title: A simple and rapid approach for screening of SARS-coronavirus genotypes: an evaluation study.
abstract: BACKGROUND
  The Severe Acute Respiratory Syndrome (SARS) was a newly emerged infectious disease which caused a global epidemic in 2002-2003. Sequence analysis of SARS-coronavirus isolates revealed that specific genotypes predominated at different periods of the epidemic. This information can be used as a footprint for tracing the epidemiology of infections and monitor viral evolution. However, direct sequencing analysis of a large number of clinical samples is cumbersome and time consuming. We present here a simple and rapid assay for the screening of SARS-coronavirus genotypes based on the use of fluorogenic oligonucleotide probes for allelic discrimination.
  
  
  METHODS
  Thirty SARS patients were recruited. Allelic discrimination assays were developed based on the use of fluorogenic oligonucleotide probes (TaqMan). Genotyping of the SARS-coronavirus isolates obtained from these patients were carried out by the allelic discrimination assays and confirmed by direct sequencing.
  
  
  RESULTS
  Genotyping based on the allelic discrimination assays were fully concordant with direct sequencing. All of the 30 SARS-coronavirus genotypes studied were characteristic of genotypes previously documented to be associated with the latter part of the epidemic. Seven of the isolates contained a previously reported major deletion but in patients not epidemiologically related to the previously studied cohort.
  
  
  CONCLUSIONS
  We have developed a simple and accurate method for the characterization and screening of SARS-coronavirus genotypes. It is a promising tool for the study of epidemiological relationships between documented cases during an outbreak.
authors.affiliation: Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong. gracehung@cuhk.edu.hk
authors.forename: Grace T Y
authors.initials: GT
authors.lastname: Chung
authors.forename: Rossa W K
authors.initials: RW
authors.lastname: Chiu
authors.forename: Jo L K
authors.initials: JL
authors.lastname: Cheung
authors.forename: Yongjie
authors.initials: Y
authors.lastname: Jin
authors.forename: Stephen S C
authors.initials: SS
authors.lastname: Chim
authors.forename: Paul K S
authors.initials: PK
authors.lastname: Chan
authors.forename: Y M Dennis
authors.initials: YM
authors.lastname: Lo
mesh_terms: D000483:Alleles; D019143:Evolution, Molecular; D005814:Genes, Viral / Q000235:genetics; D005838:Genotype; D006801:Humans; D015345:Oligonucleotide Probes / Q000032:analysis / Q000235:genetics; D010802:Phylogeny; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics*; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology / Q000821:virology*; D013997:Time Factors
chemical_list: D015345:Oligonucleotide Probes