In his State of the Union Address given on January 28, 2014, President Obama recognized the need for continued and increased investment in new technologies, including technologies specific to the biological and pharmaceutical fields.

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How would “vaccines that stay ahead of drug-resistant bacteria” fare under the new USPTO 101 Guidelines?

Vaccines typically are made from the naturally-occurring microorganism associated with the disease that the vaccine is designed to protect against, and may include a modified version of the microorganism, a killed form of the microorganism, a protein associated with the microorganism, or an antigenic fragment of a protein associated with the microorganism. For at least the last two types of vaccines, the most important component of the vaccine would be considered a “natural product” under the USPTO guidelines.

I don’t want to pick on any patents, but a search of the USPTO patent database using queries like “vaccine” and “antigen” identifies thousands of patents that might never have been granted under the new USPTO 101 Guidelines. For example, a typical patent to a vaccine based on an antigen identified by it’s amino acid sequence, which could be a naturally-occurring protein or an antigenic fragment, includes a claim like this:

  1. A pharmaceutical composition, comprising: (i) a peptide having an amino acid sequence that is at least 80% identical to SEQ ID NO: 2, and (ii) a pharmaceutically acceptable carrier.

Following the analysis outlined in the Guidelines, this claim only would be patent eligible if one of the components is structurally different from a natural product.

If SEQ ID NO:2 is the amino acid sequence of a naturally-occurring protein or a fragment of a naturally-occurring protein, component (i) could not support patent eligibility.

Whether component (ii) supports patent eligibility may depend on whether and how that component is defined in the patent. Most patents define ”pharmaceutically acceptable carriers” broadly, with reference to pharmaceutical reference books. Patents that provide specific examples of pharmaceutically acceptable carriers usually include water and other “natural products” in their lists of examples, in which case component (ii) would not support patent eligibility.

I thought the “pasteurized juice” example in the USPTO 101 Guidelines training slides might provide some hope for claims directed to sterile pharmaceutical compositions, or for compositions comprising sterilepharmaceutically acceptable carriers, but the slides find that claims to “pasteurized” juice are patent eligible only because the specification defines the pasteurized juice as being structurallydifferent:

The specification describes the pasteurization process as damaging the chemical structure of the vitamin C and flavonoids in the juice. As a result, the pasteurized juice contains about 20-30% less vitamin C and about 30% fewer flavonoids than naturally occurring juice. The pasteurized juice thus has a different taste, and lower nutritional value than the naturally occurring juice.

(Slide 77)

Even if the pharmaceutically acceptable carrier is defined as including only non-naturally occurring components (which would support patent eligibility), doesn’t a rule that bases the patent eligibility of an important new vaccine on the pharmaceutically acceptable carrier it is formulated in make a mockery of the U.S. patent system?