Tag Archives: SARS-CoV-2

The presidential election will be decided in the next month — revision for clarity

Apologies to all for the previous post which was far murkier than it could have been.  The problem was that a ‘case’ of the pandemic coronavirus can mean 3 very different things.  These distinctions are tedious but crucial.

Meaning #1 — COVID19 — People who are clinically ill with the virus (official name SARS-CoV-2).  These are the people that  may die of the illness, although most do not.

Meaning #2 — The viral genome has been found in your saliva.

Meaning #3 — You have antibodies to the virus in your blood.

Here is the distinction between #2 and #3 — Antibodies (proteins) and genomes (RNA) are completely different chemically. Finding the actual genome (RNA in this case) of a virus in an individual  is like seeing a real bear up close and personal.  This can do you some damage.  In contrast, antibodies to the virus are made by an individual who has been infected by the virus in the past.       Antibodies are like seeing the tracks of the bear without the bear itself. You can’t see tracks without the bear having been present at some point in the past.  Antibodies mean you were infected at some point whether you knew it or not.

OK, so here’s another shot at what was I saying in the previous post.

I find it very sad that loosening the restrictions on activity has become so political. The left says that it will be a disaster and that cases and deaths will spike (meaning #1). As far as I’ve seen, they never say they hope they’re wrong.  The right says that deaths will continue, but the rate won’t increase.  There is evidence for both sides, but in the coming months we’ll actually have data one way or the other.

One thing is certain.  The number of cases of positive viral culture (meaning #2) will increase.  It has to because more people will be tested. So far, we’ve only studied around 1/1,000 of the population.  No one has ever said the lockdown will prevent new infection.  It hasn’t, but it has slowed things down.

I’m hoping that cases of COVID19 and death will not explode.  Not because I want Trump to win, but because getting people back to work  would be good for the country.  Should that happen, the anger of those who lost their jobs or businesses during the shutdown will be formidable.  Trump will win.

Should deaths from COVID19 explode (meaning #1) as restrictions are lifted, Trump is toast.

We should also get some idea of the percentage of the population who have been infected (manifest by antibodies to the pandemic virus meaning #3).  It almost certainly will increase, unless those already showing the antibodies lose them (which is unheard of happening this fast inFor  the antibodies we’ve studied in the past).

I’m cautiously optimistic that not much will happen when restrictions are eased. Here’s why.  All the studies on antibodies (meaning #3) done so far show they are 10 – 100 times more prevalent than cases where the virus is cultured (meaning #2).  For example 20% of Manhattan sampled population have the antibodies.  This implies that most infections with the pandemic coronavirus are asymptomatic.  

Another viral disease with a high prevalence of antibodies is infectious mononucleosis.  90% of adults in the USA have antibodies to mono, but far fewer than 90% were ever sick.

So the number of cases with positive culture (meaning #2)  isn’t what’s important.  It’s how many of them get sick with COVID19 (meaning # 1).  I think we have very good past statistics on the number of deaths and cases of COVID19   It will be clear if there is a spike in COVID19.

However be careful not to read too much into the first week’s statistics after restrictions are lifted, as there is a lag period of 2 – 11 days between infection and clinical illness.  Also try to understand which of the 3 meanings of “case” the article you are reading is talking about — this won’t always be possible.

 

Covid19* could be coming for you — take 2

Flattening the curve (by social isolation) was never about completely preventing new infections.  It was about slowing the rate of rise in new infections so hospitals wouldn’t be overwhelmed.  That was the state of play when I wrote the following post 29 March (seems like ages ago doesn’t it?)

A friend and his wife are getting 3 days of meals delivered to their room in their retirement home.  Clearly a great way to socially isolate themselves.  This will help ‘flatten the curve’.  What that means is that the peak won’t be as high, so we won’t run out of beds and respirators.

But look at the curve in this article — https://www.flattenthecurve.com

Now integrate the area under the curve.  Looks like the number of cases is comparable (more actually under the flattened curve).

Add this to the extreme likelihood that covid19 will become endemic in the population (given the number of cases out there).  This means that absent a vaccine or a treatment, you will meet it sooner or later with whatever biologic resources you have.

