I thought I remember reading that they still count as their original metatype. For example a Troll infected with Strain III (Ghoul) would be targetable by both the Slay Ghoul spell, as well as Slay Troll. On a quick search I couldn't find the quote, but it seems reasonable.
That being said, it would mean that they are still technically metahuman.
I remember reading that too, but I'll be damned if I know where.
Ah the Joys of cross edition backtracking.
Sadly in 5th they left it sort of vague, namely Pg 134 of Run Faster
Becoming Infected does not remove a character’s
inherent metatype abilities. A dwarf becoming a gnawer
does not lose her thermographic vision, for instance.
So the Infected is still of their original metatype, though now what we call a subspecies thanks to some HMHVV-loving, though again thanks to 5th's tendency to leave out various bits in the transition, this can be pretty easy to miss.
For better clarity you need to roll it back to 4th with pg 77 in Runner's Companion:
Sufficiently Inhuman
The Infected are still metahumans (except for bandersnatchii),
and still subject to most of the things that target
metahumans, but are sufficiently different that they can be categorized
separately using magical theory. Thus, an Infected can
be targeted and affected by a spell that targets its metatype (Slay
Human, Slaughter Ork, etc.) as well as a spell that targets its
specific subspecies (Slay Vampire, Slaughter Busaw, etc.). The
character can also still take qualities and equipment restricted or
built especially to accommodate her metatype. Bandersnatchii
can be targeted and affected by a spells that target sasquatches
(Slay Sasquatch, etc.) as well as spells that target its specific subspecies
(One Less Bandersnatch, etc.).
