LOC_000SPGU.1

France/LOC_000SPGU.1/2024

M. Gasparine & A. Falchi

University of Corsica, Unite des Virus Emergents

Sample details

Collection date

2024

Earliest release date

2025-08-10

Sampling location

France

Isolate name

1002

Data use terms

Changed	User	Data use terms
2026-03-26 17:39	insdc_ingest_user	OPEN

OPEN

Data use terms URL

https://#TODO-MVP/open

INSDC

NCBI release date

2025-08-10

INSDC accession M

PV976883.1

INSDC accession S

PV976892.1

Submission details

Submission ID

PV976883.1.M/PV976892.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2026-03-26 17:39:10 UTC

Date released

2026-03-26 17:47:42 UTC

Host

Ixodoidea

Lineage

Segment S Lineage

III

Files

Annotations

LOC_000SPGU.1.embl

Alignment and QC

Total SNPs S

Length S

1672 (100%)

Variant S

False

Total SNPs M

1316

Total inserted nucs M

109

Total deleted nucs M

Total unknown nucs M

1081

Total frame shifts M

Frame shifts M

GPC:86-98(nt:347-386),GPC:207-288(nt:711-956),GPC:308-613(nt:1014-1931),GPC:619-646(nt:1947-2030),GPC:666-713(nt:2088-2231),GPC:1093-1244(nt:3369-3824),GPC:1303-1347(nt:3997-4132),GPC:1365-1385(nt:4183-4247),GPC:1394-1411(nt:4272-4325),GPC:1434-1450(nt:4392-4442),GPC:1466-1485(nt:4486-4547),GPC:1500-1513(nt:4590-4630),GPC:1530-1548(nt:4680-4736),GPC:1663-1685(nt:5077-5147)

Length M

5413 (79.9%)

Variant M

True

Nucleotide mutations

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

Substitutions

M

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

S

G1661A

Deletions

M

792-809, 1013, 2232, 3996, 4075-4077, 4182, 4485, 5076, 5166-5200

Insertions

M

ins_197:ATGTCTTCAAAC, ins_346:AGAA, ins_386:CAGAAACGCTCAGGGCTCAAAACCCAAGTACC, ins_710:AT, ins_956:C, ins_1902:TT, ins_1931:AA, ins_1946:G, ins_2006:A, ins_2030:T, ins_2087:G, ins_3368:AG, ins_3824:G, ins_4132:A, ins_4247:A, ins_4271:A, ins_4325:CG, ins_4391:A, ins_4442:ATCAT, ins_4547:CAGG, ins_4589:A, ins_4630:CC, ins_4679:C, ins_4703:G, ins_4736:G, ins_4817:ATC,...

Amino acid substitutions

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