Omicron is more transmissible but less deadly

Wazzup Pilipinas!?

Omicron cases are on the rise, but it’s clear that vaccines and boosters are making a difference. Vaccines and boosters help prevent severe illness and death — if you haven’t already, go get your vaccine and booster. 

The country will remain under Alert Level 2 from Jan. 1 to 15 despite the uptick in COVID-19 infections and growing concerns over the Omicron variant, Malacañang announces.

Don't be scared, omicron is more transmissible but is less deadly than all the strains that came before, the kids are safer than anyone else and vaxed or not so long as people are staying healthy I've heard it's about as bad as a head cold. Possible endemic in the future I hope.

Omicron is less deadly than previous coronavirus strains, and results in a quarter of the deaths recorded in earlier waves, data from South Africa suggests. 

As per the current data, Omicron is a mild infection...Oxygen requirement may not be that much...I would request everyone to refrain from hoarding oxygen cylinders, medicines. 

It sure is looking that this variant has less virulence, less chance of inducing Covid pneumonia.

Added to our immunity wall and T cell defense, this is all good. 

There’s no guarantee that Omicron is the worst this virus will throw at us. We must get past partisanship and pandemic fatigue and use the tools we have to fight Covid: vaccines, masks, ventilation, testing, effective treatments.

Although Omicron is very capable of evading antibodies and causing reinfections/breakthroughs, it barely evades T-cells at all, meaning vaxxed or recovered people are likely to retain very good protection against severe disease.

We have new results on T cell responses to Omicron, and its good news! 

Most of your T cell responses from vaccination or previous infection still recognise Omicron. 

Why did we do this study? 

Omicron has more than 30 mutations in its Spike protein, and many studies now show that this knocks out a lot of the neutralising antibody binding sites. 

We wanted to check if other parts of the immune system - T cells - still recognise Omicron Spike. 

We describe T cell responses to #Omicron compared to original SARS-CoV-2 in ppl vaxxed with JnJ (1x and 2x) and Pfizer (2x). We also studied Omicron-infected patients and compared their T cells to patients hospitalised in previous waves (n=138 participants in total). 

Unlike antibodies, which bind in hotspots, T cells can target the whole of Spike - shown as a mountain range, with Omicron mutations in red.

So we expect that T cells would still be able to target Omicron- even though it has lots of changes, there is lots of Spike NOT mutated.

 Why is this important?‼️👇🏾

While antibodies block infection, T cells come in and kill infected cells, preventing the virus from growing & spreading more & causing worse disease

They can't prevent you from getting infected, but they can minimise the damage that comes afterwards.. 

How did we do this study? 

We measured T cell responses using peptides -small chopped up bits of proteins that T cell recognise. 

We compared a pool of peptides based on the original (“Ancestral”) SARS-CoV-2 and Omicron spike protein. 

Thank you Sette Lab for sending us the peptides.

We isolate white blood cells from patient samples, mix the cells with the peptides, and then use a technique called intracellular cytokine staining and flow cytometry, to check for a T cell response. 

We measured both CD4 ‘helper’ cells and CD8 ‘killer’ cells. 

Results - First CD4 T cells: 

Compared to ancestral virus, there was a small decrease when tested against Omicron spike. 

This was a consistent decrease across all study groups.

However, most of the CD4 T cell response was still there and cross-recognised Omicron. 

Next, CD8 T cells:

Here too, compared to ancestral virus, there was a small decrease when tested against Omicron spike for some of the groups, no major change for most people. 

If we plot fold-change of Omicron responses compared to ancestral, we see that 70-80% of T cell responses are preserved.

This means that most people who were vaccinated with 1x / 2xJnJ, 2xPfizer & those who had COVID 1-6 mo ago, still have T cells that can recognise Omicron. 

Important to point out - there were a minority of CD8 T cell “knockouts”.

These represent people who may have had a narrower response targeting only a few regions in Spike, that happened to coincide with mutations in Omicron and a specific HLA bkg – we’ll be following up on these.

