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Spillover of new BA.1 sublineage from persistently infected COVID patient into the community

America, BA.1, Coronavirus, Genome, Healthcare, Immunocompromised, Infection, New York State, Omicron, Preprint, Research, Spillover, Testing, USA

“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.

 

 

 

Preprint: Increasing frequency of cryptic SARS-CoV-2 lineages in New York sewers

 

 

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