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Cont: The One Covid-19 Science and Medicine Thread Part 4

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SARS Cov-2 does not exist anymore. Covid 19 is extinct.

SARS-CoV-2 still exists and is not extinct:
SARS-CoV-2 variants of concern as of 17 May 2023 (European Centre for Disease Prevention and Control)
The COVID-19 pandemic in 2023: far from over (Lancet, Jan 14, 2023)
What made you think that it was?

We are now in 2023 and many iterations later than that.


SARS-CoV-2 is alive and well and still doing a lot of damage, including killing people. See the current U.S. numbers here. (I haven't updated the numbers since April, but my links are to Our World in Data, which still does. But remember that number of new cases is even more unreliable now than it used to be. I assume that the number of C-19 deaths is still fairly reliable. Approximately 50,000 this year, so far.)

Your "many iterations later" means that several new and more contagious variants of SARS-CoV-2 are circulating. Notice that it is still SARS-CoV-2, both in Europe and in the USA. And notice that not even the super-spreader events have disappeared. This one happened last month in a group of people that ought to know how to protect themselves but for the most part didn't appear to do so: "70% of respondents reported not wearing a mask.":

On Thursday, April 27, several in-person attendees notified conference organizers that they had tested positive for SARS-CoV-2, the virus that causes COVID-19. That same day, EIS leaders made an announcement at the conference about potential cases and took action to reduce further spread connected with the conference and related events. After the conference ended, CDC received additional reports of attendees testing positive for SARS-CoV-2
Update on Rapid Assessment of SARS-CoV-2 Transmission at 2023 EIS Conference (CDC, May 26, 2023)

In other countries:
For the second wave since April, Zhong’s modeling revealed that the XBB variant is expected to cause 40 million infections weekly by May, going up to 65 million in June. This goes against the grain of Chinese health officials’ estimate that the wave had peaked in April. In Beijing, the number of new infections recorded between May 15 and 21 grew four times in four weeks.
China Might Have 65 Million COVID Cases a Week by June. How Worried Should the World Be? (Time, May 29, 2023)

We should discuss what we have now, and if it is somehow different than the other viruses that were also once 'novel' and more deadly and then became a common and mostly innocuous illness for healthy populations. ie common cold.


The "mostly innocuous" illnesses still managed to kill and cripple a lot of children before the arrival of vaccines that are much more effective than those against the flu and SARS-CoV-2. And they are still incredibly lethal in unvaccinated children and adults in places like Samoa that haven't experienced the centuries or millennia of, for instance, measles weeding out people whose immune systems weren't effective against that particular virus.
 
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Just had it 2 weeks back for the first time. 2 days in bed, 40C, terrible throat ache, basically could not swallow, not even water. Not worse than bad case of flu, but not better either. I'm 99% sure I got it on Osaka Airport. It was super crowded and it was 3 days before onset of the symptoms.
I'd agree it's not newsworthy anymore .. but it certainly does exist.


When was your last vaccination?
I think I got the infection in early April, also for the first time if that's what it was, but I never got tested. (Danes can't get Paxlovid anyway unless they are 85+, so there's no practical point of getting tested if you are going to self-isolate anyway). The infection itself was pretty mild, two days of slightly sore throat and four days of low-temperature fever, but I kept having weird but not particularly bad headaches that took five weeks to disappear completely.
I got one jab of Soberana Plus in early October '22 and one of the updated bivalent Pfifzer (+ flu vax) five weeks later.

I would says that it's still newsworthy. It seems to have dropped out of the local news entirely even though new variants like XBB.1.16 "now in 2023 and many iterations later" are at least as contagious as ever and better at evading immunity, and it still kills. In the second half of 2020 and until now, we have had a higher rate of mortality in DK than expected in spite of booster shots in the fall. (The pale blue line marks expected mortality.)

Reports like this one seem to serve the purpose of keeping SARS-CoV-2 out of the news or to make headlines say, 'nothing to worry about':
WHO said on 17 April 2023 that, thus far, “no changes in severity have been reported in countries where XBB.1.16 are reported to be circulating…Disease severity is not higher compared to previously circulating variants” (in pre-immune populations).
In terms of clinical considerations, WHO did note a slight rise in bed occupancy in some states in India (2-4%) but emphasised that “these levels are much lower compared to the level recorded during the delta wave or omicron BA.1/BA.2 waves.”
What do we know about the Arcturus XBB.1.16 subvariant? (BMJ, May 16, 2023)
Apparently no need to mention that in many countries Delta was pre-vaccination and that many other countries were only partially vaccinated.
 
