Finally a Viral Cause of Chronic Fatigue Syndrome? Or Not? – How Results Can Vary and Depend on Multiple Factors

15 02 2010

Last week @F1000 (on Twitter) alerted me to an interesting discussion at F1000 on  a paper in Science, that linked Chronic fatigue syndrome (CFS) to a newly discovered human virus XRMV [1]ResearchBlogging.org.

This finding was recently disputed by another study in PLOS [2], that couldn’t reproduce the results.  This was highlighted in an excellent post by neuroskeptic “Chronic Fatigue Syndrome in “not caused by single virus” shock!

Here is my take on the discrepancy.

Chronic fatigue syndrome (CFS) is a debilitating disorder with unknown etiology. CFS causes extreme fatigue of the kind that does not go  away after a rest. Symptoms of CFS include fatigue for 6 months or more and experiencing other problems such as muscle pain, memory problems, headaches, pain in multiple joints and  sleep problems. Since other illnesses can cause similar symptoms, CFS is hard to diagnose. (source: Medline Plus).

No one knows what causes CFS, but a viral cause has often been suspected, at least in part of the CFS patients. Because the course of the disease often resembles a post-viral fatigue, CFS has also been referred to as post-viral fatigue syndrome (PVFS).

The article of Lombardi [1], published in October 2009 in Science, was a real breakthrough. The study showed that two thirds of patients with CFS were infected with a novel gamma retrovirus, xenotropic murine leukaemia virus-related virus (XMRV). XMVR was previously linked to prostate cancer.

Lombardi et al  isolated DNA from white blood cells (Peripheral Blood Mononuclear Cells or PBMCs) and assayed the samples for XMRV gag sequences by nested polymerase chain reaction (PCR).

The PCR is a technique that allows the detection of a single or few copies of target DNA by amplifying it across several orders of magnitude, generating thousands to millions of copies of a particular DNA. Nested PCR amplifies the resultant amplicon several orders of magnitude further. In the first round external primers are used (short DNA-sequences that fit the outer end of the piece of DNA to be amplified) and an internal set of primers is used for the second round. Nested PCR is often used if the target DNA is not abundantly present and to avoid the comtamination with products that are amplified as a spin-off due to the amplification of artifacts (sites to which the primers bind as well)

[I used a similar approach 15-20 years ago to identify a lymphoma-characteristic translocation in tonsils and purified B cells of (otherwise) healthy individuals. By direct sequencing I could prove that each sequence was unique in its breakpoint sequence, thereby excluding that the PCR-products arose by contamination of an amplified positive control. All tumor cells had the translocation against one in 100,000 or 1,000,000 normal cells. To be able to detect the oncogene in B cells, B cells had to be purified by FACS. Otherwise the detection limit could not be reached]

Lombardi could detect XMRV gag DNA in 68 of 101 patients (67%) as compared to 8 of 218 (3.7%) healthy controls. Detection of gag as well as env XMRV was confirmed in 7 of 11 CFS samples at the Cleveland Clinic (remarkably these are only shown in Fig 1A of the paper, thus not the original PCR-results).
In contrast, XMRV gag sequences were detected in 8 of 218 (3.7%) PBMC DNA specimens from healthy individuals. Of the 11 healthy control DNA samples analyzed by PCR, only one sample was positive for gag and none for env. The XMRV gag and env sequences were more than 99% similar to those previously reported for prostate tumor–associated strains of XMRV. The authors see this as proof against contamination of samples with prostate cancer associated XMRV-DNA.

Not only PCR experiments were done. Using intracellular flow cytometry and Western blot assays XMRV proteins were found to be expressed in PBMCs from CFS patients. CFS patiens had anti-XMRV antibodies and cell culture experiments revealed that patient-derived XMRV was infectious. These findings are consistent with but do not prove that XMRV may be a contributing factor in the pathogenesis of CFS. XMRV might just be an innocent bystander. However, unlike XMRV-positive prostate cancer cells, XMRV infection status did not not correlate with the RNASEL genotype.

The Erlwein study was published within 3 months after the first article. It is much simpler in design. DNA was extracted from whole blood (not purified white blood cells) and subjected to a nested PCR using another set of primers. The positive control was an end-point dilution of the plasmid. Water served as a negative control. None of the 186 CSF samples was positive.

The question then is: which study is true? (although it should be stressed that the Science paper just shows a link between the virus and CFS, not a causal relationship)

Regional Differences

Both findings could be “real” if there was a regional difference in occurrence of the virus. Indeed XMRV has previously been detected in prostate cancer cells from American patients, but not from German and Irish patients.

