Scientists say a now-dominant strain of the coronavirus appears to be more contagious than original

[Mountainmanbob]

No. This means we've learned something factual about the world. That way, we can make informed decisions.

You seem to have the answers?
When do we go back to work?

If you watch the news?
Manufacturing moving out of Calif..
Due to lockdown.
M

 

[essentialsaltes]

You seem to have the answers?
When do we go back to work?

If you watch the news?
Manufacturing moving out of Calif..
Due to lockdown.
M

If you watch the news?
Governor Newsom has a plan.
I got curbside pickup this weekend.

Elon Musk is just mad that Calif.,
Won't accept his kid's name: X Æ A-12

 

[Mountainmanbob]

If you watch the news?
Governor Newsom has a plan.
I got curbside pickup this weekend.

Elon Musk is just mad that Calif.,
Won't accept his kid's name: X Æ A-12

Thanks for that link.

Although it sure is proving to be hard to keep all on the same page, I have noticed that the plans set in motion to reopen have brought great hope for most all.

Have a good day,
Bob

 

[SelfSim]

There is one, and only one strain of SARS-CoV-2

There is only one strain of SARS-CoV-2. The first virus isolate, taken from a Wuhan patient in December 2019, is the same strain as the most recent isolate taken anywhere else in the world in May 2020. So far no one has shown that any of these virus isolates differ in any fundamental property.

I can hear some of you shouting, but isn’t a nucleotide change enough to make a strain? The answer is a resounding NO. Every virus expelled by an infected individual differs from the next by many base changes. It would be foolish and of little utility to call each patient isolate a strain. That term is reserved only for special changes that confer a new property to the virus.

Explainable via the founder effect:

There is no doubt that viruses with the D614G change are emerging in different geographical regions of the world. Until proven otherwise, their emergence is likely due to the founder effect. Let’s say a virus with D614G emerges during replication in a person’s respiratory tract. If viruses with that change infect the next person, and the next, and so on, then the D614G change will predominate. The change is simply a single nucleotide polymorphism of little consequence. It is the noise produced by error-prone RNA synthesis by the virus. Viruses with D614S are simply virus isolates. They are not strains of SARS-CoV-2.

Absence of a selective pressure:

For an amino acid change such as D614S to be positively selected, as opposed to being maintained as a consequence of the founder effect, requires selective pressure. For such an already highly transmissible virus, the nature of such selection pressure is difficult to discern.

 

[SelfSim]

One question from a scientific viewpoint I've been pondering is:
Are post-infected patients who still test positive, (ie: swab/PCR), still capable of causing infection in a community?

I don't believe the answer is at all clear .. the shedding of intact viral RNA sequences still appears to leave the potential of reinfection (given a set of specific environmental conditions into which RNA is expelled)?

 

[Tanj]

One question from a scientific viewpoint I've been pondering is:
Are post-infected patients who still test positive, (ie: swab/PCR), still capable of causing infection in a community?

I don't believe the answer is at all clear .. the shedding of intact viral RNA sequences still appears to leave the potential of reinfection (given a set of specific environmental conditions into which RNA is expelled)?

What does "post-infected" mean? If you're shedding then your'e infected.

 

[SelfSim]

What does "post-infected" mean?

Clinically evident. Or in other words, there is hard evidence that the patient displayed the set of symptoms consistent with those associated with SARS Cov-2 (fever, respiratory infection, cough, etc).

If you're shedding then your'e infected.

Dog chasing its tail here. Only relies on the respective definitions of 'shedding' and 'infected'. Definitions produce circularity. Evidence breaks that chain however ..

 

[Tanj]

Clinically evident. Or in other words, there is hard evidence that the patient displayed the set of symptoms consistent with those associated with SARS Cov-2 (fever, respiratory infection, cough, etc).

What? Mate, you can't just go around making up terms, or then deciding that they have meaning. micro evolution and macro evolution are both just evolution. There's no such thing as "post-infected". Your ability to produce virus and your clinical presentation aren't necessarily correlated in any way.

