COVID-19

[John Palmer.]

I don't think all reinfection are well documented. I don't even think that the WHO asks anything about it. It doesn't appear in their reports :
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210105_weekly_epi_update_21.pdf?sfvrsn=15359201_12&download=true

Not even straight cases are well documented. They were underreported by a factor of ten or so during the first wave, and many infections are still not being reported.

What is clear is that there is a huge disproportion between anecdotal or documented reinfections, and first-time infections. Nothing indicates that naturally acquired immunity is not extremely efficacious, at least for a period of ten months. If reinfections start to pop up in big numbers —and health professionals do notice— with old or new strains, we are f****d-up, but until then, spare me the alarms.

[Rodius]

I don't think all reinfection are well documented. I don't even think that the WHO asks anything about it. It doesn't appear in their reports :
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210105_weekly_epi_update_21.pdf?sfvrsn=15359201_12&download=true

Not even cases are well documented. They were underreported by a factor of ten or so during the first wave, and many cases are still not reported.

What is clear is that there is a huge disproportion between anecdotal/well documented reinfections and single infections. Nothing indicates that naturally acquired immunity is not extremely efficacious, at least for a period of ten months. If reinfections start to pop up in big numbers —and health professionals do notice— with old or new strains, we are f****d-up, but until then, spare me the alarms.

So your preference is to not worry about something until it is a big problem.... and THEN you do something about it.

[etienne]

I don't think we can do any valid statistics right now. The number of people healed since more than 6 months is too low, and 6 months seems to be the minimum immunity. At the beginning we had a few fast reinfections, but it could have been positive people who had a false negative.

[vox_mundi]

New Covid Variant From Brazil Detected In Japan
https://www.reuters.com/article/us-health-coronavirus-japan-variant/new-coronavirus-variant-found-in-travellers-from-brazil-japan-government-idUSKBN29F08R

A new coronavirus variant has been detected in four travellers from Brazil’s Amazonas state, Japan’s health ministry has said, in the latest recorded instance of the virus evolving, Reuters reports.

A ministry official said studies were underway into the efficacy of vaccines against the new variant, which differs from highly-infectious variants first found in Britain and South Africa that have driven a surge in cases.

Brazil’s Health Ministry said it has been notified by Japan’s authorities that the new variant has 12 mutations, and one of them has already been identified also in the variants found in the United Kingdom and in South Africa. “It implies in a potential higher virus infectiousness,” it said.

[Richard Rathbone]

I don't think we can do any valid statistics right now. The number of people healed since more than 6 months is too low, and 6 months seems to be the minimum immunity. At the beginning we had a few fast reinfections, but it could have been positive people who had a false negative.

Depends how severe the infection was and how old the patient was. Tracking antibodies over the summer in the UK found no measurable drop in younger people that had a severe enough infection to know they had it, but they not only dropped fast, they were no longer detectable in about half of older people with milder infections after 3 months. Not a particularly rigorous study, so the numbers are rough, but there's clearly a wide spread in how long immunity is maintained.
Its reasonable for someone younger that had a bad dose in April to be pretty sure they won't get another now, but an older person that got off lightly in the first wave is quite likely to be susceptible again now.

[Shared Humanity]

It would not, perhaps even should not, surprise me if this airborne respiratory coronavirus behaves like others which infect humans. The four coronavirus that are responsible for around 30% of all common colds can infect a person multiple times throughout their lifetime.

[longwalks1]

TWIV (The week in virology) podcast might be an acquired taste.   It starts slow and blah blah and can meander and the end drags on sometimes.   Recent one #705 was with the Colorado State Emily Travanty, PhD Supervisor, Public Health Microbiology and Serology Colorado Department of Public Health and Environment.   The lab that got the first usOFa variant.   

It was awesome.   Back and forth, rapid fire  quality information and she was fantastic at dealing with some of the sideways  left field , left brain questions that popped up. 

For linux   (Everyone has an updated version of youtube-dl  - eh?)

Code: [Select]

youtube-dl "https://youtu.be/yYIDr9mwfAQ"
https://www.microbe.tv/twiv/

[John Palmer.]

So your preference is to not worry about something until it is a big problem.... and THEN you do something about it.

Rodius, it seems we have started off with the wrong foot. Let me try to restart.

My name is John, I am from the USA, and have opinions of my own.

Your (user)name is Rodius, from Australia, and you have opinions of your own.

Please to meet you.

[John Palmer.]

I don't think all reinfection are well documented. I don't even think that the WHO asks anything about it. It doesn't appear in their reports :
https://www.who.int/docs/default-source/coronaviruse/situation-reports/20210105_weekly_epi_update_21.pdf?sfvrsn=15359201_12&download=true

Not even cases are well documented. They were underreported by a factor of ten or so during the first wave, and many cases are still not reported.

What is clear is that there is a huge disproportion between anecdotal/well documented reinfections and single infections. Nothing indicates that naturally acquired immunity is not extremely efficacious, at least for a period of ten months. If reinfections start to pop up in big numbers —and health professionals do notice— with old or new strains, we are f****d-up, but until then, spare me the alarms.