I got one jab of Soberana Plus in early October '22 and one of the updated bivalent Pfifzer (+ flu vax) five weeks later.

You hipster, you! And I thought I was cool getting the Moderna as opposed to Pfizer.

I've had three and a dose of Covid as well back in August. I'll probably get a booster sometime this year in a similar way to getting a flu shot.
 
I had third dose sometimes when they were first given. Long time ago. I was waiting for the omicron specific for my fourth, but they are only giving them to critical groups here at the moment.
 
Just had it 2 weeks back for the first time. 2 days in bed, 40C, terrible throat ache, basically could not swallow, not even water. Not worse than bad case of flu, but not better either. I'm 99% sure I got it on Osaka Airport. It was super crowded and it was 3 days before onset of the symptoms.
I'd agree it's not newsworthy anymore .. but it certainly does exist.

Are you sure it was Covid, not…


 
C-19 or Osaka flu? :)

I also know a couple of people who had C-19 in recent months. And unlike me, they self-tested, so in their case there wasn't much doubt that it was actually C-19.

You hipster, you!


Not really. I got to Cuba unscathed in spite of all the coughing on the plane. I masked up. Few of the coughers did. It was a year since my last booster, and I wanted to get vaccinated before the return flight. I already knew about the efficacy and safety of the Cuban vaccines, and also that the vaccine-induced immunity appeared to be pretty long lasting. I later found out that it included a tetanus shot, which I hadn't had in about 20 years.

And I thought I was cool getting the Moderna as opposed to Pfizer.

I've had three and a dose of Covid as well back in August. I'll probably get a booster sometime this year in a similar way to getting a flu shot.


Considering both waning immunity and the immune evasion of recent variants like XBB.1.16, I doubt that you have much protection left.
 
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I had third dose sometimes when they were first given. Long time ago. I was waiting for the omicron specific for my fourth, but they are only giving them to critical groups here at the moment.


In DK, boosters are reserved for 50+ - and for particularly vulnerable groups younger than that.
 
SARS-CoV-2 still exists and is not extinct:
SARS-CoV-2 variants of concern as of 17 May 2023 (European Centre for Disease Prevention and Control)
The COVID-19 pandemic in 2023: far from over (Lancet, Jan 14, 2023)
What made you think that it was?

SARS = Severe Acute Respiratory Syndrome. That is not what we have now. That virus is gone. Dead. Extinct. Just as the Spanish flu petered out and morphed into a lesser deadly virus, so did this one---- scare tactics using normal human issues with common viruses notwithstanding- or trying to use 3rd world issues that would be there anyway.

Deadlier viruses that are controlled with a near-lifetime vaccination success are not at issue here. The common cold has never had a vaccine. The flu viruses change and also do not have long term protection. Lets compare the apples to the apples please.
 
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XBB.1.16 'Arcturus' is a descendent lineage of XBB, a recombinant of two BA.2 descendent lineages of Omicron. So is XBB.1.5 'Kraken'. But they are still SARS-CoV-2, they still cause Covid-19. Newer versions of the virus tend be be more infectious - the current ones are incredibly more infectious than the original version out of Wuhan - and better at evading already acquired immunity by vaccination or previous infection. At one point, health researchers tried to figure out how many times more infectious new variants were in comparison to the first Wuhan coronavirus, but I'm not sure that anybody still does that.

As I said, SARS-CoV-2 is still very much alive, and you are mistaken when you claim that "That virus is gone. Dead. Extinct." How do you think it still manages to kill? (Some professionals have suggested that SARS-CoV-2 should be called a cardiovascular instead of a respiratory disease because it destroys other organs than the lungs, but I assume that name change wouldn't please you.)

You don't seem to understand how exactly "the Spanish flu petered out and morphed into a lesser deadly virus." It didn't. It killed people, and since it kille mainly the young, who had not yet reproduced, we are the descendants of the survivors of the Spanish flu. At an early stage of the pandemic, a poster on the forum mentioned having almost been hospitalized and almost killed by the current version of the Spanish flu. This happened fairly recently, but I don't remember the poster's name, unfortunately. There are probably still people around whose ancestors may have been vulnerable to the Spanish flu but just never encountered it, so they survived and reproduced by having been isolated from the infection.

Measles also didn't just 'peter out and morph into a lesser deadly virus'. It didn't change into a milder version. It killed, and the survivors were those who had a stronger immune response to it. How do we know that it didn't become milder in and of itself? By watching what happened when it was spread to populations, in particular in the Americas, that had never encountered it.

