Mutation T9I in Envelope conveys autophagy resistance of SARS-CoV-2 Omicron

To date five variants of concern (VOC) of SARS-CoV-2 have emerged that show increased immune evasion. While their evolving escape from humoral immune responses has been analyzed in detail, adaptation of SARS-CoV-2 to human innate immune processes like autophagy are less understood. Here we demonstrate that currently predominant mutation T9I in the structural envelope (E) protein conveys increased resistance against autophagy of recent Omicron VOCs (BA.1, BA5 and XBB.5) compared to earlier SARS-CoV-2 variants. Rare omicron isolates that do not carry E T9I are sensitive towards autophagy. Mechanistic analyses revealed that E I9 inhibits autophagic turnover more efficiently than E T9 due to increased recruitment to autophagosomes and enhanced interaction with early autophagosome markers. Using pseudotyping assays we revealed that mutation T9I in E reduces release efficiency, but protects incoming virion from autophagy. In line, introduction of E T9I into recombinant 2020 SARS-CoV-2 increases its resistance against autophagy, but also attenuates replication. Our data thus reveal autophagy as a fundamental driver of SARS-CoV-2 evolution and improved autophagy escape may have contributed to the success of the Omicron variant.