Webinar 11: March 10th, 12.00-13.00 (SAST); 11.00-12.00 (CET)
First talk:- Long-read technologies – the next rare disease revolution
Speaker: Prof. Dr. Alexander Hoischen
Abstract: Long-read genomic technologies are strongly emerging. These include mapping technologies such as optical genome mapping (OGM), but also long-read sequencing (LRS) technologies, such as PacBio HiFi genome sequencing on Revio.
OGM with its ultra-long DNA molecules allows full de novo assemblies of human genomes and genomewide assessment of structural variants (SV) down to 500bp in size for constitutional as well as acquired/somatic SVs.
LRS allow to assess the full human genome for the first time and have the potential to revolutionize human genetics. This technology could offer a comprehensive first-tier test for clinical genetics and rare disease research. To determine the clinical utility of LRS, we performed Revio HiFi genome sequencing on 1,500 human genomes with ~30-fold coverage, including 100 mutation-positive controls that are impossible or challenging to identify by standard short-read genome sequencing, 100 severe sporadic rare disease cases as patient-parent trios, and 100 severe rare disease cases as singletons who remained undiagnosed after standard-of-care testing. Finally, we run a prospective clinical utility study of 1,000 samples representing the annual germline testing of our diagnostic division.
Both approaches OGM and LRS jointly re-emphasize the need for cytogenetic-centered analyses, and allow novel insights into SV biology and emphasize a previously underestimated role for SVs in rare diseases.
Further research is needed to fully assess the clinical utility of OGM and LRS, but the results of latest studies support our enthusiasm for use of OGM and LRS as a first-tier clinical tests in the near future.
Second talk:- Dynamics and ecology of a multi-stage expansion of Oropouche virus in Brazil – a case-study for integrated modelling for climate-sensitive arboviruses
Speaker: Dr. Houriiyah Tegally
Abstract: This talk explores the integration of genomic epidemiology and phylodynamics with ecological modeling towards pandemic preparedness for climate-sensitive pathogens. These techniques can be employed to comprehensively study climate-driven transmission risks, as well as the evolutionary forces shaping the emergence and spread of arboviruses, and transmission correlates governing their spatiotemporal dispersal and growth. An interdisciplinary and integrative genomic epidemiology approach can inform both our understanding of arboviral disease dynamics and strategies for proactive epidemic preparedness and response globally.
In March 2024, the Pan American Health Organization (PAHO) issued an alert in response to a rapid increase in Oropouche fever cases across South America. Brazil has been particularly affected, reporting a novel reassortant lineage of the Oropouche virus (OROV) and expansion to previously non-endemic areas beyond the Amazon Basin.
Utilising phylogeographic approaches, we reveal a multi-scale expansion process with both short and long-distance dispersal events, and diffusion velocities in line with human-mediated jumps. We identify forest cover, banana and cocoa cultivation, temperature, and human population density as key environmental factors associated with OROV range expansion. Using ecological niche modelling, we show that OROV circulated in areas of enhanced ecological suitability immediately preceding its explosive epidemic expansion in the Amazon. This likely resulted from the virus being introduced into simultaneously densely populated and environmentally favourable regions in the Amazon, such as Manaus, leading to an amplified epidemic and spread beyond the Amazon. Our study provides valuable insights into the dispersal and ecological dynamics of OROV, highlighting the role of human mobility in colonisation of new areas, and raising concern over high viral suitability along the Brazilian coast.
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