More Info on Viruses

[Avalux]

I wrote this and posted it in the Science forum way back in 2005 when there was discussion of an avian flu outbreak (luckily, it didn't happen). My intention was to provide basic information on viruses - influenza A viruses and in particular bird influenza A. The virus causing this current "swine flu" outbreak is an influenza A virus that infects pigs, so the the information in my post is relevant. I'm so glad DU has a searchable Archives (thanks Skinner, et al).

There are a couple of other very informative posts in this forum so consider this an additional resource. I think it's important to understand the basic science so news stories are better put in context.

Here’s an unsolicited lesson in viruses and how they survive – particularly the influenza A virus causing the current outbreaks of avian flu. I’ll do my best to write an explanation without being too technical. Let me add a disclaimer here – no one can predict when a pandemic will occur but I do believe it is inevitable; either in a few years or as many as 50. As advanced as we humans are, we can’t stop mother nature - it's that pesky "E" word (evolution).

A virus is a parasite – it is comprised of genetic material enclosed in a protective coat. The genetic material may be DNA or RNA depending on the type of virus. The protective coat is called a capsid. Not only does it protect the genetic material inside, but the capsid also helps the virus infect host cells. Some viruses even have an additional outer envelope of proteins, sugars and lipids stolen from the host cell in which it has been made. The complete virus "particle" – genetic material, capsid and envelope (if it has one) - is called a virion.

We aren’t sure of the origins of viruses, but most virologists agree that each virus got started by copying a few useful genes from their host cells. Viruses are ignorant of any patent or copyright laws. They are brilliant at making copies out of whatever they find useful in the host’s genetic code and move on from there. The ‘useful’ gene that’s stolen is intimately involved in the host cell’s reproduction, food gathering, cell communication or other essential function. Viruses mutate the stolen genes and when a particularly useful mutation comes along, the virus uses it for it’s own survival, usually to the detriment of its host. Over many generations and years, viruses have the ability to switch over the other species, find new genes to copy and then continue evolving in their own selfish way.

The avian flu virus is an orthomyxovirus – it’s genetic material is RNA. When a virus with RNA replicates, the copies tend to have more errors than when a virus with DNA replicates. These extra errors provide mutations upon which natural selection may act. That means RNA viruses have a high mutation rate and can evolve quickly - faster than a DNA virus or any DNA cell. Over time these mutations accumulate and eventually the virus evolves into a new strain. This progressive accumulation of individual mutations is called antigenic drift. The shape of the viral protein (antigen) slowly drifts into a different shape with each generation of virus. Eventually they drift so much that the original antibody can no longer bind to it. That means a host can become infected with this newly evolved virus. All viruses show antigenic drift, but RNA viruses mutate faster so they drift faster. Antigenic drift is responsible for many of the localized outbreaks of different strains of influenza, especially influenza A and B. In practical terms, antigenic drift is the reason we need to develop a new flu vaccine every year for human influenza and why it’s never 100% effective.

Here’s where it get pretty amazing – influenza A. This virus has the ability to undergo a kind of gene swapping or genetic reassortment that other viruses do not have. If a host cell is simultaneously infected by two different strains of influenza A, the copies of the virion may contain mixtures of each parents' genes. This makes it very easy for influenza A to quickly evolve into new combinations of genes. This is called antigenic shift; a newly created virus strain with mixed genetic material that’s different from it’s parents. This phenomenon is different from antigenic drift which occurs slowly and without change in the gene associations. The new combinations are such a unique strain of virus that the immune system has to start all over to make new antibodies to combat it.

Influenza A can infect mammals other than humans including birds (avian flu). It's very unusual for a virus to have such a wide host range, but influenza A somehow manages this trick. It probably has to do with the fact that the virus gains entry to a host cell by using receptors common to many species. That means a strain of influenza A may infect one species for decades and then suddenly jump to a new species. This sudden jump, due to antigenic shift, can produce a very serious epidemic. For example, several years ago many seals washed up on the east coast of the US dying from a strain of influenza A that, until then, had only been found in birds. Horse and swine influenza A have turned up in humans. Influenza A is the nightmare of science fiction - a virus that normally causes only a slight illness, undergoes genetic recombination with other species and comes back as a very deadly virus.

