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_000PXND.1

Display Name: Senegal/LOC_000PXND.1/2022-09
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

Sample details

Collection date
2022-09
Collection date (lower bound)
2022-09-01
Collection date (upper bound)
2022-09-30
Earliest release date
2025-01-18
Collection country
Senegal
Isolate name
ARD407242

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-10-27 14:18insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Institut Pasteur, Dakar, Virology

INSDC

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

Host

Host taxon id
Host name scientific
Hyalomma impeltatum

Alignment and QC metrics M

Length M
5431
Total SNPs M
1544
Total inserted nucs M
79
Total deleted nucs M
14
Total ambiguous nucs M
1
Total unknown nucs M
0
Total frame shifts M
0
Completeness M
99.98%

Alignment and QC metrics S

Length S
1672
Total SNPs S
46
Total inserted nucs S
1
Total deleted nucs S
0
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
99.94%

Submission details

Submission ID
PP894727.1.M/PP894734.1.S
Submitting group
Date submitted
2025-10-27 14:18:35 UTC
Date released
2025-10-27 14:25:03 UTC

Lineage

Segment S Lineage
III

Files

Annotations

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

M

  • M:T40C
  • M:A51G
  • M:A52T
  • M:T54C
  • M:G55T
  • M:G56A
  • M:A57G
  • M:T59G
  • M:C63T
  • M:A64G
  • M:C66T
  • M:T67C
  • M:T68A
  • M:A69G
  • M:A70C
  • M:T71A
  • M:T72G
  • M:G73T

    • S

  • S:G54A
  • S:G67A
  • S:G229A
  • S:T253C
  • S:G262A
  • S:A298G
  • S:A322G
  • S:G346A
  • S:A358T
  • S:C370T
  • S:G397A
  • S:G409A
  • S:C427T
  • S:G448A
  • S:A639G
  • S:C670T
  • S:C712T
  • S:A791G
    • Deletions
    M:300-302, M:5261-5271
    Insertions
    ins_M:182:TCCCACACAGAC, ins_M:395:CCGAAA, ins_M:587:CAC, ins_M:5184:CCCTTCCCCGTCGCACTACTAAA, ins_M:5322:ACACTGCAGCGTATGTGACACTGTTACCATTTAGA, ins_S:1581:T

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    GPC

  • GPC:M1K
  • GPC:S4L
  • GPC:M6F
  • GPC:Y7C
  • GPC:A8I
  • GPC:C11Y
  • GPC:L12H
  • GPC:L14Q
  • GPC:C15W
  • GPC:G16S
  • GPC:L17T
  • GPC:E19A
  • GPC:T20S
  • GPC:H21N
  • GPC:G22T
  • GPC:S23T
  • GPC:H24I
  • GPC:N25S

    • NP

  • NP:H195R
  • NP:I246V
  • NP:S301G
    • Deletions
    None
    Insertions
    ins_GPC:31:H, ins_GPC:77:SPAT, ins_GPC:165:H

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