On TTI as a control measure:

Early 2020, we said contact tracing would not control community spread against #COVID19 once cases got high

Yet when cases got high, it was blasphemy to suggest lab PCR+contact tracing not useful to control spread.

Data is now catching up.

1/
The tweet thread above by Denis Nash @epi_dude is terrific and contains lots of wonderful data!

For me, It highlights the need for us to re-evaluate what it is we are doing. When our actions weren't working to slow spread, should we have kept forcing the same actions?

2/x
I worry that we get into group-think mentality and peer pressure is immense to "stick with the consensus"...

but when consensus is to stick to a failing test-trace-isolate as control, against our own warnings to our future selves... maybe we should've bucked the trend?

3/x
Virus kinetics are FAST for this virus

Peak virus load (and likely peak transmission) is 24-72 hours after first becoming at all PCR detectable

This swift transmission window, coupled w slow lab based PCR means contact tracing to control community spread was bound to fail

4/x
Forward contact tracing is good for some things, like identifying others around you who may have been infected but it is very unlikely to stop community spread.

I wrote about this in a thread based on a nice paper back in November.



5/x
When cases get very low, then contact tracing can start to work again, particularly backwards contact tracing, to help contain an outbreak.

But I wish we had shifted course long ago, placed less emphasis on lab PCR+contact tracing and more on widesclae rapid tests...

6/x
Widescale rapid testing can remove need for contact tracing from the equation.

If 50% of a community is already testing frequently (2x/week), then enough people will find out if they were infected and isolate far before a contact tracer would have gotten to them.

7/x
The swift window for transmission means that frequent use of rapid tests that give immediate results is very likely to be a major advance over infrequent laboratory based PCR. The latter simply didn't work. It's great for clinical medicine -but it's not a public health test

8/

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More from @michaelmina_lab

13 Feb
NEW RESEARCH

Knowing if #COVID19 cases are going up v down is needed for decision making but changes in testing make it difficult to know

We found Instead of case counts, the distribution of Ct values gives a NEW way to estimate epidemic trajectory!

1/

medrxiv.org/content/10.110…
Essentially, we created a barometer that gives the growth rate (or decay rate) of an epidemic based entirely on whether the distribution of viral loads in ppl at a single time in a population is averaging high (epidemic growing) or low (epidemic declining).

2/x
This property of epidemics (when they are going up, detected virus loads are higher on average) has caused massive confusion.

The virus itself isn’t changing nor are the actual virus loads inside of individual people...

3/x
Read 9 tweets
10 Feb
Terrific write up!

Perhaps the most thorough reporting I’ve seen on the controversies surrounding rapid tests

An extremely important point @GiorgiaWithAnI covered is one at heart of the confusion but previously not covered well..

See short thread

1/x

nature.com/articles/d4158…
I’ve spoken on sensitivity and why rapid Ag tests shouldn’t be compared to PCR

Nevertheless, we’re stuck comparing to PCR. So, to deal w this, “we” have taken to comparing rapid antigen tests to PCR results below specific Ct values that may represent contagious virus loads

2/x
In many studies, Ct of <30 or <25 are considered to be likely contagious or “high virus”, respectively

HOWEVER this is bad. We must stop assuming this

Not all labs are the same

A Ct 25 in many labs may = a Ct of 18 elsewhere

This happened in Liverpool w Innova evaluation

3/x
Read 7 tweets
8 Feb
The new variant B.1.351 is evading immunity, infecting ppl already vaccinated w AZ vaccine

I’m concerned for the others too since all have very similar design against original Spike

This should be a wake up call

#Rapidtests needed for contingency plans

nytimes.com/2021/02/07/wor…
Good thing is the mRNA vaccines provided exceptional efficacy. But that was also when plasmablasts (temporary antibody producing cells) were fully abundant. We don’t know the efficacy after a few months after they all die off. Hopefully will remain very high and protect. But..???
We also do not know (or at least so far I haven’t heard) whether people are getting severely ill or not. If the AZ vaccine prevents severe disease w the new variant, then that can be good enough. I wish this part was reported so far.
Read 5 tweets
4 Feb
Short thread:

Cases are starting to plummet quickly.

This isn’t from vaccines (yet).

Possible we may be starting see a combination of seasonality on our side and likely seeing herd effects kick in.

1/x
On seasonality:

We knew in the summer that this virus was going to roar back in the fall. It did!

While coronaviruses collectively have a broad window each year, We can see that each individual coronavirus in the graph 👆has only a few months when it peaks. And then drops

2/x
This virus started really hitting us hard a second time in November. Oct-Jan may well be this viruses peak transmission window. We could be entering a reprieve from its grasp, at least for a while. If so, could help us get vaccines out and control spread quickly.

3/x
Read 10 tweets
1 Feb
NOTE:

If you see papers/media that show very low sensitivity for rapid Ag tests (i.e. 30%-60% sensitivity) the report is most likely making a common mistake:

Comparing a test meant to detect viable virus to a test that can detect minuscule amounts of RNA is a mistake.

1/x
PCR RNA stays around long after live virus is cleared

So if you see a paper that shows very low sensitivity, ask:

"Are they comparing rapid antigen tests to "anytime" PCR RNA positivity? (Especially studies asking about sensitivity among asymptomatics)

2/x
To interpret this, you should know that only 25%-40% of the time someone is PCR positive are they infectious w live virus.

So... even a test that is 100% sensitive for live virus should only show a 25%-40% sensitivity against PCR among asymptomatic people.

3/x
Read 9 tweets
28 Jan
Important: on the resurgence of SARS-CoV-2 in a place where herd immunity was already attained.

The authors lay out 4 reasons:

1) didn’t actually attain herd immunity
2) waning immunity
3) new strains evading immunity
4) much more transmissible strains

thelancet.com/journals/lance…
Waning immunity is likely as a component. The immune system memory is just like real memory. I needs to be exercised w repetition - like studying for a test. A single event will not likely offer life long immunity.

2/x
My real concern is mutation that will evade, even If partial our immune responses to earlier versions of the virus or to vaccines being made (which are directed specifically towards mimicking earlier versions)

We have to act now on slowing spread in this case w/out immunity

3/x
Read 4 tweets

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