Showing posts with label SARS. Show all posts
Showing posts with label SARS. Show all posts

Tuesday, April 14, 2020

The Bat Behind The Coronavirus Pandemic ID'd - And Why This Plague Is Unlikely To Abate Anytime Soon


Market for bats in Yunnan province - ripe and ready to go for Bat soup.   The continued invasion of certain bat habitats to raid for food ensures endless pandemics, and is definitely connected to climate change.

The horsehoe bat (Rhinolophus affinis) the prime culprit in the spread of Covid-19.

"RaTG13 is the name, rank and serial number of an individual horseshoe bat of the species Rhinolophus affinis, or rather a sample of its feces collected in 2013 in a cave in Yunna, China. The sample was collected by hazmat -clad scientists from the Institute of Virology in Wuhan that year.  Stored away and forgotten until January this year, the sample from this bat contains the virus hat caused Covid-19."-  Matt Ridley, 'The Bats Behind The Pandemic', WSJ, April 11-12, p. C5

Matt Ridley's revelation of the bat identity that's spawned the current Covid-19 pandemic was an eye opener for many, especially as he drilled down deep to show what we're up against.   Below, I summarize some of the main findings from his must read WSJ piece;:

-  In an initial foray into Shiton Cave, south of Kumming, Chinese scientists found viruses in the bat droppings and anal swabs "that were more similar to human SARS than anything fond in palm civets, the small mammals until then presumed to be the source of the human infection."

-  Back in the lab the researchers "found that one of the viruses in the droppings, called W1V1, as able to thrive in monkey and human cells- specially engineered to activate the gene for ACE2 rcceptors.  These are the ones that provide the 'lock' to which the coronavirus' protein spike can fit as a key."  This is the lock and key that showed humans could catch SARS from bat droppings and which is the key to the horrific respiratory distress suffered by many patients.

- In 2016, Ralph Baric and collegaues at the University of North Carolina at Chapel Hill "found the same bat virus  could infect live mice that had been engineered to express the same gene for the ACE 2 receptor."  According to the paper published in the wake: "The virus was poised for human emergence,"

-  The role of an animal called the Pangolin, e.g.


was considered in terms of its possible role in the spread of the virus.This was especially given "an illegal pangolin trade  for traditional Chinese medicine brings people into close contact with sick animals."  However, while the role of pangolins in the spread of SARS-COV-2 (the virus that causes Covid-19) remains unclear, "a closer look at the genome (published last week by Maciej Boni at Penn State and David Robertson at Glasgow University)  "found that human versions of the virus were more closely related to the RaTG13 horseshoe bat sample found in a cave."  

But stunningly,  the same analysis showed that "the most recent common ancestor of the human virus and the BaTG13 virus lived at least 40 years ago."  So it is unlikely the cave in Yunnan (1,000 miles from Wuhan) is where the first Covid-19 infection happened or that the culprit bat was taken from that cave to Wuhan to be chucked into a bat soup.  And the kicker: 

"Somewhere much closer to Wuhan there is another colony of bats carrying the same kind of virus"  so that "it looks like a horrible coincidence that China's Institute of Virology - where human cells were being experimentally infected with bat viruses- happens to be in Wuhan, the origin of today's pandemic".   Never mind coincidence! Look for the Reich conspiracy mongers to use it to invent nonsense that this is a Chinese "bio-weapon" or some such rot.

Ridley in his extensive piece goes on to note that bats are "sold directly to restaurants throughout China and southeast Asia, but no direct evidence if their sale to Wuhan's wet markets have come to light."

Which is gratifying to know, so that rational people (including you, Bill Maher) -will now be justified in just calling it Covid-19 and not the lurid "Wuhan virus".   What is not gratifying to learn is that the Yunnan cave sample shows the bat virus didn't need to recombine with viruses in other species in a market to be infectious to people. Instead, "the role of the wet markets may be that other animals got infected there and produce much higher loads of virus than the bats alone would, amplifying the infection."   This, in fact, was the conclusion of one Australian virologist working at a lab with Covid-infected bats in Singapore - and featured on an MSNBC special on the pandemic. She opined to Richard Engel that virus-laden bat guano contaminated a hog pen and got on a butcher's hands - which were then indiscriminately wiped onto another surface- then picked up by an unsuspecting third party.  
More worrying even is the potential for many future pandemics, epidemics, i.e.

