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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 10 05:32:46 2021 (UTC+2)

Author: Olivier Friard - Department of Life Sciences and Systems Biology - University of Turin - Italy

We gratefully acknowledge the Authors of the Originating and Submitting laboratories of the genetic sequence and metadata shared via GISAID, on which this research is based.
The isolates collection dates are in YYYY-MM-DD format (ISO 8601).

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Number of isolates sequences available: 477

Method

When the target sequence of amplification systems is available the primers and probe are aligned against the target sequence using the Smith-Waterman local sequence alignment algorithm and the alignments are classified in 3 categories:
             Full match - All primers and probe have a 100% identity with the target sequence. In case of a 2 probes system (RdRP) at least one probe must have a 100% identity.
             The identities of forward/reverse primers AND probe are greater than or equal to 80% AND the length of the amplification product is comprised between the reference length plus/minus 8 bp.
             The identity of one primer OR the probe are less than 80% OR the length of the amplification product is NOT comprised between reference length plus/minus 8 bp.

If the target sequence is not available the The sequence is not available warning is shown.
Please note that the reverse primer sequence is shown reverted-complemented in the alignments.

Results

Move the mouse cursor over elements to see the details.

Virus name / Accession IDRegionCollection date2019-nCoV_N12019-nCoV_N22019-nCoV_N3E-SarbecoRdRP
EPI_ISL_547433
EPI_ISL_547434
EPI_ISL_547435
EPI_ISL_547436
EPI_ISL_547437
EPI_ISL_547438
EPI_ISL_547439
EPI_ISL_547440
EPI_ISL_547441
EPI_ISL_547442
EPI_ISL_547443
EPI_ISL_547444
EPI_ISL_613566
EPI_ISL_613567
EPI_ISL_613570
EPI_ISL_613636
EPI_ISL_613637
EPI_ISL_613638
EPI_ISL_613639
EPI_ISL_613640
EPI_ISL_613641
EPI_ISL_613642
EPI_ISL_613643
EPI_ISL_613644
EPI_ISL_613645
EPI_ISL_613646
EPI_ISL_613647
EPI_ISL_613648
EPI_ISL_613649
EPI_ISL_613650
EPI_ISL_613651
EPI_ISL_613652
EPI_ISL_613653
EPI_ISL_613654
EPI_ISL_613655
EPI_ISL_613656
EPI_ISL_613657
EPI_ISL_613658
EPI_ISL_613659
EPI_ISL_613660
EPI_ISL_613661
EPI_ISL_613662
EPI_ISL_613663
EPI_ISL_613664
EPI_ISL_613665
EPI_ISL_613666
EPI_ISL_613667
EPI_ISL_613668
EPI_ISL_613669
EPI_ISL_613670
EPI_ISL_613671
EPI_ISL_613672
EPI_ISL_613673
EPI_ISL_613674
EPI_ISL_613675
EPI_ISL_613676
EPI_ISL_613677
EPI_ISL_613678
EPI_ISL_613679
EPI_ISL_613680
EPI_ISL_613681
EPI_ISL_613682
EPI_ISL_613683
EPI_ISL_613684
EPI_ISL_613685
EPI_ISL_613686
EPI_ISL_613687
EPI_ISL_613688
EPI_ISL_613689
EPI_ISL_613690
EPI_ISL_613691
EPI_ISL_613692
EPI_ISL_613693
EPI_ISL_613694
EPI_ISL_613695
EPI_ISL_613696
EPI_ISL_613697
EPI_ISL_613698
EPI_ISL_613699
EPI_ISL_613700
EPI_ISL_613701
EPI_ISL_613702
EPI_ISL_613703
EPI_ISL_613704