So your preference is to not worry about something until it is a big problem.... and THEN you do something about it.

And no, that's not my position, but I don't welcome unnecessary hysteria

Of course I am concerned with the possibility of the virus mutating, reinfecting, and becoming endemic. Even more now, when infections are nearing a million per day globally. That's a lot of viruses infecting a lot of people, a lot of increased chances of mutations!

The sooner vaccines are distributed and infections diminish, the less chances for virus mutations.

Vaccine manufacturers also have said that they are capable to develop and produce polyvalent vaccines as well, targeting several SARS-CoV-2 strains, in relatively short time.

[Tom_Mazanec]

Thanks for crossing your fingers and toes, people...I am on the Summit County list for vaccination. Now I just have to wait for my phone call.

[harpy]

If you're concerned with mutations, and endemic virus, I hate to tell you this, but the year is now 2021.

In the year 2021, the virus has already mutated several times, there's the UK variant, the South African Variant, there's a new Brazil Variant.

The virus is also endemic.  China has locked down another city. 

[TeaPotty]

I don't welcome unnecessary hysteria

Its pretty clear that you reacted with hysteria to what I posted about what is justifiably somewhat alarming news, and then you project that onto others as THEIR flaw. An interesting peek into the mind of an anti-alarmist coping with an undeniably alarming reality.

Try to find some emotional maturity to handle yourself so we can discuss the facts at hand without your patronizing.

[vox_mundi]

Several Gorillas at San Diego Zoo Test Positive for Coronavirus
https://ktla.com/news/local-news/several-gorillas-at-san-diego-zoo-test-positive-for-coronavirus/amp/

Several gorillas at the San Diego Zoo Safari Park have tested positive for the coronavirus in what is believed to be the first known cases among such primates in the United States and possibly the world.

The park’s executive director, Lisa Peterson, told The Associated Press on Monday that eight gorillas that live together at the park are believed to have the virus and several have been coughing.

It appears the infection came from a member of the park’s wildlife care team who also tested positive for the virus but has been asymptomatic and wore a mask at all times around the gorillas. The park has been closed to the public since Dec. 6 as part of the state of California’s lockdown efforts to curb coronavirus cases.

While other wildlife has contracted the coronavirus from minks to tigers, this is the first known instance of transmission to great apes and it is unknown if they will have any serious reaction.

Wildlife experts have expressed concern about the coronavirus infecting gorillas, an endangered species that share 98.4 percent of their DNA with humans and are inherently social animals.

The gorillas infected at the San Diego safari park are western lowland gorillas, whose population has declined by more than 60% over the last two decades because of poaching and disease, according to the World Wildlife Fund.

The safari park tested the troop of gorillas after two apes began coughing Jan. 6. The test results were confirmed by the U.S Department of Agriculture National Veterinary Services Laboratories.

https://mobile.twitter.com/sdzsafaripark/status/1348721392624168960

[vox_mundi]

Operation Warp Speed Therapeutics: Monoclonal Antibody Playbook Version 2.0
https://info.publicintelligence.net/OWS-MonoclonalAntibodyPlaybook-11-22-2020.pdf









https://publicintelligence.net/ows-monoclonal-antibody-playbook-11-22-2020/

[vox_mundi]

COVID-19 Symptoms Often Linger 6 Months or More; Study
https://www.cidrap.umn.edu/news-perspective/2021/01/covid-19-symptoms-often-linger-6-months-or-more-study-finds

More than three quarters (76.5%) of 1,655 hospitalized COVID-19 patients in Wuhan, China, had at least one symptom 6 months after discharge, reports a Lancet study published late last week.

The most common self-reported symptoms were fatigue or muscle weakness (62.7%) and sleeping difficulties (26.4%), and physical exam follow-ups also showed lung diffusion impairment—which indicates poor oxygen exchange—in 34.1% of patients.

https://www.eurekalert.org/pub_releases/2021-01/tl-pss010721.php

Study participants were discharged from the hospital from Jan 7 to May 29, 2020, and the researchers followed-up a median of 186 days (more than 6 months) later, from Jun 16 to Sep 3. Out of 1,733 people in the cohort, 1,172 (67.6%) needed oxygen therapy, 122 (7.0%) needed ventilation or a similar procedure, and 76 (4.4%) were admitted to the intensive care unit (ICU).

Among those excluded from the study were patients who died (1.3% out of the 2,469 total possible people), had follow-up for other reasons such as psychotic disorders or readmission, or lived in nursing or welfare homes.

The researchers gave a subset of 390 patients pulmonary exams and found diffusion impairment in 21.7% of those who did not need supplemental oxygen, 29.1% of those who received supplemental oxygen, and 55.8% of those who needed ventilation of any kind or a similar procedure.

