Intrahost viral evolution during chronic sapovirus infections pietsch2019intrahost
Hospital-based study (January 2010 to September 2018) analyzing stool samples from in-patients for sapovirus RNA by real-time RT-PCR, with sequencing/phylogenetic genotyping in chronic diarrhea cases to investigate intrahost evolution during chronic sapovirus infection in immunocompromised individuals. CSV-provided participant-level longitudinal stool RT-PCR measurements are reported as cycle threshold values over time (days) relative to symptom onset.
Analytes
stool_sapovirus_ct
Sapovirus RNA detection in stool by real-time RT-PCR; values are reported as PCR cycle threshold (Ct). Genotyping (GI.2, GII.1, GII.3) was assessed by phylogenetic analysis of the capsid gene (VP1) in chronic cases (used here as participant genotype attribute, not assay target).
Fitted by censored maximum likelihood. The red line is the median individual; the shaded region is the full range of a simulated cohort drawn from the fitted population, so it shows what simulating from this dataset would produce rather than a confidence interval, with dashed lines at the central 95%. Open triangles are non-detects, drawn at the censoring limit and entering the fit as "below this value" rather than being dropped. See the modelling methods for what these estimates do and do not support.