Rapid identification of emerging pathogens: Coronavirus

Emerging Infectious Diseases

Volumn 11, Issue 3, 2005, Pages 373-379

  Sampath, Rangarajan ^a,c   Hofstadler, Steven A ^a   Blyn, Lawrence B ^a   Eshoo, Mark W ^a   Hall, Thomas A ^a   Massire, Christian ^a   Levene, Harold M ^a   Hannis, James C ^a   Harrell, Patina M ^a   Neuman, Benjamin ^b   Buchmeier, Michael J ^b   Jiang, Yun ^a   Ranken, Raymond ^a   Drader, Jared J ^a   Samant, Vivek ^a   Griffey, Richard H ^a   McNeil, John A ^a   Crooke, Stanley T ^a   Ecker, David J ^a  

^a Ibis Therapeutics   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c ISIS PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID;

ACCURACY; ARTICLE; AUTOMATION; BACTERIUM IDENTIFICATION; CORONAVIRUS; ELECTROSPRAY MASS SPECTROMETRY; FUNGUS IDENTIFICATION; HEALTH SURVEY; INFECTION; MEASUREMENT; NONHUMAN; POLYMERASE CHAIN REACTION; PROTOZOON; SARS CORONAVIRUS; SENSITIVITY ANALYSIS; SERUM; SEVERE ACUTE RESPIRATORY SYNDROME; VIRUS IDENTIFICATION; VIRUS ISOLATION; VIRUS STRAIN;

EID: 20044379044     PISSN: 10806040     EISSN: None     Source Type: Journal    
DOI: 10.3201/eid1103.040629     Document Type: Article

References (29)

1. Poutanen, SM, Low DE, Henry B, Finkelstein S, Rose D, Green K, et al. Identification of severe acute respiratory syndrome in Canada. N Engl J Med. 2003;348:1995-2005.
2. Peiris JS, Lai S, Poon L, Guan Y, Yam L, Lim W, et al. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet. 2003;361:1319-25.
3. Falsey AR, Walsh EE. Novel coronavirus and severe acute respiratory syndrome. Lancet. 2003;361:1312-3.
4. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, et al. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003;348:1953-66.
5. Schmidt TM, DeLong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991;173:4371-8.
6. Kroes I, Lepp PW, Relman DA. Bacterial diversity within the human subgingival crevice. Proc Natl Acad Sci U S A. 1999;96:14547-52.
7. Stephensen CB, Casebolt DB, Gangopadhyay NN. Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay. Virus Res. 1999;60:181-9.
8. Oberste MS, Maher K, Pallansch MA. Molecular phylogeny and proposed classification of the simian picornaviruses. J Virol. 2002;76:1244-51.
9. Mack DH, Sninsky JJ. A sensitive method for the identification of uncharacterized viruses related to known virus groups: hepadnavirus model system. Proc Natl Acad Sci U S A. 1988;85:6977-81.
10. Echavarria M, Forman M, Ticehurst J, Dumler A, Charache P. PCR method for detection of adenovirus in urine of healthy and human immunodeficiency virus-infected individuals. J Clin Microbiol. 1998;36:3323-6.
11. Fout GS, Martinson BC, Moyer MW, Dahling DR. A multiplex reverse transcription-PCR method for detection of human enteric viruses in groundwater. Appl Environ Microbiol. 2003;69:3158-64.
12. Brito DA, Ramirez M, de Lencastre H. Serotyping Streptococcus pneumoniae by multiplex PCR. J Clin Microbiol. 2003;41:2378-84.
13. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, et al. High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol. 2002;68:2535-41.
14. Wang D, Coscoy L, Zylberberg M, Avila PC, Boushey HA, Ganem D, et al. Microarray-based detection and genotyping of viral pathogens. Proc Natl Acad Sci U S A. 2002;99:15687-92.
15. Wang D, Urisman A, Liu YT, Springer M, Ksiazek TG, Erdman D, et al. Viral discovery and sequence recovery using DNA microarrays. PLoS Biology. 2003;1:257-60.
16. Sampath R, Ecker DJ. Novel biosensor for infectious disease diagnostics. In: Knobler SE, Mahmoud A, Lemon S, Mack A, Sivitz L, Oberholtzer K, editors. Learning from SARS: preparing for the next disease outbreak. Washington: The National Academies Press; 2004. p. 181-5.
17. Hofstadler SA, Sampath R, Blyn LB, Eshoo MW, Hall TA, Jiang Y, et al. TIGER: the universal biosensor. Int J Mass Spectrom. 2004. [cited 22 Dec 2004]. Available from http://www.sciencedirect.com/science/article/B6VND-4F31R2G-1/2/ 96bc83d6dec9dfdd8429 ca692be52a08
18. Wagner RW, Matteucci MD, Lewis JG, Gutierrez AJ, Moulds C, Froehler BC. Antisense gene inhibition by oligonucleotides containing C-5 propyne pyrimidines. Science. 1993;260:1510-3.
19. Barnes TW, Turner DH. Long-range cooperativity due to C5-propynylation of oligopyrimidines enhances specific recognition by uridine of ribo-adenosine over ribo-guanosine. J Am Chem Soc. 2001;123:9186-7.
20. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LLM, et al. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol. 2003;331:991-1004.
21. Jiang Y, Hofstadler SA. A highly efficient and automated method of purifying and desalting PCR products for analysis by electrospray ionization mass spectrometry. Anal Biochem. 2003;316:50-7.
22. Greig M, Griffey RH. Utility of organic bases for improved electrospray mass spectrometry of oligonucleotides. Rapid Commun Mass Spectrom. 1995;9:97-102.
23. Anderson GA, Bruce JE. ICR2LS. Richland (WA): Pacific Northwest National Laboratory; 1995.
24. Senko MW, Beu SC, McLafferty FW. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J Am Soc Mass Spectrom. 1995;6:229-33.
25. Muddiman DC, Anderson GA, Hofstadler SA, Smith RD. Length and base composition of PCR-amplified nucleic acids using mass measurements from electrospray ionization mass spectrometry. Anal Chem. 1997;69:1543-9.
26. Towner JS, Rollin PE, Bausch DG, Sanchez A, Crary SM, Vincent M, et al. Rapid diagnosis of Ebola hemorrhagic fever by reverse transcription-PCR in an outbreak setting and assessment of patient viral load as a predictor of outcome. J Virol. 2004;78:4330-41.
27. Drosten C, Gunther S, Preiser W, Van Der Werf S, Brodt HR, Becker S, et al Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N Engl J Med. 2003;348:1967-76.
28. Nitsche A, Schweiger B, Ellerbrok H, Niedrig M, Pauli G. SARS coronavirus detection. Emerg Infect Dis. 2004;10:1300-4.
29. Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol. 2002;54:156-65.