Our manuscript on #sarscov2 variant mutations in N is now out in @PLOSPathogens

bit.ly/3n8nO5W

If you are at #KSRNAVirus22 you can talk to 1st author Bryan Johnson about it (probably wearing boots & maybe shorts).

A thread on the paper:
Bryan noticed several mutations in N at pos 203-204, notably a RG->KR found in alpha and omicron & R->M in delta.

The KR mutant in WA1 augmented replication in respiratory cells and disease in vivo.

R203M mutant had similar in vitro phenotype.
We found that the KR mutation increases N phosphorylation and augments viral RNA expression.

This corresponds with larger lesion and antigen staining despite similar titers in vivo.
We also found gsk3 kinase inhibitors were less effective against the KR mutant.

Finally the disruption of the original RG motif appears critical as an alanine mutant (AA) had similar results.
Overall, the results suggest positive selection occurs in the 203-205 region of N and augment #SARSCoV2 infection and pathogenesis.

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More from @TheMenacheryLab

Dec 17, 2021
The furin cleavage site (FCS) has been linked to a nefarious origin for #SARSCoV2

Yet, our new manuscript shows the FCS alone is not sufficient to drive infection & pathogenesis.

Upstream QTQTN motif plays a critical role in SARS-CoV-2 virulence

a🧵

bit.ly/3q9cebx
An issue with #SARSCoV2 has been deletion of the FCS in stock titers. However, more common is deletion of the QTQTN motif upstream of the FCS.

Every variant we have generated has had this deletion varying from 10-100%.

We generated a dQTQTN mutant in WA1 to explore its role
dQTQTN has an advantage in Vero cells (similar to the FCS KO virus).

However, it is attenuated in respiratory cells & in hamster (similar to FCS KO)

dQTQTN disrupts spike processing & entry via TMPRSS2 despite an intact FCS

Results argue that loop length/structure important
Read 7 tweets
Aug 19, 2021
After an hour of looking, have not found convincing data that booster are needed for the majority.

My worry, is that even with a booster, breakthrough will still happen, especially with #DeltaVariant .

Some musings on the need for #COVID19 vaccine boosters
1st, the data for for immune compromised patients is convincing. A third dose drives up the serum neutralizing antibody levels with most having very low to non detectable levels of protection after 2 doses.

Data not perfect, but is consistent and clear that a third dose helps.
Similarly, older patients (>50) may also need a booster. But the data is more murky vs immunocompromised data.

Aged groups appear to have a lower overall neutralizing AB titer following vaccination. This is our best correlate for protection & consistent across vaccines.
Read 12 tweets
Jul 26, 2021
Been getting lots of questions about the #COVID19 delta variant.

While the epi data makes it clear that this variant is more transmissible, the biology is a bit different than the other VOCs.

A thread of musings about delta and why there is concern (1/9)
Like the other alpha, beta, & gamma #COVID19 variants, most focus has been on mutations in the spike protein for delta.

While there are many additional backbone mutations, none have been clearly indicated to drive emergence of delta.

Still not enough known though. (2/9)
The impactful mutations in the other VOCs are generally thought to be in the spike NTD & RBD.

While delta has a few of interest (L452R), its the furin cleavage site mutation(P681R) draws the most attention.

A similar change in alpha (P681H) may also be important (3/9)
Read 9 tweets
Jan 25, 2021
Our study examining a furin-cleavage site deletion mutant in #COVID19 is now out @Nature

With a short thread (cause who has time to read beyond twitter) (1/6

go.nature.com/2MnGlfq
First, thanks to our collaborations with @utmbhealth @WUSTLmed @ihii_utmb @bmb_utmb @SutharLab @UTMB_WRCEVA @DanieleSwetnam @AndrewRouth @KariDebbink @scottweaverutmb @VirusWhisperer @aguilar_pv and others.

Lots of effort from lots of people
2/6
- The furin cleavage site (FCS) is needed for replication in respiratory cells (Calu3) & for pathogenesis in mice & hamsters in #COVID19

- Loss of FCS shifts neutralization profiles to convalescent sera making the mutant virus less susceptible

3/6
Read 6 tweets
May 23, 2020
Let's chat about the herd immunity strategy.

The proponents are not wrong. Herd immunity is the only way #COVID19 ends. Until then, this nightmare will continue.

Question comes down to exposure, multiplication, and what's acceptable.
There are 2 ways to herd immunity:

1) People get infected and survive
2) People get a working vaccine that induces immunity and are protected

That's pretty much it.

The herd immunity strategy says we're all getting it anyway & we should cause the vaccine takes too long.
Saying we need 60-70% exposure for "herd immunity", the unknown is how many have already been exposed.

So how many people have been exposed to COVID19?

Unclear. 5%, 20%, more? The studies aren't clear & depend on region.

This number is key though. It's the multiplier.
Read 7 tweets
Apr 12, 2020
Gotten questions about reactivation/reinfection with #SARSCoV2 & wanted to see some data

But since data isn't a requirement these days for #COVID19 speculation, I'll offer:

I doubt this is some kind of herpes virus like latency/reactivation

RNA positive PCR is not live virus
So what is happening? Here are possibilities

1) These people hadn't cleared the virus in the 1st place

2) The viral RNA remains in debris/damage after virus is cleared & pushes + test as it is repaired

3) #SARSCov2 evolved a complex latency/reactivation mechanism
For 1) hadn't cleared the virus

Test sensitivity is dependent on quality of the sample & threshold of RNA observed.

If sample quality wasn't great the results could lead to false negative.

If low amount vRNA, it may also impact. Would want to know CT values to interpret
Read 7 tweets

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