Our take on process-specific vs. generic host cell protein assays

By Drs. Ray Nims and Lori Nixon 

The residual host cell protein (HCP assay) is used to determine the concentration, in process streams, of protein originating from the production cell (Chinese hamster, NS0, E. coli, etc.) used in the manufacture of a biologic. Host cell protein is considered to be a process-related impurity/contaminant. The most typical approach to quantitation of residual host cell protein in a test sample is the enzyme-linked immunosorbant assay (ELISA) platform.

Generic vs. process-specific assays.  A question that often arises is whether a process-specific HCP assay is required, or whether a generic assay can be used. Although there is a spectrum of “process specificity” that can be described, in this discussion, we are considering a generic assay to be one that is developed from a broad set of antigens from the host strain or closely-related strains, but not necessarily under specific process conditions mimicking the actual production/purification process of the protein of interest. That is, the reagents for a generic assay could be developed in advance of a defined production process. For example, it is often possible to purchase a “generic” HCP ELISA kit from a commercial provider, such as Cygnus Technologies, selecting a kit that matches the production cell line. Practically speaking, most firms start with generic HCP methods in early development for an obvious reason: you can’t have a process-specific assay until you have a defined process. Even after the process is defined, the lead time for developing custom (process-specific) HCP reagents and an assay using these can be as long as 1-2 years.

It should be appreciated from the outset that there is no perfect HCP assay. Production cells can express thousands of proteins, with expression patterns differing under different growth conditions. At each successive stage of the recovery and purification process, the population of HCPs is altered. At the final drug substance stage, there may be only a few HCPs present that have co-purified with the product. If you attempt to design an assay that only selects those few remaining HCPs, then some will argue that you might miss HCPs that might make it through under other circumstances (such as a process deviation).  If you attempt to design antibody reagents using the entire unpurified mixture of proteins from the production cell, the proteins of most interest may not elicit a good antibody response and you may have inadequate sensitivity to quantify HCP in your final drug substance. In fact, it has been reported that process-specific antibodies lead to HCP assays that are more sensitive for certain HCP species (and sometimes more broadly reactive) than the antibodies provided in a generic HCP assay. 

In recent years, there has been some regulatory pressure setting an expectation that a process-specific HCP assay must be developed for product registration. In our opinion, this is unjustified as a blanket prescription.  There are a multitude of approaches for creating antigen and antibody reagents, but the resulting assay should be judged primarily on its own merits.

Suitability of any HCP assay (whether generic or process-specific) must be evaluated on a case-by-case basis, and the assay validated for the specific product in question. One of the first characteristics to aim for is an assay that is able to readily quantitate HCP in the final drug substance. Without this sensitivity, it is difficult to get results that are meaningful to guide process optimization or ensure control of your product. If the available generic method(s) have limited sensitivity for the sample of interest (results are below the required range of quantitation), then it is a good idea to start planning the development of more process-specific reagents—which are likely to afford better sensitivity. Since the numerical values reported from these assays are semi-quantitative at best, sensitivity should be judged on the performance in actual samples rather than on the product specification. Of course there are other assay characteristics (non-reactivity to product, precision, dilutional linearity, spike recovery, etc) that are required to meet validation acceptance criteria. The antigen coverage should be determined, typically by 2D electrophoresis or 2D HPLC-ELISA. It is unrealistic to expect 100% coverage of all of the proteins present in the production cell; on the other hand, it is relatively more important to ensure response against bands that persist in the purification process.  All other things being equal, of course greater coverage is more desirable.

Example of 2D electrophoresis of E. coli proteins, from Kendrick Labs

Whether a generic or process-specific method is implemented, it is vital to ensure a consistent reagent supply that will last throughout the commercial life of the product. If using vendor-supplied antigen and antibody, be aware that by nature these are “single-source” reagents with associated supply risks. If creating a custom reagent set, make enough supplies to last for years to decades.

As mentioned above, most firms start with a generic assay and may move to a process-specific assay in later stages of development. A close evaluation of the generic assay during its characterization and validation may lead to the conclusion that the generic assay is suitable for your product.  In this case, be prepared to make a strong case in defense of your generic assay—based on empirical data with your product, rather than theoretical speculation.

