The blood DNA virome in 8,240 humans

[RogerBlack]

http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006292

Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.

A graph of how many people in the sample each virus is found in, and the estimate of abundance per 100000 human blood cells.

Some viruses can be in a latent form, integrated into human DNA, to remain latent for long periods. This shows how many are integrated versus abundance.



Caveats: This study was not aimed at finding either rare, or the similar population of RNA viruses that exist. It also shows the problem with contamination, in that most of the viruses found (70) were lab containments, with some from well understood and expected sources used for calibration, but others from a wide variety of lab sources.

 

[anciendaze]

There are quite a number of interesting things in this paper. One is that HTLV-1, a retrovirus, seems more prevalent than HIV-1. This is normally dismissed by saying HTLV is mostly harmless, except when it causes HAM/TSP or ATLL, both lethal diseases. There are problems connecting infection and disease because HTLV has a very long latency prior to producing clinical disease. Most cases are asymptomatic. It would appear HTLV is still spreading through human populations.

Even though HHV-6A and HHV-6B are not retroviruses we do see significant evidence of integration into chromosomes. (Mostly this is in telomeres, and I'm not sure what this means.) HHV-6A and HHV-6B are sufficiently different to be counted as different viruses, if we were starting from scratch, and did not have HHV-7 and HHV-8 already named.

The stunning result is that HHV-7 seems to top the list in prevalence. This virus is something of a mystery at present. Perhaps we need an HHV-7 foundation to study it.

The prevalence of clearly identified infection via DNA sequencing is at odds with results based on antibodies. Most evidence of antibodies indicating prior infection by EBV shows over 90% of humans have antibodies recognizing the virus. Since cells infected with DNA virus retain the virus for life, it seems likely some infected cells remain in other physiological compartments besides peripheral blood. Some individuals have detectable virus in circulating blood, but most do not. This indicates most people infected with EBV have immune systems capable of controlling the infection.

Prevalence of HHV-6A and HHV-6B is even more of a problem. There have been studies finding 100% of subjects infected. At the time the first studies were done there was a distinct drop in prevalence with age. The conspicuous transmission of the virus mostly takes place in infants. This seems to indicate that HHV-6A and HHV-6B are more prevalent today than a generation or two in the past. These viruses are actively spreading through human populations, and about 1% are even integrated into inherited chromosomes.

I don't know how to interpret the statements about viral contamination in standard reagents. The authors appear to have taken measures to separate the results of contamination from legitimate reads, but it is unclear how successful these have been.

My bottom line is that we still do not understand a great deal about the human virome in the bulk of the population, or how this viral load contributes to known medical problems.

 

[RogerBlack]

To clarify, this is only the virome that is in blood cells, not serum.
Whole blood will contain more viruses of different sorts. Some viruses are not in the blood in immune competant people, and latent viruses that are not latent in other than blood cells will not be found, nor will RNA viruses.

This technique is a useful adjunct to other surveys, and would ideally be in conjunction with a virome of serum, and one doing RNA.

Its major plus is that it is 'free' and requires no add-ons if you are already sequencing whole human genomes from peripheral blood cells, you just reprocess the data.

I'd meant to link http://www.microbe.tv/twiv/twiv-435/ that I realised covered this paper in a podcast, but got distracted by a tomato.

 

[anciendaze]

Granted that this was never intended to find RNA viruses or free DNA virions in serum, I still think this shows a significant discordance between different estimates of DNA viral prevalence in the general population. In particular it shows a number of known pathogens with serious effects (e.g. polyoma virus, papilloma virus, HHV-8,) which standard screening for transfusions will not detect, and common clinical practice may not even look for unless there are conspicuous clinical signs.

On the subject of RNA analysis I already have strong opinions independent of virology. There has been too much emphasis on DNA in chromosomes, which may or may not be actively transcribed, (methylation is only one limited form of regulation) and too little effort to deal with substantial sequence alteration which regularly takes place in RNA. We seldom know if transcribed mRNA is being "knocked down" by RNA interference, except in those cases where this is done deliberately in genetic experiments. This is not something invented by humans for laboratory research, it is a long-standing defense against parasitic DNA or RNA sequences. When it comes to human genes accidentally disabled by RNA interference in defense against pathogens we are still largely in the dark. This may be more important to pathology than traditional active responses against pathogens involving antibodies and immune cells.

(No, I do not know this is true. Nobody knows. With past emphasis in research on infectious diseases it seems unlikely anyone would know. Such ignorance should not be acceptable in the future.)