"This was consistent with findings that the most common abnormal CT pattern was pulmonary interstitial change (GGO [ground glass opacity] and irregular lines), which were similar to the long-term lung manifestations of SARS [severe acute respiratory disease] or influenza," the researchers write, but they noted they had no baseline data.

Patients in the most severe infection group had 4.60-increased adjusted odds (95% confidence interval [CI], 0.80 to 3.25) for diffusion impairment than those who did not need any supplemental oxygen, although the data also revealed that the lungs were continuing to heal in some instances. For instance, GGO levels decreased between 25% to 45% from the height of infection to the follow-up, depending on the infection severity.

Antibody levels fell 52.5% (96.4% seropositivity to 58.5%) in 94 patients who received blood tests at the height of their infection and during their 6-month follow-up. Seven measured antibodies had decreased amounts by the time of follow-up, but more than 90% of patients continued to test positive for N-immunoglobulin (Ig) G, S-IgG, and receptor-binding-domain-IgG antibodies.

Other physical follow-up examinations found that 13% of 822 patients had decreased kidney function after discharge (but no healthy baseline data) and 23% of 1,692 patients performed at subnormal levels at a 6-minute walking test. None of the 390 patients who received follow-up ultrasounds had deep venous thrombosis of the legs.

The researchers assessed 17 symptoms. Besides fatigue/muscle weakness and sleeping difficulties, they included low-grade fever (0.0% prevalence), disordered taste (7.3%) or smell (10.6%), palpitations (9.3%), and hair loss (21.7%). (The researchers do not know if these symptoms began after discharge or held steady or worsened from hospital discharge.) They also found that 22.2% out of 1,617 were experiencing anxiety or depression.

6-month consequences of COVID-19 in patients discharged from hospital: a cohort study
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32656-8/fulltext

[vox_mundi]

Japan Has Found a New Covid Variant. Here's How It Compares to Virus Strains In the UK, South Africa
https://www.cnbc.com/amp/2021/01/11/japan-covid-variant-how-it-compares-to-strains-in-uk-south-africa.html

LONDON — Japan's National Institute of Infectious Diseases on Sunday said it had detected a new variant of the coronavirus in four travelers arriving from Brazil.

The newly discovered mutant strain of Covid-19 was found to share some of the mutations in common with those of concern for increased infectivity, the institute said, referring to highly infectious variants recently discovered in the U.K. and South Africa.

The variant of the virus discovered in Japan belongs to the B.1.1.248 strain and has 12 mutations in the spike protein, the NIID said.

Japan's Health Ministry said studies were underway to determine the effectiveness of coronavirus vaccines against the new variant, Reuters reported Sunday, citing an unnamed ministry official.

-----------------------------------------------

https://www.niid.go.jp/niid/ja/diseases/ka/corona-virus/2019-ncov/10107-covid19-33.html

... ... The novel mutant belongs to the B.1.1.248 strain and has 12 mutations in the spike protein. Similar to VOC-202012 / 01 and 501Y.V2 of mutant strains that are concerned about increased infectivity , N501Y mutation is observed at the receptor binding site of peplomer protein, and E484K mutation is observed as with 501Y.V2.

Mutations in E484 have been reported as escape mutations from monoclonal antibodies that neutralize SARS-CoV-2 (1,2). Furthermore, experimental data (3) that the E484K mutation was found in the escape mutant strain from the recoverer plasma and the neutralizing antibody titer of the pseudotype virus in the recoverer plasma decreased by about 10 times when E484 was mutated. (4) reports that it is difficult to suppress viral cell infection in vitro ( in vitro ) even in the presence of anti-SARS-CoV-2 antibody induced in the serum of COVID-19 recoverers. Has been done. That is, there is a concern that the conventional immunity against the virus may be diminished against the virus having the E484 mutation.

In Brazil, there are reports of reinfection cases with mutant strains showing the E484K mutation of the B.1.1.248 strain (2021/01/06) (5), but they are not the same as the new mutant strain.

The mutant strain is limited to information on gene sequences. At present, it is difficult to determine the infectivity and pathogenicity in humans, the effects on testing methods, the effects on vaccines, etc., and further investigation is required.

[SimonF92]

I thought this was quite interesting;

SARS-CoV-2-induced remission of Hodgkin lymphoma

https://onlinelibrary.wiley.com/doi/epdf/10.1111/bjh.17116

[Richard Rathbone]

Two increased infectivity strains might be coincidence but three looks like a trend.

Its looking very much like while none of the individual mutations do anything much, there are combinations that increase infectivity, and now the virus had had long enough in circulation to pick up a dozen mutations, combinations which increase infectivity start to appear all over the place.

Yet another indicator that vaccines need to be used to wipe it out, not to palliate recurring epidemics like is done with flu.

2020 is near the top in most mortality measures even though the December figures are still some way from being complete. 2020 is likely to be the year in which most deaths have ever been recorded in England and Wales. Its not the sort of thing to invite a repeat of.

https://news.sky.com/story/covid-19-how-mortality-rates-in-2020-compare-with-past-decades-and-centuries-12185275

[gerontocrat]

2020 is likely to be the year in which most deaths have ever been recorded in England and Wales.

https://www.bbc.co.uk/news/uk-55631693
Covid: 2020 saw most excess deaths since World War Two

The Covid pandemic has caused excess deaths to rise to their highest level since World War Two.

