31st International Dynamics & Evolution of Human Viruses

Name: 31st International Dynamics & Evolution of Human Viruses
Start: 2024-06-19T08:00:00-07:00
End: 2024-06-22T16:00:00-07:00
Location: Squamish, BC, Canada

Jun 19 – 22, 2024

Squamish, BC, Canada

Canada/Pacific timezone

This conference is now SOLD OUT for in-person registration. Virtual registration is still available.

Maureen Helinski

mhelinsk@health.ucsd.edu

Contribution List

114. A COMBINED SUPERVISED AND UNSUPERVISED MACHINE LEARNING APPROACH WITH INTRASPECIFIC CLASSIFICATION OF HUMAN ASTROVIRUSES

Joseph Butler (Western University)

Software, tools & methods

Poster

Virtual posters

46. A FORWARD SIMULATION FRAMEWORK TO QUANTIFY INTRA-HOST VIRAL GENETIC LINKAGE STRUCTURES UNDER COMPLEX DEMOGRAPHIC SCENARIOS

Mr Dylan Clark (Department of Genome Sciences, University of Washington)

Within-host dynamics & adaptation

Poster

108. A MODELING APPROACH TO UNDERSTANDING HIV CLUSTERS IN THE GLOBAL NORTH AND SOUTHERN AFRICA

Dr Rafael Nunez (Institute for Disease Modeling, Bill & Melinda Gates Foundation)

Transmission dynamics & clusters

Poster

60. A NEW METHOD FOR FINDING CONSERVED FEATURES IN LOW-VARIABILITY RNA VIRUS GENE ALIGNMENTS, ILLUSTRATED WITH SARS-CoV AND SARS-CoV-2

Jordan Skittrall (University of Cambridge)

Software, tools & methods

Poster

34. A NEW METHOD TO CLASSIFY NOVEL HEPATITIS C VIRUS GENOTYPES AND SUBTYPES

Zena Lapp (Los Alamos National Laboratory)

Software, tools & methods

Poster

118. A NOVEL ALGORITHM FOR HIGHLY ACCURATE AND EFFICIENT HIV BIOINFORMATICS FROM RAW READ DATA VIA LOCATED K-MERS

Dr Nicholas Grayson (Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK.)

Genomics & bioinformatics

Poster

98. A NOVEL THREE-PRONGED ALIGNMENT-FREE MACHINE LEARNING APPROACH FOR TAXONOMIC CLASSIFICATION: A CASE STUDY OF HUMAN ASTROVIRUSES

Fatemeh Alipour (University of Waterloo)

Software, tools & methods

Poster

24. A QUANTITATIVE COMPARISON OF CONTINUOUS ADAPTIVE EVOLUTION IN HUMAN PATHOGENIC VIRUSES

Katie Kistler (Trevor Bedford's lab, Fred Hutchinson Cancer Center)

Vaccines & immune escape

Poster

Virtual posters

119. Alterations in RSV Epidemiology and Viral Population Structure Following the SARS-CoV-2 Pandemic

Ramon Lorenzo-Redondo (Division of Infectious Diseases, Northwestern University Feinberg School of Medicine)

Transmission dynamics & clusters

Oral

95. AN APPROACH TO HAPLOTYPING WITHIN POLIO SUBTYPES

Zoe Vance (University of Edinburgh)

Genomics & bioinformatics

Poster

55. ANTIRETROVIRAL IMPRINTS AND GENOMIC PLASTICITY OF HIV-1 POL IN NON-CLADE B: IMPLICATIONS FOR TREATMENT

Judith Torimiro (Chantal Biya International Reference Centre for Research on HIV/AIDS)

Genomics & bioinformatics

Poster

31. Assessing the phylogenetic information of SARS-CoV-2 amplicon sequences from wastewater samples

Mr Adrian Lison (Computational Evolution, Department of Biosystems Science and Engineering, ETH Zürich)

Genomics & bioinformatics

Poster

9. AUTOMATED DETECTION AND ANALYSIS OF POLIOVIRUSES USING PIRANHA

Aine O'Toole (University of Edinburgh)

