“The new BA.1 sub-lineage transmitted to five independent cases, including two reported in GISAID from a different surveillance effort”…
Gisaid: BA.1 sublineage with T6001C and S mutations: S:E96D, S:L167T, S:R346T, S:L455W, S:K458M, S:E484V, S:H681R, S:P688V, detected in New York, USA #663.
Sub-lineage of: BA.1
Earliest sequence: 02-Feb-2022 (Index case)
Most recent sequence: 02-May-2022
Countries circulating: USA – New York
This new sub-lineage contains a unique combination of amino acid substitutions within the spike Omicron BA.1 background (E96D, L167T, R346T, L455W, K458M, E484V, P681R, A688V). This sub-lineage emerged in a single host with prolonged SARS-CoV-2 (BA.1) infection acquiring 8 additional mutations across the spike N-terminal domain (NTD), the receptor binding domain (RBD), and cleavage site region (CSR). The new BA.1 sub-lineage transmitted to five independent cases, including two reported in GISAID from a different surveillance effort (CDC, through LabCorp and Quest Diagnostics). A new lineage designation will facilitate identification of further community spread.
Thanks to @PeacockFlu for pointing this out.
Might be the first time we've seen virus from a persistently infected COVID patient spillover into the community. https://t.co/fQZUtOAU1y
— John Dennehy 🇺🇦 (@DrJDennehy) May 24, 2022