We know that influenza A has been conducting random, unlicensed recombinant genetics "experiments" for centuries and will continue to do so regardless of what any of us try to do about it. We watch and wait. Avian influenza A virus has a very high mortality rate (about 75%) and that’s why the present scenario is so scary. If avian influenza A were to recombine with human influenza A within a host cell, it may give the virus the ability to pass from one human to another quite rapidly. This would cause a worldwide pandemic. We may be getting dangerously close to this reality as there were two documented cases of human to human transmission last year in Asia. Another significant change we’ve seen in bird to human transmission is the large amount of viral particles in respiratory secretions of birds where in the past the virus was only found in bird feces.

And when it comes to vaccines, there are obstacles to the rapid development of a vaccine for a pandemic outbreak. Flu vaccines are normally grown in chicken eggs, but this will not be useful because avian influenza A is deadly to the chicken embryo. The only other option will be to use ‘reverse genetics’, which involves merging selected genetic material from the natural virus with a laboratory virus, with the resulting virus stimulating an immune response, but no disease when injected into humans. This of course, is easier said than done.

I happen to respect viruses a great deal - they are amazing creatures. I ask myself frequently how a one-celled organism dependent on others for survival can be so smart – they always seem to be one step ahead of us.

My advice if an avian flu pandemic happens - stock up on supplies and stay home.

http://www.democraticunderground.com/discuss/duboard.php?az=show_topic&forum=228&topic_id=5742#6140

Please follow the link to the original post - good info in the thread too. :hi:

[Avalux]

1. kick! Anyone?

I'm not shy about asking. ;-)

[seemslikeadream]

2. Thanks

I just saw this

[Avalux]

4. Thank you -

I just read that the WHO has "very big gaps" in understanding this virus. Not sure what that means....

[Stellabella]

3. K & R

:kick:

[rhett o rick]

5. k & r

[bluedawg12]

6. K&R! You know the little buggers aren't "smart" but they sure do adapt.

It's like a hot dog.

The hot dog part has the "code" the bun is the capsid. ( stop me if I am making an ass of myself! LOL)

The code, which is the standard format for coding anything, from making proteins to making a gerbil, is called DNA or RNA.

These little buggers can, as I understand it, hack their way through living systems, by stealing code.

Just when a vaccine or anti-viral comes close to stopping them in their tracks, they switch codes, like good hackers, when an antiviral software is developed.

I guess, they are little hotdogs that act like code hackers.

This is evolution in action:

"Here’s where it get pretty amazing – influenza A. This virus has the ability to undergo a kind of gene swapping or genetic reassortment that other viruses do not have. If a host cell is simultaneously infected by two different strains of influenza A, the copies of the virion may contain mixtures of each parents' genes. This makes it very easy for influenza A to quickly evolve into new combinations of genes. This is called antigenic shift; a newly created virus strain with mixed genetic material that’s different from it’s parents."

"I happen to respect viruses a great deal - they are amazing creatures. I ask myself frequently how a one-celled organism dependent on others for survival can be so smart – they always seem to be one step ahead of us.'

Me too. This is one of the reasons that HIV is so hard to "cure," they adapt faster than our strategies for eradicate can be developed.

Once inside the host, part of the problem is the host response, as someone in another thread pointed out, the release of inflammatory chemicals called cytokines creates a terrible inflammation in the lungs. So, while supporting life, while trying anti-viral medications, doctors have to add anti-inflammatory cortico steroids, to balance the exuberant inflammatory response to the virus.

"An influenza pandemic has always been a great global infectious-disease threat. There have been 10 pandemics of influenza A in the past 300 years. A recent analysis showed that the pandemic of 1918 and 1919 killed 50 million to 100 million people,1 and although its severity is often considered anomalous, the pandemic of 1830 through 1832 was similarly severe — it simply occurred when the world's population was smaller. Today, with a world population of 6.5 billion — more than three times that in 1918 — even a relatively "mild" pandemic could kill many millions of people."
http://content.nejm.org/cgi/content/full/352/18/1839

........


http://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H1N1

"H1N1 is a subtype of the species Influenza A virus. The "H" refers to the Hemagglutinin protein, and the "N" refers to the Neuraminidase protein. H1N1 has mutated into various strains including the Spanish Flu strain (now extinct in the wild), mild human flu strains, endemic pig strains, and various strains found in birds. A variant of H1N1 was responsible for the Spanish flu pandemic that killed some 50 million to 100 million people worldwide from 1918 to 1919.<1> A different variant exists in pig populations.