Dog chasing its tail here. Only relies on the respective definitions of 'shedding' and 'infected'. Definitions produce circularity. Evidence breaks that chain however ..

Well that's easy, given both are well understood biological terms. infected means viable virus is located within you and shedding means infectious virus is being produced. Definition only produce circularity when they are made up in your head with no basis in reality. I guess we'll find out if evidence can indeed break your chain.

For reference, you can be infected and not shedding. Ask the 2/3rds of the world with CMV infection.

 

[SelfSim]

... There's no such thing as "post-infected". Your ability to produce virus and your clinical presentation aren't necessarily correlated in any way.

Well I think the symptoms associated with Covid-19 are indicative of the human immune system's reaction to infection .. Why are there all those deceased people suddenly showing up in large numbers and ICU beds are fully occupied? Something's likely afoot here, y'know(?)

We know the SARS-2 virus is present in those people because there's definitive PCR test evidence of that in the form of nasopharyngeal swab test isolates and statistically meaningful matched PCR sequence data.

Well that's easy, given both are well understood biological terms. infected means viable virus is located within you and shedding means infectious virus is being produced.

RE underlined: No .. I think you'll find that's not necessarily agreed towards the recovery phase end of the infection process.

I'm querying what is meant by 'infectious virus'. PCR testing doesn't distinguish between virions and matching RNA sequences. Shedding can include infectious virions, and they can also be absent in bodily secretion samples.

For reference, you can be infected and not shedding. Ask the 2/3rds of the world with CMV infection.

True for the generalised set of viruses.
The question I'm raising however, is specifically about what is currently known about the SARS-2 virus infection properties and those similar properties assumed to be in common with SARS-1 (but not yet verified).
Once the immune system has killed virus infected cells, the remnants are shed. These remnants are detected by the sensitive PCR/swab tests. Positive results doesn't necessarliy imply infectious virions are present .. but they may be.

 

[Tanj]

SelfSim, it is possible I was somewhat ascerbic in earlier posts. I apologise for taking some RL irritation out on you. For the record I have a PhD in virology, and 30 yeards experience in biomedical research.

Well I think the symptoms associated with Covid-19 are indicative of the human immune system's reaction to infection

I don't know what you are trying to say. Obviously the immune system is involved in the infection. It has no bearing on whether you are shedding virus whilst asymptomatic.

Why are there all those deceased people suddenly showing up in large numbers and ICU beds are fully occupied? Something's likely afoot here, y'know(?)

Again not sure what point you are trying to make, nor can I see any relevance to the ability to shed vurys whilst asymptomatic.

We know the SARS-2 virus is present in those people because there's definitive PCR test evidence of that in the form of nasopharyngeal swab test isolates and statistically meaningful matched PCR sequence data.

right....and??

I'm querying what is meant by 'infectious virus'. PCR testing doesn't distinguish between virions and matching RNA sequences. Shedding can include infectious virions, and they can also be absent in bodily secretion samples.

Ahh, OK, I am beginning to understand I think.
1. RNA is a ridiculously fragile molecule in part due the ubiquitous presence of RNAses, in fact they naturally occur on skin. It doesn't hang around anywhere naked for more than a few minutes.
2. The processing steps in getting from swab to PCR reaction assume that the RNA you are collecting was not floating around in the sample.
3. There's no real mechanism for viral RNA to become extracellular in the absence of an active infection.

Once the immune system has killed virus infected cells, the remnants are shed. These remnants are detected by the sensitive PCR/swab tests. Positive results doesn't necessarily imply infectious virions are present .. but they may be.

No, partly for the reasons mentioned above, also because immune mediated cell killing involves apoptosis, an ordered shutdown that does NOT involve uncontrolled release of DAMP and PAMP, amongst other things.

If you are detecting RNA then it is coming from an active infection, either virions or infected cells. Also, that's not what shedding means in the context of virology.

 

[SelfSim]

SelfSim, it is possible I was somewhat ascerbic in earlier posts. I apologise for taking some RL irritation out on you. For the record I have a PhD in virology, and 30 yeards experience in biomedical research.

