Friedman Stephanie D, Genthner Fred J, Gentry Jennifer, Sobsey Mark D, Vinjé Jan
U.S. Environmental Protection Agency, Gulf Ecology Division, 1 Sabine Island Drive, Gulf Breeze, FL 32561, USA.
J Virol. 2009 Nov;83(21):11233-43. doi: 10.1128/JVI.01308-09. Epub 2009 Aug 26.
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').
雄性特异性单链RNA（F RNA）大肠杆菌噬菌体属于光滑噬菌体科。它们被分为两个属（光滑噬菌体属和嗜其他光滑噬菌体属），这两个属又可细分为四个基因组群（光滑噬菌体属中的基因组群I和II以及嗜其他光滑噬菌体属中的基因组群III和IV）。相对较少的菌株得到了完全的特征描述，因此，对这个病毒家族缺乏详细的了解。在本研究中，我们对19株F RNA菌株（10株光滑噬菌体属菌株和9株嗜其他光滑噬菌体属菌株）的完整基因组进行了测序和特征分析，并将它们与GenBank中现有的11个完整基因组序列进行了比较。光滑噬菌体属基因组群I和II的菌株之间的核苷酸相似性分别为75%至99%和83%至94%，而嗜其他光滑噬菌体属基因组群III和IV的菌株之间的相似性分别为70%至96%和75%至95%。尽管基因组群I的fr菌株与基因组群III的MX1和M11菌株与各自基因组群中的菌株仅共享70%至78%的序列同一性，但对完整基因组和单个基因的系统发育分析表明，fr菌株应归入光滑噬菌体属基因组群I，而MX1和M11菌株属于嗜其他光滑噬菌体属基因组群III。每个属内的菌株共享>50%的序列同一性，而两个属之间的菌株具有<40%的核苷酸序列同一性。总体而言，氨基酸组成、核苷酸相似性和复制酶催化结构域位置有助于系统发育分类。基因组3'端一个保守的八核苷酸特征序列将光滑噬菌体（5' ACCACCCA 3'）与嗜其他光滑噬菌体（5' TCCTCCCA 3'）区分开来。
