Thread by @JonPloug

On Zoos/animal parks and the origin of Omicron.

According to @K_G_Andersen 1 of the 2 most likely hypotheses on the origin of Omicron is "reverse zoonosis, followed by a new zoonosis (human>animal>human)"

1/13 🧵

https://twitter.com/k_g_andersen/status/1465824078544048128?s=21

https://twitter.com/k_g_andersen/status/1465824077315121153

Where to look then for a place of origin?

It seems that wildlife in general don't get infected easily. When Danish mink farms experienced large outbreaks of covid
- “wildlife sampled in the vicinity of the infected farms did not test positive"
2/13

curis.ku.dk/portal/files/2…

So mink and other fur farms would be an obvious place to look. But, apparently there are so few in South Africa that WHO - who made a repport on the issue - found it "very unlikely" due to the rarity of fur farms both in SA and Africa in general.

3/13
who.int/publications-d…

A place where animals routinely are handled by human are Zoos and animal parks.

In the start of the pandemic it seemed as chance findings when some animal were tested positive, but it have evolved to be an issue we need to take serious.
4/13

https://twitter.com/JeremyFarrar/status/1467552958321680385

We have seen infected lions and tigers at the Bronx Zoo in New York, Gorillas at the Atlanta Zoo, tigers at a zoo in Knoxville, Tenn., and hippos at a zoo in Antwerp, Belgium.
5/13

But for our purpose the most interesting case was

1 "puma tested positive for SARS-COV-2 after contact with infected handler" in the zoo of Johannesburg, Gauteng, 17/07/2020.

6/13
flutrackers.com/forum/forum/af…

The time and the place is important. It was "mid-2020" the time which Andersen and others have speculated was the time when the variant, that was to become Omicron, broke of the tree of SARS-CoV-2.
And the place is Gauteng, the epicenter of Omicron.
7/13

But even if this case is a coincidence (the pumas are solitarary and don't interact with other animals) it seems rational to suspect other for us unknown infections could have happened.
8/13

There are around 10 Zoos/animal parks in Gauteng (which I could find). That's a lot of potential places for a zoonosis to happen. Perhaps SARS-CoV-2 found a place to evovle in one of those zoos?
9/13

Some of the animals, as crocodiles, are kept in winter quarters, and the zoos have been closed because of Covid, so even if there were a sustained outbreak in a population of animals, perhaps it would have gone unnoticed. Especially if the animals were asymptomatic.
10/13

There is also the issue of privately owned zoos. There is one for instance, The Endofaun Zoo in Gauteng, that had serious issues with sanitation and the the living conditions of the animals. Would they have noticed an outbreak of covid?
11/13
enca.com/south-africa/a…

So to recapitulate. The place, the timing and the circumstances seems to suggest that Omicron could have evolved in some group of animals, perhaps in a winter quarter, in one of Gautengs many animal parks and zoos.
12/13

And, it seems much easier to investigate this hypothesis compared to the one that involves immunocompromised patients.

13/13
#originofomicron #Corona #Covid_19 #covidvariant

@nicd_sa @HealthZA

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