I missed some alternative embodiments of my invention which can be considered as well known for the skilled person. I filed few national applications claiming priority over the first one. A year after the first application, I filed a PCT claiming priority and this is now published. Few days before the publication of the PCT, I filed another application claiming all the alternative embodiments along with the original embodiment of my PCT. Is it possible and how can I protect all the alternative embodiments I have come up with at least in the US and EU?
Are these alternative embodiments in the later filing only, i.e. the one taking place just before the PCT being public, or are included in the description of the PCT as well? Should it be the former, in principle you should prosecute that later application as well, or have national/regional/PCT applications claim priority from it so that you can protect those embodiments in Europe and the US.
In Europe the first PCT can only affect the patentability of those alternative embodiments if you enter into the European regional phase and are only relevant from a novelty standpoint, i.e. Art. 54(3) EPC prior art, so as long as the alternative embodiments are novel you are good to go. For the US, I am not entirely sure what will be the relevance of the PCT.
If the alternative embodiments are disclosed in the PCT, you can file divisional or continuation applications once you enter into the national/regional routes to claim those embodiments. In the US you can have multiple independent claims so maybe you can claim all the embodiments in a single patent application.
In the U.S. you can take the first PCT into the national stage, or file as a "bypass" application, and make it a continuation-in-part, claiming priority to the second application. Then the specification can be whatever blend of the two applications you like as long as you do add not any new matter to what is contained in one or the other application. Any claims fully supported by the original application should be treated according the earlier filing date.