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Melanie Prague (Univ Bordeaux Population Health Inserm Inria)Vaccines & immune escapeOral
Antibody response dynamics following Ebola vaccination remain incompletely understood, particularly regarding the continuum of initial induction to long-term persistence. This study developed a mechanistic model of B-cell stimulation post-vaccination able to infer antigen presentation kinetics and propose an identifiable model based solely on anti-ZEBOV IgG levels.
This study was based on...
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Andrew Rambaut (University of Edinburgh)Poster
The COVID-19 pandemic highlighted the importance of understanding coronavirus
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evolution and transmission dynamics. However, the evolutionary dynamics of
seasonal human coronaviruses (hCoVs) are less well-characterised. Here, we use a
phylodynamic approach to compare the spread of four seasonal hCoVs (OC43,
HKU1, NL63, and 229E) over ten years within Slovenia. The four... -
Anna ZHUKOVA (Institut Pasteur)Transmission dynamics & clustersOral
Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological parameters from time-scaled pathogen phylogenetic trees. The models used in phylodynamics typically assume that the sampling procedure is independent between infected individuals. However, this assumption does not hold for many epidemics, in particular for such sexually...
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Ali Rahnavard (The George Washington University)
Sequence data, such as nucleotides or amino acids, is essential for understanding biology. However, analyzing sequencing data and genotype-phenotype associations is challenging due to noise, nonlinear relationships, collinearity, and high dimensionality. While machine learning (ML) effectively detects patterns in this data, user-friendly tools remain limited. To address this, we developed...
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Eric Arts (Western University)
Heterogenous HIV-like particle (HLP) is a targeted, potent HIV latency reversal agent (LRA) for people living with HIV (PLWH) on ART. When using samples derived from over 50 PLWH on treatment for 2 to 22 years, HLPs at least 100-fold more effective than other latency reversal agents in clinical development. HIV primarily infects activated CD4+ T cells whose T cell receptor (TCR) recognizes HIV...
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Michael Famulare (Gates Foundation)Vaccines & immune escapeOral
A major determinant for anti-poliovirus immune response is the viral capsid protein VP1. Multiple unexpected amino acid changes within this protein have been identified in wildtype type 1 poliovirus (WPV1) circulating in Pakistan following the removal of type 2 poliovirus from the oral poliovirus vaccine. These amino acid changes map to known antigenic sites as well as a conserved region found...
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Dr Hind Zaaraoui (INSERM)
Nursing home residents pay every year a devastating tribute to respiratory virus outbreaks. While antiviral treatments are effective if administered shorty after symptom onset or, even better, as pre- or post-exposure prophylaxis (Pep or PreP, respectively), they remain dramatically underused. This is due to the limited number of studies that have evaluated their efficacy in nursing homes,...
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John Tay (Institut Pasteur | University of Melbourne)
The molecular clock is a statistical tool that we use to infer evolutionary rates and timescales from molecular sequence data, with the use of calibrations. These calibrations can include sequences sampled at different points in time for many organisms. Without calibrations, evolutionary rates and times are jointly unidentifiable and thus are required. Before inferring rates and times, it is...
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Mx Giuli Sucar (Joy Lab, BCCFE)
Bayesian phylogenetic inference is commonly used to generate distributions of phylogenies and evaluate evolutionary models from genetic data, concluding with a visual inspection of randomness in parameter sampling. Visual inspection impedes full automation of the algorithm making it inaccessible to non-experts, obstructing cloud-based runs, and impeding the running of multiple replicates. One...
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Timothy Vaughan (ETH Zurich)
Phylodynamic methods provide a coherent framework for the inference of epidemiological parameters directly from genetic data. In particular, methods based on multi-type birth-death models have been used to infer the movement of pathogens between geographic locations or host types, and the transition of infected individuals between disease stages. In these models, population heterogeneity is...
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Iheanyi Okonko (University of Port Harcourt, Choba, Port Harcourt, Rivers State, 500102 Nigeria.)
Background: There is a pressing need to monitor the circulating strains and the emergence of novel HIV-1 variants in the country, especially in the understudied South-south regions. Thus, this study aimed to characterize the genetic diversity of HIV-1, tropisms, and drug-resistant mutations (DRMs) among HIV-infected individuals in the region.
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Methods:
One hundred and six HIV-infected... -
Amjad Khan (Western University)
The latent viral reservoir (LVR) consists of transcriptionally-inactive HIV-1 proviruses within long-lived resting CD4+ T-cells, in which proviruses can persist even under fully-suppressive antiretroviral therapy (ART). The presence of this reservoir is the primary reason for viral resurgence upon ART interruption. Gaining a deeper understanding of proviral dynamics in the LVR is critical for...
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Stéphanie Dan (Hospices Civiles de Lyon, Lyon, France; Centre National de Référence virus des infections respiratoires)
Understanding transmission clusters is essential to uncovering the dynamics of viral
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epidemics, identifying outbreak drivers, and guiding effective public health responses. Cluster
analysis combines genomic and epidemiological data to trace transmission pathways and
generate actionable insights to curb disease spread.
ClusterFinder, developed within the EU-funded SEQ4EPI project, is a... -
Charlyne Bürki (ETH Zürich)
Over the 2023/2024 winter season, we employed a targeted enrichment by hybrid capture method to sequence 1’160 nasopharyngeal swabs from patients across Switzerland presenting with flu-like symptoms. We identified, extracted and produced high-quality genomes of over 25 respiratory virus strains, including strains never before sequenced and publicly shared in Switzerland. Strains ranged from...