Software, tools & methods

Oral

90. Automating Bayesian Phylodynamic Analyses: A Workflow-Based Approach

Wytamma Wirth (The Peter Doherty Institute for Infection and Immunity)

Software, tools & methods

Poster

43. Can we reconstruct the transmitted/founder virus sequence from within host HIV proviral sequences?

Bradley Jones (Simon Fraser University)

Within-host dynamics & adaptation

Oral

82. CAUSES AND IMPACTS OF THE WIDESPREAD LACK OF TOPOLOGICAL CONVERGENCE IN BAYESIAN PHYLODYNAMIC INFERENCE ON LARGE VIRAL DATASETS

Jiansi Gao (Fred Hutchinson Cancer Center)

Phylodynamics & phylogeography

Oral

79. CHARACTERISATION OF NOVEL VIRUSES USING PROTEIN LANGUAGE MODELS

Kieran D. Lamb (University of Glasgow MRC Centre for Virus Research)

Genomics & bioinformatics

Poster

107. CHARACTERIZATION OF HIV-1 WITHIN-HOST DIVERSITY DURING ACUTE INFECTION USING DEEP SEQUENCING

Yifan Li (U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD)

Within-host dynamics & adaptation

Oral

29. Characterizing the social and spatial determinants of SARS-CoV-2 transmission from clusters of identical genome sequences

Cécile Tran Kiem (Fred Hutchinson Cancer Center)

Phylodynamics & phylogeography

Poster

129. CLINICAL CASE SERIES OF INTRA-HOST VIRAL DYNAMICS IN PERISTENT SARS-COV-2 INFECTIONS

Ben Jakubczak (National Institute of Allergy and Infectious Diseases)

Within-host dynamics & adaptation

Poster

88. Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression

Wytamma Wirth (The Peter Doherty Institute for Infection and Immunity)

Software, tools & methods

Poster

41. COMMON MISSPECIFICATION OF THE GENERATION INTERVAL LEADS TO UNDERESTIMATION OF R₀ IN PHYLODYNAMIC INFERENCE

Yeongseon Park (Emory University)

Phylodynamics & phylogeography

Poster

100. DECLINE AND RISE OF HIV-1 CLUSTERS DURING PREP IMPLEMENTATION IN SPAIN

Michael M Thomson (Centro Nacional de Microbiología. Instituto de Salud Carlos III)

Transmission dynamics & clusters

Poster

Virtual posters

103. DEEP MUTATIONAL SCANNING OF THE NIPAH RECEPTOR BINDING PROTEIN

Brendan Larsen (Fred Hutch Cancer Center)

Zoonoses & emerging infections

Oral

51. DESCRIPTION OF HIV SOCIAL BEHAVIOR USING A NOVEL PHYLOGENETIC MODEL OF STRUCTURED CO-EVOLUTION

Andrea Ramirez

Within-host dynamics & adaptation

Poster

87. Detecting Positive Epistasis in Chronic Infections of SARS-CoV-2

Adi Ben Zvi (Tel Aviv University)

Within-host dynamics & adaptation

Poster

106. DOSE-DEPENDENT ANTIGENIC EVOLUTION OF THE SARS-COV-2 VIRUS

Vincent Montoya (BC Centre for Excellence in HIV/AIDS)

Within-host dynamics & adaptation

Oral

36. Dynamical modeling implicates dosage of pocapavir antiviral and host cell spatial structure as key factors driving antiviral resistance evolution in poliovirus

Alexander Robertson (University of Washington)

Within-host dynamics & adaptation

Oral

109. Dynamics of RSV in the UK: Developing surveillance of a seasonal respiratory pathogen

Kate Duggan (University of Edinburgh)

Phylodynamics & phylogeography

Poster

7. Early underdetected dissemination across countries followed by extensive local transmission propelled the 2022 mpox epidemic

Miguel Paredes (Fred Hutch Cancer Center)

