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Characterization of the within-host genetic diversity of viral pathogens is required for selection of effective treatment of some important viral infections, e.g. HIV, HBV and HCV. Despite the technical ability of detection, there are conflicting data regarding the clinical significance of low-frequency variants, partially because of the difficulty of their distinguishing from experimental artifacts. The issue of cross-contamination is relevant for all highly sensitive techniques, including deep sequencing: even trace contamination leads to a significant increase of false positives in identified SNVs. Determination of infections by multiple genotypes of some viruses, the incidence of which can be considerable, especially in risk groups, is also clinically significant in some cases. We developed a new viral reference-guided assembler, VirGenA, that can separate mixtures of strains of different intraspecies genetic groups (genotypes, subtypes, clades, etc.) and assemble a separate consensus sequence for each group in a mixture. It produced long assemblies for mixture components of extremely low frequencies (

We investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. For this investigation, we developed a composite method based on analyses of PCR amplicons containing the ribosomal intergenic spacer (RIS) and its flanking partial 16S rRNA gene. Community percent similarity was determined on the basis of RIS length polymorphism. A community succession was evident in the lagoon, indicated by a progressive community transition through seven sample locations. The most abrupt changes in community structure were associated with a temperature change from 39 to 35°C and with increases in dissolved oxygen. The temporal differences in community structure, based on summer and winter samplings, were greater than the spatial differences during either season. Clone libraries of rDNA-RIS amplicons were constructed from each of three summer samples. Among 90 clones analyzed (30 clones from each sample), 56 phylotypes were distinguished by restriction fragment length polymorphism. Indices of phylotype richness, evenness, and diversity all increased in clone libraries from the beginning to the end of the lagoon. A representative clone of each phylotype was phylogenetically analyzed on the basis of its partial 16S rRNA gene sequence (ca. 450 bp). Phylogenetic analysis confirmed the increase in diversity and further indicated increasing richness of bacterial divisions. Pioneers in the community spatial succession appeared to include thermotolerant, microaerophilic methanol-oxidizing bacteria related to the genus Methylobacillus , as well as thermotolerant, microaerophilic nitrogen-fixing bacteria related to the genus Azospirillum .

Background: Northern Ireland has a high and rising prevalence rate of multiple sclerosis (MS). The most recent survey in 1996 found a rate of 168.7/100 000. Recorded prevalence rates for the south of Ireland, including County Wexford, have been markedly lower and seemed to suggest the existence of a prevalence gradient within the island. Objectives: To compare the prevalence of multiple sclerosis in Co. Wexford in the south east of Ireland and Co. Donegal in the north west, and to establish whether a variation in prevalence of MS exists within Ireland. Methods: Patients were referred from multiple sources. Review of clinical case records and/or patient examination confirmed the diagnosis. Results: In Co. Wexford, 126 patients were found to have clinically definite or probable multiple sclerosis with a prevalence rate of 120.7/100 000 (95% confidence intervals (CI) 100.6 to 143.8), which is similar to other areas of similar latitude within the British Isles. In Co. Donegal, 240 people had clinically definite or probable MS with a prevalence rate of 184.6/100 000 (95% CI 162.0 to 209.5). The difference in prevalence rates is statistically significant (Z = 3.94, p = Conclusion: There is a latitudinal variation in the prevalence rate of MS between the north and the south of Ireland. The increased prevalence of MS seen in Co. Wexford is likely to represent better case ascertainment and improved diagnostic accuracy rather than an actual increase in prevalence. The north/south variation in prevalence may represent a variation in the genetic predisposition to MS between the background populations of the two counties.