Viral vector nomenclature

Tom Anderson via methods%40net.bio.net (by ucgatan from ucl.ac.uk)
Wed Jun 6 09:41:07 EST 2007


On Wed, 6 Jun 2007, Aawara Chowdhury wrote:

> In <mailman.1366.1181069097.5139.methods from net.bio.net>,
>  Tom Anderson <ucgatan from ucl.ac.uk> wrote:
>
> > I guess most people call them viruses, but to me, a virus means
> > something that's capable of infecting cells and making copies of
> > itself, which these things aren't. Some might call them vectors, but a
> > vector is the piece of DNA you put your gene into at the start, not
> > the finished product. One guy i worked with called them amplicons,
> > which just seems completely wrong. Any advances?
>
> The correct term would be "viral vector", just as what that you refer to
> as a "piece of DNA" should really be "plasmid vector", and not just
> vector. The plasmid that you transfect to make a viral vector, should be
> termed "viral vector DNA" or "viral vector plasmid".

Hang on, though, the vector is the thing that does the carrying, not the
thing you eventually use. pRK5 is a vector; pRK5 with actin cloned into
the MCS is no longer a vector, it's a construct. You might say that pRK5
is the vector of this construct, but the construct itself is not a vector.

In my case, deleted type 5 adenovirus is a vector, but the things i'm
using aren't. 'Viral constructs' maybe? But that sounds like i'm talking
about the DNA with which i make the blobs (even though i'd actually call
that a genome, or a genomic construct).

> The term "amplicon" is correctly applied to self-amplifying flavivirus
> vector RNAs, but not to retroviral vectors, adenoviral vectors, and
> their ilk.

Right. I could even accept that the genomes of my blobs are amplicons,
since they're units of nucleic acid which get replicated, but to call the
blobs themselves amplicons is surely wrong.

> > Can you call them viruses even though it can't cause a productive
> > infeection?
>
> Perhaps. You could call them replication-deficient mutant viruses.

I'm going to go with this. It does everything a virus does except
reproduce; you wouldn't stop calling me person if i had a vasectomy,
right? No different!

Truly gutless systems are a bit different. I might suggest 'viroid', but
that means something else; 'virus-like particle' might do, but again, has
other connotations (it means at least two different things, to mycologists
and HIV people). 'Pseudovirus' also means something quite different
(infuriatingly, it's a kind of actual virus). How about 'virid'? Doesn't
seem to be used scientifically so far (as a noun), and at least sounds a
bit like 'plasmid'; the only trouble is that the particles themselves
would be viridions, which sounds like something out of a particularly bad
Star Trek: Voyager episode. I know! I'll call it a virius, just to annoy
Dr York.

> > Also: proteins go into solution, cells go into suspension, but what do
> > viruses do? Where's the borderline?
>
> Viruses go into suspension, I think.

Well, it seems like we're lacking a consensus here! I think, as DK said,
there's no hard and fast rule. I quite like the 'does it sediment at 1g?'
test, but i'm not sure it's strong enough - how do you define 'sediment'?

tom

-- 
Tom Anderson, MRC Laboratory for Molecular Cell Biology, UCL, London WC1E 6BT
(t) +44 (20) 76797264   (f) +44 (20) 76797805   (e) thomas.anderson from ucl.ac.uk



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