Phylodynamics & phylogeography

Oral

42. EFFECTS OF BLOCKING LYMPHOCYTE ENTRY ON ANTIRETROVIRAL DRUG DISTRIBUTION IN LYMPH NODES

Sobia Anam (Biomedical Engineering, University of Delaware, Newark, DE, USA)

Within-host dynamics & adaptation

Poster

91. EMERGENCE OF OMICRON FN.1 A DESCENDENT OF BQ.1.1 IN BOTSWANA

Wonderful Choga (Botswana-Harvard Health Partnership)

Phylodynamics & phylogeography

Poster

57. ENDEMIC DOES NOT MEAN CONSTANT AS COVID-19 CONTINUES TO EVOLVE

Sarah (Sally) Otto (UBC)

Transmission dynamics & clusters

Oral

59. ESTIMATION OF HIV CASES AVERTED IN PHYLOGENETIC CLUSTERS THROUGH PRE-EXPOSURE PROPHYLAXIS AND MISSED OPPORTUNITIES FOR PREVENTION

Angela McLaughlin (British Columbia Centre for Excellence in HIV/AIDS; University of British Columbia)

Transmission dynamics & clusters

Poster

11. EVOLUTION AND TRANSMISSION DYNAMICS OF RESPIRATORY SYNCYTIAL VIRUS GROUP A IN THE PAKISTAN NEONATAL POPULATION DURING THE COVID-19 PANDEMIC

Dr Sana Tamim (Research Fellow, Fogarty International Centre, National Institute of Health, US)

Phylodynamics & phylogeography

Poster

40. EXAMINING THE WITHIN-HOST EVOLUTION OF SARS-COV-2 IN PROLONGED INFECTIONS: A FITNESS LANDSCAPE APPROACH

Amber Coats (Emory University)

Within-host dynamics & adaptation

Poster

25. EXPANDING THE KNOWN DIVERSITY OF HUMAN ANELLOVIRUSES

Dr Spyros Lytras (University of Tokyo, MRC-University of Glasgow Centre for Virus Research (CVR))

Genomics & bioinformatics

Oral

92. Exploring Recombination Dynamics in Within-Host Evolution of HIV: Implications for Evolutionary Rate Measurements

Harriet Longley (University of Oxford)

Within-host dynamics & adaptation

Oral

62. EXPLORING THE IMPACT OF IMMUNOCOMPROMISED INDIVIDUALS ON SARS-COV-2 VARIANTS EMERGENCE WITH SIMPLICITY

Pietro Gerletti (Robert Koch Institute, FU Berlin)

Software, tools & methods

Oral

125. Exploring the Role of Low-Frequency Mutations in HIV Drug Resistance Evolution

David Bonsall (Wellcome Centre for Human Genetics, Nuffield Department of Medicine & Pandemic Sciences Institute, University of Oxford, UK.)

Genomics & bioinformatics

Poster

126. FACILITATING VIRAL RESEARCH WITH ACCESSIBLE WEB-BASED PLATFORMS FOR ANALYZING AND SHARING DEEP MUTATIONAL SCANNING DATA

Will Hannon (Fred Hutch Cancer Center)

Software, tools & methods

Poster

116. FLU STRAIN COMPARE: A TOOL FOR 3D VISUALIZATION OF HA AND NA MUTATIONS

Dr Manon Ragonnet-Cronin (University of Chicago)

Software, tools & methods

Poster

117. FORECASTING COVID-19 VARIANT WAVE DYNAMICS: A STATISTICAL APPROACH LEVERAGING GLOBAL DATA

Shab Molan (Simon Fraser University)

Transmission dynamics & clusters

Poster

28. Genome Evolution and Early Introductions of the SARS-CoV-2 Omicron Variant in Mexico

Hugo Castelan (Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada)

Phylodynamics & phylogeography

Poster

52. GENOME-BASED INCIDENCE ESTIMATION OF SARS-COV-2 WITH GINPIPE

Maureen Smith (Robert Koch Institute)

Software, tools & methods

Poster

27. Genomic epidemiology of rhinovirus before and during the COVID-19 pandemic

Julia Paoli (UF)

