There are multiple documented cases of patients with chronic Covid-19 infections that last several months or more. With his colleagues at the University of Michigan, Lauring documented the infection of one man who had harboured the replicating virus for at least 119 days. By analysing the genomes of virus samples taken at different points during the patient’s infection, Lauring could see the virus steadily accumulating genetic changes – a microcosm of how Sars-CoV2-2 mutates within the global population, but this time all happening within one human host…

Those who become chronically infected tend to have something in common: their immune systems are compromised in some way that makes it impossible for them to fully get rid of an infection. The man Lauring studied was undergoing chemotherapy for cancer of the lymph nodes, which likely hampered the production of immune cells that respond to new viruses. The man who shed poliovirus for at least 28 years suffered from a disorder called common variable immune deficiency, which decreases the number of antibodies in the blood and makes it harder for the body to fight off infections.

People with weakened immune systems provide viruses like Sars-CoV-2 with a unique environment. Instead of clearing an infection quickly, an immunocompromised person might only partially wipe out an infection, leaving behind a population of genetically-hardier viruses that rebound and begin the cycle all over again. In these people, a virus can evolve at remarkable speed. “The whole time, their immune system is effectively beating [the virus] up. So the virus has a chance to learn how to live with the human immune system,” says Emma Hodcroft, a postdoctoral research at the University of Bern in Switzerland who works on Nextstrain – an open-source project that tracks the genetic changes of Sars-CoV-2 and other pathogens.