Practical application of bioinformatics by the multidisciplinary VIZIER consortium

Abstract

This review focuses on bioinformatics technologies employed by the EU-sponsored multidisciplinary VIZIER consortium (Comparative Structural Genomics of Viral Enzymes Involved in Replication, FP6 PROJECT: 2004-511960, active from 1 November 2004 to 30 April 2009), to achieve its goals. From the management of the information flow of the project, to bioinformatics-mediated selection of RNA viruses and prediction of protein targets, to the analysis of 3D protein structures and antiviral compounds, these technologies provided a communication framework and integrated solutions for steady and timely advancement of the project. RNA viruses form a large class of major pathogens that affect humans and domestic animals. Such RNA viruses as HIV, Influenza virus and Hepatitis C virus are of prime medical concern today, but the identities of viruses that will threaten human population tomorrow are far from certain. To contain outbreaks of common or newly emerging infections, prototype drugs against viruses representing the Virus Universe must be developed. This concept was championed by the VIZIER project which brought together experts in diverse fields to produce a concerted and sustained effort for identifying and validating targets for antivirus therapy in dozens of RNA virus lineages.

Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans

“…Multiple amino acid alignments, including sequences of HCoV-EMC/2012 and one representative of each of the 20 recognized species of the subfamily Coronavirinae , were produced for the following proteins, using the Viralis platform (48) followed by manual correction: ADRP, the N-terminal part of PLP2, TM1, Y domain, nsp4 to nsp16, and the C-terminal part of the spike (S) protein (S2), envelope (E) protein, membrane (M) protein, and nucleocapsid (N) protein. From each protein alignment, the most informative blocks (49) were extracted using the BAGG program (50), and only these strongly conserved alignment regions were used for further analyses.…”

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

“…These relationships stand in contrast to the shallow branching of the most populous lineage of this species, which includes all the human SARS-CoV isolates collected during the 2002-2003 outbreak and the closely related bat viruses of Asian origin identified in the search for the potential zoonotic source of that epidemic 57 . This clade structure is susceptible to homologous recombination, which is common in this species 44,58,59 ; to formalize clade definition, it must be revisited after the sampling of viruses representing the deep branches has improved sufficiently. The current sampling defines a very small median PD for human SARS-CoVs, which is approximately 15 times smaller than the median PD determined for SARS-CoV-2 (0.…”

Design and validation of consensus-degenerate hybrid oligonucleotide primers for broad and sensitive detection of corona- and toroviruses

“…1). The alignments were generated using the Muscle program (Edgar, 2004) upon support of the Viralis software platform (Gorbalenya et al, 2010). Maximum likelihood trees were compiled under the WAG amino acid substitution matrix and rate heterogeneity among sites (4 categories); for Neighbor joining trees the JC69 model was applied.…”