|
|
Letter
Tracing SARS-Coronavirus Variant
with Large Genomic Deletion
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*
*The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative
Region; and †The Chinese National Human Genome Center at Shanghai, Shanghai,
China
Suggested
citation for this article
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 frame, 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 woman 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.
|
Figure |
|
|
 |
|
|
Click to view
enlarged image
Figure. Schematic illustration of the epidemiologic
relationships between patients with the severe acute respiratory
syndrome-associated coronavirus...
|
|
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.
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.
References
- Peiris JS, Yuen KY, Osterhaus AD, Stohr K. The
severe acute respiratory syndrome. N Engl J Med. 2003;349:2431–41.
- The Chinese SARS Molecular Epidemiology Consortium. Molecular
evolution of the SARS coronavirus during the course of the SARS epidemic
in China. Science. 2004;303:1666–9.
- Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield
YS, et al. The
genome sequence of the SARS-associated coronavirus. Science. 2003;300:1399–404.
- Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation
and characterization of viruses related to the SARS coronavirus from
animals in southern China. Science. 2003;302:276–8.
- Health, Welfare and Food Bureau, Government of the Hong Kong SAR.
SARS Bulletin. 30 April 2003. [cited 2004 May 30]. Available from http://www.info.gov.hk/dh/diseases/ap/eng/bulletin0430.pdf
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 http://www.cdc.gov/ncidod/EID/vol11no01/04-0544.htm
|
