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_0019WVU.1

Display Name: Cameroon/LOC_0019WVU.1/2023-11-06
A. Namekong Fokeng, A. Paguem, M. Gasparine, K. Tanyi Manchang, F. Fewou Mfoujouem, S. Mvodo, R. Charrel, X. De Lamballerie & A. Falchi

Sample details

Collection date
2023-11-06
Collection date (lower bound)
2023-11-06
Collection date (upper bound)
2023-11-06
Earliest release date
2025-12-28
Collection country
Cameroon
Isolate name
11-2

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2026-01-30 16:06insdc_ingest_userOPEN
Data use terms URL

Authors

Author affiliations
Unite des Virus Emergents, Universite de Corse, Sciences et Techniques

INSDC

NCBI release date
2025-12-28
INSDC accession L
INSDC accession M
INSDC accession S

Host

Host taxon id
Host name scientific
Hyalomma rufipes

Alignment and QC metrics L

Length L
9395
Total SNPs L
541
Total inserted nucs L
28
Total deleted nucs L
2433
Total ambiguous nucs L
0
Total unknown nucs L
0
Total frame shifts L
11
Frame shifts L
RdRp:20-236(nt:134-784),RdRp:285-315(nt:929-1020),RdRp:321-337(nt:1036-1087),RdRp:365-381(nt:1167-1219),RdRp:509-636(nt:1601-1984),RdRp:662-719(nt:2058-2233),RdRp:771-957(nt:2386-2947),RdRp:1039-2676(nt:3189-8104),RdRp:2685-3081(nt:8129-9319),RdRp:3789-3895(nt:11439-11759),RdRp:3913-3946(nt:11813-11914)
Completeness L
97.46%
Stop codons L
RdRp:358,RdRp:385,RdRp:3578
Total stop codons L
3

Alignment and QC metrics M

Length M
1459
Total SNPs M
380
Total inserted nucs M
37
Total deleted nucs M
2295
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
6
Frame shifts M
GPC:434-511(nt:1387-1621),GPC:551-582(nt:1739-1833),GPC:1035-1102(nt:3189-3394),GPC:1330-1434(nt:4074-4389),GPC:1622-1633(nt:4952-4987),GPC:1647-1685(nt:5027-5143)
Completeness M
68.11%
Total stop codons M
0

Alignment and QC metrics S

Length S
1513
Total SNPs S
123
Total inserted nucs S
0
Total deleted nucs S
29
Total ambiguous nucs S
0
Total unknown nucs S
0
Total frame shifts S
2
Frame shifts S
NP:220-325(nt:695-1014),NP:439-483(nt:1352-1488)
Completeness S
85.38%
Total stop codons S
0

Submission details

Submission ID
PX659871.1.L/PX659870.1.M/PX659872.1.S
Submitting group
Date submitted
2026-01-30 16:05:53 UTC
Date released
2026-01-30 16:11:12 UTC

Files

Annotations

Nucleotide mutations

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

Substitutions

L

  • L:C133G
  • L:T214C
  • L:G215C
  • L:T229C
  • L:T253C
  • L:T254A
  • L:C266T
  • L:G277A
  • L:A379T
  • L:A385G
  • L:A388G
  • L:T394C
  • L:G457A
  • L:T484C
  • L:G490A
  • L:T550G
  • L:G553A
  • L:A571G

    • M

  • M:T1330A
  • M:G1331A
  • M:A1332C
  • M:A1334G
  • M:T1335A
  • M:A1338C
  • M:G1340A
  • M:C1343A
  • M:T1344C
  • M:T1345A
  • M:T1347A
  • M:T1351A
  • M:C1352G
  • M:A1353T
  • M:G1355A
  • M:T1357A
  • M:G1358A
  • M:A1360T

    • S

  • S:T116C
  • S:G118T
  • S:A162C
  • S:C183T
  • S:A186G
  • S:C192T
  • S:C201T
  • S:T219C
  • S:G231A
  • S:A255G
  • S:T279C
  • S:A309G
  • S:A311G
  • S:G330A
  • S:G339A
  • S:C342T
  • S:T369C
  • S:T384C
    • Deletions
    L:285-349, L:1162-1166, L:1220, L:1600, L:1898-1900, L:1949, L:1985-1988, L:2057, L:2234, L:2385, L:2860, L:2948, L:3188, L:3287, L:3328-3420, L:3602-3999, L:5531, L:8018, L:8198-8570, L:9320-10232, L:10874-11438, L:11812, L:11888, M:1472-1493, M:1622-1646, M:1834, M:1858-3147, M:3188, M:3295, M:3361, M:3395, M:3670-4073, M:4390-4937, M:4988, S:694, S:1015-1040, S:1350, S:1351
    Insertions
    ins_L:133:T, ins_L:784:G, ins_L:928:C, ins_L:940:C, ins_L:964:TCA, ins_L:1020:C, ins_L:1035:G, ins_L:1062:C, ins_L:1087:G, ins_L:2074:TAA, ins_L:2122:GT, ins_L:2137:G, ins_L:2152:CT, ins_L:7945:G, ins_L:8041:G, ins_L:8089:GCT, ins_L:8104:T, ins_L:8128:TG, ins_L:11759:C, ins_M:1386:CTCGGCCCATCACCCCACCCCTCCACTGTCAC, ins_M:1738:A, ins_M:3316:T, ins_M:4336:G, ins_M:4951:C, ins_M:5026:G

    Amino acid mutations

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

    Substitutions

    GPC

  • GPC:G118T
  • GPC:P121M
  • GPC:P123H
  • GPC:T124P
  • GPC:R126I
  • GPC:S128E
  • GPC:S131T
  • GPC:S132A
  • GPC:P133S
  • GPC:S134Y
  • GPC:P136A
  • GPC:T138A
  • GPC:S139H
  • GPC:Q140H
  • GPC:G141P
  • GPC:H143P
  • GPC:Y144P
  • GPC:P145L

    • NP

  • NP:V27L
  • NP:K91R
  • NP:A124T
  • NP:N125G
  • NP:Q179L
  • NP:R428K
  • NP:I436V

    • RdRp

  • RdRp:C251Y
  • RdRp:G319L
  • RdRp:H338R
  • RdRp:F357S
  • RdRp:L358*
  • RdRp:Y359H
  • RdRp:N362T
  • RdRp:Y385*
  • RdRp:K386T
  • RdRp:G389C
  • RdRp:I505T
  • RdRp:R764K
  • RdRp:T767A
  • RdRp:R3401K
  • RdRp:S3578*
  • RdRp:V3598I
  • RdRp:G3903E
  • RdRp:Q3908K
    • Deletions
    GPC:224-433, GPC:512-525, GPC:592-1021, GPC:1034, GPC:1103, GPC:1195-1329, GPC:1435-1618, GPC:1634, NP:219, NP:326-334, NP:438, RdRp:363, RdRp:364, RdRp:382, RdRp:637, RdRp:638, RdRp:661, RdRp:720, RdRp:958, RdRp:1038, RdRp:2677-2684, RdRp:3082-3386, RdRp:3600-3788
    Insertions
    ins_RdRp:317:NVG, ins_RdRp:720:XX

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