers in dynamical models - Chair: Prof Lulla Opatowski, Institut Pasteur

• Joacim Rocklöv (Heidelberg University)

Room: Floor 4, 4205

Research seminar - Modeling effect of interventions on HIV transmission among men who have sex with men in the Netherlands - Chair: Prof Lulla Opatowski, Institut Pasteur

• Alexandra Teslya (University Medical Center Utrecht)

Room: Floor 4, 4205

Research seminar - Stochastic invasion of Variants of Concern in a Population with Heterogeneous Immunity - Chair: Prof Lulla Opatowski, Institut Pasteur

• Jacob Curran-Sebastian (University of Copenhagen)

Room: Floor 4, 4205

Discussion - Modeling ecological interactions of viruses

• Lulla Opatowski
• Pejman Rohani

Room: Albano 3: 6228 - Mega (22 seats)

Practical introduction to MCMC (includes breaks)

• Lorenzo Pellis (The University of Manchester)

Room: Albano 3: 6228 - Mega (22 seats)

Research seminar - Arboviruses in a Changing Environment - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata

• Nicholas DeFelice (Icahn School of Medicine at Mount Sinai)

Room: Floor 4. 4205

Research seminar - Simplified within host and dose-response models of SARS-CoV-2 Infection - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata

• Jingsi Xu (University of Manchester)

Room: Floor 4, 4205

Research seminar - The impact of Urban Heat Islands on the outbreak potential of mosquito-borne diseases spread by Culex pipiens and Aedes albopictus in Europe - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata

• Pratik Singh (Heidelberg University)

Room: Floor 4, 4205

Research seminar - Model-based evaluation of school measures on SARS-CoV-2 transmission during the pandemic - Chair: Prof Gianpaolo Scalia Tomba, University of Rome Tor Vergata

• Benedetta Canfora (University Medical Center Utrecht & Lisbon University)

Room: Floor 4, 4205

Social activity: Nobel Prize Museum Room: Albano 3: 6228 - Mega (22 seats)

Introductory lecture - Virus evolution between transmission pairs - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht

• Katia Koelle (Emory University)

Room: Floor 4, 4205

Introductory lecture - Within-host evolution of viruses - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht

• Katrina Lythgoe (University of Oxford)

Room: Floor4, 4205

Introductory lecture - Modeling the evolutionary dynamics of novel infectious diseases - Chair: Dr Ganna Rozhnova, University Medical Center Utrecht

• Troy Day (Queen's University)

Room: Floor 4, 4205

Introductory lecture - Methods for detecting and characterizing emerging SARS-CoV-2 variants - Chair: Prof Tom Britton, Stockholm University

• Erik Volz (Imperial College London)

Room: Floor 4, 4205

Research lecture - The speed of adaptation to vaccination - Chair: Prof Katia Koelle, Emory University

• Sylvain Gandon (CNRS)

Room: Floor 4, 4205

Research lecture - Natural selection and evolution in seasonal epidemic models - Chair: Prof Katia Koelle, Emory University

• Viggo Andreasen (Roskilde University)

Room: Floor 4, 4205

Research lecture - Spatially extended SIR models and quadratic growth - Chair: Prof Katia Koelle, Emory University

• Axel Brandenburg

Room: Floor 4, 4205

Research lecture - Diversity in humans and pathogens: implications for the dynamics of epidemics and the impact of interventions - Chair: Prof Rustom Antia, Emory University

• Chiara Poletto (University of Padova)

Room: Floor 4, 4205

Research lecture - Within- and between host processes of phenotype dynamics of zoonotic pathogens - Chair: Prof Rustom Antia, Emory University

• Henrik Sjödin (Umeå University)

Room: Floor 4, 4205

Research lecture - Incorporating immune waning and boosting into models of viral infections - Chair: Dr Viggo Andreasen, Roskilde University

• Rustom Antia (Emory University)

Room: Floor 4, 4205

Research lecture - An epidemic model with short-lived mixing groups - Chair: Dr Viggo Andreasen, Roskilde University

• Frank Ball (University of Nottingham)

Room: Floor 4, 4205

Research lecture - Inferring SARS-CoV-2 virus loads in sewage in the Netherlands and quantifying its relation to hospital admission data - Chair: Dr Viggo Andreasen, Roskilde University

• Michiel van Boven (University Medical Center Utrecht)

Room: Floor 4, 4205

Research lecture - Statistical Genetics and Direct Coupling Analysis - Chair: Prof Troy Day, Queen's University

• Erik Aurell (KTH Royal Institute of Technology)

Room: Floor 4, 4205

Research lecture - Inference of fitness landscape (online) - Chair: Prof Troy Day, Queen's University

