Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource

Abstract

The Poxvirus Bioinformatics Resource Center (PBRC) has been established to provide informational and analytical resources to the scientific community to aid research directed at providing a better understanding of the Poxviridae family of viruses. The PBRC was specifically established as the result of the concern that variola virus, the causative agent of smallpox, as well as related viruses, might be utilized as biological weapons. In addition, the PBRC supports research on poxviruses that might be considered new and emerging infectious agents such as monkeypox virus. The PBRC consists of a relational database and web application that supports the data storage, annotation, analysis and information exchange goals of the project. The current release consists of over 35 complete genomic sequences of various genera, species and strains of viruses from the Poxviridae family. Sequence and annotation information for these viruses has been obtained from sequences publicly available from GenBank as well as sequences not yet deposited in GenBank that have been obtained from ongoing sequencing projects. In addition to sequence data, the PBRC provides comprehensive annotation and curation of virus genes; analytical tools to aid in the understanding of the available sequence data, including tools for the comparative analysis of different virus isolates; and visualization tools to help better display the results of various analyses. The PBRC represents the initial development of what will become a more comprehensive Viral Bioinformatics Resource Center for Biodefense that will be one of the National Institute of Allergy and Infectious Diseases' ‘Bioinformatics Resource Centers for Biodefense and Emerging or Re-Emerging Infectious Diseases’. The PBRC website is available at http://www.poxvirus.org.

Dominance and Diversity in the Primary Human CD4 T Cell Response to Replication-Competent Vaccinia Virus

“…The first is predicted to express a 96 aa long polypeptide that is 100% homologous to vaccinia Copenhagen in the antigenic region we identified (37,69,70). It is not known whether this truncated form is transcribed or translated.…”

“…Inserts in random colonies were sequenced (primers on request) with BigDye 3.0 (ABI). Vaccinia open reading frames (ORFs) are named from strain Copenhagen or Western Reserve (WR) (37). 96-well deep-dish plates (n ϭ 3) were seeded at 30 colonies/ well for the working library.…”

“…Proliferation and CTL assays showed clear-cut reactivity with the allogeneic cell line 09123 in the absence of vaccinia. a ORF names and aa from Copenhagen (GenBank M35027) except for ORFs differentially present in WR (GenBank 006998) (37). Sequences for three derivatives of Dryvax are also available (GenBank DQ377945, AY313847, and AY313848).…”

“…c Data from Lefkowitz et al (37) reviewed for primate orthopox including vaccinia Copenhagen, WR, MVA Acambis 3000, three clonal derivatives of Dryvax, monkeypox (MP) Zaire, and variola Bangladesh, accessed by Lefkowitz et al (37), and NYVAC (89).…”

“…For those ORFs not predicted to be present in Copenhagen, we followed literature precedent and used strain WR nomenclature (44,54). The three WR ORFs we report as CD4 Ags, WR148, WR149, and WR206, are each present in each of the three sequenced NYCBH clones with 95-100% sequence homology to the WR ORF (37).…”