Write about COVID, Get Harassed.

I must confess that I'm a little bit discombobulated these days.

It's no big deal, it's just that my bike is in the shop because I've once again worn the teeth down to the nub, on the cassette which is that little cluster of gears stuck right up against the back wheel.

My bike guy, S, says I've got to stop stomping down on the pedals in the higher gears, especially when I've got the chain on the big sprocket up front.

I told him I would try, but it was going to be difficult to stop myself from trying to keep up with the elderly hordes that go zooming past me on their eBikes every day.

Anyway, not having my bike means that I'm not getting the daily exercise that helps to tamp down my autonomic nervous system, especially on the sympathetic side of the ledger.

It also means that I've been taking the bus to and from the lab this week.

And, I've got to say, riding crowded buses always reminds me of how, in the great majority of instances, complete strangers manage to get along and are really very civil towards each other.

Of course, in the digital world, this isn't always the case, especially when it comes to all things COVID.

Take, for example, the case of local Lotuslandian broadcaster Jody Vance:

Vancouver broadcaster Jody Vance says she wants to see "something good" come from the years she spent fearing for her family's safety because of one man's relentless online harassment campaign.

Earlier this month, 53-year-old Richard Oliver pleaded guilty to criminal harassment for the violent and sexualized messages he sent to Vance, her colleagues and guests on her show...

{snip}

...The harassment charge concerned messages sent between March 2020 and September 2021, which were largely focused on Oliver's displeasure with Vance's reporting on the COVID-19 pandemic.

"The communications went beyond simply views and became aggressive and threatening in nature. They refer to things such as a 'day of reckoning,'" (Provincial Court Judge Peter) La Prairie wrote...

And then there is the case of Florence Debarre, the French evolutionary biologist who discovered that there were racoon dog sequences in the original Wuhan wet market DNA swabs, a finding which may turn out to support the zoonotic spillover hypothesis of how the SARS-CoV-2 originally infected people.

Now, to be very clear, Dr. Debarre was not offering the kind of opinions that a commercial broadcaster might that could upset some folks. In addition, Dr. Debarre was not out out there draping a zoonotic flag over a laboratory origin tombstone on social media. However, she was clear about the implication of her findings:

...Débarre stresses that other animal DNA was also found in the swabs, and that there is still no conclusive proof that raccoon dogs in the market were carrying the virus, or were the vehicle for its first spillover into humankind. “But now it cannot be denied that they were there,” she says...

And, for that she has been subject to a viscious onslaught online:

...Since the publication of her findings (on a pre-print server), Débarre has been set upon by online mobs and received threats to her safety. “Last night, I was crying over the horrible things I’m reading about myself on social media,” she says...

****

Now.

I obviously cannot possibly know how truly bad things got for Ms. Vance and Dr. Debarre.

And the examples you will see below are undoubtedly orders of magnitude milder than the the kind of crap Ms. Vance and Dr. Debarre had to deal with, if only because they are women.

However, I did have the temerity to write about the various COVID vaccines as they were being developed, starting back in the early 2021 when I wrote about that rare blood clotting disorder that was associated with the AZ virus-based vaccine. Not long after I started to write, carefully, about the risk/reward ratios of the RNA-based vaccines and soon thereafter the codswallop began to land on the doorstop of this blog in the form of nasty comments with some regularity.

At first I just deleted these missives from the comment threads and threw them in the trash. But it wasn't long before the volume was so overwhelming, and the narratives so unhinged, that I was forced to turn on the comment moderation feature for the first time since I started up this little F-troop listed blog way back in internet ancient times (i.e. 2004).

And with the moderation on, I also decided to archive things just in case something untoward happened down the road in the non-digital world. So far nothing like that has occurred, but now seems to be an opportune time to show you all some of this stuff so that you can see specific examples of what even a very small fish in a very, very small pond has to deal with:

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I run a holistic medical private practice, and have a background in Molecular & Cell Biology, you NEVER EVER diagnose people of pathologies using a PCR test. EVER. It’s almost Biology 101, but science was thrown under the bus from the very beginning. I presume “it had to be this way” for us to see how corrupt the ENTIRE establishment really is. The swamp runs deep and wide indeed.

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So-called authorities have disgraced themselves behind a new theology of degenerate “science” that veers back into superstition and necromancy. Proof that they don’t believe their own story shows in their desperate efforts to hide the data, confabulate numbers, ignore true facts, and lash out viciously at anyone who discloses their zealous deceits...

Be a real shame if something highly predictable were to happen to you because you are too compromised to do the right thing.

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Keep yourself firmly in the box, champ, or you might just suffer the loss of your cozy little sinecure doing nothing.

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Large numbers of injectees will see their health decline in coming weeks, and no amount of "variant" disinformation is going to change the obvious pattern.

Anybody hawking syringes under these circumstances should reasonably fear for their own safety.

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A viral out-break with a minuscule death rate is not a pandemic, no matter how many times the w.h.o.Re$ change the definition.

Injuring and killing people who were at no risk is, however, a crime and justice will be meted out.

_____

Just keep boostin'...You'll eventually get what you deserve.

