Automated, phylogeny-based genotype delimitation of the Hepatitis Viruses HBV and HCV

Background The classification of hepatitis viruses still predominantly relies on ad hoc criteria, i.e., phenotypic traits and arbitrary genetic distance thresholds. Given the subjectivity of such practices coupled with the constant sequencing of samples and discovery of new strains, this manual approach to virus classification becomes cumbersome and impossible to generalize. Methods Using two well-studied hepatitis virus datasets, HBV and HCV, we assess if computational methods for molecular species delimitation that are typically applied to barcoding biodiversity studies can also be successfully deployed for hepatitis virus classification. For comparison, we also used ABGD, a tool that in contrast to other distance methods attempts to automatically identify the barcoding gap using pairwise genetic distances for a set of aligned input sequences. Results—Discussion We found that the mPTP species delimitation tool identified even without adapting its default parameters taxonomic clusters that either correspond to the currently acknowledged genotypes or to known subdivision of genotypes (subtypes or subgenotypes). In the cases where the delimited cluster corresponded to subtype or subgenotype, there were previous concerns that their status may be underestimated. The clusters obtained from the ABGD analysis differed depending on the parameters used. However, under certain values the results were very similar to the taxonomy and mPTP which indicates the usefulness of distance based methods in virus taxonomy under appropriate parameter settings. The overlap of predicted clusters with taxonomically acknowledged genotypes implies that virus classification can be successfully automated.

The Identification of Levels of Concept Understanding Using Three-Tier Multiple Choice Diagnostic Test

This research aims at identifiying the levels of concept understanding on virus material at class X, SMA Pertiwi 1 Padang. This is a descriptive research involved 138 students from class X, SMA Pertiwi 1 Padang. This research used Three-Tier Multiple Choice diagnostic test instrument which categorized into three question levels. The results showed that students experienced the highest level of concept understanding on prevented virus infections with 53,87%, then followed with the highest level of full misconception on the role of the beneficial virus with 36,23%, the highest level of misconception false positive on the different virus and bactery with 12,32%, the highest level of misconception false negative on virus living with 14,49%, the highest level of guessing on virus’ classification with 7,61%, and the highest level of ununderstandable of virus replication’s cycles with 52,18%. Most of students experienced low criteria of the concept material of virus with 34,38%.

Animal virus ecology and evolution are shaped by the virus host-body infiltration and colonization pattern.

The current classification of animal viruses primarily relates to the virus molecular world, the genomic architecture and the corresponding host-cell infection cycle. This virus centered perspective does not make allowance for the precept that virus fitness hinges on the virus transmission success. Virus transmission reflects the infection-shedding-transmission dynamics and, with it, the organ system involvement and other, macroscopic dimensions of the host environment. This study examines the transmission ecology of the world main livestock viruses, 36 in total, belonging to eleven different families, and a mix of RNA, DNA and retroviruses. Viruses are virtually ranked in an outer- to inner-body fashion, based on the shifting organ system involvement and associated infection-shedding-transmission dynamics. As a next step, this ranking is disentangled with the aim to contrast two main host ecologies, poultry plus pig production and ruminant plus equine husbandry, as well as to create a distinction among the RNA, DNA and retroviruses, also ranked in an outer- to inner-body fashion. Spearman correlation reveals the matches among these various virus traits, as pertaining to the two host-ecologies, four infection-shedding-transmission related variables, and the three virus genomes. The collective results reveal the outer- to inner-body shifts in the interplay of host environment, virus-host interactions, and nature of the virus. Two opposing virus evolution pathways emerge, respectively for generalist type, outer-body and for specialist type, inner-body viruses. The ecological virus classification here presented is broadly consistent with the current virus classification system and offers the advantage of bringing substance and cohesion to the interrelationships among viruses and virus families.