Characterization of Farmington virus, a novel virus from birds that is distantly related to members of the family Rhabdoviridae

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Abstract

Background

Farmington virus (FARV) is a rhabdovirus that was isolated from a wild bird during an outbreak of epizootic eastern equine encephalitis on a pheasant farm in Connecticut, USA.

Findings

Analysis of the nearly complete genome sequence of the prototype CT AN 114 strain indicates that it encodes the five canonical rhabdovirus structural proteins (N, P, M, G and L) with alternative ORFs (> 180 nt) in the N and G genes. Phenotypic and genetic characterization of FARV has confirmed that it is a novel rhabdovirus and probably represents a new species within the family Rhabdoviridae.

Conclusions

In sum, our analysis indicates that FARV represents a new species within the family Rhabdoviridae.

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Most cited references 13

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SMART, a simple modular architecture research tool: identification of signaling domains.

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Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.

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Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

Gustavo Palacios, Phenix-Lan Quan, Omar Jabado … (2007)

To facilitate rapid, unbiased, differential diagnosis of infectious diseases, we designed GreeneChipPm, a panmicrobial microarray comprising 29,455 sixty-mer oligonucleotide probes for vertebrate viruses, bacteria, fungi, and parasites. Methods for nucleic acid preparation, random primed PCR amplification, and labeling were optimized to allow the sensitivity required for application with nucleic acid extracted from clinical materials and cultured isolates. Analysis of nasopharyngeal aspirates, blood, urine, and tissue from persons with various infectious diseases confirmed the presence of viruses and bacteria identified by other methods, and implicated Plasmodium falciparum in an unexplained fatal case of hemorrhagic feverlike disease during the Marburg hemorrhagic fever outbreak in Angola in 2004–2005.

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Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains.

Jeffrey Blumberg, L. Bougueleret, N Tordo … (1990)

The large (L) protein subunit of unsegmented negative-strand RNA virus polymerases is thought to be responsible for the majority of enzymic activities involved in viral transcription and replication. In order to gain insight into this multifunctional role we compared the deduced amino acid sequences of five L proteins of rhabdoviruses (vesicular stomatitis virus and rabies virus) or paramyxoviruses (Sendai virus, Newcastle disease virus and measles virus). Statistical analysis showed that they share an atypical amino acid usage, outlining the uniqueness of the negative-strand virus life style. Similarity studies between L proteins traced evolutionary relationships in partial disagreement with the present taxonomic arrangement of this group of viruses. The five L proteins exhibit a high degree of homology along most of their length, with strongly invariant amino acids embedded in conserved blocks separated by variable regions, suggesting a structure of concatenated functional domains. The most highly conserved central block contains the probable active site for RNA synthesis. We tentatively identified some other functional sites, distributed around this central core, that would naturally work together to assure the polymerase activity. This provides detailed guidelines for the future study of L proteins by site-directed mutagenesis.

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Author and article information

Contributors

Gustavo Palacios

Naomi L Forrester

Nazir Savji

Amelia P A Travassos da Rosa

Hilda Guzman

Kelly DeToy

Vsevolod L Popov

Peter J Walker

W Ian Lipkin

Nikos Vasilakis

Robert B Tesh

Journal

Journal ID (nlm-ta): Virol J

Journal ID (iso-abbrev): Virol. J

Title: Virology Journal

Publisher: BioMed Central

ISSN (Electronic): 1743-422X

Publication date Collection: 2013

Publication date (Electronic): 1 July 2013

Volume: 10

Page: 219

Affiliations

[1 ]Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD 10032, USA

[2 ]Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA

[3 ]Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA

[4 ]Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA

[5 ]Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA

[6 ]CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia

[7 ]Current address: School of Medicine, New York University, New York, NY 10032, USA

Article

Publisher ID: 1743-422X-10-219

DOI: 10.1186/1743-422X-10-219

PMC ID: 3722107

PubMed ID: 23816310

SO-VID: fbbf9c2a-a452-4251-837c-a068f4656fc8

License:

This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Characterization of Farmington virus, a novel virus from birds that is distantly related to members of the family Rhabdoviridae

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Abstract

Background

Findings

Conclusions

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Zika Virus

Most cited references 13

SMART, a simple modular architecture research tool: identification of signaling domains.

Panmicrobial Oligonucleotide Array for Diagnosis of Infectious Diseases

Sequence comparison of five polymerases (L proteins) of unsegmented negative-strand RNA viruses: theoretical assignment of functional domains.

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