The above is just a small, but representative, sample of the more than 2,000 messages I archived through 2021 and 2022 (leaving aside some of the more personal stuff about my day job work and my cognitive abilities, not to mention the voluminous levels of lunatic fringe 'proof' demonstrating the existence of the 'plandemic').

The point is, do you see how unhinged and relentless these folks can be?

And do you see why, particularly because her harasser included a member of her family in his threat messages to her, Ms. Vance is, in my opinion at least, completely justified in initiating her civil suit now that that the criminal case is over?

.

Fourth Vaccine Dose Update.

Here's the kicker from the province's announcement yesterday.

Last week I mentioned that the big data sets for fourth shots under Omicron were coming. Here's the first one, with the Pfizer mRNA vaccine, from Israel, published yesterday in the New England Journal of Medicine. The following is a description of the cohort from the paper's abstract:

...Using the Israeli Ministry of Health database, we extracted data on 1,252,331 persons who were 60 years of age or older and eligible for the fourth dose during a period in which the B.1.1.529 (omicron) variant of SARS-CoV-2 was predominant (January 10 through March 2, 2022). We estimated the rate of confirmed infection and severe Covid-19 as a function of time starting at 8 days after receipt of a fourth dose (four-dose groups) as compared with that among persons who had received only three doses (three-dose group)...

Eric Topol summarizes the paper's findings here:

So.

Given all that, I would be very surprised if the province doesn't move down to age 60 for everyone as that group approaches six months after their third jab.

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While these fourth shot data are important, especially for the large elderly at-risk portion of our population, I can't emphasize how important it is for anybody who has already had their 2nd shot but nothing more to go out and get their 3rd shot if they want to significantly reduce their risk of serious illness in the event that they get caught up in the coming (already arrived?) 2nd Omicron variant wave.

.

Fourth Dose, Booster Deux Info...

The 4th shot data, above, are from a large cohort Israeli study currently under peer review that shows that a 4th shot/2nd booster of the Pfizer mRNA vaccine significantly decreased mortality in folks 60 years old and over who received their third shot/1st booster four months earlier or more.

But those data were gathered during the big Delta variant wave in Israel.

And now we're getting ready for Omicron-2.

However, now that the US FDA has announced that 4th mRNA shots are available for folks 50 years plus in the States there is a lot of chatter about efficacy.

Unfortunately, there just aren't a lot of large cohort data sets in yet. And one of the other issues to consider is the coming of the Omicron-specific vaccines.

Eric Topol of the Scripps Institute, who has proven his bonafides over and over again during the pandemic, has this to say in his latest longform post on the subject:

"...I would recommend the 2nd booster if you are more than 4-6 months from your 3rd shot, you are age 50+, you tolerated the previous shots well, and you are concerned about the BA.2 wave where you live, or that it’s getting legs as you are trying to decide. Or if you are traveling or have plans that would put you at increased risk.

It can certainly be deferred, but the question is when is the right time, and whether an Omicron-specific vaccine will have any advantage over a 2nd booster directed at the original strain. The data from 2 animal models (macaques and mouse models) suggests there may not be advantage of the Omicron-specific vaccine but that may not correlate with its effect in people. From my discussions with FDA, it is not likely the Omicron-specific vaccine will be available before late May or June. So you can factor that uncertain added benefit and timeline into your decision..."

So, there is clearly some grey here, particularly for non-seniors, which likely explains the reason that the province of British Columbia is being cautious so far:

...B.C. Health Minister, Adrian Dix says the province is well aware many people are hitting the six month mark since their last injection in long-term care homes.

“We are generally amongst the first provinces to move on these things and I expect you’ll see soon that this is an issue under active review. When you get a dose, it is sometimes dependent on the previous doses.” said Dix.

Dix specifically points to the six month mark as a potential fourth dose roll-out date. That would be this April for long-term care residents who received their third dose back in October.

“A key priority for us continues to be ensuring those most vulnerable to COVID-19, who have been given priority at every stage in our B.C vaccination program continue to see their health protected to the maximum possible extent,” Dix said.

“I think you’ll hear something from Dr. Henry and myself very soon.”...


Here's a little more from Dr. Topol:

"...If you had 3 shots and an Omicron breakthrough infection, there’s little need for getting a 2nd booster at this point. You’ve got some hybrid immunity and you can save an extra shot, if or when there’s ultimately supportive evidence for a later time.

If you haven’t had your 1st booster, you’re long overdue to get it. It was lifesaving vs Delta for people age 50+ and vital for maintaining high level of protection vs severe disease from the Omicron family of variants..."

Finishing up, a wee bit off-topic but not really (see image at top of post)...

Honestly, for folks that have already had two jabs, why wouldn't they get their third shot/first booster given the clearly demonstrated efficacy? 

The decreased numbers in that regard in B.C. are startling and could really be a personal and public health issue when the Omicron-2 wave arrives in Lotusland:

...93.8% (4,056,892) of all eligible adults in B.C. have received their first dose, 91.5% (3,956,215) have received their second dose and 59.3% (2,564,549) have received a third dose...



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A Great Opportunity For Unity As The Loosening Begins.

Vaccines and the decreased virulence of the current viral variant have helped make it possible for our PHO to start the great loosening of restrictions.