When we compared the cross-reactivity of T cells to Omicron with Beta and Delta variants, we found that they were very similar, even though Omicron has 3-4x more spike mutations than Beta and Delta.

This emphasises just how robust the T cell response is. 

This is consistent with what we recently published on cross-reactivity of the T cell response to the Beta variant:

https://www.science.org/doi/epdf/10.1126/scitranslmed.abj6824

To get a full picture of immunity,  they measured neutralising antibody responses in the same participants. 

You can see that while neutralisation is substantially decreased in most people, overall their T cell responses are only impacted in a small way. 

South Africa’s COVID epidemic is characterised by virologically distinct waves, each dominated by a different form of the virus – first original, then Beta, Delta and now Omicron. 

Next we tested blood samples from each wave & compared them to patients from the 4th wave (Omicron).

We measured T cell responses to Spike, Nucleocapsid and Membrane proteins (viral proteins most targeted by T cells when you become infected).

Omicron-infected patients had T cell responses in the same range as patients hospitalised with ancestral, Beta or Delta virus infection. 

Finally, we also tested some Omicron-infected patients with ancestral and Omicron Spike, and there was hardly any difference between them, showing that most of the parts of Spike that people make T cell responses to are conserved - parts that are not affected by the mutations. 

Finally, we also tested some Omicron-infected patients with ancestral and Omicron Spike, and there was hardly any difference between them, showing that most of the parts of Spike that people make T cell responses to are conserved - parts that are not affected by the mutations. 

The limited effect of Omicron’s mutations on the T cell response suggests that vaccination or prior infection may still provide protection from severe disease.

Well-preserved T cell immunity to Omicron is consistent with early clinical observations from South Africa, UK and Scotland of lower severity - a decoupling of case loads from hospitalisations, and shorter hospital stays, which may be due to this remaining T cell immunity.

Finally: The resilience of the T cell response demonstrated here also bodes well in the event that more highly mutated variants emerge in the future.

We still need to see how long T cell immunity lasts, but after SARS1 it was still detectable after 17yrs..

https://www.nature.com/articles/s41586-020-2550-z

Who did the work? 

Dr Roanne Keeton is the amazing researcher who generated much of the T cell data, along with my lab team, and I co-led this work with the brilliant Dr Catherine Riou.

This work was also made possible by wonderful collaborators, and many others who contributed to this work.

Thank you to all the volunteers and patients who made this work possible, and our funders.

Shout out to Biocair for all their efforts in getting critical reagents to us when they were stuck in Dubai because of NONSENSICAL TRAVEL BANS.

From the Virus Monologues

If you're considering going to some sort of indoor event – a concert, a movie, dinner – and you're wondering how to "make it safe" – and by "safe" you mean avoid omicron?

In simple terms, the answer is "don't go to indoor events"

This incorrect, false notion has persisted that SARS-CoV-2 spreads only by droplets – but the truth is it also spreads via aerosol that can hang around in the air for quite some time.

So going to eat inside that restaurant after the lunch rush? It's probably not all that 'safe'

In order to make the kind of risk assessments I see folks trying to do? You'd need much more information about the venue than is likely available - information about indoor air quality as it relates to SARS-CoV-2, things like "air changes per hour" and "equivalent ACPH"

If the restaurant is opening up gigantic windows in December to completely change out the air? That will lower risk, sure

But if the movie theater was full for the showing before the movie you want to go to? I'd assume that the air has aerosolized SARS-CoV-2 floating around in.

That may be within your risk tolerance, but I want you to be aware of the level of risk you're actually accepting.

The only way to stop this rise is for the national government to raise the alert level in NCR. LGUs are not monitoring the people anymore. What if omicron is circulating already? 

Vaccine mandate for everyone who wants to move around. Only the vaccinated should be allowed to travel except those who have conditions who are allowed to avoid the vaccine.

It is quite saddening that data scientists did their best to provide predictions but the government seems like to wait first for the prediction to really happen before they act.

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