This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000S633.1

Senegal/LOC_000S633.1/2022-08
O. Sene, S. N. Sagne, D. Ngom, M. Bocoum, M. K. Diallo, A. Khoule, E. T. Faye, S. M. Diop, I. Diallo, C. Loucoubar, M. Diallo, N. Dia, Y. Sall, B. Diop, M. Ndiaye, A. A. Sall, M. Weidmann, M. M. Diagne, M. Fall, O. Faye, E. Simon-Loriere, D. Diallo, M. A. Barry & G. Fall

Institut Pasteur, Dakar, Virology

Sample details

Collection date
2022-08
Earliest release date
2025-01-18
Sampling location
Senegal
Isolate name
ARD401182

Data use terms

Data use terms
OPEN
Data use terms URL

INSDC

NCBI release date
2025-01-18
INSDC accession L segment
INSDC accession M segment
INSDC accession S segment

Host

Host

Submission details

Submission ID
PP894720.1.L/PP894744.1.M/PP894736.1.S
Submitting group
Date submitted
2026-11-02 13:32:02 UTC
Date released
2026-11-02 13:36:16 UTC

Clade & Lineage

Closest reference L segment
singleReference (variant)
Closest reference M segment
M (MH396653.1) (variant)
Closest reference S segment
S1 (OL774851.1) (variant)

Files

Annotations

Alignment and QC

Total SNPs L segment
304
Total inserted nucs L segment
52
Length L segment
12121 (99.7%)
Total SNPs M segment
684
Length M segment
5196 (95.2%)
Total SNPs S segment
20
Length S segment
1600 (88.6%)

Nucleotide mutations

Mutations called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

L segment

  • A50G
  • T65C
  • T70C
  • C75T
  • G93A
  • C94T
  • G130T
  • T151C
  • C244T
  • T254A
  • G286A
  • A298G
  • C313T
  • T340C
  • C343T
  • T382C
  • A409G
  • C427T

M segment

  • G103A
  • G113A
  • T115C
  • T116C
  • C118T
  • T122C
  • G124A
  • A127G
  • C133T
  • A139G
  • G142A
  • A143G
  • A149C
  • C151T
  • C155T
  • G165A
  • G166A
  • G170A

S segment

  • T16A
  • A98T
  • T165C
  • A311G
  • C327T
  • G330A
  • C573T
  • G765A
  • G822A
  • T912C
  • A945C
  • A969T
  • C1035T
  • A1182T
  • C1296T
  • T1368C
  • G1428A
  • C1574T
  • T1576C
  • T1598C
Deletions
N/A
Insertions

L segment

ins_12108:TTCATCGTCATCGTTATTATCTTGGGGTGTGGGGGGAACGATTTCTTTGAGA

Amino acid substitutions

Substitutions called relative to the NC_005301.3, MH396653.1 & OL774851.1 references

Substitutions

GPC

  • GPC:V9I
  • GPC:F10L
  • GPC:K19E
  • GPC:N21H
  • GPC:P23S
  • GPC:G26E
  • GPC:E28R
  • GPC:H29R
  • GPC:N31K
  • GPC:H33D
  • GPC:V34T
  • GPC:D39G
  • GPC:S41N
  • GPC:Q42L
  • GPC:P44S
  • GPC:P53S
  • GPC:V54I
  • GPC:S64T

NP

  • NP:Y20F
  • NP:K91R

RdRp

  • RdRp:S6N
  • RdRp:Y60N
  • RdRp:I505T
  • RdRp:T767A
  • RdRp:K809R
  • RdRp:G812E
  • RdRp:T876S
  • RdRp:A1038T
  • RdRp:G1047E
  • RdRp:V1228I
  • RdRp:N1367D
  • RdRp:N1514S
  • RdRp:M1647L
  • RdRp:P1660T
  • RdRp:T1675N
  • RdRp:R1676K
  • RdRp:I1949V
  • RdRp:I1996V
Deletions
N/A
Insertions
N/A

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