No worries .. I am not pushing any particular agenda here .. I am predominately in knowledge-seeking mode .. although I confess I have been taken to task by a vocal self-proclaimed retired doctor on another science forum, who has taken the position that positive PCR testing doesn't necessarily imply the presence of infectious virions or cells, in patients recovering from Covd-19 (which seemed odd to me).

I don't know what you are trying to say. Obviously the immune system is involved in the infection. It has no bearing on whether you are shedding virus whilst asymptomatic.

Ok .. I was assuming the raised temperature, cough, respiratory issues etc were direct signs of an active immune response to a pathogen (and thus, these are the signs that makes it obvious that the immune system is active ..)

Ahh, OK, I am beginning to understand I think.
1. RNA is a ridiculously fragile molecule in part due the ubiquitous presence of RNAses, in fact they naturally occur on skin. It doesn't hang around anywhere naked for more than a few minutes.

Looks like one has to be cautious when using the classification of 'naked' as an explanation for a short longevity of a given virus(?) Naked RNA viruses which persist in nature are clearly contagious, no? (Eg: the Norovirus)?

2. The processing steps in getting from swab to PCR reaction assume that the RNA you are collecting was not floating around in the sample.

I guess you mean its not assumed that extracellular RNA is floating around in the sample here(?)

3. There's no real mechanism for viral RNA to become extracellular in the absence of an active infection.

I get what you're saying here .. I guess some viral RNA types can still persist, perhaps inactively, for long times (inside host cells) following an initial infection though, (eg: as described in latent, lytic and lysogenic infection modes), with no outward clinical signs of infection (asymptomatic).

No, partly for the reasons mentioned above, also because immune mediated cell killing involves apoptosis, an ordered shutdown that does NOT involve uncontrolled release of DAMP and PAMP, amongst other things.

If you are detecting RNA then it is coming from an active infection, either virions or infected cells. Also, that's not what shedding means in the context of virology.

Ok .. interesting .. how does virology modify that context?

 

[Tanj]

Looks like one has to be cautious when using the classification of 'naked' as an explanation for a short longevity of a given virus(?) Naked RNA viruses which persist in nature are clearly contagious, no? (Eg: the Norovirus)?

Lol..umm, in this context, "naked" means doesn't have a lipid envelope around it's virion capsid proteins. It doesn't mean it's naked RNA out there unprotected in the wild. It means the capsid is naked.

Norovirus very much has a protective capsid. It just doesn't have an envelope as well. viroids are a better example of a truly naked RNA, but they're weird and special and muddy the waters of this conversation.

I guess you mean its not assumed that extracellular RNA is floating around in the sample here(?)

I also mean the processing might get rid of them if they existed. There's likely an RNAse step to get rid of potential contaminant in there somewhere. Any free floating extracellular RNA that somehow survived to the test tube would get washed away as rubbish. (potentially, I don't know the actual methodology for these tests).

I get what you're saying here .. I guess some viral RNA types can still persist, perhaps inactively, for long times (inside host cells) following an initial infection though, (eg: as described in latent, lytic and lysogenic infection modes), with no outward clinical signs of infection (asymptomatic).

It's very rare for RNA only viruses to do this. DNA viruses do it all the time. RNA viruses with DNA intermediates (like HIV) do it alot as well. RNA only viruses, not so much. HepC does it. I think by constantly maintaining an extremely low replication (i.e. is never truly latent).

Also, terms like lytic and lysogenic are really only used in reference to bacteriophage infecting bacteria.

Ok .. interesting .. how does virology modify that context?

Shedding specifically refers to the release of infectious virions out into the environment. You look like you meant it in terms of detritus escaping a dying cell.

 

[SelfSim]

.. Shedding specifically refers to the release of infectious virions out into the environment. You look like you meant it in terms of detritus escaping a dying cell.

So, the issue is: when people test positive (PCA) during the recovery phase, they are shedding viral genetic material, but are they necessarily shedding active (ie: intact) virions?
The alternative case is if they test negative, then there is no evidence they are shedding either of these .. Ie: there's no evidence of shedding (end of story).

