The linked paper does not support your claim. The presence of those nucleocapsid proteins doesn't necessarily mean that there was live virus. They didn't attempt to culture it.

The only confirmed cases of SARS-CoV-2 infections in humans lasting beyond a few weeks have been in immunocompromised patients. Their immune systems were able to somewhat suppress the virus, but not clear the infection. (There is a hypothesis that such patients were the sources for some of the variants because the extended infections gave the virus more time to evolve but that can't be conclusively proven.)