Genomics & bioinformatics

Poster

13. GENOMIC SURVEILLANCE OF OVER 100,000 SARS-COV-2 GENOMES REVEALS TRANSMISSION INSIGHTS WITH MATCHED EPIDEMIOLOGICAL DATA

Gage Moreno (Broad Institute of MIT and Harvard)

Genomics & bioinformatics

Oral

14. Going beyond limitations in the identification of dynamic transmission clusters

Brittany Rife Magalis (University of Florida)

Transmission dynamics & clusters

Poster

83. Graph theory approach for identifying rapidly expanding SARS-CoV-2 lineages using early genomic data

Ruian Ke (Los Alamos National Laboratory)

Genomics & bioinformatics

Oral

97. HEARTLAND VIRUS PHYLODYNAMICS IN GEORGIA, USA

Stephanie Bellman (Emory University)

Zoonoses & emerging infections

Poster

23. Hidden evolutionary constraints dictate the retention of coronavirus accessory genes

Stephen Goldstein (University of Utah)

Zoonoses & emerging infections

Oral

21. HIGH CIRCULATION OF RESPIRATORY SYNCYTIAL VIRUS IN PEDIATRIC PATIENTS HOSPITALIZED WITH SEVERE ACUTE RESPIRATORY INFECTION IN SENEGAL, 2022-2023

Mamadou Malado Jallow (Pôle de virologie, Institute Pasteur, Dakar, Sénégal)

Transmission dynamics & clusters

Poster

73. HIGH HIV DIVERSITY, RECOMBINATION, AND SUPERINFECTION REVEALED IN A LARGE OUTBREAK AMONG PERSONS WHO INJECT DRUGS IN KENTUCKY AND OHIO, USA

William Switzer (CDC)

Transmission dynamics & clusters

Poster

17. High variation in HIV ‘burst size’ from individual infected cells drives dominance of individual viral founder lineages

Steffen S. Docken (Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia)

Within-host dynamics & adaptation

Oral

112. HIGH-THROUGHPUT SINGLE-GENOME SEQUENCING COUPLED TO HIGH-FIDELITY HAPLOTYPE DETERMINATION FACILITATES DETAILED INVESTIGATION OF SARS-COV-2 EVOLUTION IN IMMUNOCOMPROMISED INDIVIDUALS

Pierce Radecki (Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health)

Genomics & bioinformatics

Poster

68. HIV-1 CLUSTER DYNAMICS IN THE ERA OF ONGOING PUBLIC HEALTH-ASSOCIATED PrEP INTERVENTION IN NSW, AUSTRALIA.

Billal Obeng (The Kirby Institute, University of New South Wales, Sydney, Australia)

Transmission dynamics & clusters

Poster

104. HIV-1 CRF01_AE WAS INTRODUCED IN THAILAND IN THE MID 1970s

Morgan Geniviva (U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)

Phylodynamics & phylogeography

Poster

127. HLA CLASS I ESCAPE DRIVES THE EVOLUTION OF SARS-COV-2 IN HUMAN POPULATION

Ekaterina Ryumina (Skolkovo Institute of Science and Technology), Evgeniia Alekseeva (Skolkovo Institute of Science and Technology), Prof. Georgii Bazykin (Skolkovo Institute of Science and Technology)

Vaccines & immune escape

Poster

Virtual posters

16. HUMAN CORONAVIRUS OC43 - THE LONG AND SHORT OF IT.

Ayushman Dobhal

Zoonoses & emerging infections

Poster

3. IDENTIFICATION OF UNIQUE MOLECULAR SIGNATURES IN THE ENVELOPE GLYCOPROTEINS OF HIV-1 TRANSMITTED/FOUNDER VIRUSES FROM EAST AFRICA

FRANK KATO (1. MRC/UVRI and LSHTM Uganda Research Unit. 2. Makerere University)

Within-host dynamics & adaptation

Poster

71. Immune escape and post-acute sequelae of COVID-19

Alex Beams (Simon Fraser University)

