Massively parallel sequencing meets the vaccine industry

Live attenuated vaccines (LAVS), such as those produced for measles, mumps and influenza viruses, must have both high safety and immunogenicity if we are ever going to prevent human infection. Those vaccines, which are deemed unsafe, will be withdrawn resulting in low uptake and increased pathogen transmission and those vaccines which are poorly immunogenic, will not be  protective and result in pathogen transmission and significant disease

The key to easily predicting how safe a vaccine is – and also how immunogenic -, may lie in our ability to infer the phenotype (safety in humans) from the genotype (nucleic acid sequence). One problem with this is the inherent genetic instability of  RNA viruses; viruses such as polio, measles and mumps which are responsible for considerable disease in humans and which we vaccinate millions of people worldwide each year. This genetic instability results in what is generally considered as a viral ‘qausipecies’; a cloud-like structure in viral genome sequence space that can have multiple phenotypic properties: one being the safety, or lack of in humans. One example is that of oral polio vaccine strains which during production in tissue culture can accumulate genomic changes resulting in neurovirulence in humans.

In order to assess the safety we must therefore assay the genetic consistency or the types and frequency of particular changes in our vaccines prior to human administration to avoid vaccine induced disease. As I mentioned previously, our ability to assess the safety relies on our means of predicting phenotype from genotype, something that for most viruses is particularly difficult and time consuming. We are therefore  in a position in which we do not know the genetic determinants of safety and so cannot predict it based on nucleic acid sequence.

[caption id="" align="aligncenter" width="257" caption="MPS analysis of two batches of type 3 OPV performed by pyrosequencing. (A) The number of times each nucleotide was read in forward (green) and reverse (red) orientations. (B and C) Mutational profiles for vaccine batches that failed and passed the MNVT, respectively. Here and in all other figures the contents of mutants is shown by colored bars: mutations to A shown in orange, mutations to C in red, mutations to G in blue, and mutations to U in green. Neverov & Chumakov.(2010)"][/caption]

Neverov and Chumakov, from the American Food and Drug association (FDA) recently published a method in which massively parallel sequencing (MPS) is used to accurately and rapidly quantify nucleotide changes across entire poliovirus vaccine genomes.  This method proved to be very sensitive at detecting low frequency changes, changes that may have led to disease in humans. The group put forward the view that we do not truly have to know the direct relationship between genome sequence and safety but what we can do is compare the genotype and frequency of each change with previous ‘safe’ vaccine sequences. Vaccines will be allowed for human use if they have similar viral populations as a previously used strain. They offer this method as a replacement to the slower and less accurate mutant analysis by PCR and restriction enzyme cleavage (MAPREC) method.

The authors admit that the wide-scale implementation of MPS will be inhibited by the high running cost of the equipment.; a cost that they say is much less than the previously used primate neuroviruelance assay. Investment in this technology is expected to lead to a rapid decrease in price and hence will result in increased uptake of this in LAV production worldwide. Neverov and Chumakov have applied this novel sequencing technology to an important area of the vaccine industry. This application will find use in not only polio vaccines but in other LAV production and may also be implemented in the discovery of new genetic determinants of viral safety and immunogenicity.

Neverov, Alexander, and Konstantin Chumakov. 2010. Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proceedings of the National Academy of Sciences of the United States of America 107, no. 46 (November). doi:10.1073