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


Update: Sun Jan 31 07:00:30 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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USA

Number of isolates sequences available: 89495

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
USA/CruiseA-1/2020 EPI_ISL_4136062020-02-17
USA/CruiseA-2/2020 EPI_ISL_4136072020-02-18
USA/CruiseA-3/2020 EPI_ISL_4136082020-02-18
USA/CruiseA-4/2020 EPI_ISL_4136092020-02-21
USA/CruiseA-5/2020 EPI_ISL_4136102020-02-21
USA/CruiseA-6/2020 EPI_ISL_4136112020-02-21
USA/CruiseA-7/2020 EPI_ISL_4136122020-02-17
USA/CruiseA-8/2020 EPI_ISL_4136132020-02-17
USA/CruiseA-9/2020 EPI_ISL_4136142020-02-17
USA/CruiseA-10/2020 EPI_ISL_4136152020-02-17
USA/CruiseA-11/2020 EPI_ISL_4136162020-02-17
USA/CruiseA-12/2020 EPI_ISL_4136172020-02-20
USA/CruiseA-13/2020 EPI_ISL_4136182020-02-20
USA/CruiseA-14/2020 EPI_ISL_4136192020-02-25
USA/CruiseA-15/2020 EPI_ISL_4136202020-02-18
USA/CruiseA-16/2020 EPI_ISL_4136212020-02-18
USA/CruiseA-17/2020 EPI_ISL_4136222020-02-24
USA/CruiseA-18/2020 EPI_ISL_4136232020-02-24
USA/CruiseA-19/2020 EPI_ISL_4144792020-02-18
USA/CruiseA-21/2020 EPI_ISL_4144802020-02-21
USA/CruiseA-22/2020 EPI_ISL_4144812020-02-21
USA/CruiseA-23/2020 EPI_ISL_4144822020-02-18
USA/CruiseA-24/2020 EPI_ISL_4144832020-02-17
USA/CruiseA-25/2020 EPI_ISL_4144842020-02-17
USA/CruiseA-26/2020 EPI_ISL_4144852020-02-24
USA/UN-UW219/2020 EPI_ISL_4173682020-03-13
USA/UN-UW276/2020 EPI_ISL_4180612020-03-13
USA/UN-UW354/2020 EPI_ISL_4189212020-03-16
USA/UN-UW358/2020 EPI_ISL_4189252020-03
USA/UN-UW382/2020 EPI_ISL_4189472020-03-16
USA/UN-UW-1312/2020 EPI_ISL_4229622020-03-16
USA/UN-UW-1331/2020 EPI_ISL_4229682020-03
USA/UN-UW-1291/2020 EPI_ISL_4229782020-03-16
USA/UN-UW-1292/2020 EPI_ISL_4229792020-03-16
USA/UN-UW-1307/2020 EPI_ISL_4229802020-03-16
USA/UN-UW-1403/2020 EPI_ISL_4229822020-03-16
USA/UN-UW-1407/2020 EPI_ISL_4229832020-03-17
USA/UN-UW-1449/2020 EPI_ISL_4230232020-03
USA/UN-UW-1402/2020 EPI_ISL_4241812020-03-16
USA/UN-UW-1486/2020 EPI_ISL_4241852020-03-18
USA/UN-UW-1773/2020 EPI_ISL_4242482020-03
USA/UN-UW-1791/2020 EPI_ISL_4242492020-03-20
USA/UN-UW-1832/2020 EPI_ISL_4242552020-03-16
USA/UN-UW-1834/2020 EPI_ISL_4242652020-03-22
USA/UN-UW-1818/2020 EPI_ISL_4242662020-03-22
USA/UN-UW-1817/2020 EPI_ISL_4242672020-03-22
USA/UN-UW-1816/2020 EPI_ISL_4242682020-03-22
USA/UN-UW-2069/2020 EPI_ISL_4260772020-03-21
USA/UN-UW-2139/2020 EPI_ISL_4260782020-03-23
USA/UN-UW-4645/2020 EPI_ISL_4296282020-04-06
USA/UN-UW-5044/2020 EPI_ISL_4296432020-04-08
USA/UN-UW-5172/2020 EPI_ISL_4296562020-04-02
EPI_ISL_430879
EPI_ISL_430881
EPI_ISL_430882
EPI_ISL_430886
EPI_ISL_430890
EPI_ISL_430897
EPI_ISL_430903
EPI_ISL_430909
EPI_ISL_430910
EPI_ISL_430916
EPI_ISL_430924
EPI_ISL_437803
EPI_ISL_437818
EPI_ISL_437819
EPI_ISL_437852
EPI_ISL_450406The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450407The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_456656
EPI_ISL_461437
EPI_ISL_461438
EPI_ISL_476904
EPI_ISL_476910
EPI_ISL_476919
EPI_ISL_476922
EPI_ISL_476923
EPI_ISL_476926
EPI_ISL_476932
EPI_ISL_477683
EPI_ISL_477684
EPI_ISL_485949
EPI_ISL_485950
EPI_ISL_485951
EPI_ISL_485952
EPI_ISL_485953
EPI_ISL_485954
EPI_ISL_485955
EPI_ISL_485956
