Biomedical subjects

Darren P Martin

Publications and source records attributed to Darren P Martin.

3 recordsLinked to original sources

PubMed2026

Global inequities in hepatitis B and C genomic surveillance revealed through an interactive data integration dashboard.

OBJECTIVES: To assess global disparities in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomic surveillance and to develop an integrated platform that links genomic data with epidemiological burden. STUDY DESIGN: Retrospective observational analysis. METHODS: We reviewed existing viral genomic repositories to identify structural and analytical limitations. Subsequently, we integrated 10 996 HBV and 3533 HCV whole-genome sequences (WGS) from public databases with Global Burden of Disease (GBD) estimates to quantify inequities in genomic surveillance across countries and genotypes. Using these data, we developed the open-access Hepatitis Dashboard, incorporating >14 000 sequences from 141 countries with GBD metrics to evaluate representativeness and sequencing coverage relative to disease burden. RESULTS: Marked inequities in hepatitis genomic surveillance were identified. Despite increasing HBV- and HCV-associated mortality, virus sequence availability remains geographically and genotypically skewed-dominated by China and the United States, with substantial underrepresentation of HBV genotype E and HCV genotypes 5 and 8. Many high-endemic countries in Africa and the Western Pacific remain severely undersampled. We detected circulating antiviral drug-resistance mutations and developed a burden-adjusted sequencing coverage metric, revealing that several high-burden countries, including China, Nigeria and India, are among the least represented in global genomic datasets. Projections to 2030 indicate that neither HBV nor HCV are currently on track to meet WHO elimination targets. CONCLUSIONS: The Hepatitis Dashboard provides an integrated, continuously updated resource that links genomic and epidemiological data to quantify and visualise global surveillance gaps. This analysis highlights a critical disconnect between sequencing efforts and public health needs, which may limit the effectiveness of surveillance-informed strategies to support progress toward WHO 2030 elimination goals. By enabling burden-adjusted prioritisation and longitudinal tracking of genomic coverage, the platform supports evidence-based sampling strategies, equitable resource allocation, and monitoring of global progress toward hepatitis elimination.

Humans↗

PubMed2025

Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models.

Most phylogenetic trees are inferred using time-reversible evolutionary models that assume that the relative rates of substitution for any given pair of nucleotides are the same regardless of the direction of the substitutions. However, there is no reason to assume that the underlying biochemical mutational processes that cause substitutions are similarly symmetrical. We consider two non-reversible nucleotide substitution models: (1) a 6-rate non-reversible model (NREV6) that is applicable to analyzing mutational processes in double-stranded genomes in that complementary substitutions occur at identical rates; and (2) a 12-rate non-reversible model (NREV12) that is applicable to analyzing mutational processes in single-stranded (ss) genomes in that all substitution types are free to occur at different rates. Using likelihood ratio and Akaike Information Criterion-based model tests, we show that, surprisingly, NREV12 provided a significantly better fit than the General Time Reversible (GTR) and NREV6 models to 21/31 dsRNA and 20/30 dsDNA datasets. As expected, however, NREV12 provided a significantly better fit to 24/33 ssDNA and 40/47 ssRNA datasets. We tested how non-reversibility impacts the accuracy with which phylogenetic trees are inferred. As simulated degrees of non-reversibility (DNR) increased, the tree topology inferences using both NREV12 and GTR became more accurate, whereas inferred tree branch lengths became less accurate. We conclude that while non-reversible models should be helpful in the analysis of mutational processes in most virus species, there is no pressing need to use these models for routine phylogenetic inference.

Models of evolution↗

PubMed2011

Recombination in eukaryotic single stranded DNA viruses.

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

Animals↗