There were close to 697,000 deaths in the UK in 2020 - nearly 91,000 more than what would be expected based on the average in the previous five years.

This represents an increase of 15% - making it the largest rise in excess deaths for more than 75 years.

When the age and size of the population is taken into account 2020 saw the worst death rates since the mid 2000s.

This measure - known as age-standardised mortality - takes into account population growth and age.

Mistakes 'cost lives' in a pandemic

Richard Murray, chief executive of The King's Fund, said the picture was likely to worsen given Covid deaths are rising following the surge in infections over recent weeks.

"The UK has one of the highest rates of excess deaths in the world, with more excess deaths per million people than most other European countries or the US.

'It will take a public inquiry to determine exactly what went wrong, but mistakes have been made.

"In a pandemic, mistakes cost lives. Decisions to enter lockdown have consistently come late, with the government failing to learn from past mistakes or the experiences of other countries.

"The promised "protective ring" around social care in the first wave was slow to materialise and often inadequate, a contributing factor to the excess deaths among care home residents last year.

'Like many countries, the UK was poorly prepared for this type of pandemic."

[SteveMDFP]

  and now the virus had had long enough in circulation to pick up a dozen mutations, combinations which increase infectivity start to appear all over the place.

Yet another indicator that vaccines need to be used to wipe it out, not to palliate recurring epidemics like is done with flu.

The virus is under selective pressure to become more contagious, and to become resistant to monoclonal antibodies.  The current vaccines generate antibodies to a small part of the virus--the spike protein. So there's now emerging evolutionary pressure to alter these proteins.

None of this should be surprising, though certainly worrisome.  The current vaccines will likely prove helpful, but insufficient in the long run.  We'll need frequently-updated, multivalent vaccines, and combination anti-viral treatments, both.  Surveillance for arising mutations is going to be a long-term challenge.

When a virus becomes widespread, probability of acquiring adaptive mutations increases as the number of infected persons increases.  Had the world acted more aggressively from the beginning, we would likely not be seeing a proliferation of problematic mutations.  That cat is out of the bag, however.

[harpy]

This report from Russia, indicates that 18 mutations were found on a single human.

The diagnostic test for these "super mutators" is a consistently positive test for the virus, over a long period of time.

https://tass.com/science/1243935

A propensity of the coronavirus to mutate in case of a weakened immunity may lead to an emergence of hundreds of new mutations of the virus in a single body which do not increase death risks for a patient but may be more contagious or resistant to treatment, Director of Kazan Federal University’s Research Clinical Center for Precision and Regenerative Medicine Albert Rizvanov told TASS on Tuesday.

[gerontocrat]

First known virus case found in apes at US zoo

One of the gorillas at the San Diego Zoo Safari Park

As many as eight gorillas have tested positive for Covid-19 at the San Diego Zoo Safari Park, in what is believed to be the first cases of their kind among apes in captivity.

Some of the gorillas have shown symptoms, including coughing, but none appear seriously ill.

While there has been one definitive positive test, all eight are presumed to have been exposed to the virus. It is presumed that the gorilla contracted it from a human handler.

"Aside from some congestion and coughing, the gorillas are doing well," Lisa Peterson, executive director of the San Diego Zoo Safari Park, said in the statement.

"The troop remains quarantined together and are eating and drinking. We are hopeful for a full recovery."

The zoo has been closed since the beginning of December due to the pandemic.

Though this is thought to be the first known case in apes, the virus has shown up in some other animals, including domestic cats and dogs.

[harpy]

Humans are apes.

An ape visiting the zoo must have sneezed in the direction of these other apes, and now all the apes are infected.

[El Cid]

The virus is under selective pressure to become more contagious

I've been thinking about this for a while. How come the R of the flu has not changed in hundreds of years (= did not become more contagious) despite being more prone to mutations???

[wili]

The Basic Reproduction Number is a 20th century concept, so no one was keeping track of it in earlier centuries, so we don't really have data on it going back 'centuries', do we?

from wiki:

The roots of the basic reproduction concept can be traced through the work of Ronald Ross [died 1932], Alfred Lotka [died 1949] and others, but its first modern application in epidemiology was by George MacDonald in 1952

[harpy]

The new coronavirus has mutated numerous times already, from what I've read there's already well over 20 mutations.

The spike proteins do appear to be affected by mutations.

[crandles]

The virus is under selective pressure to become more contagious

I've been thinking about this for a while. How come the R of the flu has not changed in hundreds of years (= did not become more contagious) despite being more prone to mutations???

Do you think centuries should mean infinitely contagious? Perhaps there is a local maximum infectivity for flu and no nearby higher maximums it could jump to?

Or maybe the most infectious strains have already spread immunity?

