GL-PCT C IV 5.2 Exemptions from top-up search

As a general rule, a top-up search will be conducted for all the claims forming the basis for the Chapter II examination, as indicated in boxes I and III of the WO/IPER.[GL/ISPE 19.15; ]
A top-up search is not conducted on:[Rule 66.1ter; ]
(a)subject-matter not searched by the ISA; [Rule 66.1(e); ]
(b)non-unity cases – inventions for which additional search fees were paid, but not additional examination fees; [Art. 34(3); ]
(c)subject-matter which, although not excluded from the search, is excluded from preliminary examination; [Art. 34(4); ]
In addition to what is mentioned in Rule 66.1ter PCT, the top-up search may be refused or limited by the EPO as IPEA:
(d)where amendments contain added matter; [Art. 34(2)(b); 19(2); ]
(e)where there is no letter explaining the basis for amendments and/or indicating what has been amended in the application; [GL/ISPE 19.17; Rule 46.5(b); 66.8; ]
(f)where the EPO as ISA would not cite any documentary evidence as to the relevant state of the art (e.g. in case of "notorious knowledge" in the field of computer-implemented inventions). 
In case (d) above, the examiner will perform the top-up search based on either the previous set of application documents or the amended set, ignoring the added subject-matter. In case (e) above, the same applies to unsupported amendments (see GL/PCT‑EPO C‑III, 4).[Rule 70.2(c); ]
Where a top-up search is made for some claims or part of claims, there is no indication of:
– which claims are not covered by the top-up search (this should be derivable from the indications in Sections I and III of the WO/IPER); or 
– why no or only a partial top-up search has been made. 

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EPO PCT GL - C Procedureal Aspects Chapter II

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