Conflict of Interest

Lombardi’s clinic [1] offers $650 diagnostic test to detect XMRV, so it is of real advantage to the authors of the first paper that the CSF-samples are positive for the virus. On the other hand Prof. Simon Wessely of the second paper has built his career on the hypothesis that CFS is a form of psychoneurosis, that should be treated with cognitive behavior therapy. The presence of a viral (biological) cause would not fit in.

Shortcomings of the Lombardi-article [1]

Both studies have used nested PCR to detect XMRV. Because of the enormous amplification potential, PCR can easily lead to contamination (with the positive control) and thus false positive results. Indeed it is very easy to get contamination from an undiluted positive into a weakly positive or negative sample.

Charles Chiu who belongs to the group detecting XMRV in a specific kind of hereditary prostate cancer, puts it like this [5]:

In their Dissenting Opinion of this article, Moore and Shuda raise valid concerns regarding the potential for PCR contamination in this study. Some concerns include 1) the criteria for defining CFS/ME in the patients and in controls were not explicitly defined, 2) nested PCR was used and neither in a blinded nor randomized fashion, 3) the remarkable lack of diversity in the six fully sequenced XMRV genomes (<6 nucleotide average difference across genome) — with Fig. S1 even showing that for one fully sequenced isolate two of the single nucleotide differences were “N’s” — clearly the result of a sequencing error, 4) failure to use Southern blotting to confirm PCR results, and 5) primary nested PCR screening done in one lab as opposed to independent screening from start to finish in two different laboratories. Concerns have also been brought up with respect to the antigen testing

Shortcomings of the Erlwein-article [2]

Many people have objected that the population of CSF patients is not the same in both studies. Sure it is difficult enough to diagnose CSF (which is only done by exclusion), but according to many commenters of the PLOS study there was a clear bias towards more depressed patients. Therefore, a biological agent is less likely the cause of the disease in these patients. In contrast the US patients had all kinds of physical constraints and immunological problems.

The review process was also far less stringent: 3 days versus several months.

The PLOS study might have suffered from the opposite of contamination: failure to amplify the rare CSF-DNA. This is not improbable. The Erlwein group did not purify the blood cells, used other primers, amplified another sequences and did not test DNA of normal individuals. The positive control was diluted in water not in human DNA. The negative control was water.

Omitting cell purification can lead to a lower relative amount of the XMRV-DNA or to inhibition (often seen this with unpurified samples). Furthermore the gel results seem of poor quality (see Fig 2). The second round of the positive PCR sample results in an overloaded lane with too many aspecific bands (lane 9), whereas the first round leads to a very vague low molecular band (lane 10). True that the CSF-samples also run two rounds, but why aren’t the aspecific bands seen here? It would have been better to use a tenfold titration of the positive control in human DNA (this might be a more real imitation of the CSF samples: (possibly) a rare piece of XMRV DNA mixed with genomic DNA) and to use normal DNA as control, not water.Another point is that the normal XMRV-incidence of 1-3,7% in healthy controls is not reached in the PLOS study, although this could be a matter of chance (1 out of 100).

Further Studies

Anyway, we can philosophize, but the answer must await further studies. There are several ongoing efforts.

References

  1. Lombardi VC, Ruscetti FW, Das Gupta J, Pfost MA, Hagen KS, Peterson DL, Ruscetti SK, Bagni RK, Petrow-Sadowski C, Gold B, Dean M, Silverman RH, & Mikovits JA (2009). Detection of an infectious retrovirus, XMRV, in blood cells of patients with chronic fatigue syndrome. Science (New York, N.Y.), 326 (5952), 585-9 PMID: 19815723
  2. Erlwein, O., Kaye, S., McClure, M., Weber, J., Wills, G., Collier, D., Wessely, S., & Cleare, A. (2010). Failure to Detect the Novel Retrovirus XMRV in Chronic Fatigue Syndrome PLoS ONE, 5 (1) DOI: 10.1371/journal.pone.0008519
  3. http://f1000biology.com/article/yxfr5q9qnc967kn/id/1166366/evaluation/sections
  4. http://neuroskeptic.blogspot.com/2010/01/chronic-fatigue-syndrome-in-not-caused.html
  5. Charles Chiu: Faculty of 1000 Biology, 19 Jan 2010 http://f1000biology.com/article/id/1166366/evaluation

Photo Credits

Nested PCR ivpresearch.org




How a Flu-Virus Invades your Body: An Animation

25 10 2009

I’ve seen “viral invasion, replication and spread” more elaborately and scientifically explained, but nothing comes near a clear visual and audible presentation of what happens on a micro-scale.

Here is a video on a Flu Attack that stirs the imagination.

And one thing or another, those kind of videos get really viral on Twitter and blogs as well.

When seeing the video you at least understand why CDC’s motto is: Cover it!

