Organ-specific genome diversity of replication competent SARS-CoV-2

SARS-CoV-2 impacts people on a broad clinical spectrum from asymptomatic to severe respiratory and systemic manifestations resulting in death. In addition, intra-host SARS-CoV-2 genomic plasticity periodically leads to emergence of new virus variants with higher transmission capacities. Here we report a detailed virological analysis of thirteen postmortem COVID-19 cases that confirms two stages of fatal disease evolution based on disease duration and viral loads in lungs and plasma. More importantly, the study is the first to provide proof of viremia and presence of replication competent SARS-CoV-2 in extrapulmonary organs of an immunocompromised patient, accompanied by tissue-specific patterns of genome diversity in organ-resident SARS-CoV-2 populations