Biology subjects

Rapadas, M.

Publications and source records attributed to Rapadas, M..

3 recordsLinked to original sources

bioRxiv2025

Between- and within-host mutation of dengue virus

RNA viruses exhibit high mutation rates due to error-prone polymerases, leading to a diverse pool of viral haplotypes (also referred to as quasi-species) within infected hosts. While haplotypes have been well studied in chronic infections like HIV and HCV, diversity remains under-explored in acute infections like dengue (DENV), which are constrained by a short viremic phase. This study aimed to characterise the mutation hotspots in DENV genomes at both consensus and haplotype levels. Near full length DENV genomes were sequenced using Oxford Nanopore Technology (ONT) from the plasma of Sri Lankan patients with dengue fever recruited between 2017 -2020. Consensus sequences were mapped with Minimap-2, and haplotypes were reconstructed with Nano-Q, a tool designed for estimation of RNA virus haplotypes and their relative abundance. The genomic variability of DENV genomes was assessed by calculating Shannon Entropy (SE). Codons undergoing diversifying selection were identified with three phylogenetics-based algorithms (FEL, MEME, FUBAR) implemented within the Datamonkey suite. From 150 samples tested, both consensus and haplotype sequences were characterised in 90 samples (DENV1: 8, DENV2: 51, DENV3: 31). The genomic variability of consensus sequences measured by SE was higher in DENV2 compared to DENV3, and the reverse was true for haplotypes. At the consensus level, the NS2A gene had the greatest number of mutable sites when adjusted for gene length across all serotypes, while at the haplotype level the NS1 gene had the same. Overall, the haplotypes sequences revealed more sites with high mutability and codons under diversifying selection than those visible at consensus level. This provides proof-in-principle that in acute RNA viruses also have high mutability in haplotypes, which may be inapparent with a consensus-level analysis.

bioinformatics↗

bioRxiv2025

Adaptively integrated sequencing and assembly of near-complete genomes

Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. Cornetto is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).

genomics↗

bioRxiv2023

The landscape of genomic structural variation in Indigenous Australians

Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference databases. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here, we apply population-scale whole genome long-read sequencing to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large indels (20-49bp; n=136,797) and structural variants (SVs; [≥]50bp; n=159,912), the majority of which are composed of tandem repeat or interspersed mobile element sequences (90%) and have not been previously annotated (73%). A large fraction of SVs appear to be exclusive to Indigenous Australians (>30%) and the majority of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short-tandem repeats (STRs) throughout the genome to characterise allelic diversity at 50 known disease loci, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among STR sequences. Our study sheds new light on the dimensions, diversity and evolutionary trajectories of genomic structural variation within and beyond Australia.

genomics↗