On the positive side, the amount of research into the way virus kills is only matched by the number of therapeutic trials underway (both enormous).  The way the journals have opened up so results are widely available gratis and freely shared is impressive.

There is no question that the virus has become endemic, with no study of the presence of antibodies to the virus coming in at less than 4%, and that in Manhattan coming in at 20%.

So those unhappy about loosening restrictions have essentially shifted the goals of social isolation from slowing the rate of new infections (which has happened) to preventing new infections, something that I think is impossible.  We’re about to see if there will be a massive explosion of new cases of covid19 (which is symptomatic infection with SARS-CoV-2 rather than just the presence of its genome) or not, in the 15 or so states starting to loosen restrictions.

The studies showing antibody prevalence greater than 3 – 4% (which is essentially all of them that I’m aware of) argue that we won’t see an explosion in symptomatic infections.  That’s just about everyone’s hope (even those predicting disaster) and it’s what I think will happen.   Nothing like data to prove you right or wrong.  We’re about to find out.

As always, watch out for premature celebrations of rightness or wrongness — see https://luysii.wordpress.com/2020/04/29/watch-the-press/

  • Actually the title is incorrect, but the first post in the series was written 5 weeks ago, when most people knew what COVID19 was, the point of these posts being communication.  The virus itself is not COVID19 which stands for the illness the virus produces.  A variety of names have been applied to the virus — Chinese flu, Wuhan virus, coronavirus2.  The correct name is SARS-CoV-2 — hardly rolls trippingly off the tongue does it?  One should also distinguish finding the genome of the virus (RNA) which implies active infection, from antibodies to the virus which imply a past infection (the difference between seeing a bear and seeing its tracks).  So the correct title is really SARS-CoV-2 is coming for you – take 2 (if you’re a pedant)

Watch the press

We are about to embark on a variety of social experiments, in removing the restrictions on our activities.  This will be accomplished many different ways, in many different locales (which is good, because if there ever was a country where one size does not fit all, it is the USA).  But beware of what you read about the effects. There are people who will be proved very wrong either way — if nothing happens, or if cases and deaths skyrocket.

It’s good to see that people are being explicit about their predictions.  Here are two, both of which can’t be right

https://www.theatlantic.com/health/archive/2020/04/why-georgia-reopening-coronavirus-pandemic/610882/ — Here’s how it begins —

Georgia’s Experiment in Human Sacrifice

https://www.theepochtimes.com/as-ccp-virus-brings-a-taste-of-fascism-trump-needs-to-end-us-overreaction_3330804.html

As CCP Virus Brings a Taste of Fascism, Trump Needs to End US Overreaction

Also beware of breathless reports of nothing happening in the first few days confirming that it was OK to lift restrictions, again because new cases will take a while to show up, and new deaths from the disease will take even longer.

They may be right, they may be wrong, but at least we’re about to find out.

 

Addendum 1 May: If you have the time, please read Matt Taibbi’s latest article — https://taibbi.substack.com/p/temporary-coronavirus-censorship.
It shows just how invested the ‘don’t relax restrictions’ side is in having the experiment fail.  Toward the end of Taibbi’s article you’ll find a series of quotes in January from the same bunch showing why you shouldn’t worry about the coronavirus.  I wish I’d saved them.  I knew better, because I’d been closely following what was going on in China  since 1 Jan because I have a son, daughter-in-law and two grandchildren living in Hong Kong. Here’s a link to that old post of 27 January — https://luysii.wordpress.com/2020/01/27/what-to-do-about-the-wuhan-flu/

Here is the last post on the subject.  Good luck to us all

Gentlemen, place your bets

It’s time for us all to think like a doc who’s ordered a bunch of tests on a fairly sick patient.  The good ones don’t wait for them to come in and then figure out what to do.  They usually concentrate on the worst cases and make plans.

Before going any further, please read the following paragraph. I’m sorry to keep putting this in, but I don’t want to leave anyone behind. Finding the actual genome (RNA in this case) of a virus in an individual  is like seeing a real bear up close and personal.  This can do you some damage.  In contrast, antibodies to the virus are made by an individual who has been infected by the virus in the past.  Antibodies (proteins) and genomes (RNA) are completely different chemically.      Antibodies are like seeing the tracks of the bear without the bear itself. You can’t see tracks without the bear having been present at some point in the past.

