Phylogenetic meta-analysis of chronic SARS-CoV-2 infections in immunocompromised patients shows no evidence of elevated evolutionary rates

Genomic sequences from rapidly evolving pathogens, sampled over time, hold information on disease origin, transmission, and evolution. Together with their sampling times, sequences can be used to estimate the rates of molecular evolution and date evolutionary events through molecular tip-dating. The validity of this approach, however, depends on whether detectable levels of genetic variation have accumulated over the given sampling interval, generating temporal signal. Moreover, different molecular dating methods have demonstrated varying degrees of systematic biases under different biologically realistic scenarios, such as the presence of phylo-temporal clustering. Chronic SARS-CoV-2 infection in immunocompromised patients has been linked to remarkably higher intra-host molecular rates than those of global lineages, facilitating the emergence of novel viral lineages. Yet, most studies reporting accelerated rates lack the evaluation of temporal signal or comparison of multiple methods of inference, both required to reliably estimate molecular rates. In this study, we use 26 previously published longitudinally sampled sequence series obtained from chronically infected immunocompromised patients to re-evaluate the rate of SARS-CoV-2 intrahost evolution. Using a range of methods, we analyse the strength of temporal signal and infer evolutionary rates from tip-calibrated phylogenies. Regardless of heterogeneity in rate estimates between sample series and methods, we find within-host rates to be in good agreement with rates derived from host-to-host transmission chains. Our findings suggest that when certain limitations of the methodology are disregarded, such as the underlying assumption of phylogenetic independence or the method's sensitivity to phylo-temporal grouping, evolutionary rates can be substantially overestimated. We demonstrate that estimating within-host rates is a challenging question necessitating careful interpretation of findings. While our results do not support faster evolution across the complete viral genome during chronic SARS-CoV-2 infection, prolonged viral shedding together with relapsing viral load dynamics may nevertheless promote the emergence of new viral variants in immunocompromised patients. ### Competing Interest Statement Sanni Oversti, Emily Gaul and Denise Kuhnert have no conflicts of interest to disclose. Bjorn-Erik Ole Jensen received consulting fees and speaker's honoraria from GSK, Gilead Sciences, MSD, Pfizer, AstraZeneca and Janssen-Cilag, as well as support for attending meetings and travel from Gilead Sciences, all out of the present work.