Of course, there is still much to be done globally and there will likely be bumps and, perhaps, even temporary reversals along the way.

And there are still the very serious matters of the immunocompromised and long COVID to deal with.

However, as was mentioned last week, now is a time of great opportunity for our political leaders to unify us all.

Because we've gotten here due to the shared sacrifice of so many that has absolutely nothing whatsoever to do with conspiracy theories and/or misinformation spigots, diesel-fueled or otherwise.

OK?

______

For the record, I'm happy about what we're not removing for the moment, including proof of vaccination and indoor masking, until we see how things go and to help facilitate continued vaccination...



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Despite The Recent Cacophony, Canada Is Not A Country Full Of 'Covid Jerks'.

SanityAndReason

HaveAlreadyWonVille

A philosopher from Southern California named Eric Schwitzgebel recently wrote a piece in the Atlantic that is provocatively titled 'The Covid Jerk'.

 Here is his lede:

We all know the type. First appearing in the spring of 2020, the COVID jerk strutted unmasked through the supermarket, exhaling clouds of risk on worried shoppers and employees, and daring low-paid workers to try to enforce the new policies. Flaunting their disdain for scientific consensus, they stepped close behind you in line, breathing on your shoulder, complaining about maximum-occupancy requirements...

The rest of the piece is much more thoughtful and nuanced and is very much worth reading in its entirety.

Regardless, given recent events up here in Canada it would be easy to think that the entire country is filled to bursting with such people.

It turns out, as the 'Covid 19 Monitor' project from McMaster University has demonstrated with longterm polling throughout the pandemic, this is most definitely not the case, including the citizenry's feelings about vaccine mandates:

The thing is...

Given how well vaccination is working to decrease the risk of serious illness coupled with the advances in treatment and the decreased virulence of the current viral variant, it would appear that the time is coming where we're going to have to all get along as we start to interact more and more as things start to (hopefully) gradually loosen up in the coming weeks and months.

Thus, it seems to me that the need for collective tolerance, rather than dunking and/or owning the other side, is something that our civic leaders might want to start talking seriously about sooner rather than later.

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Please don't misunderstand me...I'm not advocating that we stop putting bullies and jerks in their place when required...I'm just suggesting that everyone needs to think about what really matters so that they don't become a bully and/or jerk themselves as we start to engage in collective behaviours and events once more.

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Real World Data...Effectiveness Of Vaccine Booster Against Omicron BA.2 Variant In Preventing Symptomatic Disease.

From a report, posted today, from the U.K. Health Security Agency:

BA.1 is the 'original' UK Omicron variant. BA.2 is the 'new' Omicron variant that has arrived in British Columbia. 

Here the 'booster' (Dose 3) is equally effective at protecting against developing symptoms after infection regardless the version of the Omicron variant.



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How Paxlovid Works.

AllTheCellBiology

ThatFitsVille

You are likely hearing, or will hear, a lot of news about Pfizer's anti-viral drug 'paxlovid' (nirmatrelvir or PF-07321332) given that it was approved for use in Canada as reported yesterday by the CBC's John Paul Tasker:

Health Canada has approved Pfizer's COVID-19 therapeutic for use in adults 18 and older, paving the way for the distribution of a potentially lifesaving drug at a time when the country's hospitals are overwhelmed.

Pfizer's Paxlovid is an oral antiviral treatment prescribed by a doctor and administered in pill form. It is designed to help the body fight off the SARS-CoV-2 virus, reduce symptoms from an infection and shorten the period of illness...

Paxlovid does not act by boosting the immune system against the virus, which is a good thing because that means that 'immune evasion' is not an issue. 

Instead, the drug, which Pfizer has gone to great lengths to modify so that it can be taken orally rather than intravenously, blocks the ability of the virus to make more of itself once it gets into the cells, including the cells that line the inside of our airways.

More specficially,  in Step 3 of the viral life cycle (see diagram, above, from Science magazine), paxlovid/PF-07321332 inhibits the ability of the 'main protease' (MPro) of the virus to chop up long strings of proteins that have been read out (or 'translated') from the viral RNA (Step 2) inside our own cells. 

The activity of the 'MPro' is essential for the viral life cycle to continue (Steps 4 and 5) because the chopped up chunks of protein from the original long string are the functional bits of the virus that allow it to make more of itself (i.e. to 'replicate') so that it can be released from your own cells (Step 6) such that it can then infect more of your own cells or be released from your airways as aerosols which can infect other people. 

The take home message.... When you whack 'MPro' with paxlovid/PF-07321332 you make less virus, which means you have less viral load in your body. As a result, you don't get as sick and, it appears, you are also less infectious.

Thus, there are real benefits here that include:

1) you can take it easily by mouth.

2) you don't have to worry about immune escape (or, in most cases, the state of your own immune system) for it to work.

3) According to the clinical trial data released by Pfizer so far, it will work for at least five days after a virally infected person becomes symptomatic which is a decent window of time to get the drug into people in real world settings.

But could the virus mutate so that paxlovid stops working?

Well, that's possible, although, unlike the spike protein (which forms the little red bits sticking out of the virus that the virus uses attach to and enter into cells, Step 1 above) where there are many mutations, there is only one mutational change in MPro in the omicron variant. However, that could change/accelerate when paxlovid treatment causes selection pressure for variants that could escape drug effectiveness. 

