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System to auto-detect new variants will inform better response to future infectious disease outbreaks | Researchers found a new way to identify more infectious variants of viruses or bacteria that start spreading in humans - including the flu, COVID, whooping cough and tuberculosis.
Phylowave, an innovative phylogenetic approach, can identify the main circulating pathogen lineages with increased fitness and the associated genetic changes, enabling the timely identification of emergent strains and deployment of targeted interventions.
Identifying lineages with improved fitness at the population level would enable a focused public-health response, through, for example, targeted vaccination and could provide key insights into the underlying ecology of disease systems. We found that for each pathogen considered, phylowave produced evidence of lineages with clear fitness differences, as evidenced by subpopulations of genetically related strains with discrete index dynamics (Fig. Across the pathogens, previously defined subvariants that reached a maximum prevalence of less than 5% at any time in the datasets were generally not identified by phylowave (for example, Eta/B.1.525, Mu/B.1.621 and EU1 for SARS-CoV-2, clades 1* of H3N2 and Central Asian Strain and East African Indian M. tuberculosis lineages).
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