LOC_000P4LA.1

Display Name: France/LOC_000P4LA.1/2023

Piorkowski, G.; Kiwan, P.; Masse, S.; Ayhan, N.; Charrel, R.; de Lamballerie, X.; Falchi, A.

Submission details

Submission ID

PP025040.1.L/PP025039.1.M/PP025038.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2024-12-20 08:39:34 UTC

Date released

2024-12-20 08:44:19 UTC

Data use terms

Changed	User	Data Use Terms
2024-12-20 08:39	insdc_ingest_user	OPEN

OPEN

Data use terms URL

https://#TODO-MVP/open

Authors

Author affiliations

IHU mediterranee, UMR190 Unite des Virus Emergents U1207

Alignment states and QC metrics L

Completeness L

91.96%

Length L

11246

Total ambiguous nucs L

Total deleted nucs L

Total frame shifts L

Total inserted nucs L

Total SNPs L

228

Total unknown nucs L

119

Alignment states and QC metrics M

Completeness M

89.64%

Frame shifts M

GPC:63-70(nt:278-300),GPC:86-106(nt:348-408),GPC:126-130(nt:468-482),GPC:1686(nt:5147)

Length M

5075

Total ambiguous nucs M

Total deleted nucs M

155

Total frame shifts M

Total inserted nucs M

Total SNPs M

1155

Total unknown nucs M

345

Alignment states and QC metrics S

Completeness S

61.30%

Length S

1498

Total ambiguous nucs S

Total deleted nucs S

Total frame shifts S

Total inserted nucs S

Total SNPs S

177

Total unknown nucs S

495

Sample details

Earliest release date

2024-06-25

Collection country

France

Collection date

2023

Collection date (lower bound)

2023-01-01

Collection date (upper bound)

2023-12-31

Isolate name

1207

Host

Host name scientific

Ixodoidea

Host taxon id

297308

INSDC

INSDC accession L

PP025040.1

INSDC accession M

PP025039.1

INSDC accession S

PP025038.1

NCBI release date

2024-06-25

Nucleotide mutations

Substitutions

L

L:A859T

L:A901G

L:C904T

L:G951A

L:G961A

L:C1015T

L:C1016T

L:C1019T

L:A1120G

L:G1174A

L:C1240T

L:A1338G

L:A1354T

L:T1420C

L:C1495T

L:A1501G

L:C1549T

L:A1555G

M

M:A203T

M:C204G

M:G208C

M:T209A

M:T212A

M:G243A

M:T246A

M:G248C

M:T253A

M:T254C

M:T259C

M:T260G

M:C263T

M:C280A

M:C283G

M:A284G

M:A285T

M:T296A

S

S:C160T

S:T163C

S:C166T

S:G171A

S:T172C

S:T175G

S:C178G

S:T181C

S:T182C

S:G184T

S:G196A

S:T199C

S:C208T

S:A209G

S:C214A

S:G229A

S:G232A

S:C235T

Deletions

L:12026-12032, M:214-231, M:249-251, M:264-277, M:291, M:292, M:301-305, M:363-365, M:379-386, M:472, M:483, M:555-569, M:5146, M:5153-5178, M:5187-5192, M:5198, M:5199, M:5223-5230, M:5277-5295, M:5306-5309, M:5331-5349, S:1543-1546, S:1564-1572, S:1592-1594, S:1599, S:1608-1611, S:1646-1663

Insertions

ins_S:1533:C, ins_S:1530:TGTG, ins_S:1580:A, ins_S:1550:AA, ins_S:1506:C, ins_S:1554:T, ins_S:1512:GTTTTTT, ins_M:236:CCG, ins_M:5217:AT, ins_M:5261:GCACCTT, ins_M:5209:AATATT, ins_M:403:GCAGGA, ins_M:408:AACCCAAGCACCACGGCTG, ins_M:5244:CA, ins_M:5323:ATG, ins_M:5242:CTA, ins_M:347:GAAAT, ins_M:454:ACT, ins_M:432:ACACCACAT, ins_M:467:TTAGA, ins_M:356:TT

Amino acid mutations

Substitutions

GPC

GPC:L17A

GPC:G18A

GPC:H21V

GPC:V76S

GPC:Y77S

GPC:S79D

GPC:P81Q

GPC:I82T

GPC:T84N

GPC:G85R

GPC:A107N

GPC:G119S

GPC:T124I

GPC:V125L

GPC:T135G

GPC:P136T

GPC:D141T

GPC:T142A

NP

NP:S39N

NP:S52G

NP:F73Y

NP:A100T

NP:T124A

NP:G125N

NP:A154S

NP:H195K

NP:V198I

NP:D199E

NP:I220V

NP:T420S

RdRp

RdRp:R292Q

RdRp:H314Y

RdRp:N421S

RdRp:I505T

RdRp:C648R

RdRp:R764K

RdRp:L765P

RdRp:T767A

RdRp:D771E

RdRp:E776K

RdRp:K809R

RdRp:G812E

RdRp:T876S

RdRp:R896S

RdRp:G1047E

RdRp:V1228I

RdRp:N1367D

RdRp:P1660T

Deletions

GPC:22-62, GPC:71, GPC:108-111, GPC:115, GPC:122, GPC:131, GPC:155-159

Insertions

ins_GPC:61:IN, ins_GPC:119:GASTPSNTTSNKPDVNSL