The progression of SARS CoV 2 in Knysna, South Africa (Updated September 27, 2020)

I wanted to record this data as an archive of the progression of SARS CoV 2 in Knysna, South Africa.

The disease was first recorded in Knysna on Tuesday March 17, 2020 when two individuals who had returned from a vacation in Europe tested positive.

Between Monday April 6, on which day 13 new cases were confirmed and Thursday April 30, there were no new cases. However, this changed and during the months of May, June and July there was an upward trajectory of new infections in the community peaking on Monday July 20, on which day 58 new cases were reported. Thereafter the number of confirmed cases began to decline, depicted by the yellow line in the graph below.

June 129 cases
July 782 cases
August 264 cases
September 135 cases

As of Sunday September 27, 2020 the running totals are as follows:

Running total confirmed cases: 1,532
Running total recoveries: 1,402
Total new cases for the week 20/9 to 26/9: 55 (⬆️ from 23 the previous week)
Active cases: 130 (⬆️ from 104 the previous week)
Total deaths: 49

NOTE: We know of course, that the detection of new cases is solely dependent on the number of tests conducted. We do not have the data of the number of cases conducted in the town on a daily basis and so can’t measure the positivity rate another important marker. We also do not have access to the number of hospitalizations in the two hospital here. However, we do have access to another very important data point which is the number of SARS CoV 2 recorded deaths. The current data is up until Friday September 4th. The town has lost 49 people to the disease to date.

There are some deductions we can make from the number of recorded deaths so far. This working paper entitled Predicted COVID-19 Fatality Rates Based on Age, Sex, Comorbidities, and Health System Capacity estimates that the Infection Fatality Rate (IFR) for Southern Sub-Saharan Africa would be 0.69% and in this data from Discovery Health South Africa they estimate the IFR to be between 0.3 and 0.4%

Using these estimates we can reverse engineer the number of recorded deaths to understand what the true extent of the infection has been. At an estimated 0.69% IFR, 49 deaths would mean there would have had to have been at least 7,200 cases in the town, (and 14,200 infections using the Discovery IFR estimate) of which 1,532 have been confirmed by positive tests. This number of infections would mean that at least 9.2% of the towns 78,000 inhabitants have been infected to date.