Sequence Listing Requirements in Continuation-in-Part Patent Applications

1. Introduction

A continuation-in-part (CIP) application repeats a substantial portion of an earlier (“parent”) application and adds new matter. In biotechnology, that new matter often includes new nucleotide or amino acid sequences, such as new variants, primers, probes, antibodies, or vectors. Every such sequence must be handled under the sequence listing rules, which are among the most technical formalities in patent practice.

CIPs are trickier than ordinary filings because they sit between two worlds. Some content is inherited from a parent, possibly filed under an older sequence standard and some is new. Three questions arise in almost every biotech CIP: which sequence standard applies, what the CIP’s listing must contain and how a listing affects priority and new-matter analysis.

This article covers the rules, the traps and a practical workflow. It focuses on US practice, with notes on the PCT and Europe.

2. Background: What a CIP Is and Why Sequences Complicate It

A CIP is a US application (35 U.S.C. §120; MPEP §201.08) filed while the parent is pending. It shares at least one inventor with the parent, claims its benefit and includes new disclosure not in the parent. Two consequences matter for sequences:

• Claims are dated claim by claim. Claims fully supported by the parent’s disclosure get the parent’s filing date. Claims that depend on new matter, including new sequences, get only the CIP’s filing date.
• New matter is allowed in the CIP but not later. Once the CIP is filed, its own content is fixed. Adding sequences after filing without support in the CIP as filed is new matter in that application too.

A sequence listing must therefore be a faithful record of what the application discloses and it also becomes evidence in any later priority fight.

3. When Is a Sequence Listing Required?

A listing is required when the application discloses a sequence that meets the threshold, wherever it appears: in the description, claims, or drawings.

• Nucleotide sequences: 10 or more specifically defined nucleotides
• Amino acid sequences: 4 or more specifically defined amino acids (consecutive, unbranched)

Both standards exclude some items, such as branched sequences, sequences with fewer than the threshold number of defined residues and sequences composed mostly of unspecified residues. Each qualifying sequence gets its own SEQ ID NO and the specification and claims must refer to sequences by SEQ ID NO.

For a CIP, this means checking two sets of sequences: those carried over from the parent and those introduced as new matter. A CIP with even one new qualifying sequence needs a complete listing covering all sequences in the CIP.

4. The Two Standards: ST.25 and ST.26

WIPO Standard ST.25 was the long-standing format. Listings were plain text files with numeric identifiers, governed in the US by 37 CFR 1.821–1.825.

WIPO Standard ST.26 is an XML-based format that replaced ST.25 for applications filed on or after July 1, 2022. In the US it is implemented in 37 CFR 1.831–1.835. Key differences include:

• File format: XML rather than plain text, generated and validated with the WIPO Sequence tool (or compatible software).
• Feature annotation: stricter and more structured, with defined feature keys and qualifiers, for example for modified bases and modified residues.
• Treatment of unusual residues: D-amino acids, nucleotide analogues and other non-standard residues are represented as modified residues with annotation rather than by the ad hoc conventions ST.25 tolerated.
• Unspecified residues: handled through defined symbols and the rules about what counts as “specifically defined” residues are more precise.
• No paper or PDF copy: the listing is filed electronically as an XML file and it is treated as part of the description without adding to page counts or fees.

5. Which Standard Applies to a CIP?

This is the most common source of error. The standard depends on the filing date of the application being filed, not on the parent’s date.

Scenario	Governing standard
Parent filed before July 1, 2022 (ST.25); CIP filed on or after July 1, 2022	ST.26 for the CIP
Parent and CIP both filed before July 1, 2022	ST.25
Parent and CIP both filed on or after July 1, 2022	ST.26
CIP filed as a bypass application from a PCT application designating the US	Based on the CIP’s own filing date under 35 U.S.C. §111(a); check current USPTO guidance for the interplay with the PCT filing date
PCT application filed before July 1, 2022 entering the US national stage	Generally follows the international filing date

Consequently, a CIP filed today, even one that claims benefit of a 2018 parent with a perfectly good ST.25 listing, needs an ST.26 XML listing. The parent’s old listing cannot simply be reused.

6. Converting the Parent’s ST.25 Listing to ST.26

Conversion is not a mechanical exercise and it has legal consequences.

Common conversion problems

• Residues that ST.25 allowed as generic placeholders may need specific ST.26 representation or annotation.
• Modified residues, D-amino acids and unusual bases require explicit features that the original listing may have described loosely.
• Sequences that fell below or above thresholds may be treated differently.
• Feature keys used in the old listing may not exist in ST.26, which forces a choice of the closest valid equivalent.

The no-new-matter constraint. For the portion of the CIP that is supposed to be identical to the parent, the converted listing must not add information that the parent did not disclose. A conversion that “improves” or reinterprets a sequence (for example, by defining an ambiguous residue) risks introducing new matter, which could cost the claims their parent priority date. Convert conservatively and document each judgment call.

Interpretation questions. Where the ST.25 listing was ambiguous, the safest approach is to reproduce the ambiguity using the closest ST.26 convention and to avoid adding qualifiers that were not implied by the original.

7. Content of the CIP’s Sequence Listing

The CIP’s listing must contain every qualifying sequence disclosed in the CIP, meaning both the inherited and the new sequences. Points to watch:

Numbering and mapping. The CIP’s SEQ ID NOs may differ from the parent’s. Two common approaches:

1. Preserve parent numbering and append new sequences at the end. This keeps a one-to-one correspondence between parent and CIP, which simplifies proving priority support.
2. Renumber logically. This may read more cleanly but requires a mapping table and careful amendment of the specification and claims.

