Monitoring wastewater for viral load estimates outbreak size

In just a few weeks, in Pretoria S. Africa (north of Johannesburg) viral load detected in wastewater has reached similar levels as the peak of Delta

This at least indicates that transmission may be remarkably swift
More information on this metric can be found here.

IMO this offers a fairly unbiased view into viral load at a population level which, barring major changes in the viral loads within individuals, can be extrapolated to an extent to cases or prevalence across a population.
Here is the website:

nicd.ac.za/diseases-a-z-i…
From above, Many are asking a very reasonable question:

If detected cases are low but wastewater viral loads high, does this mean most cases are so mild that are going undetected?

This is one hypothesis. The other is wastewater is a leading indicator. Time will tell.
I expect wastewater is leading indicator & clinical cases/hospitalizations will rise. Do I know this for sure? Nope. But there isn’t much in this virus sequence suggesting it should be very mild

On other hand, Delta just blew through S Africa which should offer protection today

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More from @michaelmina_lab

30 Nov
Many countries are asking for proof of vax, or testing to travel

I don’t understand this. Vax work Well to stop disease…

But it’s time to clarify they do not stop transmission. They slow it down

But it simply is not appropriate to assume that vax = not infectious

1/
If we don’t appreciate this soon immediately, then we will see irresponsible policy that allows the virus to keep on spreading.

This is almost certainly even more true for Omicron which, if anything, will spread more efficiently, not less, than other variants among vax’d

2/
We can be fully transparent about what vaccines do very well (protect you!) and what they are not doing very well (stopping transmission) while still advocating for everyone to be vaccinated

Most ppl see this and any lack of transparency harms vaccine uptake even more.

3/
Read 11 tweets
30 Nov
🧵

This from ⁦@CDCgov⁩ is exactly why Rapid tests are important!

A PCR 2 days before an event, flight or (fill in blank) does NOT reflect you today

2 days ago can be neg but you can be a superspreader now

A rapid test used just before the event is always best.

1/ Image
Its remarkable & contradictory that while CDC makes this figure 👆showing that neg tests 3 days before do not mean you’re negative on thanksgiving… while still recommending testing 2-3 days before travel.

The safest approach is to recommend a rapid test hours before travel

2/
In the midst of Omicron, instead of border lockdowns, we can use rapid tests just before a flight. Could even consider a PCR 24-48 hrs before amd a rapid test just a couple hours prior to flight.

3/
Read 4 tweets
27 Nov
🧵 Why some vaccines stop transmission & others don’t:

Vaccines that stop transmission are often against viruses that replicate internally first and only then transmit (like measles). So if the vaccine stops internal replication, it stops transmission.

For COVID vaccines…

1/
For vax against upper respiratory viruses like SARS2, these viruses often don’t require “internal” replication. They just land in the nose, replicate locally & transmit on. So the vax can block “internal” replication and thus stop disease separate from stopping transmission

2/
The immune response in the upper respiratory tract is somewhat distinct from response in lungs, blood, lymph, etc.

Most vaccines create a multitude of layers of protection that can block a pathogen in lungs, blood, lymph, without offering the same in the nose/mouth/throat

3/
Read 5 tweets
27 Nov
On Omicron spread:

Vaccines keep ppl out of hospital - their most important attribute

However, vax’d can be infected & transmit. Yes, vax slow spread but by no means does vax mean you can’t be infected & spread

This is critical to acknowledge as we try to limit Omicron spread
If public health officials fail to appreciate & acknowledge clearly that vaccinated can in fact acquire and spread the virus and that this is not rare, I fear ppl will continue to believe they can’t spread if they are vax’d and do less to limit spread of Omicron where it exists.
I am 100% for vaccination. I just want public health to be transparent about what vaccines do well and don’t do well so ppl are fully informed.

For too long messaging said transmission among vax was rare. This then caused confusion and loss in confidence in the vaccines.
Read 4 tweets
26 Nov
A thread well worth reading on the new variant:

Highlights:

Omicron does not originate from Delta but ancestor from mid 2020

Maybe accumulated mutations for >1 yr before detection (perhaps) or accelerated development in immune compromised individual that couldn’t clear it

1/
The constellation of mutations suggest it is likely more immune evasive…

(but how much more is difficult to say - particularly with Vax plus the large number of exposures to Delta over the past 6+ months, our immune systems may be getting sufficiently trained)

2/
Many of the mutations that are accumulated have been seen among variants that have a more difficult time being neutralized by our immune response. And among variants that are more infectious.

More data is needed to confirm the latter.

3/
Read 5 tweets
24 Nov
🧵 When the goal is limiting transmission, timing of tests is everything

If you wait days for positive results before isolating, the time spent waiting must be factored in to the “effectiveness sensitivity” of a test.

Time is always ignored as a test metric. This is wrong

1/
If people are infectious for 6 days and you have to wait 2 days for results, then for every 3 positive people detected, you miss the equivalent of an entire infection Bc the sensitivity while waiting is 0%.

This means the “effective sensitivity” cannot break 67%. But worse…

2/
What’s particularly bad but also ignored is the **0% sensitivity** while awaiting a lab PCR result is for everyone - even people who are at absolute peak virus titers and immediate isolation is most important. For these people, rapid tests detect >95% - with immediate action

3/
Read 6 tweets

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