Ultimately, issues about protease inhibitor/paxlovid resistance due to mutation could be overcome by developing additional drugs that attack other molecular choke points in the viral cycle. This is a strategy that has been used successfully in HIV treatment, although there things are different in that the treatments are chronic/go on for long periods of time which, at least so far, is not the goal of acute paxlovid treatment against SARS-CoV-2 (i.e. you take it twice a day for five days). Regardless, there are other drugs in the pipeline, including Merck's 'molnupiravir' which works by blocking a different  enzyme called RNA dependent RNA polymerase (RdRP) that is critical for making new copies of the viral genome (see Step 4 in the diagram above).

_____

There is actually a second drug that you take with PF-07321332 in Pfizer's treatment called 'ritonavir' which acts by decreasing the activity of a molecule in your own body (including in the intestines and the liver) called cytochrome 3A4. Normally, cytochrome 3A4 acts to break down/metabolize drugs/foreign agents, so here ritonavir decreases the breakdown of paxlovid. As a result, paxlovid levels remain higher for a longer in our bodies which makes it more effective against the virus. 

Regarding Merck's 'molnupiravir'...It doesn't appear to be as effective in clinical trials as Pfizer's treatment, at least on its own. There are also some concerns that it might speed viral mutation rates because of the way it works (i.e. it mucks up the ability of the virus to copy its own RNA which is where everything, including mutations, are coded).

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Why I'm Still Taking Precautions Against SARS-CoV-2.

CurvesStill

MatterVille

I'm in my early 60's.

And I'm in decent shape.

And I'll be getting my booster on Thursday.

Thus, if I get infected over the next four-to-six weeks, very likely with the omicron variant, it's reasonably likely that I will be fine, at least acutely, even if I do develop symptoms. 

This is something I'm extremely thankful for and it is something that would have been very difficult to assume a year ago before the full tilt vaccine roll-out.

So.

Why am I doubling down and planning to be extra careful over the next four-to-six weeks?

Because I do not want to spread the highly transmissible omicron form of the virus to others, potentially many others, some of whom may then get sick and need to go to hospital.

Why does this matter?

Because...

As more people have to be treated for COVID symptoms in our hospitals as transmission skyrockets fewer people will be treated and/or or receive surgery for non-COVID issues in a timely manner due to the resulting back-up in our healthcare system (something that has already started).

Which means that by being careful re: COVID, I plan to do what I can, in a very small way as just a normal, run-of-the-mill community member, to increase the chances that someone else in my community will be able to get the treatments and/or surgeries they need.

OK?


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Full disclosure...Someone very close to me and mine is scheduled to have important non-COVID treatment in the next few months...Thus, the decision I've made to be extra careful has both community and personal implications for me and mine.


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Experimental Data Are Accruing That Omicron Exhibits Decreased Lung Infectivity.

TheData

AreVille

___________

Friday Dec 31/21 - See Update at the bottom of the post

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As we noted in our last round-up post, even if the omicron variant really does generate, on average, less severe symptoms than the delta variant, the shear number of infections due to increased transmissibility will cause significant issues for healthcare systems.

Having said that, the experimental data are piling up that, different from the situation in upper airway, omicron does not infect the lining epithelial cells within the lung nearly as well as previous versions of the virus.

Eric Topol has summarized and cited those data which has been generated by multiple reputable groups:

What does this mean? Well, if it translates to the clinical/human realm it could mean significantly reduced COVID pneumonia - the bad acute* outcome of the virus.

Thus, if we can flatten the hospitalization/ICU curve in the short term by decreasing transmission while we get vaccinations amongst kids and boosters up for the vulnerable at the same time, the omicron variant could, ultimately, help us see and move toward the lights at the end of the long term tunnel.

However, again, in the short term we've got to work to decrease transmission to prevent our healthcare systems, and stretched-to-the-breaking-point healthcare workers, from being overwhelmed.



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Please note that I am not a clinician or an epidemiologist...However, I do have some expertise in epithelial cell biology - thus, the key here is how well the experimental data translate to the clinical realm...

*Please also note that, in the case of chronic, long COVID, the clinical situation is not yet clear with respect to omicron for obvious timeframe reasons.

And, just because it continues to bear repeating given that it seems to get lost in the media shuffle...While vaccination does not prevent infection/transmission of the omicron variant it is still doing a great job of decreasing hospitalization...Hugely (scroll down a little).

Update, Fri Dec 31st...And here is an interesting pre-print, with extensive experimental data and solid analysis, from a group in Glasgow. They conclude that the omicron variant has subtly, but importantly, shifted its favourite way to get into cells (from ACE-2/TMPRSS2 cell surface binding/fusion/insertion to endosomal fusion/engulfment)...This could, perhaps, contribute to the upper vs. lower airway infectivity differences of this variant (i.e. the mechanism leading to a change in cellular 'tropism'/preference for infection).



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The Best Synthesis Of The Data On Omicron I've Read So Far...

TheData

AreVille

I know I've gone to this well a number of times already but I can't emphasize enough the fantastic job that Dr. Eric Topol of the Scripps Institute is doing keeping up to date with all the COVID data. 