 

[Tanj]

So, the issue is: when people test positive (PCA) during the recovery phase, they are shedding viral genetic material, but are they necessarily shedding active (ie: intact) virions?

Which brings me back to no. As I said earlier, there's no mechanism to excrete viral RNA into the lung, and if there was it would be degraded beyond detection before you could get to it. If your PCA returns positive it's because of virus particles...or, depending on the swab and methodology, RNA from inside cells harvested during the PCA prep.

The alternative case is if they test negative, then there is no evidence they are shedding either of these .. Ie: there's no evidence of shedding (end of story).

Right. negative means no virus...or a false negative (which is to say there is virus, but the test failed to detect it),

 

[SelfSim]

Which brings me back to no. As I said earlier, there's no mechanism to excrete viral RNA into the lung, and if there was it would be degraded beyond detection before you could get to it.

Hmm .. whilst this doesn't necessarily undo what you say there, as with most of biology, there appears to be some shades of grey in that .. see:
Intricate relationships between naked viruses and extracellular vesicles in the crosstalk between pathogen and host
.. which makes the case for viral RNA propagation by making use of extracellular vesicles (EVs). Seems to apply to non-enveloped viral capsids containing the viral genome (and even goes further in considering the idea that EV carrying viral RNA in the absence of a capsid, can lead to infection of recipient cells).

Seems to also permit evolution based speculation that such a mechanism can go either way as far as enhancing, inhibiting, speeding up or slowing down the spread of infection by means of changing its appearance as it spreads .. Interesting.

 

[SelfSim]

Interesting news report from Australia on yet another batch of unusable serotology (antibody) tests here.

The more technical comments about antibody tests in general are quite a surprise however (see emboldened quotes below):

"The reality is, at the moment, they are not useful," said Professor Carola Vinuesa, one of the authors of the government report and co-director of the NHMRC Centre for Personalised Immunology at the Australian National University.

"At the moment, the quality does not seem to be good enough for these tests to be deployed in large scale."

"The sensitivity is not very good. They are not useful in being able to say 'you were infected'."

Professor Vinuesa said no test currently developed was accurate enough to reliably detect antibodies.

"Most individual results will be false positives," she said. "You cannot have most positive results being false."

A spokesman later said the government ended up buying only 1 million tests, after a third supply contract was cancelled.

"These tests have been purchased as they may have a role to play in population level serosurveillance," the spokesman said.

The current COVID-19 test, known as PCR, can only tell if a person is currently infected. Antibody tests are considered crucial by epidemiologists because they will give, for the first time, a true estimate of the number of people who have caught COVID.

But they are extremely difficult to make 100 per cent accurate.

Antibody levels can vary significantly between people, with some having very low levels. In addition, the tests may also pick up antibodies to other viruses that are similar to COVID-19.

"That gives the potential we are identifying people who have just been exposed to the common cold," said Professor Ivo Mueller, head of immunity at the Walter and Eliza Hall Institute.

Professor Mueller's team is currently trying to make their own accurate antibody test - a process that is proving difficult.

So, from this, one is left with the impression that both the the specivity and sensivity of Covid-19 serotology tests seem to not satisfy their intended purpose (which is unsettling .. in the least)?

 

[SelfSim]

Which brings me back to no. As I said earlier, there's no mechanism to excrete viral RNA into the lung, and if there was it would be degraded beyond detection before you could get to it. If your PCA returns positive it's because of virus particles...or, depending on the swab and methodology, RNA from inside cells harvested during the PCA prep.
...

Once the immune system has killed virus infected cells, the remnants are shed. These remnants are detected by the sensitive PCR/swab tests. Positive results doesn't necessarily imply infectious virions are present .. but they may be.

No, partly for the reasons mentioned above, also because immune mediated cell killing involves apoptosis, an ordered shutdown that does NOT involve uncontrolled release of DAMP and PAMP, amongst other things.