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Viktor Müller (ELTE Eötvös Loránd University, Budapest)
The increasingly widespread application of next-generation sequencing (NGS) in clinical diagnostics and epidemiological research has generated a demand for robust, fast, automated, and user-friendly bioinformatics workflows. To guide the choice of tools for the assembly of full-length viral genomes from NGS datasets, we assessed the performance and applicability of four open-source...
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Ms Kaitlin Reid (University of Oxford)
The infected blood inquiry (IBI) carried out by the UK Government examined the incidence of mass contamination of human plasma-derived commercial clotting factors between 1970 and the early 1990’s. The inquiry demonstrated that numerous viruses, including HIV and hepatitis C virus, were transmitted via contaminated blood and blood-products. While limited understanding of bloodborne viruses...
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Ali Movasati
HIV- is a highly adaptive virus that due to its high mutation rate and yield adapts to diverse evolutionary challenges, thereby complicating containment and treatment of the virus. To further understand HIV-1’s genomic evolution, we have utilized the genomic and phenotypic data obtained from our longest HIV-1 evolution experiment, corresponding to 5 years of virus passaging, in two replicates...
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Rocío Carrasco-Hernández (Instituto Nacional de Enfermedades Respiratorias)
Effective viral transmission network analysis is crucial for controlling virus spread. Cluster size is key for prioritizing interventions. Traditional methods often miss network extent due to sampling biases. This study investigates mean pairwise genetic distance (MGEND) as a proxy for estimating "true" cluster size.
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Viral samples from an HIV clinic in Mexico City were classified into... -
Andrea Ramirez
Social microbial behavior has been recognized as a contributor to clinical challenges such as antibiotic resistance and immune evasion. In structured communities, like bacterial biofilms, cooperation among specialized subpopulations ensures survival. Growing evidence suggests social interactions may also influence viral adaptation. For example, hepatitis C virus (HCV) is hypothesized to...
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Manon Ragonnet-Cronin
Subclinical or asymptomatic influenza infections are likely to play a major role in ongoing transmission but require longitudinal cohorts to detect. The Household Influenza Vaccine Evaluation (HIVE) cohort is an ongoing study of households where participants respond to weekly symptom surveys and contribute biannual blood samples. From 2011 to 2020, 2039 participants contributed 8511 serum...
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Alex Beams (Simon Fraser University)
The accrual of nucleotide substitutions in virus genomes accompanies transmission of those viruses through their host populations. Because lineages with higher fitness tend to transmit rapidly to new hosts before incurring very many substitutions, large numbers of related sequences are usually interpreted as evidence of transmission success. Quantities like the local branching index (LBI) aim...
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Aleksandr Kuznetsov (Biozentrum, University of Basel)
Respiratory Syncytial Virus (RSV) is a single-stranded RNA virus that most people encounter as children. RSV infection generally manifests with mild, cold-like symptoms, but can cause severe complications in immunocompromised populations such as infants, the elderly, and immunosuppressed transplant patients. These
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Despite its global impact, epidemiological surveillance of RSV in Switzerland... -
Jennifer McNichol (Simon Fraser University)
Timed viral phylogenies are often used to understand geographic movements, past population dynamics, the emergence of new lineages and epidemic dynamics. These inferences are frequently done in a framework using coalescent theory. Exchangeability in coalescent theory refers to the property that each pair of lineages is equally likely to coalesce, moving back in time from the present to the...
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Daphné de Riols de Fonclare (Université de Caen Normandie / INSERM1311 DYNAMICURE)Zoonoses & emerging infectionsOral
The high species richness of bats (> 1400 species) is mirrored by the diversity of viral families they harbor. It is likely that SARS-CoV-2, a Betacoronavirus Sarbecovirus responsible for the COVID-19 pandemic, originated in Rhinolophus spp. bats. In this context, it is critical to understand the origins of Sarbecovirus diversity in wildlife and the mechanisms that favor their emergence in...
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Lester Perez (Abbott Laboratories)
Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) is a tick-borne virus recognized by the World Health Organization as an emerging infectious disease of growing concern. Utilizing phylodynamic and phylogeographic methods, we have reconstructed the origin and transmission patterns of SFTSV lineages and the roles demographic, ecological, and climatic factors have played in shaping its...
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Dr Carol Leitch (Roslin Institute, University of Edinburgh)Vaccines & immune escapeOral
Marek’s disease (MD) provides a well-documented model for researching imperfect vaccines and viral vaccine escape dynamics. Despite more than 50 years of vaccination programmes, MD remains prevalent worldwide in the chicken industry. The vaccines are “leaky”, allowing low level persistence and transmission of Marek’s disease virus (MDV), the causative oncogenic herpesvirus. Resistance has...
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Chimwemwe Mhango (Malawi-Liverpool-Wellcome programme)Zoonoses & emerging infectionsOral
Background: Rotavirus remains a leading cause of severe gastroenteritis in children under five, particularly in low- and middle-income countries (LMICs). In Malawi, G9P[6] strains re-emerged in 2017, five years after the introduction of Rotarix rotavirus vaccine, necessitating an in-depth investigation of their genetic diversity, evolutionary origins, and public health...