Cover your nose with a tissue when sneezing or coughing. Visit www.cdc.gov/h1n1 for more information.
Although the above video has the tags “swine” and “flu” and alludes to H1N1, it gives no specific information on H1N1 (Swine flu), but could be about any influenza virus. For information on H1N1 go to:

25-10-2009 16-30-34

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CMV-infection, plaques and high blood pressure

26 05 2009

A recent experimental study shows that a common virus that hides (becomes latent) after infection can trigger high blood pressure, a leading cause of cardiovascular disease.

The virus is cytomegalovirus (CMV). It belongs to the herpesviruses, hence its alternative name Human Herpesvirus 5 (HHV-5). The herpesviruses have in common that they can become latent (dormant) for a long while. Herpes simplex virus-1 (HSV-1) and varizella zoster virus usually hide in nerves (neurons) and can cause cold sores and shingles respectively after reactivation.

Cytomegalovirus (CMV) can be transmitted by sputum and other bodily fluids. After infection, it stays within the host, hiding primarily in certain white blood cells serving as a reservoir for reactivation.

The study by Cheng et al, consisted of an experimental mouse study and in vitro experiments, using mouse CMV (MCMV) and human CMV (HCMV)

  1. In the in vivo experiment, 4 groups of mice -of 12 animals each- were treated as follows:
    • V: Mice in group 1 were infected by MCMV and fed a regular diet.
    • M: Mice in group 2 were mock-infected and fed a regular diet (control group).
    • V-HD: Mice in group 3 were infected by MCMV and fed a high cholesterol diet.
    • HD: mock-infected and fed a high cholesterol diet (control group).
      systolic diastolic
  2. After 6 weeks the blood pressure, measured in the carotid artery, was significantly enhanced in mice that were infected by the MCMV compared to mock-infected controls. Thus the blood pressure was significantly higher in V versus M and in V-HD versus HD mice. This was both true for the systolic and the diastolic blood pressure (see Fig).
  3. Atherosclerotic plaque formation in mouse aortas was only observed in V-HD mice (MCMV infection and high cholesterol diet together). 3 out of 12 mice showed plaques against 0 out of 12 mice in the other groups.
  4. The serum levels of all 3 pro-inflammatory cytokines tested, IL-6, TNF-α and MCP-1, were higher in the mice infected with MCMV (V-HD and V) than in the mock-infected groups fed with either diet.
  5. CMV infection induced renin and Ang II expression (in vitro cq in vivo). Renin is a rate limiting protein of Renin-Ang-II system and Ang II is the peptide that causes the blood vessels to constrict, thereby enhancing blood pressure.
  6. The renin production was only enhanced in kidney-cells containing CMV-particles.
  7. In mice infected with CMV, Ang II was also increased in serum and in artery tissues.
  8. MCMV RNA and DNA were present in blood vessels post infection. Mice produced the latency-related CMV transcriptional product I-E1.
  9. Next, in vitro experiments were carried out with human cells. Infection of human blood vessel endothelial cells with HCMV induced renin expression in a-dose dependent manner, without lysis of the cells (non-lytic infection). This means that viral gene expression takes place in the absence of a viral cytopathic effect. Only replicating forms of HCMV could induce renin.

Conclusion of the Authors:

“In summary, CMV infection alone caused a significant increase of arterial blood pressure. Enhanced expression of pro-inflammatory cytokines, renin and Ang II underlies the pathogenic mechanism of an active CMV infection to increase blood pressure and aggravate atherosclerosis. Thus, control of CMV infection to restrict development of hypertension and atherosclerosis may provide a new strategy to prevent cardiovascular diseases associated with HCMV infection.”

Review
The present article provides interesting new insights into various mechanisms whereby CMV could ultimately cause cardiovascular disease. Many different assays were performed, both with mouse CMV in vivo and in vitro and with human CMV in vitro.

It should be noted however, that several of the reported findings are not new. CVM DNA and RNA have long been identified in atherosclerotic plaques. CMV and other herpesviruses were known to induce IL-6 and other pro-inflammatory interleukines. And a relation between CMV-infection and cardiovascular disease has been established in the past.

The main new findings are (1) that CVM-infection can raise blood pressure and (2) the demonstration of possible mechanisms involved in the increase of blood pressure: induction of renin and angiotensin by infection of endothelial and renal cells (rather than induction of plaques?) and induction of cytokines. Importantly, the cytokine-enhancing effects were restricted to CMV-infected cells only.