"All over Asia and Africa human beings encounter horseshoe bats, any one of which could be carrying a virus that could start an epidemic if amplified in a market or similar setting. Bats have supplied most of the dangerous new diseases of the past two decades including: rabies, Ebola, Marburg and other highly dangerous viruses."

Above all this shows humans need to stay out of bat habitat - invading their caves, or catching the little beasts to put into soup or other exotic dishes. As Ridley points out, even the "tasty" fruit bats carry the Hendra and Nipah viruses - and have been responsible for "small but lethal outbreaks in South Asia and Australia."    More worrisome yet is that bats are long-lived mammals like we are and often live in congested conditions - citing one single bat roost in Texas with 20 million bats  at certain times of the year.  All of which portends a nonstop battle with viruses associated with these critters, and how our encroachment into bat habitats puts us all at risk.  I.e. "One quarter of all mammal species are bats - and they have lots of different viruses. They also fly so can carry diseases long distances."

These findings also torch the claims of a wingnut  WSJ hack named Andy Kessler,  ‘Coronavirus Shatters Complacency’, April 13, p. A15) that:

“The pandemic has awakened us from climate nightmares” 

 By his arguments and clueless statements he  reveals (again)  the inability of the Journal’s stable of neolib capitalists to integrate disparate concepts, realities. In this case, failing to grasp that the pandemic, indeed, is a direct offshoot of humans’ failure to take climate change seriously – and act responsibly.  How so?
Hunting, farming and the global movement of people to cities – and concomitant invasion of wild animal habitat - has led to massive declines in biodiversity and increased the risk of dangerous viruses like Covid-19 spilling over from animals to humans.
We now know  142 viruses have been transmitted from animals to humans over many years, and many have been matched to the IUCN’s red list of threatened species.  The study, published in the journal Proceedings of the Royal Society B, found that the spillover risk was highest from threatened and endangered wild animals whose populations had declined largely due to hunting, the wildlife trade and loss of habitat.  As the paper summary put it:
“Human encroachment into biodiverse areas increases the risk of spillover of novel infectious diseases by enabling new contacts between humans and wildlife … We found that species in the primate and bat orders were significantly more likely to harbor zoonotic viruses compared to all other orders,”
In the words of lead author Christine Kreuder Johnson, director of the EpiCenter for Disease Dynamics at the One Health Institute, of the UC Davis School of Veterinary Medicine.

“Spillover of viruses from animals are a direct result of our actions involving wildlife and their habitat.  The consequence is they’re sharing their viruses with us. These actions simultaneously threaten species survival and increase the risk of spillover. In an unfortunate convergence of many factors, this brings about the kind of mess we’re in now.”
Adding:
“We need to be really attentive to how we interact with wildlife and the activities that bring humans and wildlife together. We obviously don’t want pandemics of this scale. We need to find ways to co-exist safely with wildlife, as they have no shortages of viruses to give us,”.
This comports totally with what former Vice President Al Gore told Bill Maher on last Friday night's Real Time – in respect of humans encroaching on wild animal habitat and especially using these animals indiscriminately as exotic food.  It also dovetail with Matt Ridley's excellent WSJ review article (April 11-12, p.  C 3) I summarized in this post.

  The takeaway is that only an idiot or congenital moron would fail to see the connection between climate change and  plundering endangered wildilife habitat  (or the habitats of exotic or dangerous species like horse shoe bats). The latter in a dumb effort to get strange food or make way for human engineering projects (such as depicted in the 2011 film, 'Contagion.)

Wednesday, January 29, 2020

The Chinese Coronavirus Outbreak - You Need Hard Facts, Not Alt News Hysteria

Image may contain: 1 person, food
Above - Palm civets seized in China's Anhul province earlier this month. Consuming such wild game - likely infected (by bats) with the virus, is plausibly how this latest coronavirus outbreak began.  (From WSJ, p. A17, Jan. 28th.)

"What worries me more than the new disease is that fear of a vague and terrifying new illness might spiral into panic, and that it might be used to justify unnecessarily severe limits on movement and on civil liberties, especially of racial and religious minorities around the world.


