Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa

Three lineages (BA.1, BA.2 and BA.3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's fourth Coronavirus Disease 2019 (COVID-19) wave. We have now identified two new lineages, BA.4 and BA.5, responsible for a fifth wave of infections. The spike proteins of BA.4 and BA.5 are identical, and similar to BA.2 except for the addition of 69-70 deletion (present in the Alpha variant and the BA.1 lineage), L452R (present in the Delta variant), F486V and the wild-type amino acid at Q493. The two lineages differ only outside of the spike region. The 69-70 deletion in spike allows these lineages to be identified by the proxy marker of S-gene…

• BA
  Bill and Melinda Gates Foundation

  Award: INV-018978
• RF
  Rockefeller Foundation

  Award: HTH 017
• WH
  World Health Organization

  Awards: SARS-CoV-2, COVID-19
• W
  Wellcome

  Award: 221003/Z/20/Z
• DO
  Department of Science and Innovation, South Africa
• DO
  Department of Health and Social Care
• SA
  South African Medical Research Council

  Award: 2020/049
• UO
  University of Pretoria
• FC
  Foreign, Commonwealth and Development Office
• NI
  National Institutes of Health

  Awards: U54 TW012041, 3D43TW009610-09S1, COVID-19, U01 AI151698, AI151698
• CF
  Centers for Disease Control and Prevention

  Awards: NU51IP000930, U01IP001048
• MR
  Medical Research Council

  Award: COVID-19
• NI
  National Institute of Allergy and Infectious Diseases

  Awards: 5K24AI131924, COVID-19, U01 AI151698, 5K24AI131928, AI151698
• FI
  Fogarty International Center
• CF
  Center for Information Technology

  Award: U54 TW012041