A highly divergent sample from a nearly extinct SARS-CoV-2 lineage in a patient with long-term COVID-19.

Background: Although COVID-19 is primarily an acute disease, there are cases of persistent infection, primarily in immunocompromised patients. It is hypothesized that at least some variants of concern (VOCs) have arisen in such persistent cases, with the virus "spilling over" into the general population after accumulating intra-host mutations. Additionally, a growing body of evidence hints at the gastrointestinal (GI) tract as a reservoir of long-term infection, at least in some cases. Results: We report the genomic analysis of a highly divergent SARS-CoV-2 sample obtained in October 2022 from an HIV+ patient with presumably long-term COVID-19 infection. Phylogenetic analysis indicates that the sample is characterized by a gain of 89 mutations since divergence from its nearest sequenced neighbor, which had been collected in September 2020 and belongs to the B.1.1 lineage, largely extinct by 2022. Of these mutations, 33 were nonsynonymous and occurred in the Spike protein. Of these, 17 are lineage-defining in some VOCs or are at sites where another mutation is lineage-defining in a VOC, and/or have been shown to be involved in antibody evasion, and/or have been detected in other cases of persistent COVID-19; these include some "usual suspects," such as Spike:L452R, E484Q, K417T, Y453F, and N460K. Molecular clock analysis indicates that mutations in this lineage accumulated at an increased rate compared with the ancestral B.1.1 strain. This increase is driven by the accumulation of non-synonymous mutations, with an average dN/dS value of 2.2, indicating strong positive selection during within-patient evolution. Additionally, the presence of mutations that are rare in the general population samples but common in samples from wastewater suggests that the virus had persisted for at least some time in the GI tract. Conclusions: Our analysis adds to the growing body of evidence that the evolution of SARS-CoV-2 in chronically infected patients can be a major source of novel epidemiologically important variants and points to the potential role of the GI tract in long-term infection.