Well we’re in that situation in the USA.  Based on many studies now (California, New York State, Prison systems) the number of people who’ve been exposed to the virus enough to develop their own antibodies to it, is anywhere from 10 – 100 times greater than the number of people in whom the viral genome has been found.  This means that the vast majority of infections with the new coronavirus are asymptomatic.

We’ll have a more accurate picture shortly, but what do you think will happen when New York State (and probably everyone else) repeats the test for antibodies in a few weeks?

Place your bets.

Once you have an antibody to a bug, you have it (at least for a few weeks to months).  This is not true for the elderly and my wife had to be re-vaccinated for measles so she doesn’t give it to our grandkids should she be exposed again.

So repeating the prevalence of antibody studies should show an increasing percentage of people with the antibodies.  The bets have to do with how much increase we will see.  Will NY go from 13% to 26% or higher?  The experience in nursing homes and the disaster in the Soldier’s Home in Holyoke MA, shows that in a vulnerable group the infection rate can explode — https://www.masslive.com/news/2020/04/coronavirus-at-holyoke-soldiers-home-additional-veteran-dies-infection-remains-stable-over-3-days.html. Out of 210 veterans living there 66 have died of COVID19 and 82 more have been infected (showing the genome), since the first case was discovered 21 March.

Showing the conflicting evidence docs have to deal with all the time — consider the prisoner studies — https://www.reuters.com/article/us-health-coronavirus-prisons-testing-in/in-four-u-s-state-prisons-nearly-3300-inmates-test-positive-for-coronavirus-96-without-symptoms-idUSKCN2270RX.

It isn’t clear which test was being used (viral genome or antibodies to the virus).  But this is a younger and healthier population.  Very surprisingly in four state prison systems — Arkansas, North Carolina, Ohio and Virginia — 96% of 3,277 inmates who tested positive for the coronavirus were asymptomatic.

So if healthy people won’t be made sick, what will happen when restrictions on activity (both personal and business) are lifted as they will be shortly?   You have two conflicting pieces of evidence to help you place your bets.  Fortunately the country has not adopted a one-size-fits-all approach, and lots of different experiments of nature will occur.

New York is the epicenter, with the most cases and very high population density.  Symptomatic cases appear to have stabilized even with a 10fold higher transmission rate (as measured by antibody prevalence) than that measured by finding the viral genome itself.

What would be your guidance here?

It’s time to pay our respects to Dr. Janeway who first focused on the innate immune system 30 years ago — https://en.wikipedia.org/wiki/Charles_Janeway.  Obviously if we had to wait the week or so for antibodies to develop to fight off infections, we’d all be dead.  The innate immune system is much older evolutionarily than antibodies and starts working immediately.  We are still finding out how complex it is. https://en.wikipedia.org/wiki/Innate_immune_system.

Like everything else, the innate immune system weakens with age, possibly explaining the difference in clinical outcome between the vets at the Soldier’s home and the prison inmates.

It’s hard to place a bet when you’re wishing for the best possible outcome as are most of us. Some people are highly invested in the worst possible scenarios, particularly those who’ve predicted them.  My guess is that we won’t see a surge in fatal or symptomatic cases as things open up.  What’s yours?

Gentlemen, place your bets

It’s time for us all to think like a doc who’s ordered a bunch of tests on a fairly sick patient.  The good ones don’t wait for them to come in and then figure out what to do.  They usually concentrate on the worst cases and make plans.

Before going any further, please read the following paragraph. I’m sorry to keep putting this in, but I don’t want to leave anyone behind. Finding the actual genome (RNA in this case) of a virus in an individual  is like seeing a real bear up close and personal.  This can do you some damage.  In contrast, antibodies to the virus are made by an individual who has been infected by the virus in the past.  Antibodies (proteins) and genomes (RNA) are completely different chemically.      Antibodies are like seeing the tracks of the bear without the bear itself. You can’t see tracks without the bear having been present at some point in the past.

