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Polymorphism of SARS-CoV genomes.

Lei Shang1, Yan Qi, Qi-Yu Bao

  • 1James D Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China.

Yi Chuan Xue Bao = Acta Genetica Sinica
|April 22, 2006
PubMed
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This study sequenced the SARS-CoV BJ202 genome, revealing 278 polymorphic sites across 116 genomes. Variations clustered at the 3' end, with specific regions showing high mutation rates.

Area of Science:

  • Virology
  • Genomics
  • Molecular Biology

Background:

  • Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) poses a significant public health threat.
  • Understanding SARS-CoV genome variations is crucial for tracking viral evolution and developing countermeasures.

Purpose of the Study:

  • To completely sequence the SARS-CoV BJ202 genome.
  • To perform comparative genomics analysis of 116 SARS-CoV genomes.
  • To identify and characterize sequence variations, including polymorphic sites, deletions, and insertions.

Main Methods:

  • Complete genome sequencing of SARS-CoV BJ202 from a patient's stool sample.
  • Comparative genomics analysis using 116 publicly available SARS-CoV genomes from NCBI GenBank.
  • Identification of polymorphic sites, deletions, and insertions.

Related Experiment Videos

  • Phylogenetic analysis to determine genome divergence.

    • Main Results:

    • The SARS-CoV BJ202 genome was fully sequenced.
    • A total of 278 polymorphic sites were identified across 116 SARS-CoV genomes, with 41 in BJ202.
    • Polymorphic sites showed biased distribution, with a significant cluster (50.4%) in the 3' end region (19.0 kb-29.7 kb).
    • Regions encoding Orf10-11, Orf3/4, E, M, and S proteins exhibited the highest mutation rates.
    • 18 types of deletions and 2 insertions were identified, primarily in a 300 bp region encoding parts of ORF9 and ORF10-11.
    • A novel polymorphic site (position 18379) was identified in BJ202.
    • Phylogenetic analysis placed BJ202 closer to BJ01 and LLJ-2004.

    Conclusions:

    • The study provides a comprehensive genomic analysis of SARS-CoV, highlighting significant variations and their distribution.
    • The findings contribute to understanding SARS-CoV evolution and genetic diversity.
    • BJ202 represents a distinct but related lineage within the SARS-CoV species.