Use of computer algorithms to reduce viral quasispecies sequence space.
A virus may express multiple simple mutations producing a set of viral subspecies called quasispecies: the quasispecies are considered the same species as the original virus. We are interested in reducing the point mutation space to enumerate that sequence space. We form a point mutation by applying a single bit mutation to a strand of viral DNA. How many differing viruses are possible if we allow any of the base pairs to change along the strand? For a strand of arbitrary length n we see that there is a possible sequence space of 4n-1.4 = 4n combinations. We can further remove identical sequences due to redundant amino acid codon encoding. This requires the use of a computer, but this time the complexity is a product: the number of possible amino acids times the number of codons. This substantial reduction from an exponential complexity O(4n) to a product O(n.amino-acid-number) gives us the complete list of mutant viral entities which are one mutation away from the original. Further reduction is possible, but requires biological insight regarding the viability of the mutation. By recognizing the possible sequence space, prediction can be made toward identifying future viral strains of HIV and influenza (to name two important viral particles), and perhaps develop a predictive intervention.
Epperson
E S
ES
Dept. of Electrical and Computer Engineering, University of Missouri, Columbia, USA.
Tyrer
H W
HW
D000465:Algorithms; D000595:Amino Acid Sequence; D001483:Base Sequence; D003062:Codon / Q000235:genetics; D004252:DNA Mutational Analysis; D004279:DNA, Viral / Q000235:genetics; D015497:HIV-1 / Q000235:genetics*
D003062:Codon; D004279:DNA, Viral