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4.13 MASTER SEEDS/CELLS/SEQUENCES

1. Overview

The Master Seed and Master Cell concept is used in the manufacture of biological 

products. A Master Seed may be a bacterium, virus, or recombinant organism, e.g. a 

plasmid with an exogenous insert, expressed in an E. coli bacterial host. A Master lot of 

Seed or continuous Cell line is tested extensively for identity and purity by the firm, with

confirmatory testing by the CVB laboratory. In addition, recombinant Master Seeds 

should be tested to ensure expression of the relevant antigen. Each Master lot must be 

approved by APHIS prior to use in the production of biological products. Once 

approved, all production must utilize seeds and cells that are direct passages from the 

Master lot. The maximum permissible number of passages from the Master lot is also 

defined. A single Master lot may be used in the manufacture of many different biological 

products. 

Modern biotechnology enables manufacturers to use chemically synthesized ingredients 

in biological products as well. Some examples of these are primers in PCR test kits and 

synthetic peptides in antibody test kits. For these entities, a Master Sequence (amino 

acid, nucleotide, or carbohydrate) is specified in the Outline of Production; these may be 

commercially acquired and have Quality Control documents. The Master Sequences do 

not require confirmatory sequencing by CVB, although their suitability to detect diseaseassociated isolates or antibody to them should be evaluated. This can be done, e.g., 

through sequence alignment with GenBank or other database-stored sequences, through 

consultation with subject matter experts, or through published literature, and, as far as 

possible, testing with an appropriate panel of samples. 

Other examples of Master Sequences include, but are not limited to, RNA vaccine 

sequences and therapeutic or prophylactic synthetic peptides. These injected 

biotechnology-derived biologics require confirmatory sequencing, as well as other tests 

for purity and identity. 

2. References

The following regulations and guidance documents pertain to Master Seeds (MS) and 

Master Cell Stocks (MCS): 

• 9CFR Parts 101.6, 101.7, 113.8, 113.27, 113.47, 113.52, 113.55, 113.64, 

113.100, 113.200, 113.300 

• Certain Seeds have additional requirements in product-specific sections of 

9CFR Part 113. 

• VS Memorandum 800.68: New Biotechnology for Preparation of Animal 

Biological Products (December 4, 1984) 
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• VS Memorandum 800.88: Testing for Reticuloendotheliosis Virus 

Contamination (August 23, 1999) 

• VS Memorandum 800.89: Chicken Anemia Virus (December 22, 1999) 

• VS Memorandum 800.109: Master Seed and Master Cell Stock Testing Report 

Submission 

• VS Memorandum 800.113: Production, Testing and Storage of Master Seed 

and Master Cell Stocks at Alternate Locations (September 17, 2008) 

• VS Memorandum 800.201: Backpassage Studies

• VS Memorandum 800.205: General Licensing Considerations: Biotechnologyderived Veterinary Biologics Categories I, II, and III

• Testing of Biological Products chapter of Reviewers’ Manual

• LSRTIS Program Documentation 

3. Flow of Information/ Office Procedures

3.1 Mail log entries: Submissions regarding MS and MCS should be entered into the 

mail log with a direct link to the applicable MS or MCS record in LSRTIS. This 

means that a MS or MCS record must be created when the first submission is 

received. Additionally, the submissions may be linked to the product code(s) in 

which they will be used, but this is optional. 

When creating a MS or MC record in LSRTIS, ensure the Lot ID is exactly and 

completely as it appears on the MS or MC vial. Ask the firm for the complete 

identifier if they do not provide details of the vial labels in their MS/MC report. 

Do not create LSRTIS records for “pre-master” seed submissions. These submissions 

can later be linked to the MS record for the master lot that is eventually produced, but 

pre-master submissions are simply listed as product code UNASGN at the time of 

their receipt.

3.2 Location of MS and MCS files: 

3.2.1 MS and MCS documents are filed independently of products in which they 

are used. MS and MCS files are not archived unless the CVB receives 

notification from the firm that the MS or MCS no longer will be used in 

production. 

3.2.2 Unapproved MS and MCS documents were historically filed in GREEN 

folders and placed alphabetically in the prelicense files. These historic files are 

located behind the product prelicense files for the establishment. 

The folders were identified with the MS/MCS name as it will be configured in 

LSRTIS (example: Coronavirus, chicken NOT Infectious bronchitis virus) and the 

complete lot number. Master Sequences will not be entered into LSRTIS. 

Conformance with LSRTIS format provides a standard format to ensure that 

“like” Master SC are filed together.

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3.3 Write responses to MS/MCS issues separately from those associated with 

particular products. If the two topics are combined into one letter, it will make it 

more difficult to find pertinent information related to MS/MCS in the mail log. 

3.4 If several MS and MCS are processed at the same time, ideally there should 

be a separate letter for each. This is the easiest way for the support staff to keep 

the files correct, and this will facilitate retrieval of the information from the mail 

log in the future. 