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Paul PETIT (Collège de France)
HIV remains a major public health challenge, with transmission dynamics and the evolution of drug resistance posing significant barriers to effective control. While traditional sequencing methods, such as Sanger sequencing, have been instrumental in studying specific viral regions, they often fail to capture the full genomic diversity within and between hosts. In this study, we analyze 441...
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Tanja Stadler (ETH Zürich)Transmission dynamics & clustersOral
Wastewater monitoring of pathogens offers the potential to track a wide range of infectious diseases for public health, but current methods for analyzing transmission dynamics are primarily tailored to SARS-CoV-2, which is detected at high concentrations in municipal sewage. To support robust surveillance of pathogens with lower concentrations in wastewater and limited clinical validation...
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Dr Mykola Pinkevych (Infection Analytics Program, The Kirby Institute, UNSW Sydney)Within-host dynamics & adaptationOral
Although antiretroviral therapy (ART) can effectively suppress HIV replication, infection cannot be eliminated due to the presence of long-lived, latently infected cells. Treatment interruption leads to the reactivation of latently infected cells and subsequent viral replication in plasma, which may replenish the population of long-lived latently infected cells. Understanding the timing of...
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Jessica Stockdale (Simon Fraser University)Transmission dynamics & clustersOral
The serial interval of an infectious disease – the length of time between symptom onset of an infector and infectee – is an important quantity in epidemiology, but its estimation requires knowledge of individuals' contacts and exposures, typically obtained through resource-intensive contact tracing efforts or household studies. Under partially sampled data, purported transmission pairs...
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Marius Brusselmans (KU Leuven)
When constructing phylogenetic trees for phylodynamic and phylogeographic analyses, researchers often rely on tree-building software such as IQ-TREE, BEAST, and BEAST2. The algorithms used by these tools, whether based on maximum likelihood or Bayesian principles, are inherently stochastic. As a result, repeated analyses of the same data can yield trees with unstable structures due to weak or...
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Klara Marie Anker (Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, United Kingdom; Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark)
Influenza A viruses (IAVs) remain a significant public health threat due to their ability to jump between host species, as demonstrated by the H1N1 pandemic in 2009. Despite increased genomic surveillance, knowledge of the evolutionary dynamics allowing such zoonotic events is still limited, and the genetic markers that facilitate transmission between humans and swine remain unclear. To...
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Anjalika Nande (Johns Hopkins University)
The COVID-19 pandemic saw successive emergence and spread of novel viral variants, exhibiting enhanced transmissibility or evasion from vaccine- and infection-acquired immunity. While the genotypic and phenotypic basis of SARS-CoV-2 variants have been extensively characterized, the evolutionary factors governing their patterns of emergence are less well understood. In this study we...
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Paula Magbor (Western University)
Clustering infections by genetic similarity is a common method of characterizing the risk structure of a population. A graph is constructed by connecting infections with genetic distances below a threshold, then connected components with two or more nodes are extracted as "clusters". Studies of HIV molecular epidemiology often use logistic regression to find associations between potential risk...
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Selin Sen (Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA))Zoonoses & emerging infectionsOral
Dengue fever is the most important arbovirosis for public health, with more than 6 million cases worldwide in 2023. The virus is present in the subtropical and tropical regions of the world often in co-circulation with over arboviroses. There is currently no effective treatment commercially available. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype...
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Chaoran Chen (ETH Zurich)
Interactive web dashboards have proven to be effective tools for exploring and communicating epidemiological insights obtained from genomic data. In particular, they are valuable for large and/or regularly updated datasets, facilitating real-time monitoring and the rapid identification of new variants and transmission patterns. During the SARS-CoV-2 pandemic, many new genomic epidemiological...
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Gage Moreno (Broad Institute of MIT and Harvard)
Despite intensive study, surprising gaps remain in our knowledge of transmission patterns during the COVID-19 pandemic, particularly transmission as new lineages emerge. We analyzed 134,785 SARS-CoV-2 genomes from 7 lineages collected in Massachusetts from November 1, 2021, to January 17, 2023; this includes 85,125 genomes with individualized epidemiological data across 666 testing facilities....
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Dr Adam Nitido (The Ragon Institute of Mass General Brigham, MIT, and Harvard)Software, tools & methodsOral
A characteristic feature of HIV-1 is its ability to develop a diverse population that can adapt to hostile environments. The source of this diversity is often attributed to its high mutation rate, estimated to be around 5.0x10-5 mutations per site per round of replication (mut/site/rep). However, there is high variation in the observed mutation rates across published studies. It remains...
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Sebastian Duchene (Institut Pasteur)Phylodynamics & phylogeographyOral
Phylodynamic analyses infer epidemiological parameters from pathogen genome sequences for enhanced genomic surveillance in public health. Pathogen genome sequences and their associated sampling dates are essential data in every analysis. However, sampling dates are usually associated with hospitalisation or testing and can sometimes be used to identify individual patients, posing a threat to...
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Isabel Joia (University of Basel)
Human metapneumovirus (hMPV) is among the most common causes of respiratory tract infections among humans, especially affecting children and immunocompromised patients. HMPV is closely related to human respiratory syncytial virus (hRSV), these viruses being the only two members of the pneumovirus family known to infect humans. All pneumoviruses express fusion (F) proteins on their surface...
