Compliant sequence listings for European divisionals post July 2022

Options for filing a compliant sequence listing for a European divisional patent application post July 2022, where the parent patent application was filed with an ST.25 format sequence listing.

Protein and nucleotide sequences in patent applications must be presented in a certain standardised format in order for applications containing such sequences to proceed through the patent prosecution process. From 1 July 2022, a new sequence listing standard format (known as ST.26) replaced the previous sequence listing standard (known as ST.25). Accordingly, any new patent application [1] filed after 1 July 2022 (be it an international, regional or national application) which discloses sequences over a certain minimum length requires an ST.26 format sequence listing. Such a sequence listing should be generated using the WIPO Sequence software.

For the most part, adjusting to ST.26 requires getting to grips with the new software and understanding the new features available in the ST.26 format. However, a particularly difficult issue arises in the case of European divisional applications. The European Patent Office (EPO) have decided that the ST.26 format applies to European divisional applications, even in the situation where the parent application was filed before 1 July 2022 with an ST.25 sequence listing. Therefore, if a new European divisional application is filed, and the parent application has an ST.25 format sequence listing, it will be necessary to take some steps in order to ensure that the divisional application has the correct ST.26 format sequence listing.

Those who are familiar with European patent practice will be aware that the generation of a new sequence listing in ST.26 format has the potential to cause various added matter issues, with the risk that the divisional application containing the ST.26 sequence listing will be invalid according to Article 76 EPC. There are various options for dealing with this issue, but choosing the best option is not a simple choice, and will vary case by case. In order to determine the best option, analysis and client input will be required. Accordingly, it is recommended that this matter is addressed well in advance of the deadline for filing the divisional application.

A brief summary of the various options for preparing an ST.26 compliant sequence listing for European divisional applications (where the parent application had an ST.25 sequence listing) are set out below. For each option, potential advantages and disadvantages are identified.

1. Convert the existing ST.25 sequence listing to an ST.26 sequence listing using the WIPO Sequence software, and file the ST.26 sequence listing at the same time as the divisional application (thus meaning that the ST.26 sequence listing is considered to be part of the description of the divisional application).

a. Advantages
i. Avoids the need to file a sequence listing at a later date (and thus potentially a late furnishing fee).
ii. Avoids page fees applying to the sequence listing.
iii. Although not related to the question of the sequence listing, this option allows the inclusion of the claims of the parent application as a list of “embodiments” at the end of the divisional description, as is good practice when filing a European divisional application.
iv. Since the ST.26 sequence listing forms part of the description of the divisional application, it can be used as basis to correct any errors in sequences which are disclosed elsewhere in the specification.

b. Disadvantages
i. If the conversion from ST.25 to ST.26 results in the insertion of additional subject matter (which is highly likely), then the fact that the ST.26 sequence listing is part of the description will mean that Article 76 is not complied with. N.B. The likelihood of the conversion from ST.25 to ST26 resulting in added matter can be mitigated by following the guidance in Annex VII of the ST.26 standard, which sets out conversion scenarios which might result in added matter, and recommendations to avoid such issues. However, if the sequence listing that is converted is long and/or contains complicated sequences, the required checking will be very time consuming. [On the other hand, if the ST.25 sequence listing is short and uncomplicated (and thus any checking for added matter issues is not required, or is not time consuming), this may not be a problem.]

2. Convert the ST.25 sequence listing form the parent application to pdf format and add it to the end of the description of the divisional application as filed.

a. Advantages
i. This approach should ensure that all of the subject matter in the sequence listing of the parent application will be part of the divisional application.
ii. The ST.26 compliant sequence listing can be filed at a later date, meaning that it does not form part of the description (R. 30(2) EPC) and is used for search purposes only. Thus any added matter issues that may be due to conversion from ST.25 to ST.26 should not arise.
iii. Since the ST.25 sequence listing forms part of the description, it can be used as basis to correct any errors in sequences which are disclosed elsewhere in the specification.
iv. Like option 1), this option allows the inclusion of the claims of the parent application as a list of “embodiments” at the end of the divisional description.

b. Disadvantages
i. If the existing ST.25 sequence listing is long, this will result in a large excess page fee to pay (because the ST.25 sequence listing will form part of the page count of the description of the divisional application).
ii. It will still be necessary to prepare and file a ST.26 sequence listing at a later date, and therefore there is the possibility of incurring a late furnishing fee [2].
ii. Where a sequence listing is not filed at the date of filing of an application, the late furnishing fee can be avoided if a sequence listing in the required format is filed before the EPO notices the deficiency and issues a communication under R. 30(3) EPC – see EPO GL A-IV, 5.