Well we’re in that situation in the USA.  Based on many studies now (California, New York State, Prison systems) the number of people who’ve been exposed to the virus enough to develop their own antibodies to it, is anywhere from 10 – 100 times greater than the number of people in whom the viral genome has been found.  This means that the vast majority of infections with the new coronavirus are asymptomatic.

We’ll have a more accurate picture shortly, but what do you think will happen when New York State (and probably everyone else) repeats the test for antibodies in a few weeks?

Place your bets.

Once you have an antibody to a bug, you have it (at least for a few weeks to months).  This is not true for the elderly and my wife had to be re-vaccinated for measles so she doesn’t give it to our grandkids should she be exposed again.

So repeating the prevalence of antibody studies should show an increasing percentage of people with the antibodies.  The bets have to do with how much increase we will see.  Will NY go from 13% to 26% or higher?  The experience in nursing homes and the disaster in the Soldier’s Home in Holyoke MA, shows that in a vulnerable group the infection rate can explode — https://www.masslive.com/news/2020/04/coronavirus-at-holyoke-soldiers-home-additional-veteran-dies-infection-remains-stable-over-3-days.html. Out of 210 veterans living there 66 have died of COVID19 and 82 more have been infected (showing the genome), since the first case was discovered 21 March.

Showing the conflicting evidence docs have to deal with all the time — consider the prisoner studies — https://www.reuters.com/article/us-health-coronavirus-prisons-testing-in/in-four-u-s-state-prisons-nearly-3300-inmates-test-positive-for-coronavirus-96-without-symptoms-idUSKCN2270RX.

It isn’t clear which test was being used (viral genome or antibodies to the virus).  But this is a younger and healthier population.  Very surprisingly in four state prison systems — Arkansas, North Carolina, Ohio and Virginia — 96% of 3,277 inmates who tested positive for the coronavirus were asymptomatic.

So if healthy people won’t be made sick, what will happen when restrictions on activity (both personal and business) are lifted as they will be shortly?   You have two conflicting pieces of evidence to help you place your bets.  Fortunately the country has not adopted a one-size-fits-all approach, and lots of different experiments of nature will occur.

New York is the epicenter, with the most cases and very high population density.  Symptomatic cases appear to have stabilized even with a 10fold higher transmission rate (as measured by antibody prevalence) than that measured by finding the viral genome itself.

What would be your guidance here?

It’s time to pay our respects to Dr. Janeway who first focused on the innate immune system 30 years ago — https://en.wikipedia.org/wiki/Charles_Janeway.  Obviously if we had to wait the week or so for antibodies to develop to fight off infections, we’d all be dead.  The innate immune system is much older evolutionarily than antibodies and starts working immediately.  We are still finding out how complex it is. https://en.wikipedia.org/wiki/Innate_immune_system.

Like everything else, the innate immune system weakens with age, possibly explaining the difference in clinical outcome between the vets at the Soldier’s home and the prison inmates.

It’s hard to place a bet when you’re wishing for the best possible outcome as are most of us. Some people are highly invested in the worst possible scenarios, particularly those who’ve predicted them.  My guess is that we won’t see a surge in fatal or symptomatic cases as things open up.  What’s yours?

Addendum 27 April ’20.  People who have predicted terrible things happening by opening up some of the restrictions have their egos and reputations involved if they are proved wrong.  So beware breathless reports of spikes in incidence, hospitalization, deaths occurring in the first few days after the restrictions are lifted.  Remember the mean incubation period is 5 days with a range of up to 11 days. 

The very good news from New York

Today’s news from New York is very good indeed.   But first a joke

If one man tells you that you look like a horse

Ignore him.

If a second man tells you that you look like a horse

Pause and consider

If a third man tells you that you look like a horse

Buy a collar

 

The very good news from New York is that nearly 1 in 7 New Yorkers has antibodies to the new coronavirus.

For those not sure what having an antibody to the virus means as opposed to having the virus itself — see the explanation after the **** at the end of the post.

The New York study is the third one this week.