We know that DNA sequences can be present in a genome, but not transcribed, or transcribed into mRNA, but not into polypeptides. Some sequences are regularly reordered by circular RNA to produce transcripts which you will not find in the genome. So far as we know, humans do not have the spectacular range of variations found in fruit flies, where a single gene (dscam) is now known to produce over 38,000 alternate splicings transcribed into polypeptides and proteins. Over 90% of human genes do have some alternate splicing, which makes current concentration on DNA sequences found in chromosomes somewhat ridiculous. Throw in the contributions of very common viromes of humans and you should realize what we have been studying heretofore has been a small minority of active sequences found in humans, either healthy or sick.

 

[RogerBlack]

'Yes'.

On the subject of RNA analysis I already have strong opinions independent of virology. There has been too much emphasis on DNA in chromosomes, which may or may not be actively transcribed,

I don't in principle disagree, but it's going to take a further revolution in technology to get this cheap.

http://www.brain-map.org/ - is an example of human and mouse brain transcriptome atlases, like
http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000582

We generated what is to our knowledge the first genome-wide transcriptome atlas by RNA in situ hybridization of an entire mammalian organism, the developing mouse at embryonic day 14.5. This digital transcriptome atlas, the Eurexpress atlas (http://www.eurexpress.org), consists of a searchable database of annotated images that can be interactively viewed. We generated anatomy-based expression profiles for over 18,000 coding genes and over 400 microRNAs. We identified 1,002 tissue-specific genes that are a source of novel tissue-specific markers for 37 different anatomical structures. The quality and the resolution of the data revealed novel molecular domains for several developing structures, such as the telencephalon, a novel organization for the hypothalamus, and insight on the Wnt network involved in renal epithelial differentiation during kidney development. The digital transcriptome atlas is a powerful resource to determine co-expression of genes, to identify cell populations and lineages, and to identify functional associations between genes relevant to development and disease.

As a first step, we need to understand the transcriptome of the human in the same way. This is proceeding. But then it gets nasty, as you want then to look at not merely a static map of expression levels (>20000 dimension data is fun), but expressions as they vary over time during disease, which is a whole new problem.

Time-series blood, and limited biopsies are of course possible, but the simple and most obvious things you'd like to do are often impossible for various reasons, or prohibitively expensive.

Even if you had a full transcriptome atlas for CFS patients over the course of the disease, finding what's up in this firehose of data would be challenging.

 

[anciendaze]

I never claimed this would be easy, though I can recall arguments saying the Human Genome Project would take centuries. Nor am I going to insist you need to know everything about humans to be medically useful. A great many things are possible without waiting for a next millennium breakthrough in science.

Above I've highlighted one concern, possible knockdown of host genes as a result of defense against parasitic DNA/RNA sequences of whatever origin. One result of past genetic research is that we know without question that knockdown of many important host genes would have serious consequences. Is this likely? From an absence of evidence argument it would seem far-fetched. On the other hand, there simply hasn't been much research with the potential to recognize this happening.

What about a priori arguments? Conventional wisdom says that around 8% of human genomes are of viral origin. This underestimates the number of short viral sequences scattered around. Some are even reverse-transcribed DNA from RNA viruses which are not retroviruses. This would seem to reflect past coinfections of RNA viruses and retroviruses in ancient individuals who left viable offspring. Forward transcription would then produce sequences identical to those which came from actual RNA viral infections. I don't have to argue that most of these things are complete or functional in any sense. What seems very likely is that these sequences could trigger defensive responses which would have trouble distinguishing true host genes from genes inserted by viruses. In this case a knockdown via RNA interference seems almost inevitable.

Is there any reason to think this speculative argument applies to actual people with existing illnesses? Several members of my family show partial signs of Ehlers-Danlos Syndrome, though generally without the spectacular hypermobility needed for diagnosis without genetic markers. (Several of us did have unusual mobility in childhood.) Others for whom we can't identify a common ancestor (associated by marriage) show a different connective tissue disorder associated with a channelopathy. In some cases the evidence of pathology is dramatic, but the genetic markers have simply not turned up. Something is wrong with connective tissue, but so far the cause has not been found in genes.

In correspondence with people exhibiting rare diseases (which may be found in as much as 5% of the population and still be called rare by the medical profession) I find the theme of real signs of inherited pathology without genetic markers quite common. These sound like the situation I would expect if important genes are present, but knocked down as a result of defense against an environmental threat. I am particularly suspicious of such a cause when onset does not occur until adolescence or early adulthood.