This is particularly true in the case of the Omicron variant of the virus. 

Topol has written a really great longform piece that lays it all out in straightforward language and his conclusions are all backstopped by data that matter.

The piece I'm referring to is a couple of days old now but still very relevant - you should really read it in its entirety - it will only take you a few minutes.

Here are the take home messages that I have gleaned:

1) Vaccine Effectiveness

Two doses of Pfizer gives reduced protection against symptomatic infection (34%) five months after the second shot while a boost takes it back up to 75% compared to the Delta variant (60%/95). However, it is important to realize that symptomatic infection does not appear to be tracking with disease severity (see #4, below).

2) Transmissibility

Household transmission is approximately three fold higher compared to Delta.

3) Prior SARS-Cov-2 infection

The levels of antibodies in the blood of folks who have been previously infected with the virus that can neutralize (i.e. whack) the Omicron variant are low. This likely explains why the rate of folks reinfected by Omicron that have had prior Covid has been high in both South Africa and the UK.  However 'hybrid' immunity for folks who have been both vaccinated and have had prior infection looks to be solid

4) Milder Severity of Disease

This is a point that was brought up by reader Gordie in response to a previous post.  Clearly, the proportion of hospitalizations to cases is down with Omicron compared to Delta and that's a good thing. However, it is not clear why this is the case and if it is intrinsic to the Omicron variant form of the virus itself or if it's due to the fact that lots of folks now have at least some form of immunity to the virus writ large, especially T-cell immunity which is an additional immunological tool that is separate (but works coordinately with) the antibodies produced by B-cells. Topol points out that we really won't know about this until the sample size gets large enough that we can parse out  folks over 60 who have never been infected and have never been vaccinated. Of course, in most Western countries that number is quite small proportionately. 

5) The Curve Thing, Again.

Even if Omicron is significantly less virulent (say even 10X less so than Delta) it could still lead to truly problematic crunches for health care systems that are already running near or over capacity given its potential to induce an enormous number of infections worldwide in a short period of time.

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Having said all of the above, it is important to keep in mind how far we have come re: tools for mitigation since this time last year. And that includes mitigating against Omicron. As for that new thing in the toolbox, the rapid antigen test, that hasn't been widely rolled out in British Columbia yet?...Well, much more knowledgeable folks than me on this topic are all for getting that wider roll out going, and fast...Mr. Dix said yesterday that an announcement should come early next week... There may be more on this and maybe the booster rollout also, at a health briefing by Mr. Dix and Dr. Henry tomorrow (although it may be focussed on gathering size restrictions).

Sorry about the delay for the promised post on how the antiviral treatments from Pfizer and Merck work...It's coming, just really busy with the end of term rush these days...The punchline - they don't rely on an immune response to work and thus the immune evasive component of the Omicron variant is not a factor.

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An Up-To-Date Summary... What We Know About The Omicron Variant.

Data

AreVille



From the ever vigilant Eric Topol...

Dr. Topol has also started going longform at his Substack.

It's good.




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Can The Latest European Resurgence Of COVID Cases Be Explained?

LikeVirusesPublicHealthEvolves

TooVille

Covid cases are surging in Europe again.

And that includes Western Europe where vaccination numbers, over all, have been strong.

So.

Can this latest European surge this be explained?

Eric Topol of the Scripps Institute, who has demonstrated his bonafides around here before, thinks that there is (at least) a three part explanation which he wrote about in a recent piece for The Guardian.

Number one is the issue of vaccination rates:

...(T)here (is still) a large proportion of unvaccinated individuals (including children and teenagers) in each country, and only countries such as Spain at 80% and Portugal at 88% that fully vaccinated their total populations have set a high bar and have thus far withstood the continental trend of rise in cases. Noteworthy is Belgium with 74% fully vaccinated and one of the hardest-hit countries in the world, now at 79/100,000, currently 10th highest caseload globally. That alone tells us 74% isn’t enough, and that prior Covid (without vaccination, what some refer to as “natural immunity”) is unreliable for representing a solid immunity wall against the Delta variant. In fact, it has been projected for Delta that any country needs to achieve 90-95% of its total population fully vaccinated (or with recent Covid) in order to have population-level immunity that covers, providing relative protection, for the others...

Number two is the issue of waning immunity, post vaccination (and why in BC that switch to mix and match post AZ vaccine dose #1 was likely a very good thing, population-wise). Topol also makes the case that boosters should roll out for everyone based on the Israeli data that we have discussed here before (this is also the plan in BC):

...(T)here is evidence of waning of immunity on top of the hyper-contagious Delta strain. Even though much of Europe got a later start in vaccination, a recent study showed that with the Astra Zeneca vaccine the decline in anti-spike antibody occurred quite early and there was a clear relationship between antibody levels and breakthrough infections. Decline below the anti-spike antibody threshold of 500 U/ml was reached at 96 days for AstraZeneca’s vaccine compared with 257 days for Pfizer’s. The impact of waning, and the opportunity to restore very high (~95%) effectiveness of mRNA vaccines (specifically Pfizer/BioNtech) with booster (third) shots has been unequivocally proven from the Israeli data. Yet the adoption of boosters, even in the highest-risk groups such as age 60 plus, has been very slow...