Rapid Identification of Viral Contaminants, Finally

By Ray Nims, Ph.D.


There was a time, not long ago, when it might take months to years to identify a viral contaminant isolated from a biological production process or from an animal or patient tissue sample. The identification process took this long because it involved what I have referred to as the “shotgun approach”, or it involved luck.

Let’s start with luck. That is probably the wrong term. What I mean by this is that there have been instances where an informed guess has led to a fairly rapid (i.e., weeks to months) identification of a contaminant. For instance, our group at BioReliance was able to rapidly identify contamination with REO virus (REO type 2 actually) and Cache Valley virus  because we had observed these viruses in culture previously and because these viruses had unique properties (a unique cytopathic effect in the case of REO and a unique growth pattern in the case of Cache Valley virus). The time required to identify these viruses consisted of the time required to submit and obtain results from confirmatory PCR testing for the specific agents.

The first time we ran into Cache Valley virus, however, it was a different story. This was, it turns out, the first time that this particular virus had been detected in a biopharmaceutical bulk harvest sample. In this case, we participated in the “shotgun approach” that was applied to the identification of the isolate. The “shotgun approach” consisted of utilizing any detection technique available at the lab, namely, in vitro screening, bovine screening, application of any immunofluorescent stains available, and transmission electron microscopy (TEM). The TEM was helpful, as it indicated a 80-100 nm virus with 7-9 nm spikes. A bunyavirus-specific stain showed positive, and eventually (after months of work), sequencing and BLAST alignment was used to confirm the identity of the virus as Cache Valley virus.

The “shotgun approach” was subsequently applied to a virus isolated from harbor seal tissues, with no identity established as a result. After approximately a year of floundering using the old methods, the virus was eventually found to be a new picornavirus (Seal Picornavirus 1).  How was this accomplished? During the time between the identification of the Cache Valley virus and the seal virus, a new technology called deep sequencing became available. Eric Delwart’s group used the technique to rapidly identify the virus to the species level. As this was the first time this particular picornavirus had ever been detected, deep sequencing is likely the only method that would have been able to make the identification.

Deep (massively parallel) sequencing is one of a few new technologies that will make virus isolate identification routine and rapid in the future. It has been adopted for detection of viral contaminants in cells and viral seed stocks and for evaluating vaccine cell substrates by BioReliance.The other is referred to as the T5000 universal biosensor. Houman Dehghani’s group at Amgen has been characterizing this methodology as a rapid identification platform for adventitious agent contaminations.  Each technology has its advantages. Deep sequencing is more labor intensive, but has the ability to indicate (as described above) a new species. The universal biosensor can both serve as a detection method and as an identification method. Both can identify multiple contaminants within a sample.

Since identification of an adventitious viral contaminant of a biopharmaceutical manufacturing process is required for establishment of root cause, for evaluating effectiveness of facility cleaning procedures and viral purification procedures, and for assuring safety of both workers and patients, it is critical that the identification of a viral isolate is completed accurately and rapidly. Happily, we now have the tools at hand to accomplish this.

Lesson learned: Outsource but remain in control!

By Dr. Ray Nims

In a previous posting, we described the responsibilities of the contract giver (contractee) and the contract acceptor (contractor) in outsourced pharmaceutical quality control testing. Our blog title: "Outsource it, and fuggedaboutit?" somewhat facetiously suggested that the outsourcing of quality control testing does not transfer quality control responsibility from the contract giver to the contract acceptor.

Elizabeth Meyers and I expanded upon this theme in a recent article in BioProcess International. Our conclusion in that article was more direct: “The use, by a pharma organization, of a contract testing lab to fulfill some or all of its Quality Control testing obligations does not absolve the contractee of its overall Quality responsibility of ensuring the safety, purity, identity, efficacy, and potency of its products.”

This point was illustrated nicely in a recent warning letter published on the FDA Website. The name of the firm involved is not important to this discussion. Among the other findings was the following:

“Your firm failed to properly evaluate a contract laboratory to ensure GMP compliance of operations occurring at the contract site.”