Low pathogenic H1N1 strains still exist in the wild today, causing roughly half of all flu infections in 2006.<2> When the 1918 virus was compared with human flu viruses in 2005, it was noticed that it had alterations in just 25 to 30 of the virus's 4,400 amino acids. These changes were enough to turn a bird virus into a version that was human-transmissible.<3>

In April of 2009, an H1N1 outbreak killed over eighty in Mexico, and was believed to have infected more than 1500 individuals worldwide as of April 26, 2009. The U.S. Centers for Disease Control warned that it was possible the outbreak could develop into a pandemic.<4>"

[Avalux]

9. Thanks for your input!

I like your hot dog analogy. Of course viruses don't have brains and aren't smart - but they are experts at survival. :hi:

[Psychic Consortium]

7. Under Obama's wise leadership this will not turn into a Katrina event.

Thank God.

[bluedawg12]

11. He is a pro-science guy and is going to kick butt on this, unlike that chimper!

[Avalux]

13. Presser on right now. n/t

[Psychic Consortium]

14. 100% correct. nt

[FirstLight]

8. Fascinating...

It's nice to hear it in "english"
I have a book on virology, but only understand every third word or so! lol

Yes, pandemics really DO happen...it is a natural check on population density as I see it...

Did the CDC & WHO raise the pandemic levels back during the bird flu outbreak or SARS...? I don't seem to recall the same level of intensity or seriousness earlier... and the jumping around the globe is a new thing too...the earlier outbreaks were limited to mostly south asia, right?

and now isn't there a case in britain? that is worth noting I think

[Avalux]

12. There was no pandemic from the bird flu scare in 2005 or SARS.

Bird flu didn't progress to human to human transmission and SARS was an epidemic - confined to a regional area. This swine flu is easily jumping from one person to another and is infecting young healthy people. Encouraging so far is that it appears to be mild; mortality rate low.

Right now, there are additional confirmed cases in Canada; possible in Scotland and France.

:hi:

[bluedawg12]

17. Important point about avian flu not jumping to man.

I recall how closely it was monitored by WHO.

There may have been a few anecdotals about bird flu jumping to man, from small clusters, in China. Like a woman who worked around birds got ill as did her son. But, in general it did not go from bird to man on a large scale, but was monitored.

http://en.wikipedia.org/wiki/Avian_flu

>>On January 18, 2009, A 27-year-old woman from eastern China has died of bird flu, Chinese authorities said, making her the second person to die this year from the deadly virus.Two tests on the woman were positive for H5N1 avian influenza, said the ministry, which did not say how she might have contracted the virus<15>.

Although millions of birds have become infected with the virus since its discovery, 248 humans have died from the H5N1 in twelve countries according to WHO data as of January 2009. View the most current WHO Data regarding:Cumulative Number of Human Cases<<


This particular H1N1 virus is now established in man and is infectious and deadly in some instances.

Therefore, it is being closely monitored.

In fact, this version of swine flu, is now reported in:

From that famous peer reviewed communal effort journal :P wiki!