Although the findings are very suggestive of a causal relationship, it remains to be proven whether hypertension via enhanced extrarenal production of renin and angiotensin is the causal factor of CMV-associated cardiovascular disease in the normal human situation. Some statements are not underpinned by the current data. See for instance the blue marked text in the author’s conclusion.

ahc_67444

Arterial wall depicting major inflammatory features common to CMV infection and atherosclerosis. – K. Froberg

The current prevailing hypothesis is that atherogenesis is an inflammatory response to acute or chronic endothelial injury. Possible causes for this endothelial injury include free radicals, modified LDL, hypertension, diabetes mellitus and smoking [4,5]. More recently CMV and other infections have been added to the list of risk factors. It is generally thought that the formation of plaques concurrent with the enhanced induction of cytokines can contribute to atherosclerosis and vascular disease, after many years of chronic, active inflammation of the arterial wall.

In the present model, atherosclerosis was only observed in 3 out of 12 HD-V mice. This indicates that atherosclerosis is not involved in the increase of blood pressure. Instead, the present study shows, that CMV might contribute to cardiovascular disease via an effect on blood pressure, presumably mediated through an enhanced expression of renin and Ang II.

With regard to the statistical analysis, I wonder why each virus-treated group was only compared to its mock-infected control (using the Student’s t-test)? Why weren’t all groups compared to each other, using another statistical test? Is this because another approach would have rendered most differences insignificant? The differences between groups are consistent but not very large and the standard deviations are quite overlapping. (Thus significance might be lost when more rigid test are used)

It would for instance be interesting to know the relative contribution of the fatty diet to the rise in blood pressure, or the risk in the 4 groups relative to each other.
We all have CMV (well about 70-90%), but just few of us get high blood pressure (at young age). So likely other factors come into play, that may enhance the detrimental effects of CMV or vice versa. Therefore, it would for instance be interesting to know, to which extent high fat consumption would contribute to high blood pressure as well. Is the suggested order as we see it real: V alone giving slight elevation of blood pressure, HD alone giving more elevation and VHD giving the highest rise? (2×2 table).

The study has some fascinating results, but it is too soon to think about antiviral treatment as the authors and media [3] suggest. Nor is it necessary to worry the public by stating that: You can find out if you have been infected with CMV by requesting a blood test from your GP”, as the daily mail does. This is useless, because CMV is omnipresent.

It hardly seems to be justified to suggest that everybody should be treated with antivirals. And what about the other viruses or bacteria that may play a role? Furthermore, lifestyle and other (immunological) parameters may be more important ànd lifestyle changes may be easier to implement.

Update: Tuesday 2009-05-26: 17.30 pm.

HATTIP: @microbytes (Twitter)

Figure: Kent Froberg from the University of Minesota (med.umn.edu)

References

ResearchBlogging.org

  1. Cheng, J., Ke, Q., Jin, Z., Wang, H., Kocher, O., Morgan, J., Zhang, J., & Crumpacker, C. (2009). Cytomegalovirus Infection Causes an Increase of Arterial Blood Pressure PLoS Pathogens, 5 (5) DOI: 10.1371/journal.ppat.1000427
  2. http://www.sciencedaily.com/releases/2009/05/090514221915.htm
  3. http://www.dailymail.co.uk/health/article-1186876/Heart-disease-isnt-catching-Oh-yes-scientists-warn.html
  4. Many reviews from Cathrien A. Bruggeman and colleagues, like this review in a Book.
  5. Kent Froberg from the University of Minesota (med.umn.edu)
Human Herpesvirus 5 (HHV-5)




Twitter goes Viral: Swine Flu Outbreak – Twitter a Dangerous Hype?

30 04 2009

twitter-network-and-virusTwitter has been praised for its actuality and news breaking character. Remember the earthquakes and the two recent airplane crashes (Hudson River, Schiphol). Twitter often was the first to bring the news.

Twitter’s power lies in its simplicity, -the 140 character limit-, its speed and it’s domino-effect. Tweets (twitter messages) can be read by your followers (I have appr. 650). If they find something important, funny or whatever they could “RT” or Retweet (i.e. resend) the message, and their friends could retweet it as well. Via these secondary networks Twitter can go viral (in its replication and spread).

Below a friends of a friend network of a well known twitter personality Robert Scobleizer, as obtained by Twitterfriends. Only the “relevant network” is shown, directed to someone in particular: tweets beginning with @ (followed by the twitter name of your friend). The actual reach of tweets not starting with @ is greater, because they can be read by all followers.

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Apart from following specific tweople one can also search for certain words or (hash)tags via Twitter Search or #hashtags.

Pushed by celebrities, such as Ashton Kutcher and Oprah Winfrey, who recently joined Twitter. Twitter’s traffic was poised to double and the number of tweeting people has steeply increased.

Twitter has been glorified by the stars. They created a real (meaningless) twitter mania.

But what raises high, can drop low.