I also worry that the online world may give rise to dangerous skepticism, and that in the event of an actual pandemic a large number of people may delay treatment or refuse vaccines because they don’t believe the science or are suspicious of the government."- Farhad Manjoo, 
'Beware  The Pandemic Panic',  NY TIMES, Jan. 29

"As we celebrate the Year of the Rat and the world takes on the Wuhan coronavirus, it is good for all of us to remember that we have been here before and failed to act. As one Chinese academic who was involved in research on the source of SARS pointed out: “We later published many papers and popular science articles, urging everyone to stop eating wild animals and not to have too close contact with wild animals.” Seventeen years on, that message is finally being heard by those in a position to take action."-   Christian Walzer and Aili Kang, WSJ,  'Abolish Asia’s ‘Wet Markets,’ Where Pandemics Breed', Jan. 28, p. a17.

Thanks to my psychologist post-doc niece Shayle for sending me the following article ('The Chinese Coronoavirus Is Not The Zombie Apocalypse') from Psychology Today, by Robert Bartholomew, regarding the erupting coronavirus hysteria:

https://www.psychologytoday.com/us/blog/its-catching/202001/the-chinese-coronavirus-is-not-the-zombie-apocalypse


 Excerpt:

"I am not downplaying the seriousness of the new Coronavirus that has been spreading around the world.  People are dying and every death is a tragedy, but it is not the end of civilization as we know it, contrary to some media outlets which risk causing undue alarm and panic.  The headlines are ominous: “Wuhan is Ground Zero for Deadly Coronavirus.” “Situation in China is Grave.”  One paper carried an image of a Wuhan medic breaking down in tears.  Another showing a pile of corpses was fake. 

The Daily Mail quoted a researcher as saying, “'This time I am scared,' an expert who helped tackle SARS warns.”  Another scientist reportedly simulated a similar epidemic that he projected would kill 65 million people.  What the headline didn’t say is that it was a worst-case scenario for a virus deadlier than SARS and easier to catch than the flu, an extremely unlikely scenario. "


The last is especially critical to grasp. As with the case of the  lethal 1918 Spanish flu, e.g.   
100 Years Later: A Look At The Deadliest Pandemic...

The key aspect is to know the parameters, particularly the so-called R0, ("R nought") or reproduction number, which conveys the ease of transmissibility, or the infection rate per person.  This is currently pegged by the World Health Organization at between 1.4 and 2.5.  In other words, each person infected can infect from 1.4 to 2.5 other people.  By comparison the value for SARS (a variant of coronavirus) was 5.5. and for the Spanish flu, 1.8.

Watching a video from an Alt News site called "AMTV" showed me how the right wingers are behind the sowing of a lot of hysteria on this illness-  as they have been with the Q-Anon conspiracy bull.  Certainly when I see and hear the host  on Youtube put his hands out in scare quotes and blab: "This will be eye opening for a lot of you because it plays into not just 'climate change' but also people like Bill Gates who are pro-vaccination and stand to profit in the billions and billions."

All of which is humping unproductive irrationality and hysteria.  What then are we really dealing with? Is it almost like the "Black death" or the Spanish flu as many of these crackpots claim?   People need to chill out, take a deep breath and start to process facts as opposed to concocted fictions and fake news from suspect sites.   Heck, even Holman Jenkins Jr. was correct when he wrote in his WSJ column today ('The Cure For The Chinese Flu',  p. A13):

"Americans likely face a bigger risk from fear of the disease than the disease itself."

Proving once again that even a 'broken' ideological 'clock' is right at least twice a day.

Does Jenkins have a point? Sure, and so does Mr.  Bartholomew. The current range of   R0  for this disease is nowhere near even the SARS value (5.5.), or approaching the fictional 
R0,  for the disease featured in the 2011 movie 'Contagion'  (  R0 > 4.0).  Hence, the recent blaring headline in The New York Post, e.g.
Image may contain: text

Is so much balderdash.  The  fatality rate thus far (3%) is also nowhere near that for the diseases to which this virus is compared (e.g. 80-90 % for "the Black Death"). The  truth is that from the data we have so far this virus does not appear to be any worse than the annual flu, say the H3N2 - which I got in 2014.  Yeah, it was awful and for all intents I was a literal zombie for a week, but it was not the 'zombie apocalypse" as some of these Alt news sites try to portray. Also, for perspective it's always wise to compare whatever disease outbreak there is to past flu outbreaks.  For reference, 80,000 Americans died from the H3N2 influenza outbreak in 2014, and we are in no way likely to attain such numbers with this novel virus. Nor will we see any "martial law" as the Reich bloggers and crackpots claim will occur when the health alerts reach a "level 3".   If it didn't occur with the H3N2 in 2014 it will not occur now, I promise you.  Another point from the Psychology Today piece:
"All indications are that this Coronavirus is much milder than its two cousins, SARS and MERS.  When SARS (Severe Acute Respiratory Syndrome) broke out in China in 2002, it was traced to civet cats and had a death rate of about 10%.  There were just over 8,000 cases in 17 countries. "
In the image at the top of this post I show civet cats collected in the Chinese Anbul province earlier this month.  As reported  (Jan. 28, p. A17) in The Wall Street Journal    the sale of these critters constitutes part of a "wet market" - "where live and dead animals, including many wildlife species, are sold for consumption."  Adding that:  "China has closed all such markets that sell wildlife and temporarily banned the sale and shipment of wildlife throughout the country."  As they should have.