Vaccines & immune escape

Poster

12. IMMUNOGLOBULIN G SPECIFIC ANTIBODY LEVEL AGAINST EBOLA VIRAL GLYCOPROTEIN AND NUCLEOPROTEIN IN EBOLA VIRUS DISEASE SURVIVORS AND THEIR RELATIVES

Nadege Goumkwa Mafopa (Centre International de Référence Chantal Biya pour la Recherche sur la Prévention et la Prise en charge du VIH/SIDA)

Zoonoses & emerging infections

Poster

70. IMPRINTING OF BROADLY NEUTRALISING ANTI-HCV ANTIBODIES

Prof. Rowena Bull (University of New South Wales)

Vaccines & immune escape

Oral

63. Improving in silico prediction of influenza vaccine effectiveness by genome analysis incorporating epitope information

Dr Lirong Cao (The Chinese University of Hong Kong)

Vaccines & immune escape

Poster

19. INFERRING VIRAL TRANSMISSION TIME FROM PHYLOGENIES FOR KNOWN TRANSMISSION PAIRS

Emma Goldberg (LANL)

Transmission dynamics & clusters

Oral

101. INFLAMATORY MONOCYTES INCREASE PRIOR TO DETECTABLE HIV-1 REBOUND VIREMIA

Anna Farrell-Sherman (Fred Hutch Cancer Center and the University of Washington)

Within-host dynamics & adaptation

Poster

61. INFLUENZA A PACKAGING AND PROTEIN EXPRESSION: IN SILICO IMPROVEMENTS IN MOLECULAR CHARACTERISATION

Jordan Skittrall (University of Cambridge)

Genomics & bioinformatics

Poster

94. INTEGRATED PANDEMIC-SCALE PHYLODYNAMICS WITH TIMTAM

Dr Louis du Plessis (ETH Zürich)

Software, tools & methods

Oral

44. Integrative modeling of phylodynamic, vector, human travel, and epidemiological data to infer arboviral importation and local transmission

Carla Mavian (Emerging Pathogens Institute, Department of Pathology, College of Medicine, University of Florida)

Transmission dynamics & clusters

Poster

96. Intra- host diversity of hemagglutinin 5 in a non-human primate challenge model

Dr Vanessa Guerra Canedo (Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH)

Within-host dynamics & adaptation

Poster

Virtual posters

4. INTRA-HOST EVOLUTION OF HIV ENV AFTER BROADLY-NEUTRALIZING ANTIBODY INFUSION

Dr Frida Belinky (Vaccine Research Center, National Institute of Allergy and Infectious Diseases)

Within-host dynamics & adaptation

Either

93. Limited evolution despite months of measurable viremia in an ART-treated seronegative HIV-1 positive individual

Helen Fryer (university of oxford)

Within-host dynamics & adaptation

Poster

Virtual posters

75. LONG INDEL-AWARE PARSIMONY FOR DETECTING AND VISUALISING INDEL PATTERNS IN THE HIV-1 GENOME

Clara Iglhaut (University of Zurich, Zurich, Switzerland and Zurich University of Applied Sciences, Wädenswil, Switzerland and Swiss Institute of Bioinformatics, Lausanne, Switzerland)

Software, tools & methods

Oral

47. LONG-READ SEQUENCING AND LINKAGE ANALYSIS REVEAL EXTENSIVE HIV RESISTANCE EVOLUTION TO 10-1074 BROADLY NEUTRALIZING ANTIBODIES

Elena Romero (Department of Genome Sciences, University of Washington)

Within-host dynamics & adaptation

Oral

69. Machine learning models for forecasting SARS-CoV-2 lineage frequencies

Ruian Ke (Los Alamos National Laboratory)

Software, tools & methods

Poster

89. MAPPING THE DYNAMIC HOST-PATHOGEN INTERACTIONS IN JC VIRUS INFECTION AND DISEASE AT A SINGLE CELL RESOLUTION

Poorva Jain (NIH and University of Oxford)

