Untypeable Genotype

[pjhep80]

i have posted this question before and have asked just about every g.i. and hep doc i know and nobody can give me an answer and the doctors dont even raise their eyebrows about it... like it doesnt matter????  i thought genotype was important...i have had about 5 tests and they all say the same thing - this sample is atypical and untypeable...

[willing]

you can definitely get your question answered, though you may need to persist a bit. First thing is to read up a bit on HCV genotypes. The hcv genome is about 9600 nucleotides and very variable. Like snowflakes, two hcv virions rarely look exactly the same. However, at one end of those 9600 nucleotides is a stretch of sequence that is much more conserved. In a standard genotyping test a bit of that conserved stretch, (the 5' utr) is amplified and categorized:  many copies of it are made and some property, like weight, is used to classify the result into type/subtype buckets. Not all 1as for example have the same sequence in that region but  the weight of a 1a sequences will be closer to the cluster of other 1a sequences than say to a 2. Your genotype tests are probably inconclusive because you have some unusual sequence in this conserved region.

If the commercial genotyping tests can't classify your genotype (and your VL is high enough to get a good sample) you can find a specialized lab that will sequence a couple of hundred nucleotides near the 5' utr and then compare the sequence you get back with the known hcv sequences deposited in genbank. There may be simpler/cheaper approaches, but the above will definitely work. Contacting the pathology dept. of a large research med center and asking about special-case  sequencing is probably a good starting point. For purposes of tx you just need to know whether your sequence looks most closely like a 1, 2/3 or 4.

[pjhep80]

thanks for the info but i guess its a moot point since i already treated and failed... they considered me a type 1 for the trial i was on...

the genotype is really only important for this reason correct??

thanks again for your help/reply...