A thought on vaccine technology

Graphic of H1N1 confirmed cases in the US, May 14, 2009, from the CDC

With influenza A(H1N1), or swine flu, stirring up fears of flu pandemic and a potential need for mass vaccination against H1N1, it seemed fitting to consider the technology of vaccines for various viral illnesses, from seasonal flu to HIV.

A shot every year that still doesn't keep the flu away? What happened to an apple a day?

Influenza A strains easily form new strains and quasi-species via a relatively high critical error threshold for the virus, reassortment of the segmented genome, and a much slower process of genetic drift. The resultant diversity means that a new vaccine is developed each year, and may not even include the breadth of diverse strains that the human population may see during that flu season. A group at Harvard recently published promising evidence that it may be possible to produce a smaller group of vaccines that would confer immunity to any influenza A (Sui et al 2009, Nature Structural and Molecular Biology, Vol16, No3). Influenza A virions possess two major surface proteins: hemaggglutinin, for cell entry; and neuraminidase, for cell exit. Sui et al. screened a library of antibodies to locate those with high affinity antibodies to a common epitope source: the pocket in the stem of hemagglutinin. This particular epitope has two variants, meaning that its possible that two anitbodies could recognize all hemagglutinin surface proteins of all influenza A strains across many years. The preventative influenza agent, Tamiflu, is a neuraminidase inhibitor; but it doesn't always work (if administered post-infection), and there is general concern about potential increases in strain resistance. Sui et al. demonstrated that in mice, one of the high affinity antibodies toward hemagglutinin (nAb C179) blocked membrane fusion of H5N1 (avian flu), thereby protecting the mice from viral challenge. Thus, a new era of more efficient (and maybe efficacious too) flu vaccine development seems to be on its way. The Sui et al. paper is only one of several recent breakthroughs in this emerging field of a "universal" flu vaccine (editorial: Leslie M. (27 Feb 2009) "Flu antibodies stir new hope for treatment, vaccine." Science, DOI: 10.1126/science.323.5918.1160).



A graphic from Science magazine on the structure of influenza A

What about viruses for which we have no good vaccines?

HIV, HCV, and other other viruses that cause chronic disease pathologies have not been addressed with a bad vaccine technology, let alone a good one. In January, I saw a really interesting talk at UNC by John Essigmann on "Viral Acceleration Decay" (VDA). My interest in Dr. Essigmann's talk was a studious effort at best, because I expected him to talk mainly about DNA adducts and cancer--and he did. Except he also talked about his pharma start-up, Koronis, and the team's efforts to very roughly, give HIV cancer, and kill it in the host. The general idea behind VDA is eye-opening. The replication rate of HIV is very high, and it exists close to the edge of its critical error threshold, or the number of errors within the replicated genome that are tolerable by the virus. Essigmann et al. at Koronis had an idea; give a drug that is a promutagenic nucleoside analog that is incorporated by the reverse transcriptase, and eventually, too many errors will result in an abolishing of viral replication, and a decrease in viral load, until the the virus "dies." This hypothesis and the original work to demonstrate its plausibility are detailed in Loeb et al. (1999) "Lethal mutagenesis of HIV with mutagenic nucleoside analogs."

Existing treatment for HIV includes antivirals: acyclovir, lamivadine, zidovudine (AZT) -- all of these are nucleosides with a modified sugar and unmodified bases, and are intended to block reverse transcriptase replication. Clearly they are never able to abolish viral replication completely. The Koronis nucleosides contain the natural sugar group of the nucleoside, and have a modified base. This promutagenic nucleoside results in transition mutations (A<>G, C<>T). One such nucleoside is in the clinical trials process, stalled in Phase II (see http://www.koronispharma.com/ and Harris et al KP1212/1461, a nucleoside designed for the treatment of HIV by viral mutagenesis).

I'm excited to start thinking about vaccines and viral treatment in a different way. So perhaps there is a positive outcome from the H1N1 outbreak - more funding and attention for influenza vaccines, and other vaccines technologies.

Why I sweat through the NC summer in pants

Recently I began working in a new lab to complete a side project funded by a small grant from the Society of Toxicology and Colgate-Palmolive. This has provided an interesting affirmation of ideas I've begun learning as a young scientist, as I've now only trained in at least 5 (depending on how you count it) research labs at three institutions.

The primary investigator is a well-known, successful researcher in the area of hepatobiliary toxicity of pharmaceuticals. I respect her and like her very much. What I didn't expect were the cramped, often overly-political, and under-stocked and under-funded conditions of her laboratory. There are no less than 10 people working on 2 cramped benches, with glassware and other materials everywhere. There are two stools for the lab, which means one has to bend over the bench. Safety procedures are inconsistent - it's not uncommon to see shorts, open-toed shoes, no lab coat, etc. And other procedures - such as using vinyl sleeves over lab coats at BSL2 cell culture hoods - are inconsistent (i.e. in one room we wear them, and at the other hood, we don't, with no real explanation). Training seems haphazard. Disposal rules are not clear. Tools used in radioactive experiments are not dedicated radioactive tools, and wipe tests after work are not conducted. I could go on.

Then today I read this article about a graduate student at UCLA died from lack of safety procedures in a lab.

This article aligns with my experience - that academic labs are definitively more lax about safety. Some are worse than others. The first lab I trained in at Virginia Tech was wonderful, had clear procedures, clear storage of materials, clear safety rules, etc. At EPA, I've often felt that some procedures seem overly arduous, that waste streams are complex, or that maybe it would be okay to wear capris just once! Or that it seems ludicrous to wear a lab coat to label tubes. Or that I'd love to wear shorts and flip-flops to work like my academic counterparts in the middle of 100 degree+ NC summers. However, what I'm learning is that EPA has really chosen a responsible, hard-lined approach . . . that I actually miss and love.


Importantly, the big difference I'm finding is that a great laboratory technician, who chooses to be firm on procedures, safety, and operation of the lab, is the biggest key for lab safety and productivity.