EPI_ISL_613705
EPI_ISL_613958
EPI_ISL_613959
EPI_ISL_613960
EPI_ISL_614981
EPI_ISL_614982
EPI_ISL_614983
EPI_ISL_614984
EPI_ISL_614985
EPI_ISL_614986
EPI_ISL_614987
EPI_ISL_614988
EPI_ISL_614989
EPI_ISL_614990
EPI_ISL_614991
EPI_ISL_614992
EPI_ISL_614993
EPI_ISL_614994
EPI_ISL_614995
EPI_ISL_614996
EPI_ISL_614997
EPI_ISL_614998
EPI_ISL_614999
EPI_ISL_615000
EPI_ISL_615001
EPI_ISL_615002
EPI_ISL_615003
EPI_ISL_615004
EPI_ISL_615005
EPI_ISL_615006
EPI_ISL_615007
EPI_ISL_615008
EPI_ISL_615009
EPI_ISL_615010
EPI_ISL_615011
EPI_ISL_615012
EPI_ISL_615013
EPI_ISL_615014
EPI_ISL_615015
EPI_ISL_615016
EPI_ISL_615017
EPI_ISL_615018
EPI_ISL_615019
EPI_ISL_615020
EPI_ISL_615021
EPI_ISL_615022
EPI_ISL_615023
EPI_ISL_615024
EPI_ISL_615025
EPI_ISL_615026
EPI_ISL_615027
EPI_ISL_615028
EPI_ISL_615029
EPI_ISL_615030
EPI_ISL_615031
EPI_ISL_615032
EPI_ISL_615033
EPI_ISL_615034
EPI_ISL_615035
EPI_ISL_615036
EPI_ISL_615037
EPI_ISL_615038
EPI_ISL_615039
EPI_ISL_615040
EPI_ISL_615041
EPI_ISL_615042
EPI_ISL_615043
EPI_ISL_615044
EPI_ISL_615045
EPI_ISL_615046
EPI_ISL_615047
EPI_ISL_615048
EPI_ISL_615049
EPI_ISL_615050
EPI_ISL_615051
EPI_ISL_615052
EPI_ISL_615053
EPI_ISL_615054
EPI_ISL_615055
EPI_ISL_615056
EPI_ISL_615057
EPI_ISL_615058
EPI_ISL_615059
EPI_ISL_615060
EPI_ISL_615061
EPI_ISL_615062
EPI_ISL_632797
EPI_ISL_632798
EPI_ISL_632799
EPI_ISL_632800
EPI_ISL_632801
EPI_ISL_632802
EPI_ISL_632803
EPI_ISL_632804
EPI_ISL_632805
EPI_ISL_632806
EPI_ISL_632807
EPI_ISL_632808
EPI_ISL_632809
EPI_ISL_632810
EPI_ISL_632811
EPI_ISL_632812
EPI_ISL_632813
EPI_ISL_632814
EPI_ISL_632815
EPI_ISL_632816
EPI_ISL_632817
EPI_ISL_632818
EPI_ISL_632819
EPI_ISL_632820
EPI_ISL_632821
EPI_ISL_632822
EPI_ISL_632846
EPI_ISL_637190
EPI_ISL_637191
EPI_ISL_637192
EPI_ISL_637193
EPI_ISL_637194
EPI_ISL_637195
EPI_ISL_637196
EPI_ISL_637197
EPI_ISL_637198
EPI_ISL_637199
EPI_ISL_637200
EPI_ISL_637201
EPI_ISL_637202
EPI_ISL_637203
EPI_ISL_637204
EPI_ISL_637205
EPI_ISL_637206
EPI_ISL_637207
EPI_ISL_637208
EPI_ISL_637209
EPI_ISL_637210
EPI_ISL_637211
EPI_ISL_637212
EPI_ISL_637213
EPI_ISL_637214
EPI_ISL_637215
EPI_ISL_637216
EPI_ISL_637217
EPI_ISL_637218
EPI_ISL_637219
EPI_ISL_637220
EPI_ISL_637221
EPI_ISL_637222
EPI_ISL_637223
EPI_ISL_637224
EPI_ISL_637225
EPI_ISL_637226
EPI_ISL_637227
EPI_ISL_637228
EPI_ISL_637229
EPI_ISL_637230
EPI_ISL_637231
EPI_ISL_639823
EPI_ISL_639824
EPI_ISL_671270
EPI_ISL_671271
EPI_ISL_671272
EPI_ISL_671273
EPI_ISL_671274
EPI_ISL_671275
EPI_ISL_671276
EPI_ISL_671277
EPI_ISL_671278
EPI_ISL_671279
EPI_ISL_671280
EPI_ISL_671281
EPI_ISL_671282
EPI_ISL_671283
EPI_ISL_671284
EPI_ISL_671285
EPI_ISL_671286
EPI_ISL_671287
EPI_ISL_671288
EPI_ISL_671289
EPI_ISL_671290
EPI_ISL_671291
EPI_ISL_671292
EPI_ISL_671293
EPI_ISL_671294
EPI_ISL_671295
EPI_ISL_671296
EPI_ISL_671297
EPI_ISL_671298
EPI_ISL_671299
EPI_ISL_671300
EPI_ISL_671301
EPI_ISL_671302
EPI_ISL_671303
EPI_ISL_671304
EPI_ISL_671305
EPI_ISL_671306
EPI_ISL_671307
EPI_ISL_671308
EPI_ISL_671309
EPI_ISL_671310