If you are detecting RNA then it is coming from an active infection, either virions or infected cells. Also, that's not what shedding means in the context of virology.

Well news today from here:
South Korea Says Patients Who Retested Positive After Recovering Were No Longer Infectious
says:

On Monday, the country’s Center for Disease Control (KCDC) announcedthat it had studied 400 recovered Covid-19 patients, 285 of whom retested positive for the virus after they recovered; the KCDC then traced the close contacts of those individuals and found zero new cases of infection among 790 close contacts.

Looks they are concluding false positives produced by PCR testing:

The recovered patients retested positive because the test, known as a diagnostic polymerase chain reaction (PCR) test, falsely identified dead viral matter as active Covid-19 infection, according to health officials.

It is unclear whether the country and test manufacturers are working to remedy, or have fixed, this testing flaw.

So the question remains .. How does the body excrete 'dead viral matter' which is then detectable via PCR tests, when there is no such known process? (Refer to PAMPs and DAMPs given above by Tanj, (with which I concur).

What is going on here?

 

[Tanj]

Well news today from here:
South Korea Says Patients Who Retested Positive After Recovering Were No Longer Infectious
says:Looks they are concluding false positives produced by PCR testing:
So the question remains .. How does the body excrete 'dead viral matter' which is then detectable via PCR tests, when there is no such known process? (Refer to PAMPs and DAMPs given above by Tanj, (with which I concur).

What is going on here?

Well, it doesn't have to be excreted in a dead state, it could exit live and then get inactivated. Also, it's not even clear what "dead viral matter" even means, and given the sensitivity of PCR the positives could also be due to

a) An actual false positive due to method error or contamination
b) "Live" virus which nevertheless falls below the level of infective dose.

The very existence of any viral material days or weeks after allegedly being "recovered" is a better thing to worry about. There's a woman here in Australia that seems to have a chronic relapsing disease for the last 60 days.

 

[SelfSim]

Well, it doesn't have to be excreted in a dead state, it could exit live and then get inactivated.

I think these results were produced after culture testing(?)
(Ie, for others: the 'positive' matter did not grow up sufficiently in lab-cultured isolates/patient samples to be called an 'infectious load').

Also, it's not even clear what "dead viral matter" even means, and given the sensitivity of PCR the positives could also be due to

a) An actual false positive due to method error or contamination
b) "Live" virus which nevertheless falls below the level of infective dose.

Slightly better report is here:

These tests "are very simple," said Carol Shoshkes Reiss, a professor of Biology and Neural Science at New York University, who was not involved in the testing. "Although somebody can recover and no longer be infectious, they may still have these little fragments of [inactive] viral RNA which turn out positive on those tests."

She continues:

That's because once the virus has been vanquished, there is "all this garbage of broken-down cells that needs to be cleaned up," Reiss told Live Science, referring to the cellular corpses that were killed by the virus. Within that garbage are the fragmented remains of now non-infectious viral particles.

I don't get it .. (for all the perfectly valid reasons you have provided).

The very existence of any viral material days or weeks after allegedly being "recovered" is a better thing to worry about. There's a woman here in Australia that seems to have a chronic relapsing disease for the last 60 days.

Yes .. its hard to see how that could be explained by a lack of specivity or an over-sensitivity inherent in the PCR test itself? (Ie: your (a) above) - from what I've read on the PCR test, it either singles out the spike protein sequences, and the US version looks for parts of the actual viral RNA sequence ie: nucleus/capsid .. not envelope, (they also do other cross-checks to make sure its passing the right matter onto the amplification stage), I think, so its hard to see how non-infectious partial viral RNA could return a positive other than by way of the targetted infectious virion being still intact?

Your (b) above, I suppose, depends on the lab culture process and what then determines an 'infectious' or 'non-infectious' viral load (I'm not sure how all that works at the moment).

 

[(° ͡ ͜ ͡ʖ ͡ °) (ᵔᴥᵔʋ)]

I guess I will be staying home for another year...

Or we can go all out "Mad Max" and everyone can fend for themselves.