[vox_mundi]

The virus is under selective pressure to become more contagious

I've been thinking about this for a while. How come the R of the flu has not changed in hundreds of years (= did not become more contagious) despite being more prone to mutations???

Human influenza A virus was discovered in 1933 soon after Shope succeeded in isolating swine influenza A virus in 1931. So I don't understand where you get the centuries idea from. Virology wasn't a science until the late 20's.

---------------------------------------------------

The first modern application of Rθ in epidemiology was by George MacDonald in 1952. Not centuries.

---------------------------------------------------

Vaccination against influenza began in the 1930s with large-scale availability in the United States beginning in 1945.  This has significantly tamped down the reproduction number over the past 75 years.

-----------------------------------------------

Influenza Pandemics of the 20th Century
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291411/

Three worldwide (pandemic) outbreaks of influenza occurred in the 20th century: in 1918, 1957, and 1968. The latter 2 were in the era of modern virology and most thoroughly characterized. All 3 have been informally identified by their presumed sites of origin as Spanish, Asian, and Hong Kong influenza, respectively. They are now known to represent 3 different antigenic subtypes of influenza A virus: H1N1, H2N2, and H3N2, respectively.

Not classified as true pandemics are 3 notable epidemics: a pseudopandemic in 1947 with low death rates, an epidemic in 1977 that was a pandemic in children, and an abortive epidemic of swine influenza in 1976 that was feared to have pandemic potential. Major influenza epidemics show no predictable periodicity or pattern, and all differ from one another. Evidence suggests that true pandemics with changes in hemagglutinin subtypes arise from genetic reassortment with animal influenza A viruses.

[gerontocrat]

https://www.worldometers.info/coronavirus/#countries

UK Data
7 day average of daily deaths now at a record high - nearly 1,000.

But just maybe 7 day average of daily new cases has peaked.

ps: Recovered and active cases data only just appeared on worldometers. Looks a bit dodgy and I can't be bothered to go right back in time to post the data.

[John Palmer.]

I don't welcome unnecessary hysteria

Its pretty clear that you reacted with hysteria to what I posted about what is justifiably somewhat alarming news, and then you project that onto others as THEIR flaw. An interesting peek into the mind of an anti-alarmist coping with an undeniably alarming reality.

Try to find some emotional maturity to handle yourself so we can discuss the facts at hand without your patronizing.

You are literally trying to murder my character without knowing a single iota of me. Actually you're fabricating an entire new character, that of an hysterical flawed anti-alarmist. Your entire post is basically an insult!!

No. I am seriously alarmed by reinfections, human manipulation of nature, AGW, but I wouldn't use 30 pt font size for announcing one case of B117 reinfection because... what's the point?

I am more alarmed by the near one million infections per day globally. I am genuinely alarmed that a worse strain that delays global herd immunity emerges given the current numbers of the pandemics.

B117 has delayed natural herd immunity but vaccines are still efficacious against it, and it seems people that got COVID before are not being affected by the B117 en masse. In fact, that only one B117 reinfection is documented so far gives me some hope. Thank you!

Why do people react so poorly in this Forum? Your entire response is so harsh, so unfriendly and yes, purely insulting.

Let me quote my original response to your flyer, where I use numbers and reasoning to adjust my concerns on the issue at hand. Your response above is personal, emotional, and completely disproportionate.

Whoa!
30pt font size really called our attention, didn’t it?

We are talking about one reinfection.

There are about 10 to 100 reinfections documented so far out of tens of millions of infections. You do note the factor of one million, don’t you? That means naturally acquired immunity efficacy is about 99.99999% while the best vaccine so far has an estimated efficacy of 95%.

[TeaPotty]

Palmer, don't forget you attacked first, and you got a response accordingly. Regardless, you are only getting more emo and off-topic. It sounds like you need to relax, maybe some alcohol or something. Then try to see if you can discuss the topic without attacking others.

[John Palmer.]

Palmer, don't forget you attacked first, and you got a response accordingly. Regardless, you are only getting more emo and off-topic. It sounds like you need to relax, maybe some alcohol or something. Then try to see if you can discuss the topic without attacking others.

I did not do attack to your personality or character, I just said that the use of 30 pt font size seems unnecessary, and yes, can cause certain hysteria. But I don't know you or your persona at all to attack you or your persona, and I have not.

[TeaPotty]

"can cause certain hysteria"

Nobody needs your snobby patronizing, we can handle ourselves. Grow up, and stop dragging discussion off-topic.

