Tracing SARS-Coronavirus Variant with Large Genomic Deletion

摘要

To the Editor: Severe acute respi-ratory syndrome (SARS) has been aglobal public health issue (1). Wecompleted a study on the evolutionarypath of the SARS-associated coron-avirus (SARS-CoV) during the2002–2003 epidemic (2). Most humanSARS-CoV strains, as exemplified bythe Tor2 sequence (GenBank acces-sion no. AY274119) (3), are character-ized by the deletion of a 29-nucleotide(nt) segment upstream of the nucleo-capsid (N) gene domain when com-pared with the viral strains isolatedfrom the earliest human SARSpatients (2) or from nonhuman mam-malian hosts (4). Towards the end ofthe epidemic, a variant of the SARS-CoV with a deletion of 386 nt flank-ing the 29-nt site was first demonstrat-ed by complete genomic sequencingin 2 patients in Hong Kong (GenBankaccession nos. AY394999, AY395000,AY395001, AY395002) (2). The 386-nt deleted segment corresponds to thegenomic region spanning residues27719 to 28104 of the Tor2 sequence(3). The deletion results in the disrup-tion of a putative open reading frame,orf 9, while eliminating orfs 10 and11. This deletion variant was firstisolated from 2 SARS patients withdisease onset in mid-May 2003.Patient A was a 41-year-old femalephlebotomist working in NorthDistrict Hospital, New TerritoriesEast Cluster, Hong Kong. Patient Bwas a 98-year-old woman admitted toward X of North District Hospital (2). With this finding late in the epi-demic, we studied the prevalence ofthis SARS-CoV variant to determineits origin. Twenty-one SARS patientswith disease onset dates from mid-April were identified. All cases hadbeen confirmed by positive reversetranscription–polymerase chain reac-tion (RT-PCR) detection of SARS-CoV RNA in clinical specimens orseroconversion. These patients hadbeen admitted with SARS to 4 differ-ent hospitals in Hong Kong, includingNorth District Hospital and hospitalsA and B, which were located in thesame geographic cluster as NorthDistrict Hospital, as well as hospitalC, which was geographically distantfrom the other 3 hospitals. Clinicalspecimens were retrieved, and RT-PCR was performed to specificallyamplify a genomic segment of SARS-CoV encompassing the deletion site.Specimens with shortened PCR frag-ments were sequenced to determinethe location and precise extent of thedeletion.