- Is there a difference between the population of the virus in the host and that in the amplified sample?
- If the virus is a mixture of subtypes do the experimental methods favour one subtype over another?
- Does the sequencing technique favour AT or GC rich regions?
- Can we distinguish between sequencing error and point mutations?
Recent work on improving the collection and monitoring of wild bird avian influenza has shown that birds can be infected with multiple sub-types. In these cases how do we know which segments match with which other segments? How do they mix and produce mature virus?