[TeaPotty]

Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
https://www.biorxiv.org/content/10.1101/2020.12.16.423118v3

Rafael Najmanovich (one of the paper's authors):
N501Y that we predicted to be more infective, could be one mutation away from N501W that we predict to be even more infective.
https://twitter.com/RNajmanovich/status/1348992630122835972

https://www.biorxiv.org/content/10.1101/2020.12.16.423118v3.full.pdf
The mutation that favours the open state the most in our calculations is N501W... The mutation N501W is predicted to have the largest effect in augmenting the occupancy of the open state relative to the wild type. This mutation is associated with stronger binding to ACE2 (Δlog10(KD,app)=0.11) relative to the wild type Spike (but lower than N501Y). Furthermore, N501W appears to have increased expression relative to the wild type with a Δlog(MFI) of 0.1 compared to decrease in relative expression of -0.14 for N501Y. The authors note that changes in expression correlate with folding stability. However, even with a Δlog(MFI) of -0.14, N501Y is viable and spreading. Therefore, N501W might be even more stable and infective

[gerontocrat]

You should follow the link and watch the video to see yet another reason for why perhaps the USA should be put on suicide watch.

Covid-19: Alabama crowds ignore coronavirus to celebrate championship

Fans of the University of Alabama football team gathered in the streets of Tuscaloosa in Alabama, ignoring social distancing. They were celebrating the university's third national championship in the past six years.

https://www.bbc.co.uk/news/av/world-us-canada-55641084

[kassy]

I suggest using bold text for highlights and skipping non standard letter size.

[vox_mundi]

What about straw man arguments? And wild-ass guesses?

https://forum.arctic-sea-ice.net/index.php/topic,3376.msg297808.html#msg297808

... I agree, but one scenario demands several years of natural virus evolution (accelerated by overpopulation by a factor 10?

Do you have anything to support that claim?

No, I don't. It is a wild ass guess. ...

[kassy]

I suggest discussing them on the relevant thread.

[SteveMDFP]

The virus is under selective pressure to become more contagious

I've been thinking about this for a while. How come the R of the flu has not changed in hundreds of years (= did not become more contagious) despite being more prone to mutations???

I strongly doubt that influenza has a constant R value.  We have severe and less severe seasonal epidemics.  Because of the potential for large genetic shifts in some years, some strains can be more contagious than those in other years.   Something like 20% of the world's population gets infected with influenza in a given year.  Over a few years, substantial herd immunity develops to a dominant strain.  Then a strain with genetic shift picks up the baton.

[vox_mundi]

^ related

Human influenza A virus was discovered in 1933 soon after Shope succeeded in isolating swine influenza A virus in 1931. Virology wasn't a science until the late 20's.

---------------------------------------------------

The first modern application of Rθ in epidemiology was by George MacDonald in 1952.

---------------------------------------------------

Vaccination against influenza began in the 1930s with large-scale availability in the United States beginning in 1945.  This has significantly tamped down the reproduction number over the past 75 years.

-----------------------------------------------

Influenza Pandemics of the 20th Century
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3291411/

Three worldwide (pandemic) outbreaks of influenza occurred in the 20th century: in 1918, 1957, and 1968. The latter 2 were in the era of modern virology and most thoroughly characterized. All 3 have been informally identified by their presumed sites of origin as Spanish, Asian, and Hong Kong influenza, respectively. They are now known to represent 3 different antigenic subtypes of influenza A virus: H1N1, H2N2, and H3N2, respectively.

Not classified as true pandemics are 3 notable epidemics: a pseudopandemic in 1947 with low death rates, an epidemic in 1977 that was a pandemic in children, and an abortive epidemic of swine influenza in 1976 that was feared to have pandemic potential. Major influenza epidemics show no predictable periodicity or pattern, and all differ from one another. Evidence suggests that true pandemics with changes in hemagglutinin subtypes arise from genetic reassortment with animal influenza A viruses.

[vox_mundi]

Chinese Covid-19 Vaccine Far Less Effective Than Initially Touted in Brazil
https://www.wsj.com/amp/articles/chinas-sinovac-covid-19-vaccine-is-50-4-in-late-stage-brazil-trials-11610470581

SAO PAULO (Reuters) - A coronavirus vaccine developed by China's Sinovac Biotech was just 50.4% effective at preventing symptomatic infections in a Brazilian trial, researchers said on Tuesday, barely enough for regulatory approval and well below the rate announced last week.

The latest results are a major disappointment for Brazil, as the Chinese vaccine is one of two that the federal government has lined up to begin immunization during the second wave of the world's second-deadliest COVID-19 outbreak.

Several scientists and observers blasted the Butantan biomedical center for releasing partial data just days ago that generated unrealistic expectations. The confusion may add to skepticism in Brazil about the Chinese vaccine, which President Jair Bolsonaro has criticized, questioning its "origins."

... Last week, the Brazilian researchers had celebrated results showing 78% efficacy against "mild-to-severe" COVID-19 cases, a rate they later described as "clinical efficacy."

They said nothing at the time about another group of "very mild" infections among those who received the vaccine that did not require clinical assistance.

Ricardo Palacios, medical director for clinical research at Butantan, said on Tuesday that the new lower efficacy finding included data on those "very mild" cases.

Palacios and officials in the Sao Paulo state government, which funds Butantan, emphasized the good news that none of the volunteers inoculated with CoronaVac had to be hospitalized with COVID-19 symptoms. [... polishing a turd?]

