Back to Alex Jeffries questions about determining "the correct"
sequence of a given virus. I think the problem is especially
compounded for RNA viruses. The observation of a sequence is
different from an understanding of the biological significance of that
sequence. The previous respondants to the post discussed the
scientifically prudent steps to take in reporting a virus sequence
(i.e. are we convinced that your sequence is reasonably accurate?).
The larger question remains what is the biological activity of your
sequence? Also, are any of the variants contributing to the overall
effect of the population? Addressing these questions is not trivial
as even single site mutations can play a dramatic role in the ability
of a given virus to survive.
An interesting point on error rates in RNA viruses: The sequence of
tobacco mosaic virus, reported by a group in England around 1982, was
assembled from small cDNAs. In the USA a couple of years later, an
infectious clone was generated and found to be virtually identical in
sequence. The virus stock for each lab was probably originally from
the same source, but propagated separately for about 30 years. Two
independently propagated populations of an RNA virus (with supposedly
high mutation rates) maintained the same predominant sequence. I
think there must also be tremendous selection pressure on maintaining
an optimal sequence.
DAK at apldbio.com
P.S. Hope the new news reader works
Dave (DAK) Knorr