http://en.wikipedia.org/wiki/Influenza_A_virus_subtype_H1N1
>>>
Mexican officials state that since March 2009, there have been over 1000 reported cases and put the death toll at 81, with 20 confirmed to be linked to a new swine influenza strain of Influenza A virus subtype H1N1.<9><10><11> Officials in the United States said that seven people were infected with swine flu in California, two in Texas, and two in Kansas all have recovered.<12> Kansas state health officials confirmed two cases of swine flu in Kansas on 25th April 2009, just minutes after eight school children in New York City were believed to be infected after a school trip to Mexico. The New York case has been confirmed as Influenza A Virus, which meets the Centers for Disease Control and Prevention (or CDC) definition of a probable case of swine flu. Tests are still underway to determine if this flu virus is the new strain of H1N1. In Canada, the virus has not been confirmed.<13> There are no confirmed cases outside of North America. In London a member of a British Airways cabin crew was taken to hospital with "flu-like symptoms" after falling ill on a flight from Mexico City to Heathrow, but the man's results were negative. There are ten suspected cases in New Zealand with students whom had visited Mexico. Like the US students, they tested positive for Influenza A which means swine flu is highly likely. There have also been reports of suspected infection in Canada, Chile, France and Israel. Airports worldwide are on alert, with passages from Mexico entering Japan being screened for the virus. The head of the World Health Organization will lead the agency's efforts against a deadly swine flu outbreak.<14><15> The World Health Organization warns this new swine flu has the potential to become an international influenza pandemic.<16> On April 25, 2009, the World Health Organization has issued a document called the Swine influenza frequently asked questions.<17> On 24th April 2009, the World Health Organization agreed that the current situation constitutes a public health emergency of international concern. <18><<<

[FedUpWithIt All]

10. Thank you for posting this. kicked and rec'd

:hi:

[bluedawg12]

15. I was thinking about the cytokine storm these viruses create in the host

and how, the release of cyotkines damages lung tissue, in response to the virus.

So, here is my question, that's maladaptive of the virus to kill the host.

But for our dedication to saving lives, this virus would die out in the wild, as the hosts die out.

It is our valiant effort to save human life, once infected, that allows these viruses to remain in the host and eventually re-adapt to any new anti-viral stratgey.

So, but for saving lives, this type of strain would be maladaptive and self limited and die out in the "wild?"

Thoughts from smarter folks than mois. :P

[Avalux]

16. You've got the gist of it.

This is why the ebola virus would never reach pandemic proportions. It kills the host so fast it doesn't have time to spread from one person to another effectively.

[bluedawg12]

20. Good. This means, we do see new and more adaptive strains

because, we can't let the "virus die out in nature" ethically, so we save human lives and save the virus, which comes back as another version, adapted to what has gone before.

There is no need for hoaxes or exotic theories, the very act of saving lives means we can expect readapted strains to appear.

[northernlights]

19. co-evolution

Generally, viruses and bacteria co-evolve with their hosts. I call it "survival of the less fit."

The most virulent pathogens kill their hosts too quickly and efficiently to spread, so die out themselves. That is why ebola outbreaks tend to be limited. The victims don't live long enough to spread the disease very far.

However, less virulent pathogens don't kill off their hosts, and both pathogen and host evolve to a degree of equilibrium. The host develops some immunity to the pathogen, but low levels of pathogen are overlooked by the immune system. They aren't present in large enough quantities to induce an immune response or to significantly impair host functioning. When their numbers rise to a point where the immune system notices, it beats them back to low levels. If the host becomes overstressed, however, opportunistic infection can take off. Classic example is herpes simplex, that swings between "remission" and "active infection."

In some cases, they can evolve to a symbiotic relationship or even become part of the host (as is suspected with mitochondria).

[bluedawg12]

21. That's the apple cart we have altered, because we DO expect to save lives

it's the ethical thing to do and expected by society, and in doing so, perhaps this H1N1 would die out. rather, we get the good with the bad. We save the life of the host and the parasite.

My only point is, that folks, if they understand this, then, there may not be a need for exotic explanations of why "this is happening," we have no choice but to save human life and when we do, we can expect the little buggers to stay on board and re-engineer their genetic structure, to be adapted to the last wave of anti-virals or vaccines.

[Avalux]

22. Not all viruses are especially deadly though. If this one is mild

it could continue for awhile. Keep in mind too as it moves from person to person - can mutate further and there might be a second wave after the intial outbreak. As the CDC just said, expect this to be a marathon.

[northernlights]

26. not exactly

The host survives only with ameliorative/supportive care, which provides the opportunity to develop immunity to the virus and provides the virus the opportunity to evolve to a less virulent form. Which it does do. And so we co-evolve to immunity to that particular virus.