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Dr Michael Thomson (Centro Nacional de Microbiología. Instituto de Salud Carlos III)
In an HIV-1 molecular epidemiology study in Spain, based on maximum likelihood (ML) phylogenetic analyses of protease-reverse transcriptase (PR-RT) sequences, we identified a cluster of 46 individuals from 8 regions not grouping with references of known subtypes or CRFs, which through analyses with Recombination Identification Program (RIP), bootscanning, and trees of partial fragments, was...
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Dr Baptiste Elie (Institute of Medical Virology, University of Zurich & Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland)Within-host dynamics & adaptationOral
Viral "blips" are single timepoint episodes with detectable plasma HIV-1 RNA preceded and followed by undetectable viremia in individuals on antiretroviral therapy (ART). Despite their common occurrence, the origin, biological implications, and clinical consequences of viral blips for people with HIV (PWH) remain unclear. Proposed explanations include intermittent viral release from latent...
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Emily E. Bendall (University of Michigan)Within-host dynamics & adaptationOral
SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity.However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. The low diversity within-hosts and strong genetic linkage among genomic sites make accurately detecting positive selection difficult. Longitudinalsampling is a powerful method for...
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Ramon Lorenzo-Redondo (1 Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. 2 Center for Pathogen Genomics and Microbial Evolution, Northwestern University Institute for Global Health, Chicago, IL 60611, USA.)Within-host dynamics & adaptationOral
Despite the success of antiretroviral therapy (ART) in controlling viremia, HIV-1 reservoirs persist during therapy constituting the major obstacle to a functional cure. These reservoirs lead to a rapid rebound in viremia when treatment fails or is discontinued. To eliminate this viral reservoir that mostly resides in tissues, it is key to characterize its tissue microenvironment and...
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Maria Trofimova (Freie Universität Berlin, Robert Koch-Institut)
Background: Case reporting in a pandemic or for emerging viral infections depends heavily on testing strategies and as a result the degree of under-reporting of true incidence can vary substantially. We previously developed GInPipe [1], a computational tool that allows estimation of under-reporting levels over time from time-stamped pathogen genome surveillance data, within a few minutes...
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Sobia Anam
Following initial infection, HIV spreads to regional lymph nodes within 3–6 days, and systemic dissemination occurs within 6–25 days. However, these experimental findings do not align with the results of current HIV mathematical models, which show that while viral dissemination in the blood occurs within 6–25 days, the virus appears in the lymph nodes after a delay of 50 days. We hypothesize...
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Dr Lauren Castro (Los Alamos National Laboratory)Software, tools & methodsOral
Climate change and globalization are expected to increase the frequency of infectious disease outbreaks, underscoring the need for reliable forecasting methods to inform decision-making. The COVID-19 pandemic highlighted significant limitations in forecasting accuracy, particularly in scenarios where episodic selection drives the emergence of new genetic variants—such as the Delta and Omicron...
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Dr Marina Siljic (Institute of Microbiology and Immunology, Department of Virology, Faculty of Medicine, University of Belgrade, Serbia)
Background:
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This study was aimed to understand the evolutionary and transmission dynamics of HIV-1 epidemic in Serbia and to reveal the socio-demographic and clinical factors that shaped the expansion of phylogenetic transmission clusters. The dataset of 720 HIV-1 pol sequences isolated from both newly diagnosed and therapy experienced healthcare clients, between 1997 and the end of 2023, was... -
Dr Chaoran Chen (ETH Zürich)
Viral sequencing data are collected, stored, and processed by a wide range of entities, from individual scientists and laboratories to large consortia and global databases. Yet, there has been a lack of a general, reusable software for managing pathogen sequencing data. During the SARS-CoV-2 pandemic, when many new laboratories and consortia started sequencing or analyzing data, they relied on...
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Abigail M. Jackson (Harvard-MIT Health Sciences and Technology)
HIV-1 transmission leads to lifelong infection marked by continuous viral evolution and evasion of host immunity. The specifics of this host-pathogen interaction, including the complex dynamics of transmission, quasispecies diversity, and viral recombination rate, remain unclear. To better characterize these dynamics in vivo, we engineered doubly barcoded viral libraries of three HIV-1 strains...
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Denise Kühnert (Robert Koch Institute)Genomics & bioinformaticsOral
Lassa fever, caused by the Lassa virus (LASV), has led to numerous fatalities in West Africa and cases exported intercontinentally since its discovery in 1969. Currently, there are no approved vaccines, with recent research focusing on immunotherapy. Lassa virus is grouped into different lineages that circulate in specific geographical areas, elicit varying immune responses, and display...
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Eric Lewitus (U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD)Vaccines & immune escapeOral
Antibody (Ab) accessible sites at the surface of Env include the most variable HIV-1 sites. Different patterns of Ab recognition and neutralization are observed within and between HIV-1 clades. Predicting the functional effect of epitope diversity on Ab sensitivity is important for designing population-specific prophylactic strategies. We developed a statistical framework that incorporates...
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Chris Wymant (Pandemic Science Institute, University of Oxford)
Mathematical modelling allows us to answer “if this then what” questions. For infectious disease epidemiology this has been widely used to guide interventions: if we intervene like this, how much disease will we prevent? Also important, though much less widely practised, is the use of mathematical modelling to guide the design of studies and trials: if we measure like this, how much will we...
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Katy Krupinsky (University of Michigan)
SARS-CoV-2 infection is a leading cause of death by infectious disease and continues to be a pressing public health issue due to ongoing emergence of novel variants. One factor that affects variant emergence is the transmission bottleneck size, which refers to the number of unique genetic variants from a donor host that transmit and establish the population in a recipient (defined as a pair)....