Genomics & bioinformatics

Poster

115. MODELING THE DYNAMICS OF HIV-1 REPLICATION AND LATENT RESERVOIR FORMATION: INSIGHTS INTO THE ROLES OF REVERSE TRANSCRIPTION ERRORS AND CLONAL EXPANSION

Amjad Khan (Western University)

Within-host dynamics & adaptation

Poster

120. MODELING THE TRANSMISSION MITIGATION AND SELECTION IMPACT OF TESTING FOR INFECTIOUS DISEASES

Casey Middleton

Software, tools & methods

Poster

54. MODELING THE WITHIN-HOST INFECTION DYNAMICS OF SARS-COV-2

Lea Schuh (Joint Research Centre, European Commission)

Within-host dynamics & adaptation

Poster

65. Modelling APOBEC3-mediated Hypermutation in Mpox Genome using BEAST Software.

Ifeanyi Omah (University of Edinburgh)

Software, tools & methods

Poster

Virtual posters

32. Modelling of the dynamic Immune landscape that determines SARS-CoV-2 evolution

Max von Kleist (Robert-Koch Institute; Freie Universität Berlin)

Vaccines & immune escape

Oral

58. NONSYNONYMOUS SUBSTITUTIONS EXPLAIN THE WIDE VARIATION IN WITHIN-HOST EVOLUTIONARY RATES AMONG SARS-COV-2 PERSISTENTLY INFECTED INDIVIDUALS

Mahan Ghafari (Big Data Institute and Pandemic Sciences Institute, University of Oxford)

Within-host dynamics & adaptation

Oral

81. NOVEL LONG-RANGE SEQUENCING ASSAYS FOR HIV AND HCV FOR USE IN A DIAGNOSTIC SETTING

Bethany Horsburgh (The Kirby Institute, University of New South Wales)

Genomics & bioinformatics

Poster

121. Oh Deer: Investigating Within-Host Diversity of SARS-CoV-2 in White-tailed Deer (Odocoileus virginianus)

Mr Sean Vidal Edgerton (University of British Columbia)

Zoonoses & emerging infections

Poster

8. ON THE DISCOVERABILITY OF CLUSTERS/LINEAGES/VARIANTS OF SARS-COV-2 FROM WASTEWATER

Devan Becker (Wlifrid Laurier University)

Software, tools & methods

Poster

Virtual posters

2. ORIGIN AND EVOLUTION OF SUBTYPE B VARIANTS IN THE FORMER SOVIET UNION COUNTRIES

Dr Aidana Mustafa (Department of Biomedical Sciences, Nazarbayev School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan)

Transmission dynamics & clusters

Poster

37. PHYLOGENETIC ANALYSIS OF HIV-1 ENV SEQUENCES FROM THE ANTIBODY MEDIATED PREVENTION (AMP) TRIALS HVTN 704/HPTN 085 AND HVTN 703/HPTN 081 REVEALS A HIGH FREQUENCY OF LINKED TRANSMISSION PAIRS FROM PERUVIAN PARTICIPANTS.

Dr Elena Giorgi (Fred Hutchinson Cancer Center)

Transmission dynamics & clusters

Poster

45. PHYLOGENETIC APPROACH TO INFER THE INTEGRATION DATES OF HYPERMUTATED PROVIRUSES PERSISTING DURING ART

Aniqa Shahid (Faculty of Health Sciences, Simon Fraser University, British Columbia Centre for Excellence in HIV/AIDS)

Within-host dynamics & adaptation

Poster

Virtual posters

56. PHYLOGENETIC CHARACTERIZATION OF PARAMYXOVIRUSES IN BATS

Laura Muñoz-Baena (Western University)

Zoonoses & emerging infections

Oral

105. PHYLOGEOGRAPHIC ANALYSIS OF MPOX VIRUS INTRODUCTIONS INTO NEW YORK CITY REVEALS SCALE-FREE TRANSMISSION DYNAMICS REMINISCENT OF HIV TRANSMISSION CLUSTERS

Jonathan Pekar (UC San Diego)