Several sources dethroned Twitter because of it’s viral role in the recent swine flu outbreak. One of the first and most serious critiques came from a blog (Foreign Policy: Net Effect). It’s title: Twine flu: Twitter’s power to misinform.swine-flu-totThis is a serious allegation. Evgeny Morozov‘s main critiques:

  1. The “swine flu” meme has led to misinformation, fear and panic. Wrong info includes: fear that it “could be germ warfare” or “that one should not eat pork and certainly not from Mexico”.

  2. Unlike a simple Google search Twitter gives too much noise (irrelevant or wrong information).

  3. Messages from trustworthy sources have as much weight as those from uninformed people.

  4. There is very little context you can fit into 140 characters, even less so if all you are doing is watching a stream.

  5. Evgeny also worries about a future misuse of Twitter by cyber-terrorists shaping conversations on serious topics. A number of corporations are already monitoring and partially shaping twitter conversations about particular brands or products.

In addition some posts highlight that most of the Tweets belong to the category “witty or not so witty”. (also see this post)
And after these comments many similar comments were to follow: In fact these comments and critiques were going viral as well: take a look at this Google Search for Twitter Swine Flu and note the negative sound of most of the headlines.
The CNN website quotes Brennon Slattery, a writer for PC World,

“This is a good example of why [Twitter is] headed in that wrong direction, because it’s just propagating fear amongst people as opposed to seeking actual solutions or key information (..). The swine flu thing came really at the crux of a media revolution.”

Is Twitter just a hype and useless as an information source? Is it dangerous when a wide number of people would turn to Twitter in search of information during an emergency? Or have people just found a stick to beat the dog?

I will go to several aspects of the twitter flu coverage as I have encountered it.

Number of tweets

Indeed, as brought forward by Mashable, Tweets about “Swine Flu” are *now* at 10,000 per hour!!

Yesterday, 5 out of 10 twitter buzzwords were connected to Swine Flu:

  • # · Swine Flu
  • # · swineflu
  • # · Mexico
  • # · H1N1
  • # · Pandemic

Searching for information on Twitter
You can imagine that it is hardly useful to keep track of tweets mentioning *swine flu*, nor is searching for these buzzwords or hastags useful, if not combined with other terms or names, like CDC or laikas (just to find what you tweeted yourself).
I keep track of certain words via Tweetdeck in separate columns, accepting a certain “noise”, knowing this will only yield 20-50 tweets per day. It would not come to my mind to just blindly search for swineflu on Twitter.

The official media
It is said that Twitter doesn’t give useful or correct information, and indeed it hasn’t been designed for that (being merely a social Network). In its primitive form it is just online gossip or as The Register (UK) puts it- “it is not a media outlet. But odd enough, the official media did not behave differently. Cable television programmers went into crisis mode and a look at newspaper front pages and website home pages around the world showed a range of responses, from the almost hysterical to the concerned and more measured (Reuter’s Blog).

Look at this message from AJ Cann, that I retweeted :

laikas: RT @AJCann Totally irresponsible #swineflu journalism in the Dail Mail http://tinyurl.com/cms3km (expand) >>and they say twitter evokes global panic!
Is there really no reason to be worried?
Let’s face it. We don’t know an awful lot about this new virus strain. While it is true that the common flue has killed 13,000 people in the US since in a rather unnoticed way, and while there are relatively few swine flu casualties yet, one never knows how this new H1N1 epidemic will evolve. It might just fade away or it could kill millions of people. We just don’t know. It is a new, deadly virus. Not for nothing (as I learn from Twitter), the WHO has just raised the current level of influenza pandemic alert from phase 4 to phase 5. But this is only meant to be prepared and to inform, not to cause panic.
who-message
AJCann (on twitter)Ben, a doctor writing for the Guardian, excelling in critically informing the public about science (and quack) and a real valibrity, was invited all over by the media to be a naysayer on the “aporkalypse”.
How to deal with Twitter Noise?
Suppose you would listen to all radio channels at once: that would be an unbearable noise. Usually you choose a channel, your favorite one, and just listen what comes next. But you may switch to another channel anytime. And for news you might just go to a specific channel that you know is the most informative.
It is exactly the same with Twitter. I don’t follow everyone. Since I use Twitter mostly for my work (medicine, library, science, web 2.0) and not primarily for a chat or wit, I choose the tweople I follow carefully. If they produce too much noise I might unfollow them. They are my human filter to the news.

6a00d8341bfa9853ef0105368fcb5e970c-400wi-darmano

Furthermore among the ones I follow are News or Health Sources, like @CNN Health, sanjayguptaCNN, @BBC Health, @BreakingNews, @health and recently (because of retweets of friends): @WHOnews , @CDCemergency, Reuters_FluNews, Fluheadlines.

