CEE Spring Symposium 2024

CEE Spring Symposium 2024 will be taking place in the Sir Alexander Fleming Building, Imperial College London on Tuesday 23rd April 2024 at 13:00pm.

The title for the Symposium is 'The Evolution of Viral Epidemic and Pandemics: Past, Present and Future' and has been organised by Marina Escalera Zamudio, a student from University College London, following a call for proposal submissions.

Advances in genome sequencing, coupled with tools in molecular evolution, phylodynamics, and mathematical modelling, have enabled us to address critical questions regarding the origin, establishment, and spread of both emerging and established viral epidemics and pandemics. Linked to ever-changing ecological and epidemiological scenarios, scientific advances now allow us to gain insights retrospectively, in real-time, and even project into the future.

Join us this evening to follow the work of junior scientists and emerging leaders who are shaping the future research trajectories in the field.

All staff, postdocs, students and affiliated institutions are encouraged to attend this celebatory year with other London-area researchers in ecology and evolution.

Programme:

Invited Speakers:

Dr. Diana Erazo Quintero

Post Doctoral Fellow
Spatial Epidemiology lab – SpELL - Université Libre de Bruxelles
X - @dianacerazoq

'Contribution of climate change to the spatial expansion of West Nile virus in Europe and future projections'

Abstract: West Nile virus (WNV) is an important mosquito-borne pathogen in Europe and although the causal relationship between climate change and its emergence on the continent has been reported, it has not been formally evaluated. Here, we examine whether WNV establishment in Europe can be attributed to climate change. For this purpose, we train and project ecological niche models for WNV considering historical, future, and counterfactual climate data, the latter corresponding to a hypothetical climate in a world without climate change. We show an increase in the ecologically suitable area for WNV under the historical climate evolution, whereas this area remains largely unchanged throughout the last century in a no-climate-change counterfactual. Our analyses therefore point towards climate change as one of the major drivers of the increased risk of WNV circulation in Europe, and further allows discussing potential scenarios for the future evolution of the areas at risk.

Bio: Diana Erazo is an environmental engineer interested in the effects of environmental change in infectious disease dynamics. During her PhD at the University of Los Andes (Colombia, 2018), she studied the impacts of oil palm plantations in the parasite transmission of Chagas disease. Afterwards, she did a one-year post-doc in the Vignuzzi lab at Institut Pasteur (2018-2019) and a second post-doc in the group of Andy Fenton at the University of Liverpool (2019-2021). She joined the Spatial Epidemiology lab at the University of Brussels in June 2021 and currently holds a postdoctoral researcher fellowship awarded by the Belgian Fonds National pour la Recherche Scientifique (FNRS) to uncover the historical and future impact of anthropogenic climate change and other human drivers on arbovirus spread in Europe.

Maria A. Gutierrez

MMath, PhD candidate
University of Cambridge, DAMTP- Department of Applied Mathematics and Theoretical Physics
https://mariaalegriagutierrez.com/

'Evolutionary insights from mathematical modelling of vaccine escape'

Abstract: Host immunity drives the evolution of many pathogens towards antigenic escape. However, the contribution towards this escape may differ across the population: different hosts may contribute more or less –through immune pressure and onward transmission. This heterogeneity depends on the immune status of each host, primarily through (i) vaccination, (ii) previous infection history, and (iii) general immunocompetence. Existing host immunity may increase or decrease the contribution to escape, as in other phylodynamic phenomena. I will discuss the population-level consequences of this heterogeneity, focussing on the impact of the population vaccination coverage on the selective escape pressure.

I will also discuss the stochastic invasion dynamics of antigenic escape strains and their antigenic evolution over multiple epidemic waves.

These results have implications for the design of surveillance and vaccination strategies to mitigate the risk of vaccine-immune escape in a population subject to endemic disease or future epidemic outbreaks.

Bio: Maria is a Gates Cambridge Scholar and third-year PhD student at the University of Cambridge, supervised by Julia Gog (Disease Dynamics group, DAMTP). She is interested in using mathematical models to understand virus evolution. Previously also at Cambridge, she completed Mathematics undergraduate and master's degrees, specialising in theoretical physics.

Dr. Louis Du Plessis

D-BSSE, ETH Zurich, Basel, Switzerland
X - @laduplessis

'Insights into infectious disease dynamics across time and space with phylogenetics and phylodynamics'

Abstract: Genomic surveillance of infectious disease outbreaks has become near pervasive over the past few years. We are now sequencing more genomes, of more pathogens, from more sources faster than ever before, giving us a front-row seat to observe evolution in action, since many viruses evolve fast enough to accumulate significant genetic diversity over the course of an outbreak. Besides characterising individual viruses and tracking lineage frequencies, we can use the patterns in virus genomic sequences to build phylogenetic trees that represent the evolutionary history of the virus lineages, allowing us to reconstruct events from before the first cases were detected. Phylodynamic models allow us to also infer the epidemiological dynamics behind an outbreak, such as rates of spread within and between locations.

Using examples from the COVID-19 pandemic I show how we can use phylogenetics and phylodynamics together with case and mobility data to gain a deeper understanding of an infectious disease outbreak. I show how the types of insights we can gain change as we sequence more genomes, and genomes are collected over longer periods of time. Initially, few genomes were available and genetic diversity was extremely limited, allowing only basic descriptive analyses. As the numbers of sequenced genomes grew exponentially, along with cases, we were able to resolve the lineage dynamics of SARS-CoV-2 in great detail. As more genetic diversity accumulated, we could begin to use phylodynamic methods to estimate changes in the effective reproductive number over time. Finally, I provide some outlook on where the field is heading and what we can expect as genomic surveillance becomes more commonplace and standardised.

