1/11 It's a great day! Pfizer's new SARS-CoV-2 antiviral cuts deaths by about 90%

But it's also a good time for a thread about the evolution of antiviral drug resistance.

apnews.com/article/corona…
2/ In 1987, FDA approved the first HIV antiviral, AZT. Hope quickly turned to despair though, because in patient after patient the virus quickly evolved to become resistant to AZT.

It wasn't until 1996 that the key breakthrough emerged.
3/ At a conference in Vancouver BC, researchers revealed that if patients were given "triple therapy", cocktails of drugs that attacked HIV in different ways, resistance could be averted.
4/ In addition to something like AZT, which short-circuits the viral life cycle by blocking reverse transcription of the virus's RNA genome into DNA, you might add a protease inhibitor, which prevents the virus from cutting large proteins into necessary, smaller pieces.
5/ Now, if a mutation arises in a virus within a patient, conferring resistance to AZT, the virus would still rapidly be killed by the protease inhibitor. And vice versa.

To survive, a virus essentially needs to experience separate mutations to escape both drugs simultaneously.
6/ Even for fast-evolving viruses, that is a tall order. It happens...pretty much never.

This is one of most beautiful ideas in human history, right up there with giving sugar/salt/water to kids dying from diarrhea.

Or combining oil and egg yolks to make mayonnaise.
7/ Now, Pfizer's new drug is a protease inhibitor. Could it be combined with Merck's new drug, which ramps up the mutation rate so high that the virus struggles to make viable offspring?
8/ Maybe But I would recommend some lab experiments subjecting authentic SARS-CoV-2 to both drugs to test whether Merck's actually speeds up the evolution of resistance to Pfizer's.
9/ While we wait to fill out our arsenal of anti-SARS-CoV-2 drug, however, here's an idea.

Some anti-HIV drugs used in drug cocktails are called attachment inhibitors. They bind to HIV's version of the Spike protein, preventing attachment to the the cell's receptor.
10/ This might sound familiar, because it is the same mechanism of action our own antibodies use against SARS-CoV-2.

With HIV, when you give the drugs together, attachment inhibitors put the brakes on viral reproduction and protease inhibitors then mop up the what's left.
11/ So, if you're looking for a reason to get vaccinated, do it so that you will effectively have a SARS-CoV-2 drug cocktail if you ever need the Pfizer pill.

(And vaccine rollout worldwide may be the best way to preserve to effectiveness of wonderful drugs like this.)

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More from @MichaelWorobey

1 Oct
1/ Medium thread on #SARSCoV2's furin cleavage site and a strikingly similar region in some of the new BANAL genomes from Lao, and in RmYN02 from China.

Seems worth trying to clear up the confusion of @ydeigin on this issue (even it means broadcasting my pic, below).
2/ The furin cleavage site of SC2 is the RRAR in the NSPRRAR stretch of amino acids in the alignment I'm holding up there. It is what makes the virus 'pop' in humans.

The BANAL viruses have NSPAAR. A couple other ones, including RmYN02, have NSPAAR or NSPVAR.
3/ So, having barely scratched the surface of the genetic diversity of these viruses in the wild, we've found several that are literally a *single* amino acid away from having a furin cleavage site.

For example: (NSP) ->inserted R<- AAR.
Read 11 tweets
15 Sep
1: A thread connecting the dots between:

(1) @PeterDaszak et al's fascinating recent preprint on the *many* SARS-related CoV infections in humans per year in Southeast Asia, and

(2) The furin cleavage site of SARS-CoV-2, and

(3) Why Wuhan?

medrxiv.org/content/10.110…
2: The study uses a clever combination of data streams to estimate that 400,000 people per year are being infected by SARS-related coronaviruses.
3: The authors note that not all of those infections are likely to be transmissible human to human

I strongly agree with this. We would see multiple new pandemic origins every year if even 0.1% of these were viable human to human pathogens.
Read 15 tweets
4 Sep
1: I want to follow up the thread below with some additional clarification of why we hypothesize that there may be no real #SARSCoV2 genomes transitional between lineages A and B.

2: @daoyu15 has written a thread asserting that we "toss any genomes that don't fit your conclusions away". I'm afraid this is incorrect on multiple counts.

3: What we show is that many of the putatively transitional genomes bear obvious evidence of being artefacts - probably due to bioinformatic pipelines, rather than sequencing errors per se. (Issues like calling a site with poor coverage to be the base of a reference genome.)
Read 13 tweets
4 Sep
1: We have just posted a study suggesting there may be no real #SARSCoV2 genomes that are transitional between lineages A and B. Arcane, right?

But stick with me - this stuff is *absolutely* crucial to figuring out how the pandemic got started.

virological.org/t/evidence-aga…
2: Honoured to be working on this project with an *amazing* team: @jepekar, @EdythParker, Jennifer Havens, @suchard_group, Kristian Andersen, @niemasd, @arambaut, and Joel Wertheim (leading the charge).

So, what's a 'transitional' genome?
3: To explain, let me introduce you to 'lineage A' and 'lineage B', aka 'clade II' and 'clade I', respectively, in this paper by Zhang et al. These lineages co-circulated in China during the early days of the pandemic, and they differ at two key sites.

nature.com/articles/s4158…
Read 33 tweets
28 Aug
1/4: Good piece from @NPR on the declassified summary of the 90-day intelligence community (IC) review on the origin of #SARSCoV2.

npr.org/2021/08/27/103…
2/4: A little soundbite from me:

[Worobey] would like to see the scientific and intelligence communities collaborate on the problem. "I would hope and assume that this 90-day sprint is going to turn into a nice long jog where there could be some back-and-forth."
3/4 Crucial point US IC elements agree on:

"China’s officials did not have foreknowledge of the virus before the initial outbreak of COVID-19 emerged".

So could we *please* collectively move on from claim that WIV database removal in Sept 2019 was part of a cover-up/conspiracy?
Read 4 tweets
8 Aug
SARS-CoV-2/COVID-19 in Italy in September 2019: the most important finding yet on the origin of the pandemic*.

(*or an error with big consequences.)

A thread. 1/24

papers.ssrn.com/sol3/papers.cf…
The study, led by Dr. Elisabetta Tanzi, also includes heavy-hitters of molecular evolution @sergeilkp and Sudhir Kumar. I greatly admire both but respectfully disagree with their conclusions here and feel it is important to explain why. 2/
Dr. Tanzi led an earlier study claiming to find evidence of SARS-CoV-2 in a boy in Northern Italy who presented with measles symptoms in Nov 2019. 3/

wwwnc.cdc.gov/eid/article/27…
Read 26 tweets

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