In some cases, the exact same mutations were seen in viruses from two or more of the patients. analyzed flu samples taken over several weeks from four cancer patients who had longer-than-average flu infections because of their weaker immune systems. This makes it harder to measure how the viruses change over time in a single infection.
Yet, unlike some viral infections that last months or years, flu infections are usually short and over in a few days. As such, understanding flu’s evolution within individual people may help scientists to understand and eventually predict how it changes worldwide. Mutations that help the virus aid in its ability to spread from person to person, and eventually spread around the world. Also, some years the flu vaccine is not as effective as hoped because the virus has changed in an unpredictable way.Īll of the change that happens in flu viruses around the world ultimately begins in individual infections, as random mistakes or mutations in the virus’s genetic material that arise as the viruses replicate. While a single course of vaccines will protect someone against polio or measles for their whole life, people need a new flu shot every year to be protected against influenza. Influenza or flu viruses change fast to escape the body’s defenses. Our results demonstrate surprising concordance in evolutionary dynamics across multiple spatiotemporal scales. Many of these recurrent within-host mutations also reach a high global frequency in the decade following the patient infections. These same mutations emerge repeatedly within single patients and compete with one another, providing a vivid clinical example of clonal interference. In hemagglutinin, a small set of mutations arises independently in multiple patients. We find parallel evolution across three scales: within individual patients, in different patients in our study, and in the global influenza population. We deep-sequence longitudinal samples from four immunocompromised patients with long-term H3N2 influenza infections. Here, we demonstrate that influenza evolution within infected humans recapitulates many evolutionary dynamics observed at the global scale. 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.
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