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Daniel Reeves (Fred Hutchinson Cancer Center, University of Washington)Poster
Persistence of HIV in people living with HIV (PWH) on suppressive antiretroviral therapy (ART) has been linked to physiological mechanisms of CD4+ T cells. We summarize this concept with the “passenger hypothesis”, that most persistence of the HIV reservoir during ART is due to cellular vs viral mechanisms. In order to determine which mechanisms are most important for persistence, and thus...
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Louis Colliot (CIRB)
Every time the Human Immunodeficiency Virus (HIV) replicates within a cell, errors can creep into its genome. These mutations make it possible to track an epidemic, because the more similar two virus sequences are, the closer the two individuals who bear them are likely to be in the chain of transmission.
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For more than twenty years, the field of phylodynamics has been analyzing this type of... -
Aime Bienfait Igiraneza (University of Oxford)
The discovery of very potent, broadly neutralizing antibodies (bnAbs) against HIV-1 has revived the hope for new treatment and prevention methods against the virus. Nevertheless, several clinical trials have shown that the breadth of such bnAbs is still limited by viral resistance. Here, we explore whether currently available neutralization
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datasets on bnAbs predicted to bind similar epitopes... -
Bastien Reyné (SISTM team, BPH (Inserm U1219, Inria, Univ. Bordeaux) ; Vaccine Research Institute, Faculté de Médicine, Université Paris-Est Créteil, Créteil, France ; MIVEGEC (Univ. Montpellier, CNRS, IRD))
A key question in evolutionary epidemiology is to determine differences in the conditions that may allow some mutant strains to spread in a population where a resident strain is already circulating. Evolutionary invasion analyses assume that the immunity is long-lasting for previously infected individuals making it difficult to study straits such as immune escape. We relax this last assumption...
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Alen Suljič (Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana), Ms Anja Ošep (Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana)
Background:
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Persistent SARS-CoV-2 infections in immunocompromised individuals are often associated with key features of viral evolution, including accelerated mutation rates, emergence of novel variants of concern (VOCs), cryptic lineages, reservoirs of antiviral resistance, super-spreading events and interspecies transmission. These patients represent a critical group for the... -
Fabiana Gambaro (Spatial Epidemiology Lab, Universitè Libre de Bruxelles, Belgium)Software, tools & methodsOral
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, enabling the reconstruction of the dispersal history of rapidly evolving pathogens. BEAST, a Bayesian phylogenetic inference software package, provides a discrete trait analysis (DTA) that integrates geographic information as discrete characters and infers transition events among discrete sampling...
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Dr Laura Muñoz-Baena (University of Oxford)
Endogenous Viral Elements (EVEs) originate when viruses integrate their genetic material into the host genome, becoming a permanent part of the host’s DNA. As molecular fossils of ancient viral infections, EVEs offer valuable insights into host-virus coevolution and virus diversity over evolutionary timescales.
We aim to detect EVEs across 948 mammalian genomes by performing a nested...
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Agathe Colmant (Unite des Virus Emergents (UVE: Aix-Marseille Univ, Universita di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France)
Jingmenviruses are understudied flavi-like viruses with a segmented genome. They have been detected worldwide in a wide range of hosts, such as arthropods including ticks and vertebrates including cattle and humans with febrile illness symptoms. As next-generation sequencing has become more affordable, increasing numbers of large-scale metagenomics studies have been published, alongside raw...
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Maria Belen Pisano (Instituto de Virologia Dr. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba)
Molecular epidemiology of hepatitis A virus (HAV) plays a critical role in identifying outbreak origin and conducting surveillance. Although it is mostly carried out using short partial VP1/2A genomic sequences, utilizing whole-genome sequences (WGS) provides more accurate and robust information. In Argentina, where HAV vaccination is mandatory since 2005, the local sequence information is...
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Dr Lidia Garrido-Sanz (IrsiCaixa)
Detection of HIV-1-infected cells in single-cell sequencing studies presents a significant challenge partially due to the high variability of viral genomes. Conventional alignment-based tools frequently fail to identify these cells accurately, as they rely on perfect sequence matches. We have developed a bioinformatic pipeline that integrates multiple B-clade viral genome references and...
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David Rasmussen (North Carolina State University)Phylodynamics & phylogeographyOral
Unlike other areas of modern statistical inference, genomic epidemiology lacks theory to guide decisions about how to sample pathogen genomes. This makes it difficult to answer even simple questions about how sampling choices impact the quality of inferences drawn from genomic data. Researchers therefore often resort to sampling opportunistically, leading to inefficient and unrepresentative...
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Prof. Emma Hodcroft (Swiss Tropical and Public Health Institute)Software, tools & methodsOral
The sharing of viral genomic data is critical for scientific research and public health responses. While platforms like the International Nucleotide Sequence Database Collaboration (INSDC: NCBI, ENA, DDBOJ) and GISAID facilitate data sharing, challenges remain in meeting the specific needs of the pathogen genomics community. Persistent concerns about data misuse, “scooping,” and limitations on...
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Cornelius Roemer (University of Basel and SIB)
Five years since the start of the pandemic, SARS-CoV-2 remains a leading cause of acute respiratory infections, despite most people having been infected at least once. Unprecedented levels of global genomic surveillance provide a rich basis for understanding how SARS-CoV-2 variants continue to evolve in the post-Omicron era, a critical topic for vaccine strain updates.