In the Pacific islands, to this very day, measles still kills (the unvaccinated): Measles epidemic in Samoa and other Pacific islands (Lancet). It does so because it hasn't already weeded out those most vulnerable to it in those places. Or you could say that it 'peters out' by weeding out, by killing. SARS-CoV-2 doesn't (or only very, very slowly), because it mainly (but not exclusively) kills people post reproduction age.

As for SARS-CoV-2:

Key Definitions
* Mutation: A mutation refers to a single change in a virus’s genome (genetic code). Mutations happen frequently, but only sometimes change the characteristics of the virus.
* Lineage: A lineage is a group of closely related viruses with a common ancestor. SARS-CoV-2 has many lineages; all cause COVID-19.
* Sublineage: A term used to define a lineage as it relates to being a direct descendent of a parent lineage. For example, BA.2.75 is a sublineage of BA.2.
* Variant: A variant is a viral genome (genetic code) that may contain one or more mutations. In some cases, a lineage or group of lineages with similar genetic changes, may be designated by the World Health Organization (WHO) or the U.S. SARS-CoV-2 Interagency Group (SIG) as a Variant of Interest (VOI), Variant of Concern (VOC), Variant of High Consequence (VOHC) or Variant Being Monitored (VBM) due to shared attributes and characteristics that may require public health action.
* Recombination: A process in which the genomes of two SARS-CoV-2 variants combine during the viral replication process to form a new variant that is different from both parent lineages. This may occur when a person is infected with two variants at the same time. The lineage that results from recombination is called a “recombinant.”
SARS-CoV-2 Variant Classifications and Definitions (CDC, Mar 20, 2023)


Viruses can change and alter their genetic make-up. When these changes occur, the virus may become more or less of a threat to the human host. Virologists are therefore interested in tracking the evolution of the viral genome.
In the case of the SARS-CoV-2 virus, it is designated a single species, but there are different kinds that can infect the patient with essentially the same disease. Biologists deploy specific terminologies to describe viruses and the use of these terms has seeped into the public discourse. Here different types of viruses have variously been referred to as mutants, variants, subspecies, and strains. This leads to conceptual confusion. This article looks at what we mean when we refer to a viral strain.

What is a strain?
The term strain is used to distinguish a genetically distinct lineage separated from another strain by one or more mutations. A strain is a genetic variant (not to be confused with a viral variant) or subtype of microorganism (that could be a virus, but it also applies to bacteria and fungi). This is the kind of definition to which biologists abide ––it is the scientific, biological term.
It is important to realize, though, that two genetically distinct viruses are not necessarily biologically (functionally) any different from one another. Whereas a variant differs from that of the reference organism or ‘wild type’ to be designated a strain, a variant should be in possession of unique and stable phenotypic characteristics. A variant is thus called a strain when it reveals distinct physical properties. This means that all strains are variants, but not all variants are strains.
(...)
Are there strains of SARS-CoV-2 coronavirus?
In the case of SARS-CoV-2 coronavirus, the reality is that no cause has arisen in which the term ‘strain’ need be applied. If it is being used by journalists, scientists, medical practitioners, and other professionals whose linguistic choices influence the public at large then it has technically been used inaccurately. There is only one SARS-CoV-2 coronavirus.
What is a Viral Strain? (Mar 2, 2022)


But feel free to make up your own names. It's worse when you make up your own alternative facts.
I know from earlier posts that you have decided for yourself and your child that you no longer need vaccinations or boosters against SARS-CoV-2. You are free to make that decision, but your reason for making it is wrong.
 
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Apparently, here in the USA, the FDA and CDC have different definitions of "strains."

https://www.fda.gov/medical-devices...s-cov-2-viral-mutations-impact-covid-19-tests
The SARS-CoV-2 virus has mutated over time, resulting in genetic variation in the population of circulating viral strains, also called lineages. This genetic variation may impact the virus's properties such as transmission (for example, it may spread more easily) or the severity of symptoms on infected individuals (for example, it may cause more severe disease).

Also, strains and lineages seem to be used interchangeably among the different state department of health sites.

And the Mayo Clinic uses variants and strains in their opeing paragraph.

https://www.mayoclinic.org/diseases-conditions/coronavirus/expert-answers/covid-variant/faq-20505779
Concern over variants, sometimes called strains, of the virus that causes COVID-19 is based on how the virus might change. A virus could get better at infecting people, spread faster or cause people to get sicker.

