Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance hu2013association
Study of 14 patients with novel influenza A H7N9 admitted to Shanghai Public Health Clinical Centre in April 2013. Viral RNA was quantified sequentially in throat (oropharyngeal) swabs, stool, serum, and urine; viral sequencing of neuraminidase (NA) was performed to assess emergence of resistance. Paper links reduction in viral load after antivirals with improved outcome and reports persistent high viral load and emergence of NA Arg292Lys resistance in some patients. The provided CSV contains 69 measurements from patients with IDs 1, 2, and 3 across the four specimen types.
Analytes
oropharyngeal_swab
Viral RNA quantified by real-time PCR from throat (oropharyngeal) swabs; reported as gene copies per swab.
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.
serum
Viral RNA quantified by real-time PCR from serum; reported as gene copies per mL.
Measurements only — no shedding model is fitted to this analyte, usually because it is sampled once per participant, leaving no trajectory to fit, or because nothing was ever detected. Open triangles are non-detects, drawn at the assay's censoring limit. See the modelling methods for what these estimates do and do not support.
urine
Viral RNA quantified by real-time PCR from urine; reported as gene copies per mL.
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.
stool
Viral RNA quantified by real-time PCR from stool specimens; reported as gene copies per wet gram.
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.