Using insights...
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Bastiaan Van der Roest (University Medical Center Utrecht, The Netherlands)
Background
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In 2022, an Mpox clade II outbreak affected many countries including Slovenia. To optimize control, it is important to know the extent by which such outbreaks are driven by introductions from abroad or by within-country transmission. We used sequences of all Slovenian cases in a phylodynamic model to address this question, and investigated the potential to assess the number of... -
Conor O'Hare (Saw Swee Hock School of Public Health)
Singapore faces recurring dengue outbreaks that pose substantial public health and economic burdens, with recent years seeing unprecedented case numbers. While current surveillance systems track case counts, the ability to predict outbreaks in real-time remains challenging. We propose combining real-time estimation of the effective reproduction number (Rₑ) with analysis of viral spread...
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Dr Hugo Castelan (Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada)Genomics & bioinformaticsOral
Reassortment is the exchange of genomic segments between viruses. It is a significant feature of the evolution of influenza A viruses (IAV), where it can yield new combinations between highly divergent lineages (antigenic shift). In this study, we evaluated the reliability of standard comparative methods for reconstructing reassortment events in the evolutionary history of H5Nx IAV genomes. We...
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Sophie Lockwood (University of Chicago)
Human immunodeficiency virus (HIV) causes substantial morbidity and mortality in sub-Saharan Africa. HIV cases were first reported in Madagascar, an island nation off Africa’s southeastern coast, in the 1990s, although current epidemiologic data are limited. However, high prevalence of commercial sex work, recent economic changes driving population mobility, and prevalence of other sexually...
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Yexuan Song (Simon Fraser University)
Understanding viral transmission is important for responding to infectious diseases. For example, information about the geographic spread of a virus can inform policy decisions about transportation and borders. Estimates of the host species' movements in zoonotic viruses inform our knowledge of the nature and frequency of host jumps, and hence of zoonotic risk. Geographic and host movements...
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Madeleine Gastonguay (Johns Hopkins University)Software, tools & methodsOral
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a causative agent of several lymphoproliferative diseases, particularly in immunocompromised individuals. These malignancies often originate from latently infected B cells, where KSHV persists as extrachromosomal, circularized episomes. While the viral protein LANA is essential for viral maintenance during latency, the mechanisms enabling...
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Thayer Anderson (Johns Hopkins University)
In July 2023, the WHO issued guidance indicating that individuals with HIV viral loads between 200-1000 copies/mL have a “negligible” risk of onward transmission to sexual partners, marking a shift from “undetectable = untransmittable” messaging. However, this guidance is based on limited empirical data, particularly from settings in Africa since widespread roll out of antiretroviral (ARV)...
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David Jorgensen (Imperial College London)
Enterovirus D68 (EV-D68), first discovered in the 1960s, emerged to cause outbreaks of severe respiratory disease and polio-like paralysis in 2014. The transmission dynamics of EV-D68 before its emergence are poorly understood due to its clinical similarities to other respiratory infections. These similarities also complicate detection without specific testing. Despite this, extensive genetic...
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Charu Sharma (University of Oxford, UK)
The B.1.351/Beta VOC was first identified in South Africa in October 2020. Within the United Kingdom (UK), the first two cases of Beta were detected on 10 December 2020. Thereafter, the increase in the number of cases of Beta within the country raised alarms of its rapid growth which led to the UK government closing its international borders to prevent further introductions. Additionally, in...
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Prof. Marco Salemi (University of Florida Emerging Pathogens Institute)Genomics & bioinformaticsOral
The COVID-19 pandemic has caused over 776 million cases and 7 million deaths globally, highlighting the need for predictive tools to anticipate SARS-CoV-2 evolution. The S1 subunit of the Spike glycoprotein, essential for viral entry into human cells, undergoes frequent mutations that influence transmissibility and immune evasion. Predicting such mutations could be crucial for the development...
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Simone Rancati (University of Pavia), Prof. Marco Salemi (University of Florida)
The COVID-19 pandemic has caused over 776 million cases and 7 million deaths globally, highlight-ing the need for predictive tools to anticipate SARS-CoV-2 evolution. The S1 subunit of the Spike glycoprotein, essential for viral entry into human cells, undergoes frequent mutations that influence transmissibility and immune evasion. Predicting these mutations is crucial for developing vaccines...
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Iheanyi Okonko (University of Port Harcourt, Choba, Port Harcourt, Rivers State, 500102 Nigeria.)
Background: Ever since the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-COV-2) which caused COVID-19 disease began to spread, the globe has been dealing with an unparalleled public health calamity. The entire health system is under strain as a result of the pandemic. Above all, microbiologists have experienced significant challenges in terms of diagnosis. The intriguing part that was...
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Prof. Marco Salemi (University of Florida)
Influenza remains a persistent global health threat due to its high mutability, rapid transmission, and significant socioeconomic impact. This study addresses the critical research question: How can computational frameworks overcome current limitations to accurately and robustly predict human-influenza protein-protein interactions (PPIs)? Understanding these interactions is crucial for...