This strikes me as a reasonable area for research, assuming national policy does not plan to eliminate problems by shooting the 5% with clinical signs.

 

[Knockknock]

There are quite a number of interesting things in this paper. One is that HTLV-1, a retrovirus, seems more prevalent than HIV-1. This is normally dismissed by saying HTLV is mostly harmless, except when it causes HAM/TSP or ATLL, both lethal diseases. There are problems connecting infection and disease because HTLV has a very long latency prior to producing clinical disease. Most cases are asymptomatic. It would appear HTLV is still spreading through human populations.

Even though HHV-6A and HHV-6B are not retroviruses we do see significant evidence of integration into chromosomes. (Mostly this is in telomeres, and I'm not sure what this means.) HHV-6A and HHV-6B are sufficiently different to be counted as different viruses, if we were starting from scratch, and did not have HHV-7 and HHV-8 already named.

The stunning result is that HHV-7 seems to top the list in prevalence. This virus is something of a mystery at present. Perhaps we need an HHV-7 foundation to study it.

The prevalence of clearly identified infection via DNA sequencing is at odds with results based on antibodies. Most evidence of antibodies indicating prior infection by EBV shows over 90% of humans have antibodies recognizing the virus. Since cells infected with DNA virus retain the virus for life, it seems likely some infected cells remain in other physiological compartments besides peripheral blood. Some individuals have detectable virus in circulating blood, but most do not. This indicates most people infected with EBV have immune systems capable of controlling the infection.

Prevalence of HHV-6A and HHV-6B is even more of a problem. There have been studies finding 100% of subjects infected. At the time the first studies were done there was a distinct drop in prevalence with age. The conspicuous transmission of the virus mostly takes place in infants. This seems to indicate that HHV-6A and HHV-6B are more prevalent today than a generation or two in the past. These viruses are actively spreading through human populations, and about 1% are even integrated into inherited chromosomes.

I don't know how to interpret the statements about viral contamination in standard reagents. The authors appear to have taken measures to separate the results of contamination from legitimate reads, but it is unclear how successful these have been.

My bottom line is that we still do not understand a great deal about the human virome in the bulk of the population, or how this viral load contributes to known medical problems.

!!! Waooooo impresive words!!!
You sound alot like me, there is very few people that will talk this way, this are ( FACTS) that most of the poeple constanly ingnore!!
There strong evidence that you dont need to have HIV to develope immune deficiency like AIDS, some of the herpes viruses as you said can do it, they integrate to the cromosoms, some even use thesame proteinand receptor to enter Cd4 and T, B cells.
They have in comun like hiv they persist in the body no matter how much you silent them or lower the viral load.
Therr have been alot of missleading in science, indont think everything have being told the way its, now days is when we are all starting to see reality, even thouhh there is many people that blindly trust science and govermments.
As you said HTLV infection is the greates example like hhv6 to of science and govermments missleading.
Htlv it has long latency and slow replication like mlv( that science and goverments keep denied that can infect humans, but there is enough evidence that it does and its behind most of mother auto-neuro immune ilnesess.
This retrovirus like htlv1 are slow reolication, but other viruses like cmv, ebv can accelerate replication.
They help retroviruses like htlv- mlv to come our of latency enter the cell and replicate, the envelope protein of this other herpes viruses help them.

There is not to many people with tsp/ham, but thereis millions with other illness leukemia and rare cancers as the result of it.
Science and Gov's have ignore this for decades, thesame way they have misslead me/cfs all this years.

My respect to you!!!!

 

[wastwater]

I was looking at viral chromosome integration on chromosome 6 and some interesting ones came up baboon type C DNA provirus
Avian oncogenic herpesvirus
Lentivirus intergration site
Also one about EBV integrating at 6q15

 

[Knockknock]

I was looking at viral chromosome integration on chromosome 6 and some interesting ones came up baboon type C DNA provirus
Avian oncogenic herpesvirus
Lentivirus intergration site
Also one about EBV integrating at 6q15

Were did you get this from???
very interesting..
all this viruses are in were?? were did you find them ???

 

[wastwater]

It was just a yahoo search I typed something like chromosome 6 viral integration sites I'm not sure if it means anything I confuse myself at times

 

[Knockknock]

It was just a yahoo search I typed something like chromosome 6 viral integration sites I'm not sure if it means anything I confuse myself at times

ohh ok..
it does integrate...