SARS transmission pattern in Singapore reassessed by viral sequence variation analysis.
BACKGROUND
Epidemiological investigations of infectious disease are mainly dependent on indirect contact information and only occasionally assisted by characterization of pathogen sequence variation from clinical isolates. Direct sequence analysis of the pathogen, particularly at a population level, is generally thought to be too cumbersome, technically difficult, and expensive. We present here a novel application of mass spectrometry (MS)-based technology in characterizing viral sequence variations that overcomes these problems, and we apply it retrospectively to the severe acute respiratory syndrome (SARS) outbreak in Singapore.


RESULTS
The success rate of the MS-based analysis for detecting SARS coronavirus (SARS-CoV) sequence variations was determined to be 95% with 75 copies of viral RNA per reaction, which is sufficient to directly analyze both clinical and cultured samples. Analysis of 13 SARS-CoV isolates from the different stages of the Singapore outbreak identified nine sequence variations that could define the molecular relationship between them and pointed to a new, previously unidentified, primary route of introduction of SARS-CoV into the Singapore population. Our direct determination of viral sequence variation from a clinical sample also clarified an unresolved epidemiological link regarding the acquisition of SARS in a German patient. We were also able to detect heterogeneous viral sequences in primary lung tissues, suggesting a possible coevolution of quasispecies of virus within a single host.


CONCLUSIONS
This study has further demonstrated the importance of improving clinical and epidemiological studies of pathogen transmission through the use of genetic analysis and has revealed the MS-based analysis to be a sensitive and accurate method for characterizing SARS-CoV genetic variations in clinical samples. We suggest that this approach should be used routinely during outbreaks of a wide variety of agents, in order to allow the most effective control.
Liu
Jianjun
J
Genome Institute of Singapore, Singapore. liuj3@gis.a-star.edu.sg
Lim
Siew Lan
SL
Ruan
Yijun
Y
Ling
Ai Ee
AE
Ng
Lisa F P
LF
Drosten
Christian
C
Liu
Edison T
ET
Stanton
Lawrence W
LW
Hibberd
Martin L
ML
D004279:DNA, Viral / Q000032:analysis*; D004196:Disease Outbreaks; D014644:Genetic Variation; D006801:Humans; D013058:Mass Spectrometry; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics* / Q000472:pathogenicity; D045169:Severe Acute Respiratory Syndrome / Q000453:epidemiology / Q000635:transmission*
D004279:DNA, Viral
Lancet. 2003 May 24;361(9371):1779-85
12781537
Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2542-7
14983045
Adv Biochem Eng Biotechnol. 2002;77:57-74
12227737
Science. 2004 Mar 12;303(5664):1666-9
14752165
N Engl J Med. 2004 Mar 25;350(13):1366-7
15044654
N Engl J Med. 2003 Dec 18;349(25):2468-9
14681520
Clin Chem. 2003 Dec;49(12):1976-80
14633867
J Clin Microbiol. 2004 Jan;42(1):347-50
14715775
Science. 2003 May 30;300(5624):1394-9
12730500
N Engl J Med. 2003 Dec 18;349(25):2431-41
14681510
J Clin Virol. 2003 Dec;28(3):233-8
14522060
Lancet. 2003 May 24;361(9371):1767-72
12781535
N Engl J Med. 2003 Jul 10;349(2):187-8
12853594
N Engl J Med. 2003 May 15;348(20):1967-76
12690091
Lancet. 2004 Jan 10;363(9403):99-104
14726162
Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3059-64
12624187
Clin Infect Dis. 2004 Jan 15;38(2):293-6
14699465
BMC Infect Dis. 2004 Sep 06;4:32
15347429
Emerg Infect Dis. 2004 Mar;10(3):413-8
15109406
Genome Res. 2004 Mar;14(3):398-405
14993206
J Gen Virol. 2003 Sep;84(Pt 9):2305-2315
12917450
Science. 2003 May 30;300(5624):1399-404
12730501
Lancet. 2003 Apr 19;361(9366):1319-25
12711465