Estimation of the national disease burden associated with
respiratory viruses
We reported mean annual estimates over the study period for any SRI and
ILI as well as those associated with the respiratory viruses
investigated in this study. Estimates were obtained overall and within
the following age categories: <1, 1-4, 5-24, 25-44, 45-64,
≥65, <5 and ≥5 years of age. Rates were reported per 100,000
population. The details of the estimation approach are provided in
Supplementary Material and summarized below.
Medically-attended illness
To estimate the national number of respiratory viruses-associated SRI
hospitalizations we used a four-step approach. In Step 1 we estimated
the SRI hospitalizations rates at the two hospitals mentioned above
(data source 1) during 2013-2015 as previously described
[11Tempia S, Walaza S,
Moyes J, et al.
Quantifying How
Different Clinical Presentations, Levels of Severity, and Healthcare
Attendance Shape the Burden of Influenza-associated Illness: A
Modeling Study From South Africa. Clin Infect Dis.2019 ;69(6):1036-1048. doi: 10.1093/cid/ciy1017.] and we
used the SRI hospitalization rates at the two sites as proxy for the
corresponding provinces (considered to be the base provinces in our
estimation approach). In Step 2 we estimated the SRI hospitalizations
rates for the other 7 provinces from the base provinces using a
previously described methodology that leverages provincial differences
in the prevalence of known risk factors for pneumonia and healthcare
seeking behavior (data source 3). In Step 3 we estimated the respiratory
viruses-associated SRI hospitalizations rates using available
virological surveillance data (data source 1) (i.e. detection rate of
individual viruses adjusted for the estimated AF for each virus). In
Step 4 we obtained the number of respiratory viruses-associated SRI
hospitalizations using the estimated respiratory viruses-associated
rates and the population at risk in each province (data source 4).
To estimate the national number of respiratory viruses-associated ILI
outpatient consultations we used an approach similar to those used for
SRI cases, but we did not adjust for the provincial level risk factors
for pneumonia [18].
Non-medically attended illness
To estimate the national number and rates of respiratory
viruses-associated non-medically attended ILI and SRI we used the
four-step approach described above in conjunction with HUS data (data
source 2) [18].