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

[asigore]

New Pango lineage proposal

by The Mount Sinai Pathogen Surveillance Program (MSHSPSP): Ana S. Gonzalez-Reiche, Hala Alshammary, Sarah Schaefer, Gopi Patel, Jose Polanco, Angela A. Amoako, Aria Rooker, Christian Cognigni, Daniel Floda, Adriana van de Guchte, Zain Khalil, Keith Farrugia, Nima Assad, Jian Zhang, Bremy Alburquerque, Levy Sominsky, Komal Srivastava, Robert Sebra, Juan David Ramirez, Radhika Banu, Paras Shrestha, Alberto Paniz-Mondolfi, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel. Icahn School of Medicine at Mount Sinai, New York, NY. USA

Description

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.

Please note that a preprint with more details has been submitted to medRxiv.org and should post soon.

Genomes

GISAID_accessions.txt

Evidence

Omicron tree (divergence)


Lineage cluster (time-scaled)


Proposed lineage name: BA.1.X

[FedeGueli]

Great job! One of these sequences was flagged weeks ago by Neural Network Sequence Filter (NNSF) build by @bitbyte2015 , it was so odd that
it was thought as likely contamination
and we werent able to track the further spread.
Luckily you did! Thanks!

[hvbakel]

Preprint now available at: https://www.medrxiv.org/content/10.1101/2022.05.25.22275533v1

[InfrPopGen]

Thanks for submitting. We've added lineage BA.1.23 with 8 newly designated sequences, and 1 updated designations from BA.1. Defining mutation(s) G22599C (S:R346T), A22935T (S:K458M), C23013T (S:484V).