Either way, keep a written concordance of parent SEQ ID NO to CIP SEQ ID NO. It is invaluable when defending a priority date.

Consistency across the document. Every SEQ ID NO cited in the description, claims and figures must match the listing. Renumbering without updating cross-references is a frequent source of objections and, worse, claim ambiguity.

Sequences that appear only in figures. These count too and figure legends should cite SEQ ID NOs.

Sequences of the new matter. Anything new gets its own SEQ ID NO. Confirm each new sequence has textual support in the CIP as filed, since the listing cannot be the sole source of disclosure for content missing from the description.

8. Filing Mechanics and Timing

Filing with the application. The XML listing is submitted through Patent Center as a designated document type, not embedded in the PDF specification. Filing it with the application is the cleanest approach.

Filing after the application date. A listing is not necessary to secure a filing date. If it is missing or defective, the USPTO issues a notice requiring compliance within a set period (extendable with fees). Failure to respond leads to abandonment. When a listing is supplied later, it must be accompanied by a statement that it contains no new matter, meaning it does not go beyond the disclosure in the application as filed. For a CIP, “as filed” refers to the CIP’s own disclosure, including the inherited and added text.

Incorporation by reference. Historically, a listing filed electronically with the application was incorporated by reference into the specification. Confirm the current requirements for any incorporation-by-reference paragraph when preparing the application.

Legacy ST.25 practice. For CIPs governed by ST.25, applicants could, where appropriate, refer to a listing already on file in the parent by statement instead of resubmitting it. That approach works only when the CIP’s sequences are identical to the parent’s. If the CIP adds sequences, a new complete listing is required, with the corresponding statements (for example, that the submission includes no new matter beyond the CIP and that any paper and electronic copies are identical). Amendments to an ST.25 listing generally required a full replacement listing plus a statement.

9. Priority, Prior Art and Sequence Listing Errors

Claim-by-claim priority. If a claim recites a sequence that appears only in the CIP’s new matter, the claim is entitled only to the CIP’s filing date. A claim to a sequence disclosed in the parent keeps the parent date, but only if the parent supports the claim under §112(a), including written description and enablement for the claimed sequence or genus.

Parent as prior art. The parent application, once published or patented, can be prior art against CIP claims that are only entitled to the CIP date, subject to the grace period exceptions in 35 U.S.C. §102(b)(1) where applicable. A wide gap between the two filings increases this risk. This is a strategic reason to think carefully about whether a CIP, a new application, or a continuation is the better vehicle.

Errors and mismatches. Typographical errors in a sequence can change what is disclosed. Errors introduced during the ST.25-to-ST.26 conversion can look like new matter and errors in the parent’s listing can complicate correction. Correction generally requires evidence that the correct sequence was apparent from the original disclosure and even then the CIP’s date and the parent’s date must be analyzed separately.

Sequence-defined genus claims. For claims to variants, homologs, or “at least 90% identical” sequences, check that the reference SEQ ID NO is defined in the listing and that the genus is supported by the description, particularly in light of recent US case law on functional genus claims.

10. Other Jurisdictions and the PCT

• PCT: International applications filed on or after July 1, 2022 use ST.26 and the listing is treated as part of the description. Since a CIP is a US concept, the closest PCT analogue is claiming priority to multiple earlier filings and adding new material in the later one.
• EPO: Applications filed from July 1, 2022 must supply ST.26 listings. The EPO also has its own rules on late-filed listings and on sequences not part of the description as filed. Because of the different treatment of amendments, converting an older ST.25 listing needs care.
• Other offices: Most major offices follow ST.26 for new applications, but transition rules and formal requirements vary.

11. Practical Workflow for a Biotech CIP

1. Inventory the parent. Obtain the parent’s listing and confirm which standard it used.
2. Determine the governing standard from the CIP’s filing date.
3. List all sequences in the CIP, both inherited and new, including sequences that appear only in figures, examples and claims.
4. Decide on numbering strategy and build the concordance table.
5. Convert and generate the ST.26 XML using the WIPO Sequence tool and record any judgment calls during conversion.
6. Run validation and check that the XML passes the tool’s checks.
7. Proofread against the specification. Compare every SEQ ID NO and sequence in the text against the listing.
8. File the XML properly through Patent Center with the application, not embedded in a PDF.
9. Prepare the required statements if the listing is submitted after the filing date.
10. Track priority support for each claim, noting which SEQ ID NOs are new matter.

12. Common Mistakes

• Reusing the parent’s ST.25 listing in a CIP filed after July 1, 2022.
• Treating conversion as clerical, then unintentionally adding or altering disclosure.
• Renumbering without a concordance, which makes priority analysis painful.
• Omitting figure-only sequences or short sequences that meet the threshold.
• Embedding sequences only in the PDF instead of submitting the XML.
• Assuming the listing can supply new matter that the description lacks.
• Ignoring the parent’s publication when assessing prior art against the CIP’s new claims.
• Missing the response deadline for a notice to comply.

13. Conclusion

In a CIP, the sequence listing is more than a formality. It defines what sequences the application discloses, it must follow the standard in force on the CIP’s filing date and it interacts directly with new-matter limits and claim-by-claim priority. The main risks are applying the wrong standard, introducing accidental changes when converting an older listing and losing track of which sequences belong to the parent and which are new. A disciplined workflow with clear numbering, a concordance table, careful conversion and thorough cross-checking keeps a CIP’s listing accurate and its priority position defensible.