Bio: Louis is an evolutionary biologist interested in studying the interaction between evolutionary and epidemiological dynamics. His research focuses on using phylodynamic models to investigate how patterns of spread affect the observed genetic diversity in pathogen genomic sequences. Since 2021 he is the lab manager of the Computational Evolution group in the Department of Biosystems Science and Engineering at ETH Zürich, led by Prof. Tanja Stadler. Previously he obtained a PhD from ETH Zürich and was a postdoctoral researcher at Oxford University, first in pathogen phylodynamics, and then as a fellow in the Oxford Martin school programme for pandemic genomics. During the COVID-19 pandemic he was a contributing member of the COVID-19 Genomics UK consortium, the Pango network, the Swiss National COVID-19 Science Taskforce and the Swiss SARS-Cov-2 Sequencing consortium.

Dr. Darlan Candido

Research Associate
Imperial College London
X - @candido_darlan

'Unravelling spatiotemporal heterogeneities of wild and vaccine-derived poliovirus spread: past and present'

Abstract: Background & aims of study: Since 2017, vaccine-derived poliovirus (VDPV) type 2 has become the main cause of poliovirus-associated acute flaccid paralysis (AFP) cases globally. Here, we characterise the spatiotemporal patterns of poliovirus spread in Africa and Asia by using VDPV2 epidemiological data, and historical and current wild type-1 (WPV1) genetic data. Methods: Global VDPV2 AFP cases were obtained from the Poliovirus Information System. Time difference and geodesic distance were estimated using onset date and jittered coordinates for each case and the first observed outbreak case. Wavefront Velocity of spread was estimated through interpolation of time and distance of cases that increase the outbreak wavefront velocity. To uncover geographical spread, discrete phylogeographic analysis was performed on 1534 publicly available global WPV1 VP1 sequences from 1958-2015, and continuous phylogeography was performed on 963 geocoded WPV1 VP1 sequences from Pakistan and Afghanistan from 2012-2022. Results: Since 2016, 2934 VDPV-2 cases have been reported across 76 outbreaks with median size of 4 cases (range: 1-506), median maximum spread distance of 231km (0-4442) and median duration of 202 days (0-1692). We report a median of 10 nucleotide changes (6-65) from OPV2 at first detection, suggesting cryptic VDPV2 circulation. We identify a correlation between distance and time of spread (R=0.63, p<2.2e-16). We estimate a median velocity of spread of 2.3 km/day across large cVDPV2 outbreaks using case data, and a similar velocity using the Pakistan-Afghanistan WPV1 sequences. We also identify a role for immunity in reducing poliovirus wavefront velocity. Finally, DTA identifies Nigeria as the main historical exporter of poliovirus in Africa, and highlights regional spread gatekeepers, eg. Ghana, Angola, and Chad. Implications: VDPV2 spatiotemporal spread patterns are extremely relevant for designing response vaccination campaigns, so appropriate target areas can be determined.

Bio: I am a Research Associate at Imperial College London working on the genomics and epidemiology of global poliovirus spread in support of poliovirus eradication policies. I hold a Bachelor’s in Pharmacy from the Federal University of Ceará and a Master’s in Allergy and Immunopathology from the University of São Paulo. In 2022, I was awarded a PhD in Zoology from the University of Oxford following my work on the epidemiology and genomics of arboviruses and SARS-CoV-2 in Brazil and other Latin American countries. My PhD research was developed within the scope of the Brazil-UK Centre for Arbovirus Discovery, Diagnosis, Genomics and Epidemiology (CADDE) and explored the initial spread of SARS-CoV-2 in Brazil and its evolution, including the identification, reporting and description of the P.1/Gamma variant of concern in Manaus in January 2021.

Dr. Lucy van Dorp

UKRI Future Leads Fellow, UCL Genetics Institute
Department of Genetics, Evolution & Environment, University College London
X - @LucyvanDorp

'Tracking pathogens in space and time using ancient genomic approaches'

Abstract: Infectious diseases have impacted humans throughout history, with the prevention and cure of microbial infections continuing to pose significant challenges to global health. Genomic data from current pathogens can be used to reconstruct disease outbreaks and epidemics in space and time, providing direct evidence of the source of an infection and the likely drivers of its spread. However, increasingly, genomic data can also be obtained for historical and ancient pathogens from materials such as archaeological remains and archived medical collections. Genomes of ancient pathogens can be combined with modern ones into a single analytical framework that sheds new light on the relationship between us and our pathogens. In this talk I will provide case studies that showcase the power of genomics at the ancient scale to reveal the relationship between us and some major mainstays of the pathogen repertoire infecting humans.

Bio: Dr Lucy van Dorp is a UKRI Future Leaders Fellow at UCL Genetics Institute, University College London. Her work aims to contribute to the post-genomic revolution in biology and medicine by using computational genomics methods to determine the factors giving rise to patterns of diversity in human-associated pathogens. Currently her work focuses on reconstructing the evolutionary history of significant infectious diseases, including COVID-19, Tuberculosis, Malaria and multidrug-resistant hospital infections, making use of both modern and historical genomics data.