Number three is the issue the issue of the relaxation of mitigation measures (and it is here that I worry about most in both present, full house event BC as well as in future,  household small gathering BC):

... (T)here has been relaxation or abandonment of mitigation measures. Countries such as Denmark and Norway completely reopened and have seen resurgence of cases since that occurred. Throughout the world, the profound pandemic fatigue has led to the irresistible notion that the pandemic end is nigh, that masks, distancing, and other measures have run their course, essentially that enough is enough. It is hard to imagine fighting a foe as formidable as Delta that a vaccine-only strategy can be effective. We’ve seen a dramatic improvement in Japan, with full return to baseline after their worst outbreak, by the combination of high level of vaccination and the continued use of masks and mitigation measures...

The other thing that Topol points out is how we in (North) America previously ignored or, at the very least, reacted slowly to what happened in Europe when the first big viral outbreaks occurred in March of 2020, the alpha variant emerged in late 2020, and the delta variant emerged in the summer of 2021.

So.

Will we ignore/react slowly to what is happening in Europe this time as well?


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Dr. Topol is, in my opinion, the best Twittmachine follow when it comes to COVID public health and research updates.

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Real World Vaccination Efficacy Update For B.C.

Numbers

AreVille

British Columbia has started to release the COVID-19 case and hospitalization numbers broken down into folks who are not and who are vaccinated. Essentially the efficacy is similar to what we noted for Ontario a couple of weeks ago.

First, here are the numbers, per 100K per week (i.e. essentially all for the Delta variant given the recency) as analyzed by the CBC's Justin McElroy:

Second, Jens von Bergman, who is part of the non-governmental BC COVID-19 Modelling Group, has gone deeper and has done an age-based stratification for partial/one shot and full/two vaccination  efficacy - (note that the Y-axes here is are log scales such that each increment is a doubling of risk reduction compared to unvaccinated folks; SES = 'socio economic status'):

Thus, the protection is solid for full vaccination with some drop-off for protection for seniors - all of which is good. 

However, again, don't forget that the vaccinated can still be infectious even, potentially, if they are asymptomatic which means that the reason for masking and social distancing is to protect your friends, family members, colleagues and, well, pretty much everyone.

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Meanwhile in Florida, concerns have been raised by the Miami Herald that the method of reporting the numbers for the very worst outcome have been changed recently.


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An Interesting Bit Of Cell Biology With Variant Spike Proteins.

SequenceIsJust

TheBeginningVille

Sequencing the nucleotides of genes allows you to determine the coded for sequence of amino acids  in the protein concerned.

As a result, changes in the nucleotides in the gene sequence (i.e. mutations) lead to changes in the amino acids in the protein. Such changes are how the SARS-Cov-2 viral variants are generated.

Once the amino acid sequences are known that structural biologists jump in and try to figure out how changes in variants alter protein topology and, potentially, the way the protein works.

But, even with all this important and elegant 'molecular' work, the next step is to test the function of those mutated/changed/variant proteins in cells.

And a group from Boston has deposited a pre-print wherein they present some interesting data with the various SARS2-Cov-2  S-protein variants.

One of the interesting things these folks did was make funky 'pseudo' viruses that are decorated with the various S protein variants from SARS2-Cov-2. They then looked to see how fast those variants decorated pseudoviruses fuse with cells expressing the ACE2 receptor on their surface.

Here are the data which show that the Delta variant S protein (red line) causes more rapid membrane fusion in their experiments:

This group also did this with cell-cell fusion which led them to make the following conclusion:

...Our findings from both cell-based and pseudovirus-based assays suggest that the Delta variant can infect a target cell substantially more rapidly than the other variants we tested, either by more effective attachment or faster fusion kinetics...

It will be very interesting to see if this finding holds up and if it explains, at least in part, why the Delta variant virus is more infectious in people.

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Again, while I'm a biologist our group does not do research on viruses....We do, however, develop all kinds of assays to test gene/protein variant function in various cell models.




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The Apparent End Of The Port Alberni To Bamfield Ferry Service.

IfIt'sNotScottish

It's(S)crap!Ville

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Update: Looks like the service has been saved!

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Our Dad first took us on the Westcoast Trail in 1973, I think.

Back then there was little boardwalk and very few cable cars crossing over rushing water which meant that there was a whole lot of, as my younger brother, later the fireman, said at the time 'Mud a blowdowns!' as well as raft building for the fording of swollen creeks*. 

Given all this we decided that the only way that sane people travelled the trail was to start from Port Renfrew and trudge from south to north to get the worst of the thing behind you during the first few days before it all got a little easier once you crossed Nitinat Narrows, hung out at Tsusiat Falls for a bit, and then started heading towards the end at Bamfield.

I honestly can't remember if it was the first or the second time after finishing the trail that we took the trip on the M.V. Lady Rose, the old Glasgow-built combination people/cargo ferry, from Bamfield down Barkley Sound to Port Alberni on the way to civilization re-entry. 

The Lady Rose herself was taken out of operation about ten years ago and she sat tied up on the Tofino docks for quite awhile before she was towed over to Sechelt where a bunch of folks, spearheaded by a guy named Dick Clayton, are hoping to restore her.

