Since class I and II alleles elicit different types of immune responses and recruit different types of immune effector cells (CTL v Th cells), why does it make sense biologically to group them together to calculate population
coverage, i.e. the option of class I and class II combined in population coverage tool?
Combining class I and class II responses to define population coverage is not intuitive. The rationale for doing such is largely in response to feedback from users and reviewers of the website (and the original publication of the tool). Some users find utility in finding combined coverage for applications such as vaccine design, where it may be attempted to elicit responses to a set of class I epitopes in the context of help from class II epitopes. In these scenarios, for example, one may design a DNA construct encoding a string of CTL epitopes, where the construct may also encode for a promiscuous HTL epitope such as PADRE or HBV core 50. Here, the tool may provide an estimate of how well your vaccine covers not just the class I response, but also how broad the response may be in the context of specific help. As a further example, see also the reference below. We are sure users will have other applications requiring such flexibility from the tool, and it is easier to make these options part of the design up from rather that have to post engineer the software.
Design and preclinical development of a recombinant protein and DNA plasmid mixed format vaccine to deliver HIV-derived T-lymphocyte epitopes.
Walker LE, Vang L, Shen X, Livingston BD, Post P, Sette A, Godin CS, Newman MJ.
Vaccine. 2009 Nov 23;27(50):7087-95. doi: 10.1016/j.vaccine.2009.09.059. Epub 2009 Sep 26.