1/ The origin of SARS-CoV-2 has yet another riddle:
How did the pre-pandemic variant manage to confer immunity to entire countries in Asia but bypass most cities in Europe/America?
Answer: At least 3 concatenated waves.
This sends the origin date of SARS-CoV-2 to before 2016.
How did the pre-pandemic variant manage to confer immunity to entire countries in Asia but bypass most cities in Europe/America?
Answer: At least 3 concatenated waves.
This sends the origin date of SARS-CoV-2 to before 2016.
2/ Cities that did have a pre-pandemic variant wave (called here *D614) easily avoided G614 pandemic waves.
See below how Madrid could have suppressed G614 spreading (until the vaccine) with the help of *D614 (simulation A) resulting in much lower deaths than without *D614 (B).
See below how Madrid could have suppressed G614 spreading (until the vaccine) with the help of *D614 (simulation A) resulting in much lower deaths than without *D614 (B).
3/ Since *D614 spread undetected; it must have been less severe than D614 and G614, and most likely less transmissible (i.e. lower Ro and higher generation interval Go).
Casually, the spread of D614 in Wuhan puts an upper bound to the Ro of *D614:
Casually, the spread of D614 in Wuhan puts an upper bound to the Ro of *D614:
4/ With a plausible Ro of 1.26 *D614 builds 38% immunity (higher than HIT=20% due to overshooting).
In a city of 1M and with Go 11 days, 95% of the infections occur between months 13 and 23 (the probability to spread to another city is much lower during the first 12 months.)
In a city of 1M and with Go 11 days, 95% of the infections occur between months 13 and 23 (the probability to spread to another city is much lower during the first 12 months.)
5/ The first infected city (e.g. in China) spread the virus to other cities, but it is impossible that almost all small cities in Japan could have got infected DIRECTLY from that first wave when almost none of the large cities in the US did.
6/ What happened is that the first city spread it to a few cities in Japan (and no cities in the US because they're less connected) and then those few cities spread it to all the small ones within Japan.
For a city C the probability of getting infected P(C) is:
For a city C the probability of getting infected P(C) is:
7/ P(C) = 1 - {(1-P(SC))**SC * (1-P(DNC))**DNC * (1-P(DFC))**DFC}
where
P(SC): probability of transmission between cities of the Same Country
SC: amount of cities infected in the Same Country
and similarly
DNC for a Different Near Country
DFC for a Different Far Country
where
P(SC): probability of transmission between cities of the Same Country
SC: amount of cities infected in the Same Country
and similarly
DNC for a Different Near Country
DFC for a Different Far Country
8/ See below how 3 concatenated waves starting in China with:
P(SC): 23.6%
P(DNC): P(SC)/25
P(DFC): P(SC)/625
manage to infect all cities in China (0% susceptible), almost all in Japan (3% susceptible), and only 12% in the US (88% susceptible).
P(SC): 23.6%
P(DNC): P(SC)/25
P(DFC): P(SC)/625
manage to infect all cities in China (0% susceptible), almost all in Japan (3% susceptible), and only 12% in the US (88% susceptible).
9/ On the other hand, a higher P(SC), required to infect all cities in China after only 2 waves, fails to simultaneously infect most in Japan and almost none in the US.
10/ More than 3 waves also do the trick:
11/ So, assuming a plausible generation interval of 18 months (initial spread to peak) for the first 2 waves, and that the 3rd wave of *D614 must have started before Feb 1 2018 to avoid G614 pandemic waves,
Sends the likely date of origin of SARS-CoV-2 to before Feb 2015.
Sends the likely date of origin of SARS-CoV-2 to before Feb 2015.
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