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Journal of Virology, January 2005, p. 554-568, Vol. 79, No. 1
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.1.554-568.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Evolutionary Trace Residues in Noroviruses: Importance in Receptor Binding, Antigenicity, Virion Assembly, and Strain Diversity

Sugoto Chakravarty,1 Anne M. Hutson,2 Mary K. Estes,2 and B. V. Venkataram Prasad1,3*

Verna and Marrs Mclean Department of Biochemistry and Molecular Biology,1 Keck Center for Computational Biology,2 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas3

Received 20 January 2004/ Accepted 30 August 2004

Noroviruses cause major epidemic gastroenteritis in humans. A large number of strains of these single-stranded RNA viruses have been reported. Due to the absence of infectious clones of noroviruses and the high sequence variability in their capsids, it has not been possible to identify functionally important residues in these capsids. Consequently, norovirus strain diversity is not understood on the basis of capsid functions, and the development of therapeutic compounds has been hampered. To determine functionally important residues in noroviruses, we have analyzed a number of norovirus capsid sequences in the context of the Norwalk virus capsid crystal structure by using the evolutionary trace method. This analysis has identified capsid protein residues that uniquely characterize different norovirus strains and provide new insights into capsid assembly and disassembly pathways and the strain diversity of these viruses. Such residues form specific three-dimensional clusters that may be of functional importance in noroviruses. One of these clusters includes residues known to participate in the proteolytic cleavage of these viruses at high pH. Other clusters are formed in capsid regions known to be important in the binding of antibodies to noroviruses, thereby indicating residues that may be important in the antigenicity of these viruses. The highly variable region of the capsid shows a distinct cluster whose residues may participate in norovirus-receptor interactions.

* Corresponding author. Mailing address: Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030-3498. Phone: (713) 798-5686. Fax: (713) 798-1625. E-mail: vprasad{at}bcm.tmc.edu.

Journal of Virology, January 2005, p. 554-568, Vol. 79, No. 1
0022-538X/05/$08.00+0     doi:10.1128/JVI.79.1.554-568.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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