In fact, it's entirely possible that the current virus has already evolved to a less virulent mutation, which would explain why the Mexican cases have a 6-7% mortality rate and the U.S. cases to date are mild with 0 mortality.

We've upset the apple cart only in sometimes succeeding in depriving nature of a way of pruning the human population. That just leaves more targets for the next mutation.

[bluedawg12]

31. Thank you for clarifying my thinking! :)

I missed the step where the virus and host survive due to intervention and the virus can evoolve to a less virulent form.

Man, I love it when I can learn stuff. Thank you!! :)

My basic premise is that it is not in the interest of the virus to kill the host, say for ex., like Ebola.
You explained what I was thinking and made it more logical.

[Odin2005]

30. I've read that something like 14% of our DNA is derived from retroviruses.

That's a scary thought...

[Lisa0825]

18. Medical research was my first career, and while I have been away from it

for years, I still consider myself a science geek at heart. I too have a "healthy" respect for viruses. Amazing buggers! Actually not even considered cells at all... in that gray area between alive and not.

Part of me can maintain professional distance from it and recognize it as the planet's population control... but only when it doesn't hit close to me. Then I am your run of the mill human being, cursing mother nature.

I don't worry about dying. I only worry about people I care about dying.

[Avalux]

23. I am trying to take in all this information from a scientific point of view -

but two of the cases are in Cibolo TX - a few miles up the road. I just told my daughter that if there's even a suspected case at her school, they will close it. So part of me is worried for my family and those I care about. :hi:

[bluedawg12]

24. Yupper! Well said. n/t

[bluedawg12]

25. As predicted- this President is not doing a "fly over" the white house presser

is sound, a great start, they call this a "pre-pandemic" and they are on top of it.

What a relief to have a President who does not ignore 20 confirmed swine flu cases in the US and they are kicking ass and making plans!

After 8 years of anti-science, right wing disinformation, finaly a leader who does not ignore science and display apathy, rather he is on it and taking a leadership role.

[mzmolly]

27. Thanks for the interesting and informative post. What are your thoughts on the following article?

http://www.medicalnewstoday.com/articles/51913.php

Hope-Simpson had no way of knowing that vitamin D has profound effects on human immunity, no way of knowing that it increases production of broad-spectrum antimicrobial peptides, peptides that quickly destroy the influenza virus. We have only recently learned how vitamin D increases production of antimicrobial peptides while simultaneously preventing the immune system from releasing too many inflammatory cells, called chemokines and cytokines, into infected lung tissue.

In 1918, when medical scientists did autopsies on some of the fifty million people who died during the 1918 flu pandemic, they were amazed to find destroyed respiratory tracts; sometimes these inflammatory cytokines had triggered the complete destruction of the normal epithelial cells lining the respiratory tract. It was as if the flu victims had been attacked and killed by their own immune systems. This is the severe inflammatory reaction that vitamin D has recently been found to prevent.

[Avalux]

28. I was reading this and other info on Vitamin D yesterday.

In response to what I think - bought Vitamin D at Walgreens; instructed my family to take 1000 mg a day. ;-)

[mzmolly]

29. Good plan! We're taking it daily, but not nearly enough at 400mg.

:hi:

[bluedawg12]

32. Avalux. Take a look at this.

BTW- the recommended daily dose of VitD is 2000 IU currently ( not sure what it is in mg's) or 1 hour of sunlight on a Caucasian face.

Now, Mexico is pretty sunny and where is Dr. Cannell, who practices in California, when they need him?


I am very skeptical of VitD as a treatment for a viral infection, based on this research, as published, rather than a science digest type format.

Your thoughts?

http://www.democraticunderground.com/discuss/duboard.php?az=show_mesg&forum=389&topic_id=5532051&mesg_id=5536120

JJ Cannel is a psychiatrist, not an infectious disease doctor.

Here is the article he had published in 2006, which your OP cites.

Now, it says Dr. Cannell practices in California, on the edge of the swine flu that seems to be coming north from Mexico. This would be a great time to tell the good people down in Mexico that they need more sunshine, VitD and same for the towns on the border and Texas.

Let's keep on eye out for him on the news, this kind of great research should not be hidden!

He could prevent a pandemic.
...........