Why?  Because  (WSJ, p. A17, Jan. 27)  "bats are the likely origin for the virus itself and it got from bats to people in the wildlife market".    

https://www.livescience.com/new-coronavirus-origin-bats.html

 Here is where the final five minutes of the film 'Contagion' can be instructive.  It shows a flock of bats (originally perched on trees)  which then fly over a pig farm in Guangdong province and drop bat guano over the pig feeding area. The guano is already infected with the virus. The pigs then consume the guano, and become infected themselves.  In the film the Chinese hog butcher slaughters one of these pigs, gets pig blood all over his hands - wipes it off.  He then greets Gweneth Paltrow's character (on a visit on behalf of her corporation) and she shakes the butcher's hand.  She then becomes "Patient zero" - which we learn only at the end- though we suspect it earlier.  

The moral of this story? It is not a good idea for humans to be eating wild meat or game, especially from the Chinese wet markets.   This brings us to the question of how a potential epidemic in the U.S., can be properly contained.  Here we can thank Betsy McCaughey for her WSJ article 'U.S. Hospitals Aren't Ready'' (January 27, p. A17).  In the piece she compares the lessons for two different Canadian cities (Vancouver and Toronto) during the SARS outbreak of 2003.  

We learn therein: "In Vancouver the disease didn't spread. But in Toronto, one infection was allowed to become a deadly outbreak which killed 44 people in two months"

The difference arose because in Toronto, "infection control was not a high priority ...in Vancouver, by contrast, 'a robust worker safety and infection control culture' enabled the virus to be contained.."

She goes on to note that here in the U.S. infection control is just as lax as in Toronto. For example, a 2017 literature review of shortcomings in U.S. ERs found: "a lack of adequate distance between patients, use of contaminated equipment, failure to use shields to protect healthcare workers, e.g. who are intubating patients and failure to ask coughing patients to wear masks."  

Another infection breakdown point noted is when nurses, doctors wear their uniforms home after work,  infecting their families. That nonsense needs to stop if this latest Chinese virus is to be successfully contained.  And of course, let's not neglect the washing of hands which is the best way to prevent viral spread, e.g.
 As well as not touching one's face every five seconds! Below I show a summary  piece on what to know about this virus, taken from the WSJ, in yesterday's paper (p. A4):

No photo description available. Read through it carefully, using your time profitably,  as opposed to going to wacko websites that only inflame panic.

See Also:

Sunday, July 7, 2013

Did I Contract the Corona Virus in Europe?

An electron microscope image of a coronavirus
"Unless the many barriers to a transparent international research and information system disappear...the world could be dragged into another Black Death, and MERS could easily spread far beyond the bounds of the region for which it is named."
- Laurie Garrett, The Denver Post, today, 'Plague in the Middle East Could Spread Globally', p. 1D

Entering now the 6th week since developing probably the most severe respiratory infection I’ve ever had (other than the Hong Kong H1N1 flu in 1968), my lungs are finally starting to return to normal. I can breathe, walk and talk without descending into a prolonged coughing fit. (Heck, yesterday, for the first time in 6 weeks I was able to go to the cinema with wifey, to see ‘World War Z’). I also no longer am finding it necessary to take a mix of cough medicines just to get a decent night’s sleep.


All this echoes back to the 2nd day after returning from Munich, Germany, and speaking to my middle brother Jerome about my brother John’s recent death and plans for cremation. He noted my constant hacking before being able to even speak a few syllables and said: “You really ought to get that checked out! You might have that corona virus, and it’s been infecting people in Germany!” (He might have been referencing this report: http://www.cidrap.umn.edu/news-perspective/2013/03/germany-saudi-arabia-report-new-novel-coronavirus-cases )


I said I would, but feeling that I could cope with it, like the flu- I didn’t bother – preferring to “ride it out” despite having a fever that reached 101.7 several days in a row accompanied by severe nausea (I ‘broke’ the fever each time by popping a 361 mg tab of aspirin).


