Virus protein coat

[snow88]

I am currently dealing with IHHNV virus in M. rosenbergii. My task is to clone the capsid gene of IHHNV. However, i am facing problem with getting the capsid gene out from the genome. The primers i used are designed from Peneaus spc. May i know how often does virus protein coat undergo mutation? Is it feasible if i use protein coat sequence from other related species to design primers for my species?

[magicsiew]

Yes, you may do that, try to collect as much sequences as possible from related species of your particular gene and find the conserved region.

[magicsiew]

http://www.ncbi.nlm.nih.gov/pmc/article ... 011799.pdf

Seems that the mutation can occur in a relatively high rate.