The FDA then provided the following detail: "...we are concerned about your firm’s fundamental understanding of what is required by your Quality Unit and the regulatory expectations for a firm that enters into agreements with contract testing laboratories. Although you have agreements with other firms that may delineate specific responsibilities to each party, you are ultimately responsible for the quality of your products and the reliability of test results. Regardless of who tests your products or the agreements in place, you are required to manufacture these products in accordance with section 501(a)(2)(B) of the Act to assure their identity, strength, quality, purity, and safety."

The take-home message from this is that in the outsourcing of quality control testing, responsibility for the outsourced testing is retained by the contract giver. Responsibilities of the contract giver include the following: selecting and qualifying the contract lab, ensuring the suitability of methods used (through qualification, transfer, verification, or validation); putting in place a Quality and business agreement; scheduling and submitting samples (including communicating expectations for sample results); providing in-life guidance; and monitoring of contract lab performance.

There is no denying that fulfilling these responsibilities requires a significant and ongoing effort on the part of the contract giver. In this respect, outsourcing of quality control testing is not so different from doing that testing in-house.

Cell Culturists….Are your human cells authenticated?

by Dr. Ray Nims

Until fairly recently, it has been common practice to authenticate human cell cultures using phenotypic status (e.g., receptor or protein expression) and animal species of origin testing. This level of authentication is better than none, but it is not sufficient to unambiguously identify a human cell culture. The result has been that we are still hearing about cases of misidentified human cells being used for biomedical research.

There are now methods available that are capable of rapidly and unambiguously identifying human cell lines, tissues, and cell preparations to the individual level. The recent demonstration of the potential utility of molecular technologies such as short tandem repeat (STR) and single nucleotide polymorphism (SNP) profiling for cell authentication has provided the impetus for development of a new standardized method for human cell authentication.

To this end, an ATCC Standards Development Organization workgroup with international representation has spent the past two years developing a consensus standard for the Authentication of Human Cell Lines through STR Profiling. The forthcoming Standard will provide guidance on the use of STR profiling for authenticating human cells, tissue, and cell lines. It will contain methodological detail on the preparation and extraction of the DNA, guidance on the appropriate numbers and types of loci to be evaluated and on interpretation and quality control of the results. Associated with the standard itself will be the establishment of a public STR profile database which will be administered and maintained by the National Center for Biotechnology Information (NCBI). The database primarily will contain STR profiles of commonly used cell lines.

                                            STR Profiling of Hela Cells

 An announcement that the Standard is now available for public 45-day review, comment, and vote was published in the October 22, 2010 issue of the ANSI newsletter Standards Action.

The benefits of the Standard will depend on the degree to which it is adopted and followed in the biomedical research and development and biopharmaceutical  communities. Taking a broader view, it is hoped that funding agencies and journals will begin to use such authentication standards as important considerations for funding or publishing research employing human cells. The quality and validity of funded and published research should benefit greatly as a result of the reduction in frequency of use of misidentified human cells.

The deadline for comments is December 6, 2010. There is still time to review the draft Standard and to voice your opinions and concerns.

Assessing rapid microbial detection systems

by Dr. Ray Nims

With each passing year, it seems that there are more options available for rapid microbial detection. These rapid systems come in a variety of “flavors”, that is - they differ with respect to a set of key attributes. For instance, how rapid is rapid? What is the sensitivity? What is the maximum sample volume that may be tested? Is it quantitative or qualitative? What units are the results given in? Is it destructive or non-destructive (i.e., can the organism, once detected, be identified)? When one considers the variety of applications for which rapid methods may potentially replace existing culture methods, it rapidly becomes clear that there may not be “one shoe that fits all”.

In order to select an appropriate rapid method for use in one of the many microbial detection applications, one must first assess the available rapid systems for the key attributes mentioned above. This then provides the opportunity to rule out systems which for one reason or the other will not suit the application. There may be some applications for which no rapid system currently meets all requirements. Those rapid systems which do appear to possess the attributes required may be further evaluated for cost and for performance capabilities using specific sample matrices.

In the table below, we have listed some of the currently available rapid microbial detection systems. These include only systems which are 48 hours in duration or less, and therefore some of the sterility replacement assays involving reduced incubation durations (e.g., BacT/ALERT®, Growth Direct™) are not listed.

