Rhinovirus Genomics

Infection with human Rhinovirus (HRV) causes ~50% of the asthma and COPD exacerbations. There are >100 distinct HRV strains, and we feel that HRV genomic variation represents a missing piece of the asthma puzzle in terms of pathogenesis and treatment. To close this gap, we sequenced the full genomes of all known HRV serotypes. Using crystal structure superimposition and RNA minimal energy conformation modeling we then established what we refer to as a “structure-based” alignment of the RNA and amino acid sequences. This effort led to the first phylogenetic tree of the reference HRV set based on full genomes, and several unsuspected findings regarding HRV structure/function, potential anti-viral therapy, revolution and recombination.

• Bochkov YA, Palmenberg AC, Lee WM, Rathe JA, Amineva SP, Sun X, Pasic TR, Jarjour NN, Liggett SB, and Gern JE. Molecular modeling, organ culture and reverse genetics for a newly identified human rhinovirus C. Nature Medicine 17: 627-632, 2011.

• Palmenberg AC, Rathe JA, and Liggett SB. Analysis of the complete genome sequences of human rhinovirus. J Allergy Clin Immunol125: 1190-1199; quiz 1200-1191, 2010.

• Rathe JA, Liu X, Tallon LJ, Gern JE, and Liggett SB. Full-genome sequence and analysis of a novel human rhinovirus strain within a divergent HRV-A clade. Arch Viro 155: 83-87, 2010.

• Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, Fraser-Liggett CM, and Liggett SB. Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324: 55-59, 2009.