Characterization and genomic analysis of ValSw3-3, a new Siphoviridae bacteriophage infecting Vibrio alginolyticus.

A novel lytic bacteriophage ValSw3-3, which efficiently infects pathogenic strains of Vibrio alginolyticus, was isolated from sewage water and characterized by microbiological and in silico genomic analyses. Transmission electron microscopy indicated that ValSw3-3 had the morphology of siphoviruses. This phage can infect four species in the Vibrio genus and has a latent period of 15 min and a burst size of 95 ± 2 PFU/infected bacterium. Genome sequencing results show that ValSw3-3 has a 39,846-bp double stranded DNA genome with a GC content of 43.1%. The similarity between the genome sequences of ValSw3-3 and other phages recorded in GenBank database was below 50% (42%), suggesting that ValSw3-3 significantly differed from previously reported phages at the DNA level. Multiple genome comparisons and phylogenetic analysis based on major capsid protein revealed that phage ValSw3-3 was grouped in a clade with other five phages, including Listonella phage phiHSIC (NC_006953.1), Vibrio phage P23 (MK097141.1), Vibrio phage pYD8-B (NC_021561.1), Vibrio phage 2E1 (KX507045.1), and Vibrio phage 12G5 (HQ632860.1), which was distinct from all known genera within the Siphoviridae family that have been ratified by ICTV. An in silico proteomic comparison of diverse phages from the Siphoviridae family supported this clustering result and suggested that ValSw3-3, phiHSIC, P23, pYD8-B, 2E1, and 12G5 could be classified as a novel genus cluster of Siphoviridae A subsequent analysis of core genes also revealed the common genes shared within this new cluster. Overall, these results provide a characterization of Vibrio phage ValSw3-3 and support our proposal of a new viral genus within the family Siphoviridae ImportancePhage therapy has been considered as a potential alternative to antibiotic therapy in treating bacterial infections. For controlling the vibriosis-causing pathogen, Vibrio alginolyticus, well documented phage candidates are still lacking. Here we characterize a novel lytic Vibrio phage ValSw3-3 based on its morphology, host range and infectivity, growth characteristics, stability under various conditions, and genomic features. Our results show that ValSw3-3 could be a potent candidate for phage therapy to treat V. alginolyticus infections due to its strong infectivity and better pH and thermal stability compared with previously reported Vibrio phages. Moreover, genome sequence alignments, phylogenetic analysis, in silico proteomic comparison, and core-gene analysis all support that this novel phage ValSw3-3 and five unclassified phages form a clade distant from other known genera ratified by ICTV. We thus propose a new viral genus within the Siphoviridae family to accommodate this clade with ValSw3-3 as a representative member.