Background
Although documented, the mutational dynamics of SARS-CoV-2 in immunocompromised patients remain relatively understudied. This study examined a cohort of immunocompromised patients hospitalized with SARS-CoV-2 infection to assess the distinct evolutionary trajectories of SARS-CoV-2 in these individuals compared to their immunocompetent counterparts. We compared the genetic diversity of SARS-CoV-2 between these groups over time.
Methods
87 immunocompromised hospitalized patients and 52 non-immunocompromised subjects from Pitié-Salpêtrière Hospital (Paris, France) diagnosed with SARS-CoV-2 infection by RT-PCR were enrolled. Samples were collected at the time of infection (D0) and during their follow-up. Whole genome sequencing was performed using Oxford Nanopore technology (ONT). Consensus sequences were generated using a pipeline including minimap2 and DeepVariant. We performed a sparse principal component analysis (sPCA) and a t-student stochastic neighbor embedding (t-SNE) to identify trends in longitudinal data. We used univariate analyses to catch differentially detected single mutations. We built a global and specific models on isolated mutation to measure the association with follow-up time and immunosuppression.
Results
The median follow-up time for immunocompromised patients was longer than for the controls (6 days vs. 4 days, respectively). Immunocompromised patients and controls were mainly infected by Omicron BA.1. Univariate analyses of the emergence of minor mutations showed an overexpression of 5 mutations in immunocompromised patients and the absence of minor mutations in the control group at the end of the follow-up period: N:R13C, ORF1ab:L896S, ORF1ab:N5591K, ORF1ab:P557T and the N:136delG deletion (see figure). Multivariate analyses confirmed the impact of immunodeficiency status on the emergence of these mutations (N:136delG p<0.01, N:R13C p<0.01, ORF1ab:L896S p<0.05, ORF1ab:N5591K p<0.01, ORF1ab:P5557T p<0.01). These mutations were observed in patients infected with clades BQ.1 and BA.5.
Conclusions
The univariate and multivariate analyses suggested a greater genetic diversity, which increased over time in immunocompromised patients. Isolated mutations in N and ORF1ab gene could affect protein structure therefore an in-silico and in-vitro approaches could be interesting to investigate the effect on protein structure.