Transmission dynamics & clusters

Oral

77. Phylogeography and evolutionary history of hepatitis A virus genotype IA in Argentina

Anabella Fantilli (Instituto de Virología “Dr. J. M. Vanella”, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Córdoba, Argentina)

Phylodynamics & phylogeography

Poster

66. Plumbing the temporal and spatial structure of SARS-CoV-2 genomic variation in Ontario wastewater samples

Paula Magbor (Western University)

Genomics & bioinformatics

Poster

50. POPULATION DYNAMICS OF HIV DRUG RESISTANCE DURING TREATMENT SCALE-UP IN UGANDA: A POPULATION-BASED LONGITUDINAL STUDY

Michael Martin (Johns Hopkins Medicine)

Transmission dynamics & clusters

Poster

39. Predicting the fitness of SARS-CoV-2 variants using a protein language model

Jumpei Ito (Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo)

Genomics & bioinformatics

Poster

64. PREVALENCE OF HIGH-LEVEL HIV DRUG-RESISTANT MUTATIONS AMONG THE FORMER SOVIET UNION COUNTRIES

Ms Nurzhanna Bakuova (Nazarbayev University)

Phylodynamics & phylogeography

Poster

10. Prospects for a molecular taxonomy of influenza A virus subtypes

Art Poon (Western University)

Genomics & bioinformatics

Oral

113. REAL-TIME TRACKING OF VARIANT EVOLUTION AND DYNAMICS FOR PUBLIC HEALTH DECISION-MAKING: PROGRESS AND CHALLENGES

Carmen Lia Murall (Public Health Agency of Canada)

Phylodynamics & phylogeography

Oral

123. Recombination patterns reveal epidemiological dynamics

Dr Nicola Mueller (University of California San Francisco)

Software, tools & methods

Oral

86. RSV lineage dynamics revealed by novel ARTIC sequencing approach.

Daniel Maloney (University of Edinburgh / NHS Lothian)

Genomics & bioinformatics

Oral

74. SARS-CoV-2 dynamics in New York City during March 2020 – August 2023

Wan Yang (Columbia University)

Transmission dynamics & clusters

Poster

99. SARS-COV-2 VARIANT REPLACEMENT CONSTRAINS VACCINE-SPECIFIC VIRAL DIVERSIFICATION

Bethany L Dearlove (U.S. Military HIV Research Program, CIDR, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA)

Vaccines & immune escape

Oral

33. Selective forces in HIV reservoirs estimated by simultaneous modeling of HIV- and CD4 TCR- levels and clonality

Daniel Reeves (Fred Hutchinson Cancer Center, University of Washington)

Within-host dynamics & adaptation

Oral

110. Simultaneous virus-vector genomics for mosquito-borne diseases with COSMOS

Dr Tanya Golubchik (University of Sydney)

Genomics & bioinformatics

Oral

84. SMALL VIRAL RNA EVOLUTION AND THE ORIGIN OF SARS-COV-2: INSIGHTS FROM FUNCTIONAL GENOMICS

Dr Amber R. Paulson (University of British Columbia, British Columbia Centre for Excellence in HIV/AIDS)

Zoonoses & emerging infections

Oral

80. SPATIOTEMPORAL DISPERSION OF DENV1 GENOTYPE V LINEAGES IN COLOMBIA

Tyshawn Ferrell (Department of Microbiology and Immunology, Emory University school of Medicine), Diana Rojas Gallardo (Department of Biology, Emory University, Atlanta, GA, USA)

Phylodynamics & phylogeography

Poster

Virtual posters

30. Sweden surpasses the UNAIDS 95-95-95 Target: Estimating HIV-1 incidence between 2003-2022

Macauley Locke (Los Alamos National Laboratory)

Software, tools & methods

Oral

111. T-shaped alignments can improve phylodynamic inference of HIV transmission clusters

August Guang (Brown University)

Genomics & bioinformatics

Poster

85. THE CURIOUS CASE OF S-GENE TARGET FAILURE SWITCHING