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_000YS43.1

Display Name: Cameroon/LOC_000YS43.1/2023-11-06
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
2025-12-30 23:57insdc_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
387
Total inserted nucs M
48
Total deleted nucs M
2263
Total ambiguous nucs M
0
Total unknown nucs M
0
Total frame shifts M
3
Frame shifts M
GPC:468-1033(nt:1493-3191),GPC:1092-1416(nt:3366-4340),GPC:1621-1685(nt:4953-5147)
Completeness M
68.47%
Stop codons M
GPC:43
Total stop codons M
1

Alignment and QC metrics S

Length S
1513
Total SNPs S
44
Total inserted nucs S
1
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:711-1030),NP:439-483(nt:1369-1504)
Completeness S
92.17%
Total stop codons S
0

Submission details

Submission ID
PX659871.1.L/PX659870.1.M/PX659872.1.S
Submitting group
Date submitted
2025-12-30 23:57:05 UTC
Date released
2025-12-31 00:08:42 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

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:T1380A
  • M:T1382A
  • M:G1386T
  • M:T1387A
  • M:T1390A
  • M:A1391C
  • M:T1393C
  • M:C1394A
  • M:A1395C
  • M:A1396C
  • M:A1397C
  • M:T1398A
  • M:C1399G
  • M:A1400T
  • M:C1401G
  • M:G1404A
  • M:T1405A
  • M:T1409A

    • S

  • S:T132C
  • S:G134T
  • S:G189A
  • S:C208T
  • S:C217T
  • S:G229A
  • S:A298G
  • S:A322G
  • S:A325G
  • S:A327G
  • S:G346A
  • S:A358T
  • S:C370T
  • S:T385C
  • S:G397A
  • S:C523T
  • S:A639G
  • S:A649G
    • 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:1482-1492, M:1660-1665, M:1838, M:1862-3151, M:3192, M:3365, M:3396, M:3674-4077, M:4406-4952, M:4992, S:710, S:1031-1056, S:1367, S:1368
    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:1553:CCTCTGCCGGGACACTACAGCTCTCCTGCTAGACCGGCACACAAC, ins_M:1733:G, ins_M:4340:G, ins_M:5035:A, 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:D33N
  • GPC:T34R
  • GPC:M35H
  • GPC:T36Y
  • GPC:T37D
  • GPC:P38T
  • GPC:G39P
  • GPC:D40S
  • GPC:N41D
  • GPC:P42N
  • GPC:S43*
  • GPC:S44A
  • GPC:E45P
  • GPC:P46N
  • GPC:P47S
  • GPC:V48Q
  • GPC:S49L
  • GPC:T50H

    • NP

  • NP:V27L
  • NP:R45K
  • NP:K91R
  • NP:H195R

    • 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:218-467, GPC:1034, GPC:1439-1620, 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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