• Igor Rouzine (Sechenov Institute of Evolutionary Physiology and Biochemistry)

Room: Lecture room 5

Computer Woskhop 1 - Who infected whom? Hands-on experience on outbreak analysis with phybreak to combine genetic and epidemiological data

• Mirjam Kretzschmar
• Martin Bootsma

Room: Floor 4, 4205 Knowledge of who infected whom during an outbreak of an infectious disease is important to determine risk factors for transmission and to design effective control measures. Our software package phybreak infers transmission links that show how an infection went from person to person, based on both epidemiological and genetic data. During this workshop you will get experienced with phybreak and how to use it yourselves. Requirements: you need to bring your laptop. Materials are attached. The link to the google colab is: bit.ly/phybreakworkshop_colab

Discussion - Anticipating and identifying adaptive evolution in SARS-CoV-2 and other acute viral pathogens

• Katia Koelle
• Katrina Lythgoe
• Sylvain Gandon

Room: Albano 3: 6228 - Mega (22 seats)

Computer workshop 2 - Introduction to BEAST: phylodynamic analysis of molecular sequences

• Jantien Backer
• Ganna Rozhnova

Room: Floor 4, 4202 Summary: A phylodynamic analysis uses molecular sequences sampled at different times to learn about the population history of a virus. We will use BEAST 2 (Bayesian Evolutionary Analysis by Sampling Trees) to guide you through all steps of the analysis, from reconstructing phylogenies to choosing the appropriate population model. At the end of the course you will do a phylodynamic analysis by yourself. Requirements: Participants are requested to have the following programs installed prior to the workshop: BEAST 2: a program for Bayesian analysis of molecular sequences using MCMC. You can download the latest version from http://beast2.org/ This download will also include Beauti and TreeAnnotator that will be used during the practical. Tracer: a program to inspect the trace file of parameters that are logged during the BEAST analysis You can download the latest version from http://beast.community/tracer FigTree: a program to view annotated phylogenetic trees You can download the latest version from https://github.com/rambaut/figtree/releases Note that under Windows you need to be allowed to run .exe files for these programs to run.

Social activity: Boat trip (times TBA) Room: Albano 3: 6228 - Mega (22 seats)

Research seminars - Host Heterogeneity and Punctuated Evolution of SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht

• Bjarke Frost Nielsen (Roskilde University)

Room: Floor 4, 4205

Research seminars - Inferring epidemiological dynamics using temporal patterns of genetic variation, with application to SARS-CoV-2 - Chair: Dr Michiel van Boven, University Medical Center Utrecht

• Yeongseon Park (Emory University)

Room: Floor 4, 4205

Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of vaccination and human behavior - Chair: Dr Michiel van Boven, University Medical Center Utrecht

• Troy Day
• Mirjam Kretzschmar

Room: Floor 4, 4205

Discussion - Modeling evolutionary and epidemiological dynamics of viruses: role of host immune system - Chair: Dr Michiel van Boven, University Medical Center Utrecht

• Rustom Antia
• Viggo Andreasen
• Michiel van Boven

Room: Floor 4, 4205

Research lecture - Multiscale time-since-infection models in epidemiology and evolution - Chair: Prof Frank Ball, University of Nottingham

• Lorenzo Pellis

Room: Floor 4, 4205

Research lecture - Pathogen evolution and emergence in zoonotic spillover events - Chair: Prof Frank Ball, University of Nottingham

• Peter Fransson (Heidelberg University)

Room: Floor 4, 4205

Research lecture - The importance of vaccinated individuals to population- level evolution of pathogens - Chair: Prof Erik Aurell, KTH Royal Institute of Technology

• Maria Gutierrez (University of Cambridge)

Room: Floor 4, 4205

Research lecture - Early warning signals for SARS-CoV-2 epidemic waves - Chair: Prof Erik Aurell, KTH Royal Institute of Technology

• Kieran Drake (Imperial College London)

Room: Floor 4, 4205

Research lecture - A fitness landscape model for understanding why chronic infections contribute to population-level SARS-CoV-2 evolution: Chair - Prof Tom Britton, Stockholm University

• Amber Coats (Emory University)

Room: Floor 4, 4205

Research lecture - The evolution of infectious diseases: connecting within- and between-host processes: Chair - Prof Tom Britton, Stockholm University

• Willian T. A. F. Silva (Swedish University of Agricultural Sciences)

Room: Floor 4, 4205

Discussion - Household, network and other models with heterogeneity: Chair - Prof Tom Britton, Stockholm University

• Frank Ball
• Tom Britton

Room: Albano 3: 6228 - Mega (22 seats)

Social activity: Royal Palace Room: Albano 3: 6228 - Mega (22 seats)