GRAViTy-V2: a grounded viral taxonomy application.

Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence motifs in conserved genes. Classification at lower taxonomic ranks, such as genus or species, is usually based on nucleotide sequence identities between genomic sequences.

Quantifying the impact of a novel virus on the economic value of pathogen reduction technology for platelets.

Background: Pathogen reduction technology (PRT) is an intervention designed to proactively reduce the amount of known and unknown pathogens in donated blood. As current screening for known pathogens is highly effective, some previous evaluations have found that the value of PRT largely hinges on a previously unknown pathogen, most likely a novel virus, emerging and entering the blood supply. In such situations, the risk of emergence can and should be modeled and presented transparently in the cost-effectiveness results for deliberation by decision-makers.

A critique of the use of species and below-species taxonomic terms for viruses-time for change?

The International Committee for the Taxonomy of Viruses (ICTV) regulates assignment and names of virus species and higher taxa through its taxonomy proposal and ratification process. Despite using similar taxonomic ranks to those used elsewhere in biology, the ICTV has maintained the principle that species and other taxa are strictly categories with a formal nomenclature, whereas the viruses as objects are referenced through a parallel inventory of community-assigned virus names. This is strikingly different from common and scientific name synonyms for species used elsewhere in biology.

Enterovirus A71 and coxsackievirus A6 circulation in England, UK, 2006-2017: A mathematical modelling study using cross-sectional seroprevalence data.

Enterovirus A71 (EV-A71) and coxsackievirus A6 (CVA6) primarily cause hand, foot and mouth disease and have emerged to cause potential fatal neurological and systemic manifestations. However, limited surveillance data collected through passive surveillance systems hampers characterization of their epidemiological dynamics. We fit a series of catalytic models to age-stratified seroprevalence data for EV-A71 and CVA6 collected in England at three time points (2006, 2011 and 2017) to estimate the force of infection (FOI) over time and assess possible changes in transmission.