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Mr Martin Wohlfender (Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland)
Background
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The COVID-19 pandemic has highlighted the need for real-time infectious disease surveillance and forecasting systems to identify trends in transmission. In this study, we compare short-term forecasting models for COVID-19 hospital admissions that make predictions 1 to 4 weeks ahead based on retrospective electronic health record data from the Bern region of... -
Pierce Radecki (Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health)
High-Throughput Single-Genome Amplification and Sequencing (HT-SGS) enables detailed measurements of intra-host virus genotypes via barcoding of individual virus genomes during reverse transcription (RT) followed by PCR amplification, sequencing, and bioinformatic error correction procedures. However, the absence of “ground-truth” RNA reference samples makes it challenging to evaluate...
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Dr Brittany Magalis (University of Louisville)
During infection, human immunodeficiency virus (HIV) maintains a stably integrated reservoir of proviruses that persist within the host genome despite combined antiretroviral therapy (cART). Characterizing these reservoirs remains challenging due to insufficient phylogenetic resolution, particularly under cART, which limits our ability to assess proviral integration and replication competency...
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David A Kennedy (Penn State University)Zoonoses & emerging infectionsOral
Spillover of infectious diseases is a significant issue for human, animal, and plant health, in part due to their potential to establish in the new host population, thus achieving a host jump. Current approaches to predict and prevent host jumps are structured around discovering new viruses, drawing associations between pathogen characteristics and host jump risk, and managing spillover, but...
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Charlie Hamilton (Pandemic Sciences Institute, Nuffield Department for Medicine, University of Oxford)Phylodynamics & phylogeographyOral
Selection pressures on SARS-CoV-2 molecular phenotypes have changed dramatically in time since the virus’s emergence. Initially, for example, the greatest pressure was on enhancing the virus's intrinsic biological traits in order to increase its transmissibility in the naive population. Then, as population immunity grew from previous infections and vaccination, immunity became the primary...
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Isobel Guthrie (University of Oxford)Within-host dynamics & adaptationOral
Insertions and deletions (indels) have appeared frequently during SARS-CoV-2 evolution, including as lineage defining mutations. However, indels are difficult to study, particularly at the within-host level, due to differing processes of alignment and consensus genome generation, making it difficult to evaluate their evolutionary significance and compare between individuals. We have developed...
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Jonathan Pekar (UCSD)Zoonoses & emerging infectionsOral
A widespread outbreak of H5N1 avian influenza A virus was detected in U.S. dairy cattle in 2024, causing significant illness in cattle, reduced milk production, and economic damage. We analyze 537 H5N1 genomes from birds and non-human mammals leading up to the emergence of H5N1 in cattle, and 1,739 genomes from cattle, poultry, humans, and other mammals involved in the 2024 outbreak for which...
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Macauley Locke (Los Alamos National Laboratory)
HIV-1 has nine main subtypes that persist in infected populations; however, the overall diversity of HIV-1 is much larger due to recombination amongst these original subtypes. Recombination has led to many unique recombinant forms and over 100 circulating recombinant forms (CRFs), which may become more prevalent than the two parent strains in a given region. We analysed sequences taken from...
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Georg Angehrn (Biozentrum, University of Basel)
RNA viruses like SARS-CoV-2 have a high mutation rate, which contributes to their rapid evolution. The rate of mutations depends on the mutation type (e.g., A→C, A→G, etc.) and can vary between sites in the viral genome. Understanding this variation can shed light on the mutational processes at play, and is crucial for quantitative modeling of viral evolution. Using the millions of available...
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Vincent Garot (CIRB / LCQB)
The way a virus spreads leaves footprints in its genome. Phylodynamics leverages these footprints to estimate epidemiological parameters from collected virus genetic data. The estimation is typically done in a likelihood-based framework. The epidemiological process is modeled on a virus transmission tree. This tree is approximated by time-scaled phylogenetic trees reconstructed from virus...
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90. TRANSMISSION CLUSTER ANALYSIS OF DRUG RESISTANCE MUTATIONS IN HIV-1 SUBTYPE A6 IN THE FSU REGIONAnastasiia Nefedova (Nazarbayev University)
The HIV epidemic in the Former Soviet Union (FSU) is growing rapidly, with 140,000 new infections reported in 2023, marking a 20% increase since 2010. Despite ongoing efforts to expand HIV prevention and treatment programs, AIDS-related deaths are on the rise in this region, underscoring the need for a better understanding of transmission dynamics and drug resistance mutations (DRMs) to inform...
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Meriadeg Ar Gouilh (Université de Caen Normandie / CHU / INSERM1311 Dynamicure)
The measles virus, renamed Morbillivirus hominis in 2023 (Paramyxoviridae), is subjected to a global elimination program established by the World Health Organization since 2012. However, despite these efforts, two significant epidemic resurgences occurred in France (2008-2012 ; 2017-2019). Based on a rich collection of samples, this work illuminates the evolutionary dynamics of...
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Dr Frida Belinky (Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health)Phylodynamics & phylogeographyOral
HCoV-OC43 is a common cold coronavirus that has persisted in the human population for decades. This study investigates HCoV-OC43's genomic diversity and recombination patterns to elucidate the emergence of new genotypes and shed light on intra-host diversification, which underpins the ongoing evolution of HCoV-OC43. Employing consensus sequencing and high-throughput single genome sequencing...
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Florence Débarre (CNRS)
The unprecedented number of PCR tests and viral genomic sequences generated during the COVID-19 pandemic offers an unprecedented amount of data to follow the dynamics and evolution of a pathogen. While largely used during the pandemic, in particular to follow potential changes in vaccine efficacy, the full potential these community data remains to be exploited. For this project, building on a...
