PPD_001W4G4.1

Display Name: Cameroon/PPD_001W4G4.1/2023-11-06

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

Country

Cameroon

Isolate name

11-2

Data use terms

Changed	User	Data use terms
2026-01-10 16:05	insdc_ingest_user	OPEN

OPEN

Data use terms URL

https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations

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

INSDC

INSDC accession L

PX659871.1

INSDC accession M

PX659870.1

INSDC accession S

PX659872.1

NCBI release date

2025-12-28

Host

Host taxon ID

72862

Host name - scientific

Hyalomma rufipes

Alignment and QC metrics S

Length S

1513

Completeness S

92.17%

# of SNPs S

# of inserted bases S

# of deleted bases S

# of ambiguous bases S

# of unknown bases S

# of frame shifts S

# of stop codons S

Frame shifts S

NP:220-325(nt:711-1030),NP:439-483(nt:1369-1504)

Alignment and QC metrics L

Length L

9395

Completeness L

97.46%

# of SNPs L

541

# of inserted bases L

# of deleted bases L

2433

# of ambiguous bases L

# of unknown bases L

# of frame shifts L

# of stop codons L

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)

Stop Codons L

RdRp:358,RdRp:385,RdRp:3578

Alignment and QC metrics M

Length M

1459

Completeness M

68.47%

# of SNPs M

387

# of inserted bases M

# of deleted bases M

2263

# of ambiguous bases M

# of unknown bases M

# of frame shifts M

# of stop codons M

Frame shifts M

GPC:468-1033(nt:1493-3191),GPC:1092-1416(nt:3366-4340),GPC:1621-1685(nt:4953-5147)

Stop Codons M

GPC:43

Submission details

Submission ID

PX659871.1.L/PX659870.1.M/PX659872.1.S

Submitting group

Automated Ingest from INSDC/NCBI Virus by Loculus

Date submitted

2026-01-10 16:04:36 UTC

Date released

2026-01-10 16:31:39 UTC

Earliest release date

2025-12-28

Lineage

Segment S Lineage

III

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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Organisms

PPD_001W4G4.1

Sample details

Data use terms

Authors

INSDC

Host

Alignment and QC metrics S

Alignment and QC metrics L

Alignment and QC metrics M

Submission details

Lineage

Nucleotide mutations

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

L

M

S

Amino acid mutations

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

GPC

NP

RdRp

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