Why are subtypes specified for sequences that are gene fragments when they might be embedded in a recombinant genome?
When a short region of sequence has a subtype designation, one should be aware that the subtype designation often refers only to that fragment of sequence, and the virus that it is derived from may be recombinant. There are some exceptions. Sometimes the sequence is known to come from an isolate from which other fragments are also sequenced; in that case, we try to indicate both subtypes; i.e. if we have an env sequence that is subtype A and a gag sequence that is subtype B, we try to assign ‘AB’ to both. However, because of the manual effort involved, we don’t always manage to do this consistently.
