June 29, 2008 A team of molecular biologists and computer scientists at Stony Brook University has designed and synthesized a new class of weakened polioviruses. They used their synthesizing method with computer software to systematically re-code the poliovirus genome. In doing so, the team is the first to demonstrate that a synthetic weakened virus can immunize an animal. These results show promise in the creation of new attenuated (‘live virus’) anti-viral vaccines and are reported in the June 27 issue of Science.
Six years ago, Eckard Wimmer, Ph.D., Distinguished Professor, Department of Molecular Genetics and Microbiology at Stony Brook University, and colleagues synthesized and generated poliovirus, the first artificial synthesis of any virus. Dr. Wimmer and other scientists within the Department built on that finding in their recent work.
“Synthesizing the wild-type poliovirus was an essential and important first step toward our current research,” says Dr. Wimmer, noting that the new method involves impeding the synthesis of viral proteins, a new approach to developing attenuated vaccines. This type of vaccine is created by mutating the virus so it cannot cause disease. Generally, attenuated vaccines are easy to administer, inexpensive, and sometimes offer the best protection against disease.
“As all viruses depend on their host’s cellular machinery to produce their proteins, targeting the synthesis of viral proteins by the host may be universally applicable to creating weakened strains of other viruses,” says Steffen Mueller, Ph.D., Senior Author and Research Assistant Professor of Molecular Genetics and Microbiology, referring to the implications of the research results.
Because of the redundancy of the genetic code, there are an unimaginably large number of ways to encode any given protein. For poliovirus proteins, there are more possible encodings (10442) than atoms in the universe. Using a powerful computer algorithm, the team found particular re-codings of the genome predicted to weaken the virus.
The researchers made hundreds of small mutations in the genome that perfectly preserved the viral proteins but changed the way those proteins were encoded by RNA (ribonucleic acid), so that pairs of amino acids were added by transfer RNAs (tRNAs) that rarely work together in normal proteins. They call the process “Synthetic Attenuated Virus Engineering,” or “SAVE.” The resulting virus contains completely authentic, wild-type poliovirus proteins. However, each of the hundreds of mutations causes a tiny defect by creating an obstacle – a genetic “speed bump” – in translating the genetic code into a protein.
“Translation of this unusual genome into viral proteins was inefficient, and the most highly re-coded virus was weakened to the point where it was unable to infect cells,” says J. Robert Coleman, Lead Author and a graduate student in Molecular Genetics and Microbiology.
The reduced translational efficiency of these chimeric viruses reduced their ability to cause disease. The team injected mice with the re-coded polioviruses. Most mice showed no signs of disease but did produce anti-polio antibodies. These mice were then immune against infection by the normal, fully virulent poliovirus.
“Ultimately we created a wimpy poliovirus that can be customized and does not cause disease unless given at high doses,” explains Bruce Futcher, Ph.D., Co-author and Professor of Molecular Genetics and Microbiology. “These viruses are still far from suitable vaccines for humans, but there is a lot of potential for this approach,” continues Dr. Futcher. “A virus modified using ‘SAVE’ might act as a vaccine by providing immunity against the normal virus.”
The inclusion of computer programming essential to developing these synthetic polioviruses featured the work of Steven Skiena, Ph.D., Professor of Computer Science. Dr. Skiena, in collaboration with his graduate student Dimitris Papamichail, developed the sequence design algorithm.
“Sophisticated computer algorithms are necessary to design the hundreds of changes to sufficiently cripple the virus for our ‘death by a thousand cuts’ approach,” summarizes Dr. Skiena. “Because of the large number of changes, the weakened virus can never mutate back to wild-type.”
The research team hopes this “death by a thousand cuts” virus mutation strategy can be applicable to attenuating many kinds of viruses. They are looking into applications with other viruses.