Epidemiol Infect. 2006 Dec;134(6):1129-40. Epub 2006 Sep 7.
Comment in:
Epidemiol Infect. 2007 Oct;135(7):1091-2; author reply 1092-5.
Epidemiol Infect. 2007 Oct;135(7):1095-6; author reply 1097-8.
Epidemic influenza and vitamin D.Cannell JJ, Vieth R, Umhau JC, Holick MF, Grant WB, Madronich S, Garland CF, Giovannucci E.
Atascadero State Hospital, 10333 El Camino Real, Atascadero, CA 93422, USA.

In 1981, R. Edgar Hope-Simpson proposed that a 'seasonal stimulus' intimately associated with solar radiation explained the remarkable seasonality of epidemic influenza.
....An interventional study showed that vitamin D reduces the incidence of respiratory infections in children. We conclude that vitamin D, or lack of it, may be Hope-Simpson's 'seasonal stimulus'

.
................
Another article in 2006 on Vit.D


Cannell JJ, Vieth R, Umhau JC, Holick MF, Grant WB, Madronich S, Garland CF, and Giovanucci E. Epidemic Influenza and Vitamin D. Epidemiol Infect. 2006 Sep 7;:1-12 (Epub ahead of print)

Altern Med Rev. 2008 Mar;13(1):6-20.
Use of vitamin D in clinical practice.Cannell JJ, Hollis BW.

The recent discovery--from a meta-analysis of 18 randomized controlled trials--that supplemental cholecalciferol (vitamin D) significantly reduces all-cause mortality emphasizes the medical, ethical, and legal implications of promptly diagnosing and adequately treating vitamin D deficiency.

Theoretically, pharmacological doses of vitamin D (2,000 IU per kg per day for three days) may produce enough of the naturally occurring antibiotic cathelicidin to cure common viral respiratory infections, such as influenza and the common cold, but such a theory awaits further science.



.............
Let's see if the hypothesis is any further along by 2008


Virol J. 2008 Feb 25;5:29.
Comment in:
Virol J. 2008;5:149.
On the epidemiology of influenza.Cannell JJ, Zasloff M, Garland CF, Scragg R, Giovannucci E.
Department of Psychiatry, Atascadero State Hospital, 10333 El Camino Real, Atascadero, CA 93423, USA.

We hypothesize that two factors explain the nine conundrums: vitamin D's seasonal and population effects on innate immunity, and the presence of a subpopulation of "good infectors." If true, our revision of Edgar Hope-Simpson's theory has profound implications for the prevention of influenza.


............
And Vit D. is also implicated in autism for this author.


Med Hypotheses. 2008;70(4) 50-9. Epub 2007 Oct 24. Links
Autism and vitamin D.Cannell JJ.
Atascadero State Hospital, Psychiatry, 10333 El Camino Real, Atascadero, CA 93423, United States.

Autism is more common in areas of impaired UVB penetration such as poleward latitudes, urban areas, areas with high air pollution, and areas of high precipitation. Autism is more common in dark-skinned persons and severe maternal vitamin D deficiency is exceptionally common the dark-skinned. Conclusion: simple Gaussian distributions of the enzyme that activates neural calcitriol combined with widespread gestational and/or early childhood vitamin D deficiency may explain both the genetics and epidemiology of autism.

.........

Some of the peer reviewed comments that I could acces were not supportive of this hypothesis, either.

http://www.democraticunderground.com/discuss/duboard.php?az=show_mesg&forum=389&topic_id=5532051&mesg_id=5536394

[bluedawg12]

33. One other question about VitD as an antiviral or for prevention.

I listened to the white house presser today, they never mentioned taking VitD at all. Unless i missed it.

If this were a legitimate treatment or preventative, I would expect them to advise people to take their daily recommended dose, or just go out and get some sun, for an hour or two.

The experts from the white house never said anything about VitD today.

:shrug:

[Avalux]

34. Vitamin D has no activity against viruses.

However - there may be some validity to its effect on the immune system although no clinical trials have been done to prove it (that's why officials don't recommend it). In my own mind I know taking a Vitamin D supplement won't hurt so why not do it.

[bluedawg12]

35. Kick for useful info. n/t