EPI_ISL_671311
EPI_ISL_671312
EPI_ISL_671313
EPI_ISL_671314
EPI_ISL_671315
EPI_ISL_671316
EPI_ISL_671317
EPI_ISL_671318
EPI_ISL_671319
EPI_ISL_671320
EPI_ISL_671321
EPI_ISL_671322
EPI_ISL_671323
EPI_ISL_671324
EPI_ISL_671325
EPI_ISL_671326
EPI_ISL_671327
EPI_ISL_671328
EPI_ISL_671329
EPI_ISL_671330
EPI_ISL_671331
EPI_ISL_671332
EPI_ISL_671333
EPI_ISL_671334
EPI_ISL_671335
EPI_ISL_709948
EPI_ISL_709950
EPI_ISL_709951
EPI_ISL_709952
EPI_ISL_709953
EPI_ISL_709954
EPI_ISL_709955
EPI_ISL_709956
EPI_ISL_709957
EPI_ISL_709959
EPI_ISL_709960
EPI_ISL_709961
EPI_ISL_709962
EPI_ISL_709963
EPI_ISL_709964
EPI_ISL_709965
EPI_ISL_709966
EPI_ISL_709967
EPI_ISL_709968
EPI_ISL_709969
EPI_ISL_709970
EPI_ISL_709971
EPI_ISL_709972
EPI_ISL_709973
EPI_ISL_709974
EPI_ISL_709975
EPI_ISL_709976
EPI_ISL_709977
EPI_ISL_709978
EPI_ISL_709979
EPI_ISL_709980
EPI_ISL_709981
EPI_ISL_709982
EPI_ISL_709983
EPI_ISL_709984
EPI_ISL_709985
EPI_ISL_709986
EPI_ISL_709987
EPI_ISL_709988
EPI_ISL_709989
EPI_ISL_709990
EPI_ISL_709991
EPI_ISL_709992
EPI_ISL_709993
EPI_ISL_709994
EPI_ISL_709995
EPI_ISL_709996
EPI_ISL_709997
EPI_ISL_709998
EPI_ISL_709999
EPI_ISL_710000
EPI_ISL_710001
EPI_ISL_710002
EPI_ISL_710003
EPI_ISL_710004
EPI_ISL_710005
EPI_ISL_710006
EPI_ISL_710007
EPI_ISL_710008
EPI_ISL_710009
EPI_ISL_710010
EPI_ISL_710011
EPI_ISL_710012
EPI_ISL_710013
EPI_ISL_710014
EPI_ISL_710015
EPI_ISL_710016
EPI_ISL_710017
EPI_ISL_710018
EPI_ISL_710019
EPI_ISL_710020
EPI_ISL_710021
EPI_ISL_710022
EPI_ISL_710023
EPI_ISL_710024
EPI_ISL_710025
EPI_ISL_710026
EPI_ISL_710027
EPI_ISL_710028
EPI_ISL_710029
EPI_ISL_710030
EPI_ISL_710031
EPI_ISL_710032
EPI_ISL_710033
EPI_ISL_710535
EPI_ISL_710536
EPI_ISL_766057
EPI_ISL_766058
EPI_ISL_766066
EPI_ISL_766103
EPI_ISL_766242
EPI_ISL_766318
EPI_ISL_766319
EPI_ISL_766320
EPI_ISL_766321
EPI_ISL_766322
EPI_ISL_766323
EPI_ISL_766324
EPI_ISL_766325
EPI_ISL_766326
EPI_ISL_766327
EPI_ISL_766328
EPI_ISL_766329
EPI_ISL_766330
EPI_ISL_766331
EPI_ISL_766332
EPI_ISL_766333
EPI_ISL_766334
EPI_ISL_766335
EPI_ISL_766336
EPI_ISL_766337
EPI_ISL_766338
EPI_ISL_766339
EPI_ISL_766340
EPI_ISL_766341
EPI_ISL_766342
EPI_ISL_766343
EPI_ISL_766344
EPI_ISL_766345
EPI_ISL_766346
EPI_ISL_766347
EPI_ISL_766348
EPI_ISL_766349
EPI_ISL_766350
EPI_ISL_766351
EPI_ISL_766352
EPI_ISL_766353
EPI_ISL_766354
EPI_ISL_766355
EPI_ISL_766356
EPI_ISL_766357
EPI_ISL_766358
EPI_ISL_766359
EPI_ISL_766360
EPI_ISL_766361
EPI_ISL_766362
EPI_ISL_766363
EPI_ISL_766364
EPI_ISL_766365
EPI_ISL_766366
EPI_ISL_766367
EPI_ISL_766368
EPI_ISL_766369
EPI_ISL_766370
EPI_ISL_766371
EPI_ISL_766372
EPI_ISL_766373
EPI_ISL_766374
EPI_ISL_766375
EPI_ISL_766376
EPI_ISL_766377
EPI_ISL_766378
EPI_ISL_766379
EPI_ISL_766380
EPI_ISL_766381
EPI_ISL_766382
EPI_ISL_766383
EPI_ISL_766384
EPI_ISL_766385
EPI_ISL_766386
EPI_ISL_766387
EPI_ISL_766388
EPI_ISL_766389
EPI_ISL_766390
EPI_ISL_766391
EPI_ISL_766392
EPI_ISL_766393
EPI_ISL_766394
EPI_ISL_769871
EPI_ISL_769872

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