@BreakingNews and @health mentioning real casualties and the WHO calling an emergency meeting, I realized the seriousness of the problem. I was also pointed to @WHOnews and @CDCemergency, the most trustworthy sources to follow.
I also understood that the swine flu might be difficult to contain.

laikas: RT @BreakingNews: BULLETIN — WORLD HEALTH ORGANISATION CALLS EMERGENCY MEETING TO DISCUSS DEADLY SWINE FLU OUTBREAKS IN MEXICO AND THE U.S.

laikas: RT @health WHO, CDC concerned about possible epidemic following reports of 60+ people killed by new flu strain in Mexico http://bit.ly/d3JsO
laikas: RT @TEDchris: Swine flu outbreak. This is how it was SUPPOSED to have been contained. http://is.gd/us6r Worrying. >> WHO protocol
laikas: RT @BreakingNews: Reports of flu outbreak in New Zealand. 22 students may have been infected after a trip to Mexico. BNO trying to confirm. 3:25 AM Apr 26th from TweetDeck

laikas: RT @dreamingspires: RT @AllergyNotes Map of H1N1 Swine Flu of 2009 http://bit.ly/P2mcc (expand) 4:41 AM Apr 26th from TweetDeck

laikas: Map of H1N1 Swine Flu of 2009 http://bit.ly/P2mcc _ New Zealand added to the map. 4:42 AM Apr 26th from TweetDeck


Direct Link to H1N1 Swine Flu Google Map:

Somewhat later came the informative phase. Long before the official media were giving any useful information, some of my twitterfriends alerted me to their own or other (official) news.

@ajcann already wrote a post on his blog Microbiology Bytes (a blog with the latest news on microbiology) :10 things you should know about swine flu. (April 25th)

laikas: Reading @sciencebase Swine Flu http://bit.ly/y5Xqz 7:47 AM Apr 26th from web

laikas: RT @sanjayguptaCNN: I’ll answer your swine flu Q’s LIVE on CNN at 7:30a ET. call 1-800-807-2620. thanks 4he gr8 tweet Q so far.

laikas: RT @consultdoc: Great swine flu summary via @ubiquity http://bit.ly/DK0xV (expand) Thanks Greg.1:18 PM Apr 26th from TweetDeck

laikas: RT @BreakingNews: The WHO is holding a news conference on swine flu. Michael van Poppel is covering it live @mpoppel.
laikas: RT @stejules: RT @mashable HOW TO: Track Swine Flu Online http://tinyurl.com/dh68n8 (expand) (via @tweetmeme) (

At that point I became saturated with all information. I just follow the main news and read some good overviews

end-tweet-flu
Conclusion
For me, Twitter was the first and most accurate news source to get informed and updated on the swine flu pandemics. It was reliable, because “my friends” filtered the news for me and because I follow some trustworthy sources and news sites. Indirectly other tweople also pointed me at good and actual information.
And in my turn I kept my followers informed. The news has alarmed me, but I’m not in panic or frightened. I just feel informed and at the moment I can do nothing more than “wait and see”.

It has often been said: Twitter is what you make of it.
But keep in mind the golden rule:

Information on Swine Flu

News and Blogs

Photo Credits:

* wonderful those different names.





The Real Sputnik Virus

15 08 2008

I just rewrote the “about” section, saying that this blog was started as part of the web 2.0 SPOETNIK (EN: Sputnik) course, that I saw this blog as an experiment, but that I am now irreversibly infected by the blog/Sputnikvirus.

Coincidentally a real Sputnik virus has been discovered.¹ The virus is called Sputnik (Russian for “travelling companion”), because it “accompanies” the mamavirus, the big ‘mama’ among the recently discovered giant mimiviruses. Both the mamavirus and its satellite were present in an amoeba-species, found in a water cooling tower. Strikingly Sputnik cannot infect the amoeba on its own, but needs the companion of a mimivirus. In fact Sputnik hijackes the ‘viral factory’ of the mimivirus in order to replicate, making the mimivirus less infective. Therefore the Sputnik virus is said to actually “infect” another virus

Wait a minute…!! A virus that ‘lives’ from an other virus and takes over his replicating machinery? This means that the virus that is being ‘infected’ (the mamavirus) is a living organism??? But viruses are ‘dead’, at least that is what I learned.

Definition of a virus in one of my studybooks (Genes IV, Benjamin Lewin, 1990, p41).

“Viruses take the physical form of exceedingly small particles. They share with organisms the property that one generation gives rise to the next; they differ in lacking a cellular structure of their own, instead needing to infect a host cell. Both prokaryotic and eukaryotic cells are subject to viral infections; viruses that infect bacteria are usually called bacteriophages”

Thus ‘per definition’ viruses are not alive ànd they do not infect other viruses?!