The key attributes of these rapid systems are displayed in the table below. The systems are arranged by principle of detection, as in the table above. For certain methods (e.g., Micro Pro™) increased sensitivity can be gained through increasing the duration of the incubation time. For non-destructive methods, the ability to identify the organism(s) detected is facilitated by an additional incubation post-detection.

What is the regulatory position on rapid microbial detection methods? The U.S. FDA Guidance for Industry: Sterile Drug Products Produced by Aseptic Processing states that other suitable microbiological tests (e.g., rapid methods) may be considered for environmental monitoring, in-process control testing, and finished product release testing after it has been demonstrated that these new methods are equivalent or better than conventional (e.g., USP) methods. Additionally, the FDA Process Analytical Technology (PAT) initiative encourages the voluntary development and implementation of innovative approaches in pharmaceutical development, manufacturing, and quality assurance (from MJ Miller, PDA Journal 45: 1-5, 2002).

Are rapid methods being used in the pharmaceutical industry? ScanRDI was approved by the FDA for water testing at GSK and for sterility testing at Alcon; Pallchek has been approved by the FDA for bioburden testing at GSK; and Wyeth received approval for use of Celsis for microbial limits testing.

Like all methods proposed to replace existing “gold standards”, these rapid microbial detection systems must be demonstrated through comparability protocols to be equivalent to or better than the existing methods. The effort required should pay dividends in terms of shortened turnaround times and reduced costs.

Using porcine trypsin in biologics manufacture?

by Dr. Ray Nims

On March 22, 2010, a press release from GlaxoSmithKline (GSK) announced that porcine circovirus 1 (PCV 1) DNA had been detected in their rotavirus vaccine. On May 6, Merck disclosed that it had found DNA fragments of both PCV types 1 and 2 in its rotavirus vaccine. The PCV 2 findings in Merck's vaccine may be of greater concern, due to the fact that this virus causes disease in pigs, while PCV 1 apparently does not. However, the relative amounts of PCV DNA found in the GSK vaccine appear to be much greater (the lab discovering the PCV DNA in the GSK vaccine did not detect any in the Merck vaccine), and the worry in this case is that some of the genomic material may be associated with infectious PCV 1 virus. In both cases, the presence of the PCV genomic material has been attributed to the use of porcine trypsin at some point in the vaccine manufacturing process.


The FDA convened an advisory committee meeting on May 7th to discuss the findings of PCV DNA in the two licensed rotavirus vaccines. What was the result of the advisory committee meeting? The advisory committee felt that the benefits of the rotavirus vaccines clearly outweigh the risks. This, added to the fact that there appears to be little human health hazard associated with these viruses, led to the FDA clearing the two vaccines for continued use on May 14th. The product labels will be updated to reflect the presence of the PCV DNA in these products. In the longer term, these products may need to be "reengineered" to remove the PCV DNA. This may involve the preparation of new Master and Working cell banks and thus will take some time.

Another likely outcome of the advisory committee’s meeting may be heightened expectations, going forward, for PCV screening of porcine raw materials and of Master and Working cell banks which were exposed to porcine ingredients (e.g., trypsin) at some point in their development. Porcine-derived raw materials which are used in the production of biologics are to be tested per 9 CFR 113.53 Requirements for ingredients of animal origin used for production of biologics for a variety of viruses of concern. In the case of ingredients of porcine origin, those viruses of concern are listed in 9 CFR 113.47 Detection of extraneous viruses by the fluorescent antibody technique. These include rabies, bovine viral diarrhea virus, REO virus, porcine adenovirus, porcine parvovirus, transmissible gastroenteritis virus, and porcine hemagglutinating encephalitis virus. While porcine circovirus may not be specifically mentioned in the 9 CFR requirements, it will be prudent to add a nucleic acid-based assay for detection of this virus to the porcine raw material testing battery going forward. Similarly, Master and Working cell banks exposed to porcine raw materials (e.g., trypsin) during their developmental history should be assayed for PCV prior to use.

Routine nucleic acid-based testing for PCV should detect the genomic sequences for this virus should intact infectious or non-infectious PCV be present in the test materials. Now that this virus is one of concern to the FDA and to the public, performing the appropriate raw material and cell bank testing for it will most likely become an expectation for vaccine and biologics manufacturers.