3. File the divisional application by reference to the parent application under Rule 40(1)(c) EPC.

a. Advantages
i. Utilising this option means that the full description of the parent application is used as the description of the divisional application. If the description of the previously filed application contained a sequence listing in ST.25 format on its date of filing, then that sequence listing formed part of the description of the parent application, and will thus automatically form part of the description of the divisional application. This method is therefore a quick and easy way of including the parent application’s (ST.25 format) sequence listing with the divisional application.
ii. Since the ST.25 sequence listing forms part of the description, it can be used as basis to correct any errors in sequences which are disclosed elsewhere in the specification.
iii. The necessary ST.26 compliant sequence listing can be filed at a later date, meaning that it does not form part of the description (R. 30(2) EPC) and is used for search purposes only. Thus any added matter issues that may be due to conversion from ST.25 to ST.26 should not arise.

b. Disadvantages
i. Since the description of the parent application cannot be amended in any way, this option does not allow basis for the claims of the parent application to be included as a list of “embodiments” at the end of the description of the divisional.
ii. An additional page fee may be due.
iii. It will still be necessary to submit an ST.26 format sequence listing at a later date, with the attendant risk of incurring a late furnishing fee.

4. File the divisional application without either an ST.25 or an ST.26 format sequence listing, but only if the specification of the parent application as originally filed contained all of the sequences (as part of the “normal” text and/or drawings).

a. Advantages
i. The necessary ST.26 compliant sequence listing can be filed at a later date, meaning that it does not form part of the description (R. 30(2) EPC) and is used for search purposes only. Thus any added matter issues that may be due to conversion from ST.25 to ST.26 should not arise.
ii. A later-filed ST.26 sequence listing does not form part of the description and thus does not count towards page fees.
iii. Like options 1) and 2), this option allows the inclusion of the claims of the parent application as a list of “embodiments” at the end of the divisional description.

b. Disadvantages
i. If there are a large number of sequences, it will be time consuming to cross-check with the ST.25 sequence listing of the parent application to make sure that all the sequences are present and correct in the “normal” text and/or drawings of the parent specification.
ii. Since neither the ST.25 sequence listing from the parent, nor the ST.26 listing from the divisional will form part of the description, they cannot be used as basis to correct errors elsewhere in the specification.
iii. It will still be necessary to prepare and file a ST.26 sequence listing at a later date, and therefore there is the possibility of incurring a late furnishing fee.

Conclusion

The appropriate option for a particular divisional application should be determined on a case by case basis. Of the options presented here, Option 3 should probably be disregarded on the basis that it does not allow the inclusion of the claims of the parent case as a list of “embodiments” at the end of the description of the divisional application. Option 4 is only possible if it is possible to be confident that the “normal” text and/or drawings of the parent application do in fact contain all of the correct sequences. However, that option is otherwise attractive. Option 2 is probably the “safest” option in terms of making sure that no subject matter from the parent application is lost and that added matter issues arising from the sequence listing are avoided. However, it will result in hefty page fees if the ST.25 sequence listing contains many pages when converted to pdf format. Option 1 can be a valid choice if the ST.25 sequence listing from the parent application is short and uncomplicated (although Option 2 would appear to be better in that situation), or if it is possible to spend the time (and the budget) checking the converted ST.26 file in advance of divisional filing, in order to identify and remove added matter issues.

Notes

• EPO source material:
  FAQ - WIPO Standard ST.26: divisional applications and notification of sequence listings in the communication under Rule 71(3) EPC

• Notice from the European Patent Office dated 9 December 2021 concerning the filing of sequence listings

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[1] The requirement to use the ST.26 format applies even if the priority date of the application predates 1 July 2022.

[2] Where a sequence listing is not filed at the date of filing of an application, the late furnishing fee can be avoided if a sequence listing in the required format is filed before the EPO notices the deficiency and issues a communication under R. 30(3) EPC – see EPO GL A-IV, 5.