But what is in a definition/name?
According to Aristotle a definition of an object must include its essential attributes or its “essential nature”. However humans may only observe part of the essential attributes, especially when it concerns the infinitely small or infinitely large (which limitates the accuracy of our observations). Nature made his own definitions/categorizations and we just trying to find the rules, if any, to bring some order into chaos. But in science rules and concepts can be falsified and this rule may be one of them.

That viruses may be at the boundaries of life is no new discussion. According to wikipedia:

Biologists debate whether or not viruses are living organisms. Some consider them non-living as they do not meet all the criteria used in the common definitions of life. For example, unlike most organisms, viruses do not have cells. However, viruses have genes and evolve by natural selection. Others have described them as organisms at the edge of life.

As you can see from the scheme above (from wikipedia) the classification of living organisms has never been rigid and as time goes more ‘kingdoms’ have been discovered.

The Mimivirus seems to be at “the edge of life”, because it

Besides the what-is-a-living-organism-issue the discovery of the Mimi-Sputnik virus couple raises some other interesting points.

  • The paradigm that viruses are evolutionary latecomers, evolving as parasites after the archaea, bacteria and eukaria had formed is challenged by comparative genome-analysis which suggests that the virus world is the most ancient.
  • There is an abundance of Mimi-like genetic sequences in the (virus-rich) ocean leading to a suspicion that giant viruses are a common parasite of plankton.
  • Sputnik-like DNA is also found in the ocean, raising the possibility that satellite viruses could play a role in regulating the growth and death of (Mimi-infected) plankton. Therefore these marine viruses could be mayor player in the global ecosystem
  • Although Mimiviruses primarily infect amoeba, antibodies have been found to the virus in some human pneumonia cases. If these mimiviruses have their own satellites…. then this might perhaps be therapeutically exploited against large DNA viruses in human.

Finally I would like to close this post with an apt poem of Jonathan Swift (often cited in this context):

So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ‘em;
And so proceed ad infinitum.

And another coincidence: There is a popgroup sigue-sigue-sputnik that has an number called virus (on the album ray-of-light.)

NOTES
¹The Sputnikvirus has been detected by the team led by Jean-Michel Claverie and Didier Raoult (CNRS UPR laboratories in Marseilles), the same team that identified the mimivirus as a virus.
²Some of the finding are not completely new, e.g. Sputnik was not the first virus-satellite: Satellite Tobacco Mosaic Virus had been discovered before. Some researches don’t regard a satelite virus as a virus, however, but as subviral

SOURCES
La Scola, B et al The virophage as a unique parasite of the giant mimivirus, Nature DOI:10.1038/nature07218; announced in ‘Virophage’ suggests viruses are alive – Nature News, 2008 august 6th
Other news-coverages:
NRC-handelsblad, 2008-08-09 en wetenschapsbijlage 2008-08-10
telegraph.co.uk 2008-08-06
sciencenow daily news 2008-08-06

BACKGROUND INFO and HYPOTHESES
about the sputnikvirus
:
findingdulcinea.com: good starting point for further information about Sputnik and mimiviruses with links to other sources
scienceblogs.com/grrlscientist/
the-scientist.com/blog/
about the mimivirus :
a general overview in
http://www.microbiologybytes.com (last update 2007)
and “unintelligent-design at discovermagazine.com/2006

about the origin of viruses and their presence in the sea: again….
Nice overview
Viruses in the sea’ in Nature by Curtis A. Suttle et al(2005)
Hypothesis: The ancient Virus World and evolution of cells by Eugene V Koonin in Biomedcentral (2006) (pdf-open access)
General: Wikipedia, ie about Viruses and Bacteriophages

—————

Ik heb net de “about” pagina herschreven: ik schrijf dat ik dit blog ben gestart in het kader van de web 2.0 SPOETNIK cursus, dat ik dit blog als een experiment zag, maar dat ik inmiddels voor altijd geinfecteerd ben met het blog/Spoetnikvirus.

Toevallig las ik afgelopen zaterdag in het NRC dat er een echt Spoetnik virus is ontdekt.¹ Van de Spoetnikcursus weet ik nog dat Spoetnik in het Russisch metgezel betekent. Het virus kreeg deze naam omdat het zich samen met het mamavirus, het grootste virus onder de reusachtige minivirussen, in een amoebe ophoudt. Opmerkelijk genoeg is het Spoetnik virus helemaal niet in zijn eentje in staat om de amoebe te infecteren, maar heeft jij daarbij de hulp van het mimivirus nodig, in die zin dat Spoetnik de virusfabriekjes van het mimivirus inpikt om zichzelf te vermenigvuldigen. Met andere woorden, het Sputnik virus is in staat een ander virus te infecteren.

