What does 'virus prototype strain' mean?
A prototype virus may or may not be the first isolated virus of a group. It's essentially the same as a "reference" virus -- in fact, the International Committee on Taxonomy of Viruses
(ICTV) uses the terms interchangeably, as in the  Hepeviridae Study Group which has a column entitled "Prototype/Reference Strain".  

In many cases the reference virus is the first isolate, but it isn't necessarily the case. The ICTV is the official body that determines reference strains, and they may choose a different virus as the reference/prototype. For example the first isolate may turn out to be unusual or an outlier in same way, so that a more typical strain may be chosen as a reference or prototype (I don't know offhand of examples of this though).  

"Prototype" is often used in a broader sense as well, where a group of viruses can act as prototypes for a still broader group.  For example, "The genomic structure of Pencillium chrysogenum virus (PcV), the prototype of the genus Chrysovirus ... " (pdf link) uses "prototype" to refer to all the viruses in the Pencillium chrysogenum group, as compared to the broader genus.