4. Procedure for Approving a Master Seed or Cell

4.1 Ideally, the Master Seed or Cell should not be introduced into production facilities 

until it is approved by the CVB. Some firms, however, need to introduce a candidate 

Master Seed or Cell into production facilities in order to prepare the Master lot or to test 

it. If a firm makes a request to introduce an unapproved Master Seed or Cell into 

production, the reviewer should determine whether the unapproved seed/cell poses a 

material risk to the integrity of other production processes occurring in the facility. The 

reviewer should also consult with IC, as per ICSOP0018 to ensure that the new fraction 

can be introduced into the licensed premises with no disruption of the current production 

procedures and without cross contamination of products. Research facilities that are 

entirely separate and apart from facilities used for the preparation of licensed biological 

products will not be considered part of the licensed premises for these purposes. If not, 

permission may be granted to introduce the Master Seed or Cell into production facilities

at the firm’s own risk. Letters written to authorize moving the Seed into production 

should include a statement to update facility documents as necessary. 

 

4.2 The firm must submit an acceptable report of their evaluation of the Master Seed 

or MCS candidate. Although an APHIS Form 2008 may be used to summarize test 

results, a 2008 is not required and is NOT sufficient to document the firm’s testing. 

A complete report, with materials and methods, should be submitted, per VS 

Memorandum 800.109. 

All tests codified in the 9CFR, plus any additional tests deemed necessary to assess 

the identity and purity adequately, must be completed. Specialized testing that the 

firm is not equipped to perform may be completed by outside laboratories. 

The two key areas of testing are identity and purity. Identity testing of Master Seeds 

should adequately define the taxonomic type of the agent (e.g., bacteria to the species 

level in most cases) and should confirm any special characteristics of the agent (e.g., 

pilus or toxin expression, special serotype (e.g., E. coli O157:H7), or mutation (e.g., 

J-5 E. coli).

Purity testing for bacterial agents is relatively simple (9CFR 113.27) because they are 

grown in acellular medium in which contaminating viruses will not survive. Purity 

testing for viruses and other intracellular organisms, as well as cells, is more complex. 

Viruses, other obligate intracellular organisms, and cells must be tested for different 
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extraneous agents, depending on the species of animal from which they were derived, 

how they will be propagated during production, and in what type of biological 

product they will be used. For example, a feline virus, propagated on canine cells, for 

use in a feline vaccine must be tested for feline and canine extraneous agents. Some 

unique considerations for testing fish Master Seed Viruses include:

• When testing fish Master Seed Viruses, fish red blood cells should be used to 

testing for hemadsorbing agents as per 9 CFR 113.46(b). 

• When testing aquatic Master Seed Viruses for cytopathic agents as per 9 CFR 

113.55(c), fish cell lines should be maintained for at least 28 days. 

The standard list of extraneous agents, divided by animal species, is found in 9CFR 

113.47, but testing for additional agents may be required in individual cases, 

depending on risk factors. Some specific considerations for unique cell lines are 

listed below:

• Considerations for Avian cell lines

o Agents of concern regarding chicken derived cell lines: 

 Reticuloendotheliosis virus (REV), and Chicken Anemia Virus 

(CAV): PCR tests are available for these viruses and protocols 

are available from the CVB laboratory. 

 Avian leukosis virus (ALV): An ELISA test is available, and 

the protocol is available from the CVB laboratory. To use this 

test, an exemption to 9 CFR 113.31 must be requested. The 

exemption request should be accompanied by data to support 

that the ELISA test conducted by the firm is at least as 

sensitive as the codified test. 

 Marek’s disease virus (MDV): Very important because many 

of the poultry cell lines have been immortalized via MDV 

infection. Papers such as “Transactivation of Latent Marek’s 

Disease Herpesvirus Genes in QT35, a Quail Fibroblast Cell 

Line, by Herpesvirus of Turkeys,” by T. Yamaguchi et al in 

Journal of Virology 74:10176-10186 may be helpful. 

o Agents of concern regarding duck cells 

 Duck hepatitis virus: Should be detected in 9 CFR 113.37 

testing

 Duck enterovirus: This virus causes CPE in DEF cells 

 Duck parvovirus: Only grows in Muscovy duck fibroblasts 

and embryo fibroblasts 

• Agents of concern for fish cell lines

o Viral Hemorrhagic Septicemia Virus (VHS)

o Infectious Hematopoietic Necrosis Virus (IHN)

o Spring Viremia of Carp Virus (SVC)

o Infectious Salmon Anemia Virus (ISA) 

o Infectious Pancreatic Necrosis Virus (IPN)

o Channel Catfish Virus (CCV) 





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11.1 Correspondence relating to the additional testing should be formatted to show 

the Seed or Cell is approved, even though the expanded approval has not yet been 

given. 

11.2 When the expanded approval is given, update the LSRTIS record as appropriate.