Wacht even?!……… Een virus dat een ander virus infecteert en ‘ziek maakt’? Dat betekent dat het virus dat geinfecteerd wordt ‘leeft’. Maar virussen zijn dood, dat heb ik tenminste zo geleerd.

Definitie van een virus in een oud studieboek (Genes IV, Benjamin Lewin, 1990, p41).

“Viruses take the physical form of exceedingly small particles. They share with organisms the property that one generation gives rise to the next; they differ in lacking a cellular structure of their own, instead needing to infect a host cell. Both prokaryotic and eukaryotic cells are subject to viral infections; viruses that infect bacteria are usually called bacteriophages”

Dus viruses leven per definitie niet en kunnen andere virussen niet infecteren?!

Maar “what is in a definition/name”?
Volgens Aristoteles moet een een definitie van een voorwerp/begrip essentiële elementen of de ware aard omvatten. Maar mensen zien misschien maar een deel van deze kenmerken, vooral als het om oneinig grote of oneindig kleine dingen gaat. De natuur maakt zijn eigen indelingen en wij proberen om wetten te achterhalen, voor zover deze er zijn, om orde in de chaos aan te brengen.
Volgens de regels der wetenschap zijn wetten en concepten echter toetsbaar en falsifieerbaar. Dat virussen levenloos zijn zou dus ook ontkracht kunnen worden.

Het al dan niet ‘levend zijn’ van virussen is geen nieuwe discussie. Sommige biologen zien virussen als niet-levend, omdat ze niet àlle belangrijke kenmerken van leven hebben, ze hebben bijvoorbeeld geen cellen. Virussen hebben echter wel genen en evolueren door natuurlijke selectie waardoor ze volgens anderen wel op het randje van het leven balanceren.

Het Mimivirus lijkt nog het meest op het randje te balanceren. Het

Behalve bovenstaande implicaties voor wat we ‘leven’ noemen, maakt het Mimi-Spoetnik-koppel nog meer discussie los.

  • Op basis van vergelijkend genoomonderzoek lijkt het onwaarschijnlijk dat virusen evolutionaire nakomertjes zijn, maar meer dat ze aan de voet van de archaea, de bacteriën en de eukaryoten hebben gestaan.
  • Er is heel veel Mimi-achtige genmateriaal in de oceanen gevonden, hetgeen zou kunnen betekenen dat reuzevirussen wel eens een algemene parasiet van plankton zouden kunnen zijn.
  • Spoetnik-achtig DNA wordt óók in de oceaan gevonden. Misschien dat satelliet-virussen wel een slutelrol spelen in de regulatie van de hoeveelheid plankton.
  • Hoewel Mimivirusen vooral amoeben infecteren, zijn antistoffen tegen dit virus ook bij enkele patienten met longontsteking gevonden. Als deze mimivirusen hun eigen satellieten hebben, kunnen deze wellicht ingezet worden tegen de ziekteveroorzakende virussen.

Tenslotte een zeer toepasselijk gedicht van Jonathan Swift (veelvuldig in deze kwestie aangehaald):

So, naturalists observe, a flea
Has smaller fleas that on him prey;
And these have smaller still to bite ‘em;
And so proceed ad infinitum.

Nog een toevalligheid Er is een band sigue-sigue-sputnik met een (vrij heftig) nummer virus (album ray-of-light).

NOTES
¹het Spoetnik- en het mimivirus zijn ontdekt door Jean-Michel Claverie en Didier Raoult (CNRS UPR laboratories in Marseilles) en zijn team.
²Niet alle bevindingen zijn echt even nieuw. Vòòr Spoetnik waren er al andere virussatellieten ontdekt, zoals de satelliet(virus)van tabaksmozaïekvirus. Door velen wordt zo’n virus niet als ect virus gezien, maar als subviraal beschouwd.





Virus attack

8 06 2008

The recent Google Doc spam attack made me think of the video my daughter (14) recently showed me. She gave me the link to ongein.nl, but I found a better version on Youtube, that can be enbedded.

It is Animator vs. Animation 2 by Alan Becker

Enjoy it! Watch it till the END. Lol firefox!

——–

NL flag NL vlagDit spreekt voor zich. Een hele leuke animatie, waar mijn dochter me een tijd geleden op attendeerde Ik moest er weer aan denken nadat ik eergisteren zo’n vervelende spam binnenkreeg. Het begin is wat traag, maar daarna gebeurt er zoveel. Ik zie er steeds meer in. Vooral firefox is prachtig, maar ook The END. Herkenbaar. Geniet ervan!








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