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Bradley Jones (Department of Mathematics, Simon Fraser University)
Tree metrics are measures to compare the similarity between two tree topologies. Effective sample size (ESS) is a statistic that quantifies the amount of autocorrelation in Markov chain Monte Carlo (MCMC) and is used to assess run convergence. With tree metrics, Lanfear et al showed that we can compute an ESS for tree topologies. From the plethora of tree metrics that have been developed,...
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Rocío Carrasco-Hernández (Instituto Nacional de Enfermedades Respiratorias)
Epidemiological models are key tools for understanding infectious disease dynamics. Traditional SIR models assume that all individuals in a host population are initially susceptible, limiting their ability to predict complex outbreak patterns observed in real-world epidemics. Here, we introduce the USIR model, which incorporates the concept of evolutionary niche expansion—an adaptation of...
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Zoe Vance (University of Edinburgh)
Genomic surveillance of pathogens has become a critical element of modern public health. A key step in most surveillance pipelines is amplification of a target pathogen or locus through PCR, particularly in samples where higher sensitivity is desirable. Despite widespread usage of amplicon sequencing, the potential for errors introduced during amplification to mislead an analysis is...
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Nicolas Tessendier (Collège de France)Within-host dynamics & adaptationOral
Human papillomavirus (HPV) infections drive one in twenty new cancer cases,
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exerting a particularly high burden on women. Most anogenital HPV infections are
cleared in less than two years, but the underlying mechanisms that favour persistence
in around 10% of women remain largely unknown. Notwithstanding, it is precisely this
information that is crucial for improving treatment, screening... -
Sneha Sundar (Department of Environmental Systems Sciences, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland)Within-host dynamics & adaptationOral
Whether or not there is a limit to adaptation is one of the fundamental questions of evolutionary biology. To what degree can a viral population evolve to be fitter in a constant environment? In a long-term evolution experiment with HIV-1 in two T-cell lines (MT-2 and MT-4), we have been observing the accumulation of majority mutations and fixations at an almost constant rate for more than...
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Mr Michael P. Hogarty (University of Pennsylvania)Within-host dynamics & adaptationOral
BACKGROUND: Modelling HIV evolution can illuminate mechanisms of viral persistence and predict resistance to antiretroviral therapies. However, current models do not take into account viral population size. Here, we examine in a large cohort of simian-human immunodeficiency virus (SHIV) infected rhesus macaques the relationship between viral population size and rates of virus...
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Roland Regoes (ETH Zurich)
Phylodynamic methods are widely used to infer the population dynamics of viruses between and within hosts. For HIV-1, these methods have been used to estimate migration rates between different anatomical compartments within a host. The methods typically assume that there is no selective pressure acting on the virus, even though it is known that viruses often experience strong selection...
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John Coffin (Tufts University)Genomics & bioinformaticsOral
Human endogenous retroviruses (HERVs) comprise about 8% of our genome and provide us with a valuable fossil record of host-retrovirus interaction in our primate ancestors. The most recently active HERV-K(HML-2) 5Hs group, although now apparently extinct as an infectious agent, has some members that entered our ancestral genome less than 1 million years ago and retain one or more viral ORFs,....
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Anika John (ETH Zürich)Vaccines & immune escapeOral
Influenza A virus (IAV) has placed a significant strain on public health systems by causing seasonal outbreaks and, in severe cases, pandemics. This burden is compounded by its rapid evolution, which drives immune escape and requires the frequent redesign of vaccines and antiviral drugs. Therefore, genomic surveillance of IAV is crucial for monitoring its evolution and informing vaccine and...
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Auguste Rimaite (1. Department of Biosystems Science and Engineering, ETH Zurich; 2. SIB Swiss Institute of Bioinformatics)
Respiratory syncytial virus (RSV) is a highly contagious, enveloped, single-stranded RNA respiratory virus that primarily causes mild, cold-like symptoms. However, it can lead to severe illness, hospitalization, or death in infants and immunocompromised individuals. RSV is classified into two subtypes, RSV-A and RSV-B, with one subtype typically dominating a given season that begins in the...
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Zena Lapp (Los Alamos National Laboratory)
Simulating within-host viral sequence evolution allows for the investigation of factors such as the role of recombination in viral diversification and the impact of selective pressures on virus evolution. Here, we add another model to the toolbox of within-host sequence simulators: wavess (within-host agent-based viral evolution sequence simulator), a discrete-time agent-based model and a...
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Ms Premmarin Inmonthian (Faculty of Associated Medical Sciences, Chiang Mai University)Transmission dynamics & clustersOral
Background: In 2022, Thailand lifted lockdown and isolation measures, and SARS-CoV-2 was declared endemic by the Ministry of Public Health. The spread of the Omicron variant raised questions about the relative contributions of community versus household transmission to ongoing infections. We analyzed SARS-CoV-2 transmission within the Thailand VERDI-RECOVER study and conducted whole genome...
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Mrs Rose Marin (CIRB, Collège de France)
Human papillomaviruses (HPVs) are common sexually transmitted viruses. Most infections they cause clear naturally within a few months or years, but can become chronic and can cause many ano-genital cancers, especially cervical cancers. Although safe and effective vaccines are available, the genetic bases of persistence and pathogenicity remain poorly understood. Some HPV genotypes, such as...
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