Hot Tubs and Bioreactors

By Dr. Ray Nims

Contaminating organisms which most commonly are under the radar for biopharmaceutical manufacturing operations include bacteria, mollicutes (mycoplasmas and acholeplasmas), and viruses. Various in-process and lot-release detection assays are mandated by the FDA and the International Conference on Harmonisation to ensure that such contaminants are detected in bulk harvests and/or final products as part of assuring patient safety (specified in ICH Q5A R1 and the 1993 Points to Consider in the Characterization of Cell Lines used to Produce Biologics). There is, however, an additional group of organisms which may threaten biologics production (one which is not normally associated with such manufacturing activities) namely, the Mycobacterium fortuitum complex.

The what?? The fortuitum complex is a group of relatively rapid-growing (non-tuberculosis) mycobacteria which is more typically associated with hot tub disease, and the contamination of industrial cutting fluids and foot baths used for pedicures. The group includes M. fortuitum, M. chelonae, M. abscessus, M. immunogenum, M. mucogenicum, M. peregrinum, and a few others. These mycobacteria, as well as other groups of non-tuberculosis mycobacteria, can be pathogenic in humans, even those who are immuno-competent. The organisms of the fortuitum complex represent a potential risk to the biopharma industry due to their propensity for forming biofilms, their ability to proliferate in water under relatively low nutrient conditions, their resistance to typical water disinfection methods, and their relatively slow growth in nutrient media.

                    Mycobacteria growing at the liquid/air
                       interface of a growth medium.


These characteristics render the organisms capable of existing in water piping and other surfaces in contact with water or aqueous media. Their slow growth in nutrient media may result in these agents being overlooked in biopharmaceutical manufacturing operations, especially when surveillance methods such as short-term bioburden assays are employed. A few cases of contaminated vaccines and tissue extracts have been reported in the literature (Mycobacterium chelonei in abscesses after injection of diphtheria-pertussis-tetanus-polio vaccine. Am. Rev. Respir. Dis. 1973 Jan; 107:1-8; Abscesses due to Mycobacterium abscessus linked to injection of unapproved alternative medication. Emerg. Inf. Dis. 1999; 5: 681-687).

Are there other examples? It is, unfortunately, difficult to estimate the frequency of occurrence of mycobacterial contamination in biologics manufacturing, since many episodes may lead to premature bioreactor termination, with little evidence to implicate a mycobacterium. It is also likely that episodes may have occurred without being reported in the literature.

Outsource it, and fuggedaboutit?

By Ray Nims

Much has been written about the rationales and advantages for outsourcing of manufacturing and/or testing services; about the selection of outsourcing partners; and about the optimization of the pharma/contractor relationship. In any pharma/contractor relationship, there are responsibilities associated with the pharma as well as contractor responsibilities. These include both business as well as compliance responsibilities. The business realities and regulatory expectations associated with the use, by a pharma company, of a contract testing organization must be considered when the decision is made to outsource. A contract testing organization desiring to provide services for a pharmaceutical must be aware of the expectations and responsibilities associated with such a partnership. The optimal and most defensible programs will be those in which the various practices to be described below are formalized within internal Quality Systems, policies, and/or standard operating procedures as well as Quality Agreements.


Responsibilities falling upon the pharmaceutical partner include: 1) the selection of the contract testing lab; 2) commissioning and providing test samples of raw materials and products for method verification (compendial methods) and method qualification (non-compendial methods); 3) instituting of a Quality Agreements, business agreement, and/or confidentiality agreement with the contractor; 4) scheduling and shipping of test samples in accordance with the requirements of the testing lab and the test system; 5) providing in-life guidance and oversight of investigations of unexpected and out of specification results; and 6) ongoing monitoring of the performance of the contract lab and its methods.

Responsibilities primarily falling upon the testing lab include: 1) attaining and maintaining GLP or GMP compliance as appropriate for the intended use of the method; 2) providing assurance that the methods offered will be available to the client over the long term; 3) responsiveness to the sponsoring pharma and adherence to the terms of the Quality and/or business agreements; 4) method validation, verification, and or qualification as appropriate for the intended use of the method; 5) control of reagent, raw material, control, and standard inventory and quality; 6) assuring secure and retrievable data archiving; and 7) retention of staff possessing the appropriate expertise for direction of operators and the methods.