Parallel evolution of influenza across multiple spatiotemporal scales

Abstract

Viral variants that arise in the global influenza population begin as de novo mutations in single infected hosts, but the evolutionary dynamics that transform within-host variation to global genetic diversity are poorly understood. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population. In hemagglutinin, a small set of mutations arises independently in multiple patients. These same mutations emerge repeatedly within single patients and compete with one another, providing a vivid clinical example of clonal interference. Many of these recurrent within-host mutations also reach a high global frequency in the decade following the patient infections. Our results demonstrate surprising concordance in evolutionary dynamics across multiple spatiotemporal scales.DOI: http://dx.doi.org/10.7554/eLife.26875.001

Potency and timing of antiviral therapy as determinants of duration of SARS CoV-2 shedding and intensity of inflammatory response

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A decade of RNA virus metagenomics is (not) enough

“…To put it scientifically, it is nuts that all this and much more have happened in only approximately a decade. If they were not already, RNA viruses have become the star child of evolutionary biologists, whether for day-by-day or eon-by-eon examples of evolution (Koonin, 2007;Koonin et al, 2008Koonin et al, , 2015Shi et al, 2016;Xue et al, 2017). With our world expanded and our place in it shrunk, there is still much to do regarding viral sequencing for our own quotidian human RNA viruses (Tang et al, 2017).…”

Extreme Competence: Keystone Hosts of Infections

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