SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient

Abstract

Objectives: Intra-host SARS-CoV-2 evolution during chronic infection in immunocompromised hosts has been suggested as being the possible trigger of the emergence of new variants.

Methods: Using a deep sequencing approach, we investigated the SARS-CoV-2 intra-host genetic evolution in a patient with HIV over a period of 109 days.

Results: Sequencing of nasopharyngeal swabs at three time points demonstrated dynamic changes in the viral population, with the emergence of 26 amino acid mutations and two deletions, 57% of them in the Spike protein. Such a combination of mutations has never been observed in other SARS-CoV-2 lineages detected so far.

Conclusion: Our data confirm that persistent infection in certain immunocompromised individuals for a long time may favor the dangerous emergence of new SARS-CoV-2 variants with immune evasion properties.

Keywords: Immunocompromised patient; Intra-host evolution; Prolonged infection; SARS-CoV-2; Sequencing.

Figure 1

SARS-CoV-2 mutation accumulation during chronic infection in a patient with HIV over 109 days. (A) Genome coverage profiles for the three nasopharyngeal swabs analyzed in this study. Y-axis is in logarithmic scale. (B) Schematic representation of amino acid mutations found in patient swabs compared with the Wuhan-Hu-1 reference sequence (GenBank accession number NC_045512.2). The heatmap summarizes the variant frequencies; bordered squares represent consensus mutations (frequency >50%), and the mutations written in blue are those typical of the AH.3 lineage. (C) Phylogenetic analysis of the sequences obtained from patient swabs at the three time points. The sequences were aligned to a set of representative SARS-CoV-2 genome sequences belonging to AH.3 lineage and the main lineages and VOCs identified so far. The maximum-likelihood phylogenetic tree was constructed with IQ-TREE (GTR+F+R2) and rooted on the Wuhan-Hu-1 reference genome. Ultra-fast bootstrap supports are indicated above the nodes. (D) Histograms representing the amino acid frequency at the positions that differ between the three time points. Amino acids are indicated above the columns for each position. VOCs = variants of concern.

Figure 2

Genome variants identified in nasopharyngeal swabs collected from the patient at three time points in comparison to the Wuhan-Hu-1 reference sequence (GenBank accession number NC_045512.2) in the nucleotide positions that differed between the three consensus sequences. When present, amino acid mutations are indicated. The rectangle marks two different mutations present at the same nucleotide position (26,767; Membrane protein).