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Applied and Environmental Microbiology, January 2006, p. 207-211, Vol. 72, No. 1
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.1.207-211.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Evaluation of Affymetrix Severe Acute Respiratory Syndrome Resequencing GeneChips in Characterization of the Genomes of Two Strains of Coronavirus Infecting Humans

Irshad M. Sulaiman,1* Xin Liu,2 Michael Frace,1 Nikhat Sulaiman,1 Melissa Olsen-Rasmussen,1 Elizabeth Neuhaus,1 Paul A. Rota,2 and Robert M. Wohlhueter1

Biotechnology Core Facility Branch, Scientific Resources Program,1 Respiratory and Enteric Viruses Branch, Division of Viral and Rickettsial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 303332

Received 24 June 2005/ Accepted 11 October 2005

Severe acute respiratory syndrome (SARS) was discovered during a recent global outbreak of atypical pneumonia. A number of immunologic and molecular studies of the clinical samples led to the conclusion that a novel coronavirus (SARS-CoV) was associated with the outbreak. Later, a SARS resequencing GeneChip was developed by Affymetrix to characterize the complete genome of SARS-CoV on a single GeneChip. The present study was carried out to evaluate the performance of SARS resequencing GeneChips. Two human SARS-CoV strains (CDC#200301157 and Urbani) were resequenced by the SARS GeneChips. Five overlapping PCR amplicons were generated for each strain and hybridized with these GeneChips. The successfully hybridized GeneChips generated nucleotide sequences of nearly complete genomes for the two SARS-CoV strains with an average call rate of 94.6%. Multiple alignments of nucleotide sequences obtained from SARS GeneChips and conventional sequencing revealed full concordance. Furthermore, the GeneChip-based analysis revealed no additional polymorphic sites. The results of this study suggest that GeneChip-based genome characterization is fast and reproducible. Thus, SARS resequencing GeneChips may be employed as an alternate tool to obtain genome sequences of SARS-CoV strains pathogenic for humans in order to further understand the transmission dynamics of these viruses.

* Corresponding author. Mailing address: Biotechnology Core Facility Branch, Scientific Resources Program, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Mailstop G-36, 1600 Clifton Road, Atlanta, GA 30333. Phone: (404) 639-1644. Fax: (404) 639-1331. E-mail: isulaiman{at}cdc.gov

Applied and Environmental Microbiology, January 2006, p. 207-211, Vol. 72, No. 1
0099-2240/06/$08.00+0     doi:10.1128/AEM.72.1.207-211.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Sulaiman, I. M., Sammons, S. A., Wohlhueter, R. M. (2008). Smallpox Virus Resequencing GeneChips Can Also Rapidly Ascertain Species Status for Some Zoonotic Non-Variola Orthopoxviruses. J. Clin. Microbiol. 46: 1507-1509 [Abstract] [Full Text]  
  • Pandya, G. A., Holmes, M. H., Sunkara, S., Sparks, A., Bai, Y., Verratti, K., Saeed, K., Venepally, P., Jarrahi, B., Fleischmann, R. D., Peterson, S. N. (2007). A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip(R) whole-genome resequencing platform. Nucleic Acids Res 35: e148-e148 [Abstract] [Full Text]  
  • Sulaiman, I. M., Tang, K., Osborne, J., Sammons, S., Wohlhueter, R. M. (2007). GeneChip Resequencing of the Smallpox Virus Genome Can Identify Novel Strains: a Biodefense Application. J. Clin. Microbiol. 45: 358-363 [Abstract] [Full Text]  
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