Public health experts said that alone will be a relief for Brazilian hospitals that are buckling under the strain of surging case loads. However, it will take longer to curb the pandemic with a vaccine that allows so many mild cases.

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[vox_mundi]

Immunological characteristics govern the transition of COVID-19 to endemicity
https://science.sciencemag.org/content/early/2021/01/11/science.abe6522.full



We are currently faced with the question of how the CoV-2 severity may change in the years ahead. Our analysis of immunological and epidemiological data on endemic human coronaviruses (HCoVs) shows that infection-blocking immunity wanes rapidly, but disease-reducing immunity is long-lived.

Our model, incorporating these components of immunity, recapitulates both the current severity of CoV-2 and the benign nature of HCoVs, suggesting that once the endemic phase is reached and primary exposure is in childhood, CoV-2 may be no more virulent than the common cold. We predict a different outcome for an emergent coronavirus that causes severe disease in children.

These results reinforce the importance of behavioral containment during pandemic vaccine rollout, while prompting us to evaluate scenarios for continuing vaccination in the endemic phase.

[Sebastian Jones]

Canada has considerable pharmaceutical and virological expertise:
'Canada has been a global leader in vaccine development before. In the middle of the last century, public labs in Ontario and Quebec provided the ability to produce them here at home. Toronto's Connaught Laboratories played a key role in developing the polio vaccine in the 1950s, for example.'
Canada lost its facilities during a period of austerity minded governments. The current pandemic has led us to realize this was a short sighted and ultimately expensive action. So, Canada is now building its capabilities back up.
Ultimately it aims to have the capacity to produce up to a billion doses a year, and thus able to help supply vaccines to the world in general.
https://www.cbc.ca/news/health/vaccine-development-production-in-canada-1.5868398

[El Cid]

The virus is under selective pressure to become more contagious

I've been thinking about this for a while. How come the R of the flu has not changed in hundreds of years (= did not become more contagious) despite being more prone to mutations???

I strongly doubt that influenza has a constant R value.  .....

Influenza has a very low R:

https://bmcinfectdis.biomedcentral.com/articles/10.1186/1471-2334-14-480

"Twenty-four studies reported 51 R values for the 1918 pandemic. The median R value for 1918 was 1.80 (interquartile range [IQR]: 1.47–2.27). Six studies reported seven 1957 pandemic R values. The median R value for 1957 was 1.65 (IQR: 1.53–1.70). Four studies reported seven 1968 pandemic R values. The median R value for 1968 was 1.80 (IQR: 1.56–1.85). Fifty-seven studies reported 78 2009 pandemic R values. The median R value for 2009 was 1.46"

This is pretty stable between 1,5-1,8. And I am sure the R could not have been much lower in previous centuries (as that would have made the R too low for it to meaningfully spread). So influenza likely has a very low R for a very long time.

Everyone said upthread that covid will select for higher R because that is what always happens with contagious diseases (less deadly, spreads quicker). This does not seem to be the case for the flu despite being around for centuries! 

[Richard Rathbone]

Everyone said upthread that covid will select for higher R because that is what always happens with contagious diseases (less deadly, spreads quicker). This does not seem to be the case for the flu despite being around for centuries!

If there is a readily accessible mutation series that leads to a better variant, that variant will occur and then be selected for, but if it needs a dozen mutations, and ten of these are detrimental unless all twelve are present, it isn't going to get there.

COVID lineages mutate about once a month on average, so any advantage that only took one mutation to achieve was probably already found between when it was in a bat in October and noticed in Wuhan in December. This process was seen in mink farms when sequencing was done close enough to the species jump to catch it happening, but there weren't enough sequences done soon enough after it jumped into humans to spot the initial adaptation.

What we are seeing now is combination effects, variants that require multiple mutations that are individually neutral but help the virus spread when they are all present. Its seems there are multiple combination options that it takes roughly a year's worth of random walking to stumble across, but which are powerful enough to take over once they have happened.

[John Palmer.]

What about straw man arguments? And wild-ass guesses?

https://forum.arctic-sea-ice.net/index.php/topic,3376.msg297808.html#msg297808

... I agree, but one scenario demands several years of natural virus evolution (accelerated by overpopulation by a factor 10?

Do you have anything to support that claim?

No, I don't. It is a wild ass guess. ...

Why do you drag this here? Just to add some gratuitous discrediting to me? I did not engage with you not even once, and certainly you had not engaged with me before. So your first interaction is to just throw one more stone, Vox_mundi?

I am, genuinely, flipping out about the normal behavior around here.

[SteveMDFP]

This is pretty stable between 1,5-1,8. And I am sure the R could not have been much lower in previous centuries (as that would have made the R too low for it to meaningfully spread). So influenza likely has a very low R for a very long time.

Everyone said upthread that covid will select for higher R because that is what always happens with contagious diseases (less deadly, spreads quicker). This does not seem to be the case for the flu despite being around for centuries!

An R value of 1.5 - 1.8 is not "very low."  It's quite high, when you consider exponential growth.  Probably about 5 days from time of infection to time of spread to another.