But the ferry service itself is still going, using a different ship, the M.V. Francis Barkley, under the auspices of the Lady Rose Marine Services.

Still going until the end of the month, that is.

Susie Quinn wrote that story for the Alberni Valley News recently. Here's her lede:

An icon of Vancouver Island’s West Coast is poised to take its final voyage.

Lady Rose Marine Services will close its doors as of Aug. 31, after 75 years of freight and passenger service down the Alberni Inlet.

The company is yet another victim of the coronavirus pandemic and the economic strain of extended closures and restrictions, owner Mike Surrell said Monday, Aug. 9. The company posted a brief statement on its Facebook page after rumours started circulating about the closure.

“Seventeen months of basically no income going into the winter, which is traditionally slow…maintaining and running these vessels is very, very expensive,” he said.

“With COVID-19 we managed to hang on for 17 months. We’re not able to maintain this pace. Unfortunately, the Frances Barkley will stop sailing at the end of the month.”

Surrell bought the company and all its operations in 2008. He said while COVID-19 was the final strike, it has also been difficult finding employees with the proper certification to help keep the ship running. Working as a mariner is a specialty, and government regulations demand a certain amount of current training and certification...

Here's hoping something can be worked out for all those affected that decreases the impact of this latest development - There is a road up the inlet** but it is not great and there are remote stops that will likely lose their regular, scheduled goods delivery service pretty much entirely.

Now.

Don't get me wrong, based on the evidence, I'm still all in favour of getting as much of the population vaccinated as possible, invoking vaccine mandates in situations where folks will be interacting, indoors in close quarters, and to practice social distancing + masking + rapid testing when your interacting with folks outside your pod. However, unless things go completely off the rails due to new data emerging regarding the Delta variant or the wide, rapid spread of a new even more problematic variant (which doesn't look like it will be Lambda), I would be concerned if any future hard lockdowns were not geographically targeted and for as short a duration as possible. After all, we are not, unfortunately, not New Zealand.

Lastly, it really is important to understand and have empathy for a whole lot of folks, including small business folks, who have been truly negatively impacted by the steps we've taken, especially pre-vaccine, to deal with the pandemic so far. This is something that has to be kept in mind as the PHO and we all struggle to choose the best and most prudent way(s) forward.

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*The bare bottomed, pack-over-the-head crossing of the Cheewhat River, before they built the bridge, by my youngest brother, later the musician, would come on the next trip. 

**For one of our trips home from Bamfield our Mom actually drove that road, I think in the VW (notso) microbus, to pick us up. We probably still owe her for that one.

And here's something crazily modern, and I'm not sure actually good...Big chunks of the trail can now be traversed virtually via Google Street View...

Sub-header?...Blame it on Mr. Myers.

Tip O' The Toque to reader E.G. for the heads-up on the update.

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There Are Some Things That Should Not Be Crowd Sourced...

...And this is one of them, especially by a medical doctor and a member of the ruling federal government.

Link

To be fair, much of the rest of Dr. Fry's recent timeline, excluding the slew of tweets that are run-up to election announcement-type stuff, is solid and factual regarding COVID-19. 

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An update on COVID-19 from Dr. Eric Topol, in terms of vaccine protection against the Delta variant is important...The data on the solid protection from severe illness has not changed, but the protection against break through infections has decreased probably to ~50% protection based on a number of studies from different jurisdictions...It's here.



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What To Tell Folks Who Ask About Vaccines And The Delta Variant.

DecreasingHesitancy

MattersVille

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Update: Aug 12th...Regarding points one and two, below...Eric Topol has aggregated the data from a number of studies on vaccine protection numbers against the Delta variant...They are dropping to approximately 50% protection...The protection against severe disease, and worse, however remain solid.

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As we predicted a couple not long ago, the American CDC's concern about vaccinated folks who suffer breakthrough SARS-CoV-2 infections that are themselves infectious has muddied the public perception significantly, thanks in no small part in my opinion, to the media's inability to walk and chew gum at the same time.

So.

Let's say you run into someone who is hesitant and you want to calmly explain to them why it is still a very, very, very, very good idea to get vaccinated.

You could try the following five point plan...

First, yes, it is true, vaccinated folks who suffer breakthrough infections of the Delta variant (which is now dominant in North America) can be infectious.

Second, as is clear from the chart directly below from San Diego county, where slightly more than half of folks are fully vaccinated, far fewer vaccinated folks suffer these breakthrough infections:

Third, many fewer folks who are vaccinated and suffer breakthrough infections go on to get sick enough that they have to enter hospital:

Fourth, many fewer folks who are vaccinated and suffer breakthrough infections, who then go on to get sick, actually die. San Diego also has these data, but the graph below is more of a zoom out, done by the Wall Street Journal (paywalled), looking at America's truly tragic real world vaccination experiment county-by-county:

Fifth, getting vaccinated doesn't just protect you but it also protects everyone else in your household, your workplace and your community as well as your loved ones because it decreases spread as was demonstrated by home grown modellers in British Columbia modellers recently:

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If you want a nice summary of all the data for all the vaccines, Eric Topol, who really tracks all of this stuff and is a fantastic Twittmachine follow, has it.