Study #1 was from Santa Clara County California, by people from Stanford which is located there.  Briefly, the authors advertised for people to be tested for antibodies (hardly a random sample).  They projected that about 4% of the people in a 2 million population county having antibodies to the new coronavirus.

To say the study was not universally loved is an understatement — https://statmodeling.stat.columbia.edu/2020/04/19/fatal-flaws-in-stanford-study-of-coronavirus-prevalence/

And

The Stanford one will likely have to be retracted as it’s been widely reported that there were severe methodological errors and even some basic math errors in the analysis. Also, the current antibody tests are essentially worthless given the high false positive rate (I believe the CEO of Roche made that exact claim today).

The joke tells us to Ignore him.  

Study #2 was from LA and also found that about 4% of the study group had antibodies to the virus  Unlike the Stanford (SF) study — The LA study was composed differently in that its 863 adults were selected through a market research firm to represent the makeup of the county.

A friend  sent me the following “Last week I attended (virtually) a Princeton talk by Prof. Edward Felton dealing with COVID-19 pandemic issues.  Prof. Felton mentioned in his talk that the SARS-CoV-2 antibody tests have about a 5% false positive rate (and likewise, about a 5% false negative rate.  If this is true than the 4% antibody prevalence measured in the California tests is meaningless, right?”

The joke tells us to pause and consider

Study #3 Today’s study is from New York State—- here’s a link –https://www.cnbc.com/2020/04/23/new-york-antibody-study-estimates-13point9percent-of-residents-have-had-the-coronavirus-cuomo-says.html.

The State randomly tested 3,000 people at grocery stores and shopping locations across 19 counties in 40 localities to see if they had the antibodies to fight the coronavirus, indicating they have had the virus and recovered from it. With more than 19.4 million people residents, according to U.S. Census data, the preliminary results imply that at least 2.7 million New Yorkers have been infected with Covid-19.

Buy a collar

All 3 studies are saying the same thing — most people aren’t terribly bothered by the virus.  In another context the following was said “It’s hard to argue with data. We’re scientists. We pay attention to data, we don’t try to un-explain them.”

How can I say that the news is good?  After all,Governor Cuomo is right; the numbers are horrible — 19,453 fatalities and 263,754 cases in the state. But the numbers also mean that the overall mortality is under 1% of those who have been infected with the virus.

This means that we are far closer than we thought to relaxing the restrictions on personal and economic activity than we thought, and that most people are naturally immune to severe complications of the virus.

Addendum 24 April — Today’s Science has critiques of study #1 and study #2 and several more (but not including the NY study) — here’s the link https://science.sciencemag.org/content/368/6489/350 — Not mentioned in the article is the fact that all the studies point the same way — at least a 10 fold increase in the percentage of antibodies vs. the percentage of patients in whom the viral genome can be found.

****

The 263,754 ‘cases’ in New York State, were determined by finding the actual genome (RNA in this case) of the virus in a person.  It’s like seeing a real bear which can do you some damage.  Antibodies to the virus are made by an individual who has been infected by the virus.  Antibodies (proteins) and genomes (RNA) are completely different chemically.      Antibodies are like seeing the tracks of the bear without the bear itself.

A bombshell that wasn’t

Yesterday, a friend sent me the following

” Chinese Coronavirus Is a Man Made Virus According to Luc Montagnier the Man Who Discovered HIV

Contrary to the narrative that is being pushed by the mainstream that the COVID 19 virus was the result of a natural mutation and that it was transmitted to humans from bats via pangolins, Dr Luc Montagnier the man who discovered the HIV virus back in 1983 disagrees and is saying that the virus was man made.”

Pretty impressive isn’t it?  Montagnier says that in the 30,000 nucleotide sequence of the new coronovirus SARS-CoV-2 he found sequences of the AIDS virus (HIV1).  Worse, the biolab in Wuhan was working both on HIV1 and coronaviruses.  It seems remote that a human could have been simultaneously infected with both, but these things happen all the time in the lab, intentionally or not.

It really wouldn’t take much to prove Montagnier’s point.  Matching 20 straight nucleotides from HIV1 to the Wuhan coronavirus is duck soup now that we have the sequences of both.  HIV1 has a genome with around 10,000 nucleotides, and the Wuhan coronavirus has a genome of around 30,000.  Recall that each nucleotide can be one of 4 things: A, U, G, C.  In the genome the nucleotides are ordered, and differences in the order mean different things — consider the two words united and untied.

