2. Dilution effects for SARS-CoV-2
Here we assume a 14 day window period inside of which SARS-CoV-2 can be detected
with sensitivity Se in individual specimens; that viral load increases by 1 log10
viral copies every day for the first 7 days (so if viral load is 50 copies/unit on day 1, it is 500 on
day 2, etc.) and then that viral load decreases by 1 log10 viral copies every day
for the last 7 days.
Further assuming that the virus is only detectable within
the 14-day window (again, with sensitivity Se), a pool of size 10 (tenfold dilution) would result
in non-detectability of virus on days 1 and 14 of that window period - a loss
of two days out of 14, and therefore a dilution of individual assay sensitivity of 14%.
A pool size of 100 (hundredfold dilution) would result in non-detectability on days 1-2 and 13-14,
a loss of four days out of 14, and a dilution of individual assay sensitivity of 29%.
In general, pooling size is related to dilution of individual assay sensitivity by dilution = [log10(pooling size)/7].
In general, then, the user must set the maximum allowable dilution factor (MAD)
a priori and then calculate the maximum acceptable pool size as
MAPS = 10 (7 x MAD). So if
MAD is 0.1, MAPS is 5;
MAD is 0.2, MAPS is 25;
MAD is 0.3, MAPS is 125;
MAD is 0.4, MAPS is 631;
The user must enter MAPS by hand - we include no default and do not autocalculate
MAPS below, because our assumptions (immediately above) for SARS-CoV-2 viral dynamics
are preliminary and may change over the next weeks and months
(updated: 15 April 2020).
WARNING: THIS ALLOWS THE USER TO ENTER INCOMPATIBLE VALUES OF MAD & MAPS.
Finally, note that if the optimal master pool size returned by our code is smaller
than the MAPS, there will be less dilution than the maximum allowable dilution.
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