Biomedical Engineering Reference
In-Depth Information
brane
[
M
], and
nucleocapsid
[
N
]-3') and short untranslated regions at both
termini
(
4
,
5
)
.
With this sequence information, rapid PCR-based molecular diagnostic tests
of SARS-CoV infection were designed
(
1
,
6-10
)
. Besides offering molecular
diagnosis and quantitative measurement of viral load, PCR-based technologies
have also been exploited to amplify the genomic fragments of SARS-CoV for
sequence analysis. The high sensitivity and specificity of PCR has made this
genomic sequence analysis possible even for uncultured clinical specimens.
Unlike the conventional microbiological methods, PCR-based technologies
may not require viral culture, which could introduce culture-derived artifacts
in the genomic sequence. The specific PCR primers selectively amplify SARS-
CoV sequences from the background of other nucleic acid sequences contrib-
uted by the patient or other microbes. Moreover, the PCR-based method is
versatile in terms of the type of clinical specimens. In our hands, we have suc-
cessfully analyzed the SARS-CoV genome directly from uncultured samples
of serum, nasopharyngeal aspirate, and stools
(
11
)
. This obviates any concern
about the poor or even unsuccessful viral culture of the precious clinical speci-
mens. The risk in handling large-volume and hazardous viral culture could
also be avoided.
Genomic sequence variations were observed in the SARS-CoV obtained
from different patients in this epidemic. Based on these sequence variations,
most of the isolates are typified by two groups: isolates obtained from patients
who were epidemiologically linked to the Metropole Hotel in Hong Kong, and
those who were not
(
3
,
12
,
13
)
. For example, there are seven sequence varia-
tions that can distinguish isolate CUHK-Su10, which is linked to the Metropole
Hotel, from isolate CUHK-W1, which is not linked to this hotel case cluster
(
Table 1
). Among them, four variations at nucleotide positions 17564, 21721,
22222, and 27827 (according to the Tor2 sequence in GenBank, accession no.
AY274119
[
5
]
) were suggested by The Chinese SARS molecular epidemiol-
ogy consortium
(
14
)
as part of a haplotype configuration that marks the differ-
ent phases of a tri-phasic SARS epidemic in Guangdong Province of China.
CUHK-W1 carried a haplotype G:A:C:C that typified the middle phase. Nota-
bly, the same haplotype was observed in CUHK-L2, which was one of the
earliest confirmed case of SARS in Hong Kong, having been documented even
before any report of the hotel case cluster
(
15
)
. CUHK-Su10 carried a haplo-
type T:T:T:T that typified the late phase, marked by the hotel case cluster that
spread the virus to many other parts of the world.
Genomic sequence variations in SARS-CoV have also revealed the route of
infection from within communities and across cities. For instance, compared
with isolate CUHK-Su10, two mutations, T3852C and C11493T, first appeared
