Selection analysis of GISAID SARS-CoV-2 data

SARS-CoV-2 coronavirus nCoV-2019 Evolutionary History
2

April 1st update.

SEVEN (maybe eight) sites currently showing some evidence of selection

  • S D614G : has some reversions, toggle-like behavior; HLA/CTL?
  • ORF3a Q57H : additional line of evidence – intrahost NGS variation data
  • ORF8 84L/S : may be toggling
  • ORF1a T265I (nsp2 T85I) : late and multiple introductions (high frequency)
  • ORF1a L960F (nsp3 L142F) : late and multiple introductions (low frequency)
  • ORF1a L3606F (nsp6 L37F) : additional line of evidence – intrahost NGS variation data
  • ORF1b T1729I (exonuclease T206I) : late and multiple introductions (low frequency)
  • (Maybe) ORF1a L1599F (nsp3 L781F) : this variant appears to have gone extinct

Details at http://covid19.datamonkey.org/2020/04/01/covid19-analysis/

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