THE SARS VIRUS GENOME

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THE SARS VIRUS GENOME
The Quick and the Dead?
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SARS

• Severe Acute Respiratory Syndrome
• First identified in Guangdong Province, China
• Mortality 3-6 (45-63 in persons over-60)
• Associated Coronavirus SARS-HCoV

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Coronavirues

• Enveloped
• Replicates in cytoplasm of animal cells
• Single-strand 30 kb RNA genome
• 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

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Application of Genomics to Pandemic

• Competing Interests CDC BCCA
• Draft Sequence 12 April 2003
• Complete Sequence 1 May 2003

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Look! I stay up all night studying genomics, too!
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Genomics Strategy for SARS-HCoV

• 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 5end of genome
• Large cDNAs cloned bidirectionally sequenced
• Sequence Alignment and Consensus Analyses

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Surprising Not-So-Surprising Features
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The Power of Analyzing Sequences for Consensus

• 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 149amino 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).

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Conclusions and Summaryfrom SARS-HcoV Genome
Project

• 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

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SARS HistoryGuangdong to Genome in Six
MonthsVirus to Genome in 38 Days

• 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.

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What to do after getting sequence?
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Knowledge of Sequence will

• 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

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The Next Genome Project?
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Antennalope
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