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THE
SARS
VIRUS
GENOME
The Quick and the Dead?
SARS
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Severe Acute Respiratory Syndrome
First identified in Guangdong Province,
China
Mortality 3-6% (45-63% in persons
over-60)
Associated Coronavirus SARS-HCoV
Coronavirues
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Enveloped
Replicates in cytoplasm of animal cells
Single-strand 30 kb RNA genome
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With 5’ cap & poly-A tail
Respiratory, enteric, hepatic, neurological
Cause 30% respiratory infections
Can acquire genes by horizontal transfer and
co-infection
Three main classes
Application of Genomics to Pandemic
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Competing Interests: CDC & BCCA
Draft Sequence: 12 April 2003
Complete Sequence: 1 May 2003
Look! I stay up all night
studying genomics, too!
Genomics Strategy for SARS-HCoV
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Virus isolated from bronchioalveolar sample
from fatal case from Toronto (Tor2 isolate)
Virus particles purified & RNA extracted
Converted to cDNA by oligo-dT priming
RACE used to obtain far 5’end of genome
Large cDNAs cloned & bidirectionally
sequenced
Sequence Alignment and Consensus
Analyses
Surprising & Not-So-Surprising Features
• Sequence nearly identical to CDC isolate
• No evidence for mutability
• Major genes conserved among coronaviruses
• replicases 1a and 1b
•Membrane (M) glycoprotein
• S protein
•Nucleocapsid (N) protein
• the small envelope (E) protein
• s2m motif common to avian bronchitic and equine rhinitic viruses
• Suggests horizontal transfer
• 9 unique ORFs
• some overlap, some nested
• do not readily align with other coronaviruses
• suggests new coronavirus class
The Power of Analyzing Sequences for
Consensus
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ORF 3 (Fig. 2; base pairs 25,268 to 26,092) encodes a predicted protein of
274 amino acids that lacks significant BLAST (24), FASTA (25), or PFAM
(26) similarities to any known protein. Analysis of the N-terminal 70 amino
acids with SignalP provides weak evidence for the existence of a signal
peptide and a cleavage site (probability 0.540). Both TMpred (27) and
TMHMM predict the existence of three transmembrane regions spanning
approximately residues 34 to 56, 77 to 99, and 103 to 125. The most likely
model from these analyses is that the C terminus and a large 149–amino
acid N-terminal domain would be located inside the viral or cellular
membrane. The C-terminal (interior) region of the protein may encode a
protein domain with ATP-binding properties (ProDom ID PD037277).
Conclusions and Summary
from SARS-HcoV Genome Project
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SARS defines unique class of coronavirus.
No evidence of intervirus recombination between
known coronaviruses
Besides s2m motif, no evidence of intervirus
recombination from non-coronaviruses.
Suggests recent mutation of existing animal
(nonhuman) virus caused ability to infect humans.
Demonstrates how fast technology and expertise
has grown and can be applied
CDC & BCCA have filed for patents
SARS History:
Guangdong to Genome in Six Months
Virus to Genome in 38 Days
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November 2002: An outbreak of a mysterious respiratory illness occurs
in Guangdong Province, China, making hundreds seriously ill and
killing dozens.
Mid-February 2003: Virus spreads to Vietnam and Hong Kong;
international travel blamed.
Mid-March: Virus spreads to Singapore and Canada.
March 15: A Singaporean doctor travels through New York on his way
to Germany, becoming ill en route; he is diagnosed with SARS in
Frankfurt.
March 17: World Health Organization facilitates the collaboration of 11
laboratories in 10 countries to identify the cause of SARS.
March 24: Centers for Disease Control and Prevention announces that
a coronavirus strain causes SARS.
March 29: Dr. Carlo Urbani, a WHO officer who treated the earliest
cases in Hanoi, dies of SARS.
May 1: CDC and the British Columbia Cancer Agency in Canada
publish near-identical sequences of the SARS virus in Science.
What to do after getting sequence?
Knowledge of Sequence will…
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allow precision diagnosis of virus presence by
specific DNA amplification of virus regions
help consolidate association of virus with
disease
facilitate development of antiviral treatments
(including neutralizing antibodies) and vaccines
help understand epidemiology of rapid viral
mutation and host changing
The Next Genome Project?
Antennalope
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