According to the CDC website:

"Coronaviruses are common throughout the world. They can infect people and animals. Five different coronaviruses can infect people and make them sick. They usually cause mild to moderate upper-respiratory illness. But, some coronaviruses, like the one that caused SARS in 2003, can cause severe illness..."


There is also a more recent mutation, and according to CDC, is:


“a novel coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the cause of respiratory illness in people. Investigations are being done to figure out the source of MERS-CoV and how it spreads. So far, there are no reports of anyone in the U.S. getting infected with MERS-CoV.  The Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) decided in May 2013 to call the novel coronavirus Middle East Respiratory Syndrome Coronavirus 


Evidently, this is a much more severe strain. According to today’s Denver Post (‘Perspective’, p. 1D, 'Plague in the Middle East Could Spread Globally')  MERS-CoV may well be the precursor to a new global "plague". 79 have so far been documented as contracting it and 40 have died- often after kidneys have shut down. If such stats hold it would make it a more prolific killer than Avian flu. But then, as the article also notes, there may be milder symptoms which have not yet been fully documented say in longitudinal studies. Meanwhile, there has been a CDC update of the MERS-CoV, e.g.  http://www.cdc.gov/mmwr/preview/mmwrhtml/mm6223a6.htm?s_cid=mm6223a6_w

Excerpt:

"The continued reporting of new cases indicates that there is an ongoing risk for transmission to humans in the area of the Arabian Peninsula. New reports of cases outside the region raise concerns about importation to other geographic areas. Nosocomial outbreaks with transmission to health-care personnel highlight the importance of infection control procedures. Recent data suggest that mild respiratory illness might be part of the clinical spectrum of MERS-CoV infection, and presentations might not initially include respiratory symptoms. In addition, patients with comorbidities or immunosuppression might be at increased risk for infection, severe disease, or both. Importantly, the incubation period might be longer than previously estimated. Finally, lower respiratory tract specimens (e.g., sputum, bronchoalveolar lavage, bronchial wash, or tracheal aspirate) should be collected in addition to nasopharyngeal sampling for evaluation of patients under investigation. An Emergency Use Authorization (EUA) was recently issued by the Food and Drug Administration (FDA) to allow for expanded availability of diagnostic testing in the United States”


This is important and could well mean that, while in Munich (or other places) I may well have contracted a “milder respiratory illness” – though from my perspective, “milder” isn’t a term I'd choose to use – not when coughing spasms have been triggered where I could barely catch my breath and sometimes spat up blood. My wife at times compared it to Whooping cough. Yes, she also contracted what I have had (nosocomial transmission?) and said it was the worst respiratory infection she’s ever had, and even worse than her H1N1 flu that scuttled our Xmas plans last year. Though I took pains to cover my mouth, nose whenever I coughed or sneezed, it is possible she contracted it from using the mutual laptop without first applying disinfecting wipes  (the CoV can last up to 24 hrs. outside the host)


Still, it’s necessary to be cautious in trying to ascribe blame. As the UK Guardian site noted: “In confirmed cases, patients had a fever, cough, shortness of breath and breathing difficulties. It is not known whether these symptoms are typical or whether the virus may be circulating more widely but causing milder illness.”

Therein lies the rub, or quandary. Until we know if the symptoms ARE typical, how can one differentiate them from say something like severe, acute bronchitis? And incidentally that was the self-diagnosis I finally settled on, but again it could be wrong. I mean how accurate a diagnosis can one make using only Google?


"Why don’t you go to the doc then?"

Well, maybe because I believe I’ve already had enough medical interventions the past two years (including for prostate cancer treatment) and don’t want to help run up national health care costs any more than they are! Especially on the eve of the implementation of the Affordable Care Act. The Neoliberals are already big on accusing those of us on Medicare of "over using" it!


Anyway, bottom line, I am still here and getting better: the lassitude is now the main hurdle. As to whether I actually had CoV (at least the MERS-CoV form), I don’t know. My take so far is that it likely wasn’t, and perhaps only a mild CoV or an acute case of bronchitis after all. Aggravated badly by a bout with smoke from the Black Forest fire. Stay tuned.