Suppose Montagnier found a 20 nucleotide sequence from HIV1 in the new coronavirus genome. How many possibilities are there for such a sequence?  Well for a 2 nucleotide sequence there are 4 x 4 == 4^2 = 16,  for a 3 nucleotide sequence 4 x 4 x 4 == 4^3 = 64.  So for 20 nucleotides there are 4^20 possible sequences == 1,099,511,622,776 different possibilities.  So out of the HIV1 genome there are 10,000 – 20 such sequences, and in the coronavirus sequence there are 30,000 -20  such sequences so there are 10,000 times 30,000 ways for a 20 nucleotide sequence to match up between the two genomes.  That 300,000,000 ways for a match to occur by chance — or less than .1%.  If you’re unsatisfied with those odds than make the match larger.  25 nucleotides should satisfy the most skeptical.

But there’s a rub — as Carl Sagan has said  “Extraordinary claims require extraordinary evidence.”  Apparently Montagnier hasn’t published the sequence of HIV1 he claims to have found in the coronavirus.   If anyone knows what it is please write a comment.

Then there’s the fact that Montagnier appears to have gone off his rocker. In 2009 he published a  paper (in a journal he apparently built) which concludes that diluted DNA from pathogenic bacterial and viral species is able to emit specific radio waves” and that “these radio waves [are] associated with ‘nanostructures’ in the solution that might be able to recreate the pathogen”.

Sad.  Just as one of the greatest chemists of the 20th century will be remembered for his crackpot ideas about vitamin C (Linus Pauling), Montagnier may be remembered for this.

On second thought, there is no reason to need Montagnier and his putative sequence at all. The sequences of both genomes are known.     Matching any 20 nucleotide sequence from HIV1 to any of the 30,000 – 20 20 nucleotide sequences from the Wuhan flu is a problem right out of Programming 101.  It’s a matter of a few loops, if thens and go to’s.  . If you’re ambitious  you could start with smaller sequences say 5 – 10 nucleotides, find a match, move to the next largest size sequence and repeat until you find the largest contiguous sequence of nucleotides in HIV1 to be found in the coronavirus.

You can read about the Wuhan lab in an article from Nature in 2017 — https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487

A way to end the pandemic

Could infecting people with the four or so coronaviruses that cause the common cold protect them against the new coronavirus causing the pandemic?   The official name for the new virus is SARS-CoV-2, the name for the disease is COVID-19.

“According to Marie-Louise Landry, MD, an infectious disease expert at Yale Medical School and the Director of the Yale Clinical Virology Laboratory, four common human coronaviruses cause 15-30% of common colds”

https://www.health.com/condition/infectious-diseases/coronavirus/coronavirus-symptoms-vs-cold

Now ask yourself how she could make a statement like this.  I’m going to try to get in touch with her tomorrow, but it is very likely that these cold causing coronaviruses are detected by measuring antibodies to them, carried in the blood of people who have been infected by them in the past.

Could one coronavirus (even a benign one) give partial immunity to others?  It’s possible and it’s time to find out.  We could know  in a few weeks.

Assume the test to measure the antibodies to cold coronaviruses exists.  Then measure them in our real, honest to God, modern day heroes on the front lines  — the nurses, docs, EMTs, orderlies, housekeeping, cops, etc. etc.  who are exposed every day to COVID-19.

Every hospital in the country could at least draw blood on them, look to see if antibodies are present and wait.   I doubt that many would refuse the test.

Sadly, it wouldn’t be long before some of them became infected with SARS-CoV-2.  Then investigators couldlook to see if those with the antibodies to the cold causing coronaviruses were protected.

If so, then make a cocktail of the 4 or so coronaviruses and give it to everyone.   It would be Edward Jenner and the cowpox all over again — https://en.wikipedia.org/wiki/Edward_Jenner

Even if the protection was only partial, decreasing the number of susceptible individuals would be enough to slow the pandemic and possibly even stop it.