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_000PZWV.1

Display Name: Senegal/LOC_000PZWV.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
ARD407551

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2025-11-26 16:57insdc_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 S

Length S
1687
Total SNPs S
319
Total inserted nucs S
17
Total deleted nucs S
0
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
0
Completeness S
99.88%
Total stop codons S
0

Alignment and QC metrics M

Length M
5368
Total SNPs M
1530
Total inserted nucs M
82
Total deleted nucs M
62
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
1
Frame shifts M
GPC:86-96(nt:347-380)
Completeness M
99.66%
Total stop codons M
0

Submission details

Submission ID
PP894723.1.M/PP894731.1.S
Submitting group
Date submitted
2025-11-26 16:57:46 UTC
Date released
2025-11-26 17:06:07 UTC

Lineage

Segment S Lineage
I

Files

Annotations

Nucleotide mutations

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

Substitutions

M

  • M:G50T
  • M:A51G
  • M:A52T
  • M:G56T
  • M:A57G
  • M:T58A
  • M:T59A
  • M:G60A
  • M:A64G
  • M:T65A
  • M:C66T
  • M:A69G
  • M:A70T
  • M:T71G
  • M:T72A
  • M:C74G
  • M:G76A
  • M:A80G

    • S

  • S:C38A
  • S:T39C
  • S:G54A
  • S:A61G
  • S:G67A
  • S:G73A
  • S:T79C
  • S:G91A
  • S:A92C
  • S:G94T
  • S:G99A
  • S:G100A
  • S:A109G
  • S:A118G
  • S:T127C
  • S:A130G
  • S:C142T
  • S:T163C
    • Deletions
    M:663-689, M:5166-5200
    Insertions
    ins_M:224:ATGTCTGTGCTG, ins_M:346:AGAA, ins_M:380:AAGAGTCAGAAATGCTCAGGGCTCAAAACCCA, ins_M:815:TTCATAAGCCCT, ins_M:5253:TGCCCCAACTAT, ins_M:5295:CAACTTTGCT, ins_S:1541:TGCTTCTGCTTCT, ins_S:1582:AAC, ins_S:1616:G

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:M1E
  • GPC:H2F
  • GPC:I3M
  • GPC:S4L
  • GPC:M6T
  • GPC:Y7N
  • GPC:A8F
  • GPC:I9F
  • GPC:L10F
  • GPC:L12Q
  • GPC:Q13L
  • GPC:C15W
  • GPC:L17G
  • GPC:E19G
  • GPC:T20V
  • GPC:H21A
  • GPC:G22S
  • GPC:S23G

    • NP

  • NP:M13L
  • NP:R15K
  • NP:S39N
  • NP:S52G
  • NP:F73Y
  • NP:K91R
  • NP:A100T
  • NP:T124A
  • NP:G125N
  • NP:A154S
  • NP:H195K
  • NP:V198I
  • NP:D199E
  • NP:V205I
  • NP:I220V
  • NP:I246V
  • NP:D248E
  • NP:N258K
    • Deletions
    GPC:26-54, GPC:182-206
    Insertions
    ins_GPC:131:ESEMLRAQNPSTTAGSGASTPINTTSNKPDVNSPTSPILEAKSSP, ins_GPC:221:SKQINTTTLGIPPKIQATQS

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