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August 11, 2021

Analysis of 329,942 SARS-CoV-2 Records Retrieved from GISAID Database

Quantori is excited to share research findings that are available on Cold Spring Harbor Laboratory's bioRxiv preprint server for biology “Analysis of 329,942 SARS  — CoV-2 records retrieved from GISAID database”

Research Highlights

  • The analysis yielded 155 genome variations (SNPs and deletions) in more than 0.3% of the sequences.
  • Nine common SNPs were present in more than 20% of the samples.
  • Clustering results suggested that a proportion of people (2.46%) were infected with a distinct subtype of the B.1.1.7 variant.
  • The subtype may be characterized by four to six additional mutations, with four being a more frequent option (G28881A, G28882A, and G28883С in the N gene, A23403G in S, A28095T in ORF8, G25437T in ORF3a).
  • Two clusters were formed by mutations in the samples uploaded predominantly by Denmark and Australia, which may indicate the emergence of “Danish” and “Australian” variants.
  • Five clusters were linked to increased/decreased age, shifted gender ratio, or both.
  • Metadata mining analysis has led to a hypothesis about gender inequality in medical care in certain countries.
  • ORF6 and E were the most conserved genes (96.15% and 94.66% of the sequences totally match the reference, respectively), making them potential targets for vaccines and treatment.

Kudos to Yuriy GankinMaria ZelenovaAnna Ivanova and Semyon S. on their work!

Read the preprint here


Image Description: Forty-three clusters were revealed by HDBScan. Legend on the right contains cluster numbers and color schemes.