Complete genome sequences of Mycobacterium smegmatis phages Ashballer and Bombitas.

We report the discovery of two mycobacteriophages isolated from soil in Rock Hill, South Carolina. Ashballer has a genome sequence length of 52,231 bp, while Bombitas is relatively larger at 110,129 bp. Both have siphovirus morphologies and have temperate lifecycles.

Rogue taxa phenomenon: a biological companion to simulation analysis.

To provide a baseline biological comparison to simulation study predictions about the frequency of rogue taxa effects, we evaluated the frequency of a rogue taxa effect using viral data sets which differed in diversity. Using a quartet-tree framework, we measured the frequency of a rogue taxa effect in three data sets of increasing genetic variability (within viral serotype, between viral serotype, and between viral family) to test whether the rogue taxa was correlated with the mean sequence diversity of the respective data sets. We found a slight increase in the percentage of rogues as nucleotide diversity increased. Even though the number of rogues increased with diversity, the distribution of the types of rogues (friendly, crazy, or evil) did not depend on the diversity and in the case of the order-level data set the net rogue effect was slightly positive. This study, assessing frequency of the rogue taxa effect using biological data, indicated that simulation studies may over-predict the prevalence of the rogue taxa effect. Further investigations are necessary to understand which types of data sets are susceptible to a negative rogue effect and thus merit the removal of taxa from large phylogenetic reconstructions.

Complete Genome Sequences of Mycobacterium smegmatis Phages MelsMeow, Yorick, Virgeve, and Mikro.

Mycobacterium phages Mikro, Yorick, Virgeve, and MelsMeow were isolated from soil in Rock Hill, South Carolina. Mikro is a myovirus with a comparatively large genome of 157,166 bp. The remainder are siphoviruses with genome lengths ranging from 59,227 bp to 68,563 bp. All phages were isolated on Mycobacterium smegmatis.

Complete Genome Sequences of Microbacterium liquefaciens Phages Mercedes, Leafus, Nebulous, and Ixel.

Microbacterium phages Mercedes, Leafus, Nebulous, and Ixel were isolated from soil in Rock Hill, SC. All are lytic phages with Siphoviridae morphotypes and similar genome sequence lengths that range from 40,200 bp to 42,000 bp. The four bacteriophages were isolated using the host Microbacterium liquefaciens.

Genomic diversity of bacteriophages infecting Microbacterium spp.

The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.

Serotype-specific differences in antigenic regions of foot-and-mouth disease virus (FMDV): a comprehensive statistical analysis.

Although vaccines are available for prophylaxis of foot-and-mouth disease virus (FMDV), few cases of escape mutants have been reported. To develop serotype-specific FMDV vaccination strategies it is imperative to understand how host selection has influenced evolution of FMDV. This study identified several possible targets for serotype-specific FMDV vaccines using a novel statistical approach. Pairs of closely related FMDV genomes identified in a phylogenetic analysis representing all seven serotypes were examined in order to understand the long term effects of host selection on well-characterized and predicted antigenic regions of importance (B, T(H), and T(C)). Estimates of synonymous and non-synonymous substitution rates for antigenic and non-antigenic regions were calculated for individual pairs of FMDV genomes. We found that on average, both antigenic and non-antigenic regions were subject to purifying selection acting at non-synonymous sites and that several antigenic sites showed a pattern of nucleotide substitution suggesting repeated positive selection across the population. In addition, we found that antigenic regions from the individual FMDV serotypes differed with respect to the extent of amino acid conservation. For a capsid T(H) epitope currently used in one synthetic vaccine, we found that serotypes SAT1-3 had significantly greater non-synonymous nucleotide substitutions than the other serotypes. In contrast, in a second well-studied B-cell epitope, there were no serotype-dependent differences in synonymous or non-synonymous nucleotide substitutions. These results support the hypothesis that host selection acting on individual serotypes has been an important factor in the long-term evolution FMDV and needs to be considered for vaccine design.

Evolution of cytotoxic T-lymphocyte epitopes in hepatitis B virus.

In hepatitis B virus (HBV), while mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been described it has been difficult to determine how natural selection by host CTL has influenced long-term evolution of HBV. We used statistical analysis of published HBV genomic sequences to examine the role of natural selection in evolution of CTL epitopes. Based on a phylogenetic analysis, we identified 25 pairs of closely related genomes isolated from different HBV genotypes and examined pattern of nucleotide substitution in genomic regions encoding well-characterized CTL epitopes. On average, both epitope and non-epitope regions are subject to purifying selection acting at non-synonymous sites. However, certain CTL epitopes showed a pattern of nucleotide substitution suggesting repeated positive selection across the population. The results support the hypothesis that CTL-driven selection has been an important factor in long-term evolution of HBV.

Origin of the 1918 Spanish influenza virus: a comparative genomic analysis.

To test the avian-origin hypothesis of the 1918 Spanish influenza virus we surveyed influenza sequences from a broad taxonomic distribution and collected 65 full-length genomes representing avian, human and "classic" swine H1N1 lineages in addition to numerous other swine (H1N2, H3N1, and H3N2), human (H2N2, H3N2, and H5N1), and avian (H1N1, H4N6, H5N1, H6N1, H6N6, H6N8, H7N3, H8N4, H9N2, and H13N2) subtypes. Amino acids from all eight segments were concatenated, aligned, and used for phylogenetic analyses. In addition, the genes of the polymerase complex (PB1, PB2, and PA) were analyzed individually. All of our results showed the Brevig-Mission/1918 strain in a position basal to the rest of the clade containing human H1N1s and were consistent with a reassortment hypothesis for the origin of the 1918 virus. Our genome phylogeny further indicates a sister relationship with the "classic" swine H1N1 lineage. The individual PB1, PB2, and PA phylogenies were consistent with reassortment/recombination hypotheses for these genes. These results demonstrate the importance of using a complete-genome approach for addressing the avian-origin hypothesis and predicting the emergence of new pandemic influenza strains.