Inferring viral quasispecies spectra from 454 pyrosequencing reads

<p>Abstract</p> <p>Background</p> <p>RNA viruses infecting a host usually exist as a set of closely related sequences, referred to as quasispecies. The genomic diversity of viral quasispecies is a subject of great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software was originally designed for single genome assembly and cannot be used to simultaneously assemble and estimate the abundance of multiple closely related quasispecies sequences.</p> <p>Results</p> <p>In this paper, we introduce a new <b>Vi</b>ral <b>Sp</b>ectrum <b>A</b>ssembler (ViSpA) method for quasispecies spectrum reconstruction and compare it with the state-of-the-art ShoRAH tool on both simulated and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. Experimental results show that ViSpA outperforms ShoRAH on simulated error-free reads, correctly assembling 10 out of 10 quasispecies and 29 sequences out of 40 quasispecies. While ShoRAH has a significant advantage over ViSpA on reads simulated with sequencing errors due to its advanced error correction algorithm, ViSpA is better at assembling the simulated reads after they have been corrected by ShoRAH. ViSpA also outperforms ShoRAH on real 454 reads. Indeed, 7 most frequent sequences reconstructed by ViSpA from a real HCV dataset are viable (do not contain internal stop codons), and the most frequent sequence was within 1% of the actual open reading frame obtained by cloning and Sanger sequencing. In contrast, only one of the sequences reconstructed by ShoRAH is viable. On a real HIV dataset, ShoRAH correctly inferred only 2 quasispecies sequences with at most 4 mismatches whereas ViSpA correctly reconstructed 5 quasispecies with at most 2 mismatches, and 2 out of 5 sequences were inferred without any mismatches. ViSpA source code is available at <url>http://alla.cs.gsu.edu/~software/VISPA/vispa.html</url>.</p> <p>Conclusions</p> <p>ViSpA enables accurate viral quasispecies spectrum reconstruction from 454 pyrosequencing reads. We are currently exploring extensions applicable to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations.</p

Invasive species control: incorporating demographic data and seed dispersal into a management model for Rhododendron ponticum

Rhododendron ponticum is a serious invasive alien plant in the British Isles and is of significant conservation and economic concern. Here, we integrate information on both the life-history and spatial dynamics of this species within an individual-based, spatially-explicit model and investigate the effectiveness of different control strategies. Importantly, we simulate seed movement and dispersal using a mechanistic seed dispersal model. We investigate the effectiveness of initiating control at the edge versus the core of the infestation, with and without returning each year to remove seedlings. We compare these results to an age-dependent strategy whereby the oldest plants are removed each year. Age-dependent control, in which the oldest plants were removed first, was the most effective strategy investigated, both in terms of the probability of successful eradication and the number of years taken to control. We demonstrate that this is because the older (and taller) plants towards the core produce more seeds that, on average, travel further. Indeed, our results suggest that the expansion of the invading front is actually driven as much by seeds that disperse long distances from these larger plants as by the seed rain from recently matured plants located much closer to the front. Finally, we investigate the potential use of ‘quarantine lines’ - corridors of unsuitable habitat that are sufficiently wide to contain an infestation, preventing spread to vulnerable areas. This study has provided generic insights into best practice for management based on the current understanding of the biology and ecology of this pernicious, invasive plant

Does public awareness increase support for invasive species management?:Promising evidence across taxa and landscape types

Management of invasive species often raises substantial conflicts of interest. Since such conflicts can hamper proposed management actions, managers, decision makers and researchers increasingly recognize the need to consider the social dimensions of invasive species management. In this exploratory study, we aimed (1) to explore whether species’ taxonomic position (i.e. animals vs. plants) and type of invaded landscape (i.e. urban vs. nonurban) might influence public perception about the management of invasive species, and (2) to assess the potential of public awareness to increase public support for invasive species management. We reviewed the scientific literature on the conflicts of interest around the management of alien species and administered two-phased questionnaires (before and after providing information on the target species and its management) to members of the public in South Africa and the UK (n = 240). Our review suggests that lack of public support for the management of invasive animals in both urban and non-urban areas derives mainly from moralistic value disagreements, while the management of invasive plants in non-urban areas mostly causes conflicts based on utilitarian value disagreements. Despite these general trends, conflicts are context dependent and can originate from a wide variety of different views. Notably, informing the public about the invasive status and negative impacts of the species targeted for management appeared to increase public support for the management actions. Therefore, our results align with the view that increased public awareness might increase the public support for the management of invasive species, independent of taxonomic position and type of landscape

Can Pediatric Orthopaedic Surgery be Done Safely in a Freestanding Ambulatory Surgery Center? Review of 3780 Cases

Background:The purpose of this study was to determine the intraoperative and 30-day postoperative complication rates in a large consecutive cohort of pediatric patients who had orthopaedic surgery at a freestanding ambulatory surgery center (ASC). The authors also wanted to identify the rates of same-day, urgent hospital transfers, and 30-day hospital admissions. The authors hypothesized that pediatric orthopaedic procedures at a freestanding ASC can be done safely with a low rate of complications.Methods:A retrospective review identified patients aged 17 years or younger who had surgery at a freestanding ASC over a 9-year period. Adverse outcomes were divided into intraoperative complications, postoperative complications, need for the secondary procedure, unexpected hospital admission on the same day of the procedure, and unexpected hospital admission within 30 days of the index procedure. Complications were graded as grade 1, the complication could be treated without additional surgery or hospitalization; grade 2, the complication resulted in an unplanned return to the operating room (OR) or hospital admission; or grade 3, the complication resulted in an unplanned return to the OR or hospitalization with a change in the overall treatment plan.Results:Adequate follow-up was available for 3780 (86.1%) surgical procedures. Overall, there were 9 (0.24%) intraoperative complications, 2 (0.08%) urgent hospital transfers, 114 (3%) complications, and 16 (0.42%) readmissions. Seven of the 9 intraoperative complications resolved before leaving the OR, and 2 required return to the OR.Neither complications nor hospitalizations correlated with age, race, gender, or length or type of surgery. There was no correlation between the presence of medical comorbidities, body mass index, or American Society of Anesthesiologists score and complication or hospitalization.Conclusions:Pediatric orthopaedic surgical procedures can be performed safely in an ASC because of multiple factors that include dedicated surgical teams, single-purpose ORs, and strict preoperative screening criteria. The rates of an emergency hospital transfer, surgical complications, and 30-day readmission, even by stringent criteria, are lower than those reported for outpatient procedures performed in the hospital setting.Level of Evidence:Level IV - case series