Why is the subtype B consensus sequence used rather than a particular isolate, the consensus sequence for a different subtype, or the consensus sequence for Group M sequences?
This is a commonly adopted convention that dates back to the late 1980s and early 1990s when subtype B viruses were the most common viruses in the U.S. and Europe. Using a different subtype of a group M consensus would cause too much confusion at this time. Using a particular isolate would also be confusing as nearly every common laboratory isolate has one or more unusual mutations that would always need to be noted. For example, the common laboratory strain HXB2 has a rare I3V mutation in protease. Therefore, if HXB2 was used for the consensus, nearly every sequence would have a V3I mutation in protease.
Related Questions
- Why is the subtype B consensus sequence used rather than a particular isolate, the consensus sequence for one of the more common subtypes (e.g. subtype C), or the consensus sequence for group M?
- I used an oligonucleotide in a cloning experiment an when I sequence through the area represented by the oligo the sequence is different from the sequence I ordered. Why?
- How do I obtain an alignment of all sequences of a particular gene with a particular subtype or country of origin?