From the virus' perspective, a higher R value could mean that a given village all comes down with the flu, everyone goes to bed and recovers, and the virus never gets to spread to the next village.  It wants to circulate in a community for a longer time, for more opportunities to spread to the next community.

Covid is contagious for longer for an individual, so a higher R does not have this disadvantage.  As long as people can be contagious for more than a week, then the higher the better.  All the better if some people are asymptomatic.  Those people will travel rather than take to their beds.  This virus functions extremely well for producing the problems it has.  A tough nut to crack.

[harpy]

The human incubation "super mutator" is a dangerous factor.   The human incubation chamber (see my previous article, of a human being infected for 6+ months but never actually killing the virus due to immune issues).  This will change the natural selection factors the virus experiences, with ZERO incentive to behave like a typical virus, that mutates when spread between humans.

What could emerge from this situation are virus mutations that are quite different from its original form, but no incentive to reduce fatality, since it's being incubated in an artificial environment.
 The host develops partial (incomplete) immunity at first, which protects the human incubation chamber from death, but the virus itself is then allowed to mutate into more harmful forms.

Look out for more and more mutations in the coming months and years.

We're not even close to the end, and if this trend continues, the virus will permanently end our previous way of living.

On the other hand, one big accomplishment thus far is a 10% reduction in CO2 emissions.   

[vox_mundi]

US Sees New Record of 4,327 Covid Deaths In a Single Day
https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

The US recorded its highest single daily death toll of the pandemic on Tuesday, according to figures published by Johns Hopkins university.

According to the new figures, yesterday the US recorded 215,805 new coronavirus cases, and 4,327 further deaths. This takes the total death toll in the pandemic in the US to 380,485, and is the highest daily death figure recorded by the university since the pandemic began. The previous highest figure of 4,194 was recorded on 7 January.

The Covid Tracking Project reports that 131,326 people are currently hospitalized in the US with Covid-19. It is the 42nd day in a row that the figure has exceeded 100,000.

The pandemic has killed more than 1,963,557 million people worldwide

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New Study Suggests College Campuses Are COVID-19 Superspreaders
https://medicalxpress.com/news/2021-01-college-campuses-covid-superspreaders.html



College campuses are at risk of becoming COVID-19 superspreaders for their entire county, according to a new vast study which shows the striking danger of the first two weeks of school in particular.

Looking at 30 campuses across the nation with the highest amount of reported cases, experts saw that over half of the institutions had spikes—at their peak—which were well above 1,000 coronavirus cases per 100,000 people per week within the first two weeks of class.

In some colleges, one in five students had been infected with the virus by the end of the fall term. Four institutions had over 5,000 cases.

"At the University of Notre Dame, for instance, all 12,607 students were tested before the beginning of class and only nine had tested positive. Less than two weeks into the term, the seven-day incidence was 3083, with a reproduction number R0 of 3.29.

Senior author, Ellen Kuhl, adds: "Strikingly, these local campus outbreaks rapidly spread across the entire county and triggered a peak in new infections in neighbouring communities in more than half of the cases.

In 17 of the campuses monitored, a new computer model developed by scientists at Stanford University shows outbreaks translated directly into peaks of infection within their home counties.

Out today, the team's research—published in the peer-reviewed journal Computer Methods in Biomechanics and Biomedical Engineering—crucially shows, however, that tight outbreak management, for example the immediate transition from in person to all online learning, can reduce the peaks within about two weeks


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UK May Move Patients Into Hotels to Ease Hospital Strain
https://medicalxpress.com/news/2021-01-uk-patients-hotels-ease-hospital.html

Health Secretary Matt Hancock said Wednesday that the National Health Service was looking at various ways to reduce the strain on hospitals, including moving patients to hotels when appropriate. Discussions about the issue were first reported by the Guardian newspaper.

"We would only ever do that if it was clinically the right thing for somebody," Hancock told Sky News. "In some cases, people need sit-down care, they don't actually need to be in a hospital bed."

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British Virus Variant Now In 50 Countries
https://medicalxpress.com/news/2021-01-british-virus-variant-countries.html

The coronavirus mutation first found in Britain has now spread to 50 territories, according to the World Health Organization, while a similar South African-identified strain has now been found in 20.

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Google Urgently Investigating Android Coronavirus Tracking App Issues
https://www.theverge.com/2021/1/13/22228594/google-coronavirus-tracking-app-exposure-notifications-issues-problems

Google says it’s working quickly to investigate issues with Android apps that use the Android Exposure Notifications System to track the spread of COVID-19. An unknown issue is causing apps to take longer to load or conduct regular exposure checks. The NHS COVID-19 app that’s used across England and Wales is affected by this Android issue, with a loading notification stuck in the notifications area for many users.



These issues are affecting all apps worldwide that use the Android Exposure Notifications System.

[gerontocrat]

UK deaths today 1,564.
To put that in perspective, an equivalent figure for the USA based on population would be around 7,500.