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Volume 11, Number 1—January 2005


Tracing SARS-Coronavirus Variant with Large Genomic Deletion

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To the Editor: Severe acute respiratory syndrome (SARS) has been a global public health issue (1). We completed a study on the evolutionary path of the SARS-associated coronavirus (SARS-CoV) during the 2002–2003 epidemic (2). Most human SARS-CoV strains, as exemplified by the Tor2 sequence (GenBank accession no. AY274119) (3), are characterized by the deletion of a 29-nucleotide (nt) segment upstream of the nucleocapsid (N) gene domain when compared with the viral strains isolated from the earliest human SARS patients (2) or from nonhuman mammalian hosts (4). Towards the end of the epidemic, a variant of the SARS-CoV with a deletion of 386 nt flanking the 29-nt site was first demonstrated by complete genomic sequencing in 2 patients in Hong Kong (GenBank accession nos. AY394999, AY395000, AY395001, AY395002) (2). The 386-nt deleted segment corresponds to the genomic region spanning residues 27719 to 28104 of the Tor2 sequence (3). The deletion results in the disruption of a putative open reading frames, orf 9, while eliminating orfs 10 and 11. This deletion variant was first isolated from 2 SARS patients with disease onset in mid-May 2003. Patient A was a 41-year-old female phlebotomist working in North District Hospital, New Territories East Cluster, Hong Kong. Patient B was a 98-year-old female admitted to ward X of North District Hospital (2).

With this finding late in the epidemic, we studied the prevalence of this SARS-CoV variant to determine its origin. Twenty-one SARS patients with disease onset dates from mid-April were identified. All cases had been confirmed by positive reverse transcription–polymerase chain reaction (RT-PCR) detection of SARS-CoV RNA in clinical specimens or seroconversion. These patients had been admitted with SARS to 4 different hospitals in Hong Kong, including North District Hospital and hospitals A and B, which were located in the same geographic cluster as North District Hospital, as well as hospital C, which was geographically distant from the other 3 hospitals. Clinical specimens were retrieved, and RT-PCR was performed to specifically amplify a genomic segment of SARS-CoV encompassing the deletion site. Specimens with shortened PCR fragments were sequenced to determine the location and precise extent of the deletion.


Thumbnail of Schematic illustration of the epidemiologic relationships between patients with the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) variant with the 386-nt deletion. Patients are grouped according to the most probable site where SARS infection was acquired. Blocked arrows indicate the potential epidemiologic relationships between subgroups of patients. Patients who are suspected of being an epidemiologic link between particular subgroups are indicated by their as

Figure. Schematic illustration of the epidemiologic relationships between patients with the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) variant with the 386-nt deletion. Patients are grouped according to the most probable site where...

RT-PCR products were not observed in 2 specimens. Gel electrophoresis of the RT-PCR products for each of the remaining 19 specimens showed a single genomic fragment; 13 of these fragments were shortened. Direct sequencing of the short amplicons showed a deletion of 386 nt identical to that isolated from patients A and B. The patients’ histories were reviewed. Patients A, B, and the 13 patients appeared to be epidemiologically related. The epidemiologic relationships and clinical details of the 15 cases are illustrated in the Figure. Most of the cases were part of a documented outbreak at North District Hospital traceable to an 85-year-old woman, L, in whom SARS was not initially suspected but was subsequently confirmed by seroconversion. Patient L had been admitted to ward Y of North District Hospital; subsequently SARS developed in 7 fellow inpatients (patients 3, 4, 5, 6, 8, D, and E) and 2 healthcare workers (patients 7 and A) (Figure). Patient A had been working in both wards X and Y, and patient D was transferred from ward Y to X before symptom onset. Soon afterwards, SARS developed in 2 other inpatients (patients B and 11) in ward X (Figure). Patient E was transferred from ward Y to Z, where symptoms later developed in another inpatient (patient 2) (Figure).

Patients 1, 9, and 10 had not been admitted to North District Hospital but were admitted directly to hospital A. Patients 9 and 10 were household contacts of patient 8 (Figure). Patient 1 had no documented contact with other SARS patients, but coincidentally, patients 1 and L resided in the same estate, T, where a cluster of SARS cases had been documented by the local government (5). The deletion variant was absent in 6 of the studied cases. These case-patients had no identifiable relationship with the cohort of patients illustrated in the Figure and did not reside in the same geographic region as patients L and 1. Three of the patients were admitted to and treated in hospital C. None of the 6 patients had been admitted to North District Hospital.

Therefore, we have isolated a SARS-CoV variant with the largest genomic deletion reported to date in a total of 15 SARS patients, 14 females and 1 male, with ages ranging from 26 to 98 years (median 73 years) (Figure). Nine (60%) of the 15 patients, 8 of whom were known chronic disease patients, died (Figure). This mortality rate is consistent with previous observations where the death rate in patients >65 years generally exceeded 50% (1). Despite the disruption of several putative orfs, as evident from this study, this SARS-CoV variant remained effective in propagating among persons, particularly in the healthcare setting. The predicted orfs 9, 10, and 11 of the SARS-CoV thus may not be functionally important, although further studies are required. We were able to document 3 generations of transmission and traced the first appearance of this deletion variant to mid-April 2003, possibly at Estate T. Investigation on the origin of this enigmatic variant should be continued by studying its prevalence among the earlier human SARS-CoV isolates and potential mammalian hosts.

Rossa W.K. Chiu*, Stephen S.C. Chim*, Yu-kwan Tong*, Kitty S.C. Fung*, Paul K.S. Chan*, Guo-ping Zhao†, and Y.M. Dennis Lo*Comments to Author 
Author affiliations: *The Chinese University of Hong Kong, Shatin, Hong Kong SAR; †The Chinese National Human Genome Center at Shanghai, Shanghai, China


The project team is supported by the Research Fund for the Control of Infectious Diseases from the Health, Welfare and Food Bureau of the Hong Kong SAR Government.


  1. Peiris JS, Yuen KY, Osterhaus AD, Stohr K. The severe acute respiratory syndrome. N Engl J Med. 2003;349:243141. DOIPubMed
  2. The Chinese SARS Molecular Epidemiology Consortium. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004;303:16669. DOIPubMed
  3. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, The genome sequence of the SARS-associated coronavirus. Science. 2003;300:1399404. DOIPubMed
  4. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science. 2003;302:2768. DOIPubMed
  5. Health, Welfare and Food Bureau, Government of the Hong Kong SAR. SARS Bulletin. 30 April 2003. [cited 2004 May 30]. Available from


Suggested citation for this article: Chiu RWK, Chim SSC, Tong Y-k, Fung KSC, Chan PKS, Zhao G-p, et al. Tracing SARS-coronavirus variant with large genomic deletion [letter]. Emerg Infect Dis [serial on the Internet]. 2005 Jan [date cited]. Available from

DOI: 10.3201/eid1101.040544

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Table of Contents – Volume 11, Number 1—January 2005

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Y.M. Dennis Lo, Department of Chemical Pathology, The Chinese University of Hong Kong, Room 38023, 1/F Clinical Sciences Building, Prince of Wales Hospital, 30-32 Ngan Shing St, Shatin, New Territories, Hong Kong Special Administrative Region, China; fax: 852-2636-5090

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