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PPD_00SQZD2.1

Kenya/AFI-LAM-1993/2024-09-11
G. Kimita, B. K. Mutai, E. A. Omuseni, C. A. Masakhwe, S. Ocholla, A. P. Lemtudo, G. O. Awinda & J. N. Waitumbi

WRAIR-Africa, Basic Science Laboratory

Sample details

Collection date
2024-09-11
Sampling location
Kenya (Lamu, Lamu West sub-County, Kashmiri)
Isolate name
AFI-LAM-1993

Data use terms

Data use terms
OPEN
Data use terms URL

Clade

Clade
Asian

INSDC

INSDC accession
NCBI release date
2024-11-06
NCBI update date
2024-11-26

Host

Host

Submission details

Submission ID
PQ551088.1
Submitting group
Date submitted
2026-08-28 15:00:59 UTC
Date released
2026-08-28 15:03:29 UTC
Earliest release date
2024-11-06

Alignment and QC

Length
10666 (98.7%)
# of SNPs
235
# of deleted bases
1
# of ambiguous bases
1

Nucleotide mutations

Mutations called relative to the NC_035889.1 reference

Substitutions
  • A50G
  • T188C
  • A254G
  • T299C
  • G423A
  • G444A
  • A523G
  • T545C
  • T558C
  • T578C
  • C617T
  • G653A
  • T719C
  • T773C
  • A803G
  • A884G
  • C947T
  • A953G
Deletions
81
Insertions
N/A

Amino acid substitutions

Substitutions called relative to the NC_035889.1 reference

Substitutions

E

  • E:I169V
  • E:A280T
  • E:D348N
  • E:T470A
  • E:M473L

M

  • M:I67M

NS1

  • NS1:V84I
  • NS1:H113Y
  • NS1:E146K
  • NS1:L154I
  • NS1:A233T
  • NS1:V349M

NS2A

  • NS2A:F180L

NS3

  • NS3:I109V
  • NS3:T215A
  • NS3:H584Y

NS4B

  • NS4B:I240T

NS5

  • NS5:Y74H
  • NS5:V114M
  • NS5:I322V
  • NS5:R515K
  • NS5:K560R
  • NS5:S749A
  • NS5:V787A
  • NS5:H825Y
  • NS5:V902A

ancC

  • ancC:A106T
  • ancC:V113I

pr

  • pr:N17S

prM

  • prM:N17S
  • prM:I160M
Deletions
N/A
Insertions
N/A

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