There was certainly a phenotype change (upper respiratory) between Delta and Omicron. What authority decides a change is enough for a new "strain"? Seems to be the most common term is lineage.
 
A friend of mine has had Covid twice and is currently being absolutely hammered by RSV.

It's the latest insult in an already awful year for him.

He's currently wondering if Covid has damaged his immune system because of the severe infections he's had recently.

I still appear to be living a charmed life after five Covid vaccines.

:D
 
For my latest visit to the VA (Veteran's Administration) hospital for a blood draw (which I get done every few weeks), it's the first time since the lockdown that they didn't require masks for normal visits and activities. That just takes a giant load off of stress reminders each time I went there. Oh, I'm still at a higher risk than most, but I'm OK with going maskless in most situations now.
 
Also, strains and lineages seem to be used interchangeably among the different state department of health sites.


I think that's the point. You can add variants to strains and lineages. (I have referred to new variants as new strains or even versions of SARS-CoV-2.) How many of us (other than biologists) know and use the list of biological classification correctly when we are talking about animals?
 
The Cleveland Clinic study has now been published:

Effectiveness of the Coronavirus Disease 2019 Bivalent Vaccine
https://academic.oup.com/ofid/article/10/6/ofad209/7131292

Among 51 017 employees, COVID-19 occurred in 4424 (8.7%) during the study. In multivariable analysis, the bivalent-vaccinated state was associated with lower risk of COVID-19 during the BA.4/5-dominant (hazard ratio, 0.71 [95% confidence interval, .63–79]) and the BQ-dominant (0.80 [.69–.94]) phases, but decreased risk was not found during the XBB-dominant phase (0.96 [.82–.1.12]).

So the bi-valent vax is not very useful for the current variants. At least for symptomatic disease.

That said what gets the most attention is the unexpected association between number of vaxxes and increased rate of symptomatic disease with approx doubling after 3 vaxes. See figure 2.

The association of increased risk of COVID-19 with more prior vaccine doses was unexpected.

One possible explanation is discussed in icpcovid's site, a collection of experts that have been weighing in on Covid-19 since March 2020. I've looked at their takes at various points in the pandemic and found them quite good. Most interesting to see how their analsysis has evolved as new info arrived.

https://www.icpcovid.com/en/news/7-...covid-vaccine-effectiveness-during-successive

After discussing Simpson's paradox the risk of prior infection among the unvaxxed was zeroed in on.

Back to the problem, which is different, but there is a relationship. Only I am thinking less about age (which is already taken into account) but about history of infection. Someone who is less vaccinated may have had more infections, and gets the protection from that.

In any case there may well be an ADE effect at work in regards to symptomatic disease. It just isn't known. And it is well estblished that vaxxes reduce serious disease/risk of death.
 
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The Cleveland Clinic study has now been published:

Effectiveness of the Coronavirus Disease 2019 Bivalent Vaccine
https://academic.oup.com/ofid/article/10/6/ofad209/7131292



So the bi-valent vax is not very useful for the current variants. At least for symptomatic disease.

That said what gets the most attention is the unexpected association between number of vaxxes and increased rate of symptomatic disease with approx doubling after 3 vaxes. See figure 2.



One possible explanation is discussed in icpcovid's site, a collection of experts that have been weighing in on Covid-19 since March 2020. I've looked at their takes at various points in the pandemic and found them quite good. Most interesting to see how their analsysis has evolved as new info arrived.

https://www.icpcovid.com/en/news/7-...covid-vaccine-effectiveness-during-successive

After discussing Simpson's paradox the risk of prior infection among the unvaxxed was zeroed in on.



In any case there may well be an ADE effect at work in regards to symptomatic disease. It just isn't known. And it is well estblished that vaxxes reduce serious disease/risk of death.

Hmmm… that’s disappointing.
 
CDC's MMWR report of a large blood donor database shows an interesting skew of age v prior infection. See Figure 2

https://www.cdc.gov/mmwr/volumes/72/wr/mm7222a3.htm?s_cid=mm7222a3_w#T1_down

Figure 2 is a chart of percentages in 4 groups by age category and time frames. Infected and vax, infected w/o vax, not infected with vax and not infected w/o vax.

Time frames and distribution is consistent with the San Diego data I've reviewed the last 2 years which showed lower infection rates amongst the elderly. Good thing too or there would have been a lot higher mortality given the Covid-19 severity age skew.
 
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