PP_0080FTQ.1

Kenya/PP_0080FTQ.1/2025-09-06
A. Nyunja, S. K. Langat, G. Pilarowski, E. Chepkorir, V. Ofula, P. Oluniyi, H. Koka, J. Lomeringole, E. Koskei, O. Arach, F. Musili, B. Chelangat, J. Mutisya, C. M. Tato, J. Lutomiah, S. Khamadi & K. Limbaso

Kenya Medical Research Institute (KEMRI), Centre for Virus Research

Sample details

Collection date
2025-09-06
Sampling location
Kenya (Mombasa)
Isolate name
028/06/2025

Data use terms

Data use terms
OPEN
Data use terms URL

Clade

Clade
II-ECSA

INSDC

INSDC accession
NCBI release date
2026-10-06
NCBI update date
2026-10-06

Host

Host

Submission details

Submission ID
PZ661954.1
Submitting group
Date submitted
2026-10-07 09:00:17 UTC
Date released
2026-10-07 09:01:22 UTC
Earliest release date
2026-10-06

Files

Annotations

Alignment and QC

Length
11746 (99.4%)
# of SNPs
390
# of inserted bases
3
# of deleted bases
17

Nucleotide mutations

Mutations called relative to the NC_004162.2 reference

Substitutions
  • G68T
  • T163A
  • T244C
  • T268C
  • T271C
  • T319C
  • A337G
  • C358T
  • C409T
  • C448A
  • C459A
  • T490C
  • A493C
  • G520T
  • A575G
  • T590G
  • A604T
  • T610C
Deletions
11445-11458, 11628-11630
Insertions
ins_11531:AGG

Amino acid substitutions

Substitutions called relative to the NC_004162.2 reference

Substitutions

6K

  • 6K:V8I
  • 6K:I54V

C

  • C:P23S
  • C:V27I
  • C:K63R
  • C:K97R

E1

  • E1:I55V
  • E1:K211E
  • E1:M269V
  • E1:D284E
  • E1:V322A

E2

  • E2:G57K
  • E2:I74M
  • E2:G79E
  • E2:N160T
  • E2:A164T
  • E2:L181M
  • E2:S194G
  • E2:I211T
  • E2:V264A
  • E2:M267R
  • E2:S299N
  • E2:T312M
  • E2:A344T
  • E2:S375T
  • E2:V386A
  • E2:M390I
  • E2:I415V
  • E2:I418V

E3

  • E3:I23T

nsP1

  • nsP1:T128K
  • nsP1:I167V
  • nsP1:L172V
  • nsP1:E234K
  • nsP1:M383L
  • nsP1:I384L
  • nsP1:L407S
  • nsP1:T481I
  • nsP1:Q488R
  • nsP1:L507R

nsP2

  • nsP2:S54N
  • nsP2:H374Y
  • nsP2:C642Y
  • nsP2:S643N

nsP3

  • nsP3:I171V
  • nsP3:V175I
  • nsP3:Y217H
  • nsP3:P326S
  • nsP3:V331A
  • nsP3:T337I
  • nsP3:K352E
  • nsP3:I376T
  • nsP3:A382I
  • nsP3:L461P
  • nsP3:S462N
  • nsP3:P471L
  • nsP3:R524*

nsP4

  • nsP4:T75A
  • nsP4:P110S
  • nsP4:T254A
  • nsP4:Q500L
  • nsP4:I514T
  • nsP4:V555I
  • nsP4:V604I
Deletions
N/A
Insertions
N/A

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