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Journal of Virology, November 2009, p. 11233-11243, Vol. 83, No. 21
0022-538X/09/$08.00+0     doi:10.1128/JVI.01308-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Gene Mapping and Phylogenetic Analysis of the Complete Genome from 30 Single-Stranded RNA Male-Specific Coliphages (Family Leviviridae){triangledown}

Stephanie D. Friedman,1,2* Fred J. Genthner,1 Jennifer Gentry,2 Mark D. Sobsey,2 and Jan Vinjé3

U.S. Environmental Protection Agency, Gulf Ecology Division, Gulf Breeze, Florida 32561,1 University of North Carolina at Chapel Hill, Department of Environmental Sciences and Engineering, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina 27599,2 National Calicivirus Laboratory, Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 303333

Received 25 June 2009/ Accepted 14 August 2009

Male-specific single-stranded RNA (FRNA) coliphages belong to the family Leviviridae. They are classified into two genera (Levivirus and Allolevivirus), which can be subdivided into four genogroups (genogroups I and II in Levivirus and genogroups III and IV in Allolevivirus). Relatively few strains have been completely characterized, and hence, a detailed knowledge of this virus family is lacking. In this study, we sequenced and characterized the complete genomes of 19 FRNA strains (10 Levivirus strains and 9 Allolevivirus strains) and compared them to the 11 complete genome sequences available in GenBank. Nucleotide similarities among strains of Levivirus genogroups I and II were 75% to 99% and 83 to 94%, respectively, whereas similarities among strains of Allolevivirus genogroups III and IV ranged from 70 to 96% and 75 to 95%, respectively. Although genogroup I strain fr and genogroup III strains MX1 and M11 share only 70 to 78% sequence identity with strains in their respective genogroups, phylogenetic analyses of the complete genome and the individual genes suggest that strain fr should be grouped in Levivirus genogroup I and that the MX1 and M11 strains belong in Allolevivirus genogroup III. Strains within each genus share >50% sequence identity, whereas between the two genera, strains have <40% nucleotide sequence identity. Overall, amino acid composition, nucleotide similarities, and replicase catalytic domain location contributed to phylogenetic assignments. A conserved eight-nucleotide signature at the 3' end of the genome distinguishes leviviruses (5' ACCACCCA 3') from alloleviviruses (5' TCCTCCCA 3').

* Corresponding author. Mailing address: U.S. Environmental Protection Agency, Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL 32561. Phone: (850) 934-2468. Fax: (850) 934-9201. E-mail: friedman.stephanie{at}epa.gov

{triangledown} Published ahead of print on 26 August 2009.

Journal of Virology, November 2009, p. 11233-11243, Vol. 83, No. 21
0022-538X/09/$08.00+0     doi:10.1128/JVI.01308-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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