Proposal for novel B.1 sublineage associated with White-Tailed Deer in Canada

[fmaguire]

Description

Sub-lineage of: B.1 (high degree of divergence from closest mink/human relatives)
Earliest sequence: 2021-11-03 (Canada: Ontario)
Most recent sequence: 2021-12-01 (Canada: Ontario)
Countries circulating: Canada
Epidemiological Significance: Highly divergent lineage in deer suggestive of long circulation, evidence of transmission from deer to human
Pre-print Data: 10.1101/2022.02.22.481551

Deposited Consensus Sequences:

• Canada/ON-WTD-wcov-04658-2372/2021 EPI_ISL_10176284
• Canada/ON-WTD-wcov-04645-24062/2021 EPI_ISL_10174960
• Canada/ON-WTD-wcov-04662-2575/2021 EPI_ISL_10177537
• Canada/ON-WTD-wcov-04581-2582/2021 EPI_ISL_10174207
• Canada/ON-WTD-wcov-04649-D3262/2021 EPI_ISL_10175390
• Canada/ON-PHL-21-44225/2021 EPI_ISL_8323174

Global ML Tree

Local ML Tree

Numbers correspond to wcov-XXXX part of GISAID accession (with 2 additional partial genomes not uploaded included in this phylogeny)

Conserved Non-synonymous Mutations

Gene	Mutation
ORF1a	T265I (C1059T) / NSP2_T85I
ORF1a	T708I (C2388T) / NSP2_T528I
ORF1a	A1283V (C4113T) / NSP3_A465V
ORF1a	A1314V (C4206T) / NSP3_A496V
ORF1a	N2038delinsMRASD (A6377ATGCGTGCGTCGG) / NSP3_ins1219MRAS
ORF1a	N2038delinsMRASD (A6377ATGCGTGCGTCGG) / NSP3_N1220D
ORF1a	S2255F (C7029T) / NSP3_S1437F
ORF1a	S2500F (C7764T) / NSP3_S1682F
ORF1a	L3116F (C9611T) / NSP4_L353F
ORF1a	S3149F (CC9711TT) / NSP4_S386F
ORF1a	K3353R (A10323G) / NSP5_K90R
ORF1a	S3983F (C12213T) / NSP8_S41F
ORF1a	L4111F (C12596T) / NSP8_L169F
ORF1a	T4164I (C12756T) / NSP9_T24I
ORF1a	T4174I (C12786T) / NSP9_T34I
ORF1b	I201V (A14041G) / NSP12_I201V
ORF1b	P323L (C14408T) / NSP12_P323L
ORF1b	V373L (G14557T) / NSP12_V373L
ORF1b	V1280L (G17278T) / NSP13_V348L
ORF1b	M1702I (G18546T) / NSP14_M169I
ORF1b	P1736S (C18646T) / NSP14_P203S
ORF1b	D2151Y (G19891T) / NSP15_D91Y
ORF1b	K2588R (A21203G) / NSP16_K182R
S	H49Y (C21707T) / Spike_H49Y
S	T95I (C21846T) / Spike_T95I
S	V143_Y145DELINSD (GTTTATT21989G) / Spike_V143/V145del
S	F486L (T23020G) / Spike_F486L
S	N501T (A23064C) / Spike_N501T
S	D614G (A23403G) / Spike_D614G
ORF3a	Q57H (G25563T) / NS3_Q57H
ORF3a	L219V (T26047G) / NS3_L219V
E	P71S (C26455T) / E_P71S
ORF8	D35Y (G27996T) / NS8_D35Y
ORF8	E106* (G28209T) / NS8_E106stop
N	P168S (C28775T) / N_P168S
N	S206P (T28889C) / N_S206P
N	T391I (C29445T) / N_T391I
ORF10	L37F (C29666T)

[shay671]

Hi @fmaguire - Very interesting.
I could not find : EPI_ISL_10177537
Is there another reference for this sequence ?

[fmaguire]

Ah sorry, that one seems to have been flagged for curation by GISAID for a possible frameshift and we still have to respond. Will update this when it has gone through.

[fmaguire]

The flagged frameshift in EPI_ISL_10177537 has been confirmed on GISAID and its available.
Raw data for all sequencing (including subset of high coverage genomes uploaded to GISAID and referenced above) is available: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA812959&o=acc_s%3Aa

[chrisruis]

Thanks @fmaguire We've added this as B.1.641 in v1.2.139