Again, please not that, while I am a life scientist, I am neither a virologist nor an epidemiologist...In the spirit of full disclosure, however, I am acquainted with a couple of the home grown modellers cited above.



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America's Very Unfortunate Real World Vaccine Experiment.

Unfortunately, and truly sadly, America and Americans are engaged in a real world COVID-19 vaccine experiment.

The following are the numbers for cases, hospitalization and deaths in the ten jurisdictions with the highest rates of full vaccination as reported by the New York Times for yesterday, August 1st.

And the following are the same categories of numbers for the ten jurisdictions with the lowest rates of full vaccination:

As has been noted recently, the now dominant Delta variant of the SARS-CoV2 virus can be transmitted by both vaccinated and unvaccinated folks. Given this, the percent change in case numbers may become less the issue over time. Regardless, based on the ability of full vaccination to prevent serious illness, the differences in hospitalizations and, most tragically, death rates really matter.

So, regarding hospitalizations, please note that only one of the high vax jurisdictions compared to five of the low vax jurisdictions had an increase of greater than 100% over the last 14 days.

And with respect to deaths, none of the high vax jurisdictions vs. eight of the low vax jurisdictions had daily death rates over 0.1 per 100,000 people. And a number of the daily death rates in the latter category were shockingly high.

****

Here in Canada full vaccination rates are quite uniform across all jurisdictions, except for a dip in Newfoundland Labrador and PEI. Thus, it is unlikely that we will engage in the same real world experiment with jabs themselves as is occurring in our neighbours and friends to the south. However, it would appear that, unfortunately, we here in Canuckistanmikitaville may be gearing up to embark on a non-pharmaceutical intervention experiment in at least one jurisdiction.  

We can only hope that our full vax rates get to Vermont-like levels before any large increase in case numbers results.

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One thing to consider (and perhaps emphasize in the media?)...If dominant Delta variant infections occur among the vaccinated as well as the unvaccinated and if many more folks in the latter group gets seriously sick as a result, who is being most protected by, say, the maintenance of masking?

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The Lagging Indicator That Matters Most.

The graph above is from a piece in today's New York Times by Lauren Leatherby  comparing COVID-19 outcomes across U.S. counties with either high (left) or low (right) vaccination rates.

The grey under the curves represent deaths.

Of course, some folks might be wondering how this can be given all the hullabaloo over U.S. CDC concerns that vaccinated people can still transmit virus to others after a breakthrough infection occurs?

Well, it is because the vaccinated that do develop a relatively rare breakthrough infection themselves rarely go on to develop symptoms. Additionally, only a small percentage of the vaccinated who develop symptoms progress to a stage where they get severely ill and die.

Eric Topol, who really knows what he's talking about and really stays on top of this stuff, recently gave kudos to a fellow named Darren Lu for his truly impressive graphic that demonstrates the protective multiplier effect of vaccination that contributes to real world differences in death rates like those shown at the top of the post:

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So, what's the issue with the vaccinated who do suffer breakthrough infections who do not get sick but can transmit the Delta variant of the virus to others?....Well, the big issue there is that those folks will not know that they are infectious (i.e. they are asymptomatic) which will likely drive spread to both the vaccinatated and, worse, the unvaccinated given the high R0 value of this particular version of the bug. Thus, the CDC's change in mask recommendations this week....How to really deal with this?...Dr. Topol suggests widespread rapid antigen testing so those vaccinated who do get infected but not sick will know to self-isolate...I reckon this is an apporoach that institutions with large numbers of young people, including those with large numbers of young adult people, returning in, say, September might want to consider.

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Get Ready For A Media Onslaught On The Transmissibility Of The Delta Variant.

TheTurningOfTheNewscycle

ThumbscrewsVille


Earlier today the New York Times foreshadowed a coming announcement from the U.S. CDC that they have data that the Delta variant can be spread by both the unvaccinated and the vaccinated.

Then, early this evening the Washington Post spelled it out:

The (internal CDC) document strikes an urgent note, revealing the agency knows it must revamp its public messaging to emphasize vaccination as the best defense against a variant so contagious that it acts almost like a different novel virus...

{snip}

...It cites a combination of recently obtained, still-unpublished data from outbreak investigations and outside studies showing that vaccinated individuals infected with delta may be able to transmit the virus as easily as those who are unvaccinated. Vaccinated people infected with delta have measurable viral loads similar to those who are unvaccinated and infected with the variant...

So, if the CDC is correct, this means that anyone can be infectious, regardless vaccination status. Thus the rationale for the CDC's reinstitution of a mask mandate in areas where infection rates are high earlier in the week.

The hard part here, I reckon, is going to be keeping the message clear regarding the fact that there are no data to significantly alter the conclusion that vaccination protects against significant illness due to Delta variant infection.

To wit:

...The (document) highlights the daunting task the CDC faces. It must continue to emphasize the proven efficacy of the vaccines at preventing severe illness and death while acknowledging milder breakthrough infections may not be so rare after all, and that vaccinated individuals are transmitting the virus...

Lets hope that critical message doesn't get lost in the media volcano that is about to erupt, probably by tomorrow/Friday morning.

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