Abstract
Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization.
MeSH terms
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Adaptation, Physiological
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Amino Acid Substitution
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Animals
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Base Sequence
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Carnivora / virology
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China / epidemiology
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Cluster Analysis
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Coronavirus / genetics
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Coronavirus / isolation & purification
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Coronavirus M Proteins
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Disease Outbreaks*
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Evolution, Molecular*
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Genome, Viral*
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Genotype
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Humans
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Membrane Glycoproteins / genetics
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Molecular Sequence Data
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Mutation
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Nucleic Acid Conformation
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Open Reading Frames
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Phylogeny
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Point Mutation
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RNA, Viral / genetics
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Selection, Genetic
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Sequence Deletion
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Severe Acute Respiratory Syndrome / epidemiology*
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Severe Acute Respiratory Syndrome / virology*
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Severe acute respiratory syndrome-related coronavirus / genetics*
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Severe acute respiratory syndrome-related coronavirus / isolation & purification
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Severe acute respiratory syndrome-related coronavirus / physiology
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Spike Glycoprotein, Coronavirus
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Viral Envelope Proteins / genetics
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Viral Matrix Proteins / chemistry
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Viral Matrix Proteins / genetics
Substances
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Coronavirus M Proteins
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M protein, SARS-CoV
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Membrane Glycoproteins
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RNA, Viral
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Spike Glycoprotein, Coronavirus
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Viral Envelope Proteins
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Viral Matrix Proteins
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spike glycoprotein, SARS-CoV