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Lipkin & CII: Diagnostics Breakthrough Brings Viral Sequencing to Doctors’ Toolkit

Simon

Senior Member
Messages
3,789
Location
Monmouth, UK
I do think we are lucky to have Ian Lipkin and co doing mecfs research, it's not like he's short of other interesting stuff to do - like this (Lipkin has pioneered a lot of viral detection techniques, so he has form in this area).
NEW YORK (Sept. 22, 2015)—Until now, there hasn’t been a fast, efficient way to broadly screen for viral infections. A breakthrough genetic testing method promises change this situation by giving clinicians a powerful new tool to detect and sequence viruses. Developed by scientists at the Center for Infection and Immunity (CII) at Columbia University’s Mailman School of Public Health, the Virome-Capture-Sequencing platform for Vertebrate viruses (VirCapSeq-VERT) is as sensitive as the gold standard polymerase chain reaction (PCR) assays while enabling simultaneous testing for hundreds of different viruses and providing near complete sequence of their genomes.

The system and its capabilities are described for the first time in a paper in the journal mBio:

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

Captures Viruses Even After They Mutate

The method’s ability to detect a broader swath of the genome is especially useful in screening for viruses, which mutate many times faster than bacteria. VirCapSeq-VERT is able to detect and collect genetic information about viruses even if the sample doesn’t exactly match the probe. According to its developers, VirCapSeq-VERT can detect a novel virus when as much as 60 percent of its sequence doesn’t match the probe. When the suspect virus mutates, the technology is still able to catch it.
 

Never Give Up

Collecting improvements, until there's a cure.
Messages
971
I do think we are lucky to have Ian Lipkin and co doing mecfs research, it's not like he's short of other interesting stuff to do - like this (Lipkin has pioneered a lot of viral detection techniques, so he has form in this area).
Do you know how this differs from the VirScan product in terms of method, accuracy, discernment of length and extent of infection, price, and speed?
 

msf

Senior Member
Messages
3,650
Simon, you seem to pay close attention to the big ME studies - how did Lipkin rule out viruses in ME if this hadn´t been invented yet?
 

RL_sparky

Senior Member
Messages
379
Location
California
From Stanford's Newsletter dated June 1st, 2015:

High Throughput Sequencing/Pathogen Discovery: Through our continued partnership with Holden Maecker

PhD at Stanford and W. Ian Lipkin MD and Mady Hornig MA, MD at Columbia University, our effort of

looking for pathogens present or abundant in ME/CFS patients has yielded exciting results. We are in the

process of preparing a manuscript for submission to a peer-reviewed journal.

http://med.stanford.edu/content/dam/sm/chronicfatigue/documents/MECFSNewsletter_Spring_2015.pdf
 

Simon

Senior Member
Messages
3,789
Location
Monmouth, UK
Simon, you seem to pay close attention to the big ME studies - how did Lipkin rule out viruses in ME if this hadn´t been invented yet?
He used established high-tech methods (see @RL_sparky post above), the breakthrough about this new method is that it allows clinicians to quickly screen for a large number of viruses, work that take a long time using conventional methods in a lab. As Halycon said, only results from plasma have been released (but not yet published):
Until now, there hasn’t been a fast, efficient way to broadly screen for viral infections. A breakthrough genetic testing method promises change this situation by giving clinicians a powerful new tool to detect and sequence viruses

Do you know how this differs from the VirScan product in terms of method, accuracy, discernment of length and extent of infection, price, and speed?
You don't ask much! Sorry, I don't know, but did wonder myself. The technology is quite different. This new method detects viral DNA/RNA, while the VirScan approach detects viral proteins. As for the rest, I don't know but am interested if anyone has more information.
 

Sean

Senior Member
Messages
7,378
We get bogged down in details sometimes here. Please keep in mind that we are still in the early stages of serious ME/CFS research, and a lot of what is going on currently is exploratory and not definitive.
 

Bob

Senior Member
Messages
16,455
Location
England (south coast)
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Never Give Up

Collecting improvements, until there's a cure.
Messages
971
Slightly off-topic (and I don't know if they used their new technology to make this finding) but Lipkin's team seem to have discovered a new human virus.

It looks a little like the hepatitis C virus, which can cause permanent liver damage, and a little like the human pegivirus, which appears to be harmless, the team reports in the journal mBio.

They've named it human hepegivirus-1 (HHpgV-1).

Am I the only one that finds this name choice humorous?
 

beaker

ME/cfs 1986
Messages
773
Location
USA
We get bogged down in details sometimes here. Please keep in mind that we are still in the early stages of serious ME/CFS research, and a lot of what is going on currently is exploratory and not definitive.

That seems rather insulting to those who have been doing research( yes serious research !) for the last 30 years --DeFreitas,Cheney, Bell, Peterson, Kilmas,Grufferman, Rowe, Stratton, Streeten, Stewart,Jessop, and so many more in so many countries, And for those who came before them ( Ramsey, Parish ) and the Icelandic outbreak before that certainly had doctors working on it.
This is not a new disease. They were all "serious" researchers.

Their groundwork, and unwillingness to give up on their patients and /or lab work laid the groundwork for what is going on now.

Yes, we have new technology -- as there has a been along the way-- and new insights. But this is not early serious research. I hope we will look back and see this as the beginning of the last chapter. Who knows.
 

Sean

Senior Member
Messages
7,378
I think you have misinterpreted what I am saying, particularly given my track record over many years of supporting those people (including financially, to the extent I can,) and arguing for that kind of research.

But IMHO it is beyond dispute that we currently have no definitive answers and are still in the early stages of serious research (especially compared to other major diseases), and I do not accept that saying that in any way impugns the work and dedication of those names you have listed (and others).

I see nothing in my original statement that needs modifying, other than perhaps to add that the situation seems to be changing in our favour, in the USA at least.

:grumpy:
 

acer2000

Senior Member
Messages
818
Perhaps this should be its own new headline, but its interesting this came right before this other announcement:

Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses

http://mbio.asm.org/content/6/5/e01466-15

Also collaboration with Lipkin lab.
 
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