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Viral discovery and sequence recovery using DNA microarrays.

Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL - PLoS Biol. (2003)

Bottom Line: Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery.During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient.This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, USA.

ABSTRACT
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

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Related in: MedlinePlus

Prototypical Coronavirus Genome StructureRed bars indicate physical location of virus microarray DNA elements mapped to a generic coronavirus genome. Portions of the coronavirus genome sequenced by physical recovery and PCR methods are highlighted with homologies to known coronaviruses. Abbreviations: aa, amino acid; nt, nucleotide
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pbio.0000002-g001: Prototypical Coronavirus Genome StructureRed bars indicate physical location of virus microarray DNA elements mapped to a generic coronavirus genome. Portions of the coronavirus genome sequenced by physical recovery and PCR methods are highlighted with homologies to known coronaviruses. Abbreviations: aa, amino acid; nt, nucleotide

Mentions: During the initial phase of research into the etiology of SARS, an unknown virus was cultured in Vero cells from a patient suffering from SARS (Ksiazek et al. 2003). Total nucleic acid purified from this viral culture, as well as a control culture, was obtained from the Centers for Disease Control and Prevention on March 22, 2003. These two samples, along with additional controls (HeLa cell RNA and water alone), were amplified and hybridized within 24 h to the virus DNA microarray. The strongest hybridizing array elements from the infected culture were derived from two families: astroviridae and coronaviridae. Table 1 lists the oligonucleotides from these families with the greatest hybridization intensity. By comparison, these oligonucleotides yielded essentially background levels of hybridization in the various control arrays performed in parallel. The initial suggestion from this hybridization pattern was that members of both of these viral families might be present. However, alignment of the oligonucleotides using ClustalX revealed that all four hybridizing oligonucleotides from the astroviridae and one oligonucleotide from avian infectious bronchitis virus (IBV) (GenBank NC_001451), an avian coronavirus, shared a core consensus motif spanning 33 nucleotides (data not shown); thus, these five oligonucleotides behaved essentially as multiple redundant probes for the same sequence. This motif is known to be present in the 3′ UTR of all astroviruses and the avian coronaviruses (Jonassen et al. 1998), but appears to be absent in the available sequenced mammalian coronaviruses (bovine coronavirus, murine hepatitis virus [MHV], human coronavirus 229E, porcine epidemic diarrhea virus, and transmissible gastroenteritis virus). The other three hybridizing oligonucleotides were derived from three conserved regions within the ORF1AB polyprotein common to all coronaviruses (Figure 1). Based on the aggregate hybridization pattern, the virus appeared to be a novel member of the coronavirus family.


Viral discovery and sequence recovery using DNA microarrays.

Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman DD, Mardis ER, Hickenbotham M, Magrini V, Eldred J, Latreille JP, Wilson RK, Ganem D, DeRisi JL - PLoS Biol. (2003)

Prototypical Coronavirus Genome StructureRed bars indicate physical location of virus microarray DNA elements mapped to a generic coronavirus genome. Portions of the coronavirus genome sequenced by physical recovery and PCR methods are highlighted with homologies to known coronaviruses. Abbreviations: aa, amino acid; nt, nucleotide
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC261870&req=5

pbio.0000002-g001: Prototypical Coronavirus Genome StructureRed bars indicate physical location of virus microarray DNA elements mapped to a generic coronavirus genome. Portions of the coronavirus genome sequenced by physical recovery and PCR methods are highlighted with homologies to known coronaviruses. Abbreviations: aa, amino acid; nt, nucleotide
Mentions: During the initial phase of research into the etiology of SARS, an unknown virus was cultured in Vero cells from a patient suffering from SARS (Ksiazek et al. 2003). Total nucleic acid purified from this viral culture, as well as a control culture, was obtained from the Centers for Disease Control and Prevention on March 22, 2003. These two samples, along with additional controls (HeLa cell RNA and water alone), were amplified and hybridized within 24 h to the virus DNA microarray. The strongest hybridizing array elements from the infected culture were derived from two families: astroviridae and coronaviridae. Table 1 lists the oligonucleotides from these families with the greatest hybridization intensity. By comparison, these oligonucleotides yielded essentially background levels of hybridization in the various control arrays performed in parallel. The initial suggestion from this hybridization pattern was that members of both of these viral families might be present. However, alignment of the oligonucleotides using ClustalX revealed that all four hybridizing oligonucleotides from the astroviridae and one oligonucleotide from avian infectious bronchitis virus (IBV) (GenBank NC_001451), an avian coronavirus, shared a core consensus motif spanning 33 nucleotides (data not shown); thus, these five oligonucleotides behaved essentially as multiple redundant probes for the same sequence. This motif is known to be present in the 3′ UTR of all astroviruses and the avian coronaviruses (Jonassen et al. 1998), but appears to be absent in the available sequenced mammalian coronaviruses (bovine coronavirus, murine hepatitis virus [MHV], human coronavirus 229E, porcine epidemic diarrhea virus, and transmissible gastroenteritis virus). The other three hybridizing oligonucleotides were derived from three conserved regions within the ORF1AB polyprotein common to all coronaviruses (Figure 1). Based on the aggregate hybridization pattern, the virus appeared to be a novel member of the coronavirus family.

Bottom Line: Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery.During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient.This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Biophysics, University of California San Francisco, USA.

ABSTRACT
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.

Show MeSH
Related in: MedlinePlus