EPI_ISL_485957
EPI_ISL_485958
EPI_ISL_485959
EPI_ISL_485960
EPI_ISL_485961
EPI_ISL_485963
EPI_ISL_485964
EPI_ISL_485967
EPI_ISL_485968
EPI_ISL_485969
EPI_ISL_491002
EPI_ISL_491003
EPI_ISL_501084
EPI_ISL_501085
EPI_ISL_514062
EPI_ISL_514063
EPI_ISL_514064
EPI_ISL_514065
EPI_ISL_514066
EPI_ISL_514067
EPI_ISL_514068
EPI_ISL_514069
EPI_ISL_514070
EPI_ISL_514071
EPI_ISL_514072
EPI_ISL_514073
EPI_ISL_514074
EPI_ISL_514075
EPI_ISL_514076
EPI_ISL_514077
EPI_ISL_514078
EPI_ISL_514079
EPI_ISL_514080
EPI_ISL_514081
EPI_ISL_514082
EPI_ISL_514083
EPI_ISL_514084
EPI_ISL_514085
EPI_ISL_514086
EPI_ISL_514087
EPI_ISL_514088
EPI_ISL_514089
EPI_ISL_514090
EPI_ISL_514091
EPI_ISL_514092
EPI_ISL_514128
EPI_ISL_576399
EPI_ISL_576400
EPI_ISL_576401
EPI_ISL_576402
EPI_ISL_576403
EPI_ISL_576404
EPI_ISL_576406
EPI_ISL_576489
EPI_ISL_576490
EPI_ISL_576491
EPI_ISL_576492
EPI_ISL_576493
EPI_ISL_576494
EPI_ISL_576495
EPI_ISL_576496
EPI_ISL_576497
EPI_ISL_576498
EPI_ISL_576499
EPI_ISL_576500
EPI_ISL_576501
EPI_ISL_576502
EPI_ISL_576503
EPI_ISL_576504
EPI_ISL_576505
EPI_ISL_576506
EPI_ISL_576507
EPI_ISL_576508
EPI_ISL_576509
EPI_ISL_576510
EPI_ISL_576511
EPI_ISL_576512
EPI_ISL_576513
EPI_ISL_576514
EPI_ISL_576515
EPI_ISL_576516
EPI_ISL_576517
EPI_ISL_603256
EPI_ISL_603259
EPI_ISL_735466
EPI_ISL_759860
EPI_ISL_759861
EPI_ISL_759862
EPI_ISL_759863
EPI_ISL_759864
EPI_ISL_759865
EPI_ISL_801537
EPI_ISL_884445
EPI_ISL_884446
EPI_ISL_884447
EPI_ISL_884448
EPI_ISL_884449
EPI_ISL_884450
EPI_ISL_884451
EPI_ISL_884452
EPI_ISL_884453
EPI_ISL_884454
EPI_ISL_884455
EPI_ISL_884456
EPI_ISL_884457
EPI_ISL_884458
EPI_ISL_884459
EPI_ISL_884460
EPI_ISL_884461
EPI_ISL_884462
EPI_ISL_884463
EPI_ISL_884464
EPI_ISL_884465
EPI_ISL_884466
EPI_ISL_884467
EPI_ISL_884468
EPI_ISL_884469
EPI_ISL_884470
EPI_ISL_884471
EPI_ISL_884472
EPI_ISL_884473
EPI_ISL_884474
EPI_ISL_884475
EPI_ISL_884476
EPI_ISL_884477
EPI_ISL_884478
EPI_ISL_884479
EPI_ISL_884480
EPI_ISL_884481
EPI_ISL_884482
EPI_ISL_884483
EPI_ISL_884484
EPI_ISL_884485
EPI_ISL_884486
EPI_ISL_884487
EPI_ISL_884488
EPI_ISL_884489
EPI_ISL_884490
EPI_ISL_884491
EPI_ISL_884492
EPI_ISL_884493
EPI_ISL_884494
EPI_ISL_884495
EPI_ISL_884496
EPI_ISL_884497
EPI_ISL_884498
EPI_ISL_884499
EPI_ISL_884500
EPI_ISL_884501
EPI_ISL_884502
EPI_ISL_884503
EPI_ISL_884504
EPI_ISL_884505
EPI_ISL_884506
EPI_ISL_884507
EPI_ISL_884508
EPI_ISL_884509
EPI_ISL_884510
EPI_ISL_884511
EPI_ISL_884512
EPI_ISL_884513
EPI_ISL_884514
EPI_ISL_884515
EPI_ISL_884516
EPI_ISL_884517
EPI_ISL_884518
EPI_ISL_884519
EPI_ISL_884520
EPI_ISL_884521
EPI_ISL_884522
EPI_ISL_884523
EPI_ISL_884524
EPI_ISL_884525
EPI_ISL_884526
EPI_ISL_884527
EPI_ISL_884528
EPI_ISL_884529
EPI_ISL_884530
EPI_ISL_884531
EPI_ISL_884532
EPI_ISL_884533
EPI_ISL_884534
EPI_ISL_884535
EPI_ISL_884536
EPI_ISL_884537
EPI_ISL_884538
EPI_ISL_884539
EPI_ISL_884540
EPI_ISL_884541
EPI_ISL_884542
EPI_ISL_884543
EPI_ISL_884544
EPI_ISL_884545
EPI_ISL_884546
EPI_ISL_884547
EPI_ISL_884548
EPI_ISL_884549
EPI_ISL_884550
EPI_ISL_884551
EPI_ISL_884552
EPI_ISL_884553
EPI_ISL_884554
EPI_ISL_884555
EPI_ISL_884556
EPI_ISL_884557The sequence is not available
EPI_ISL_884558
EPI_ISL_884559The sequence is not available
EPI_ISL_884560
EPI_ISL_884561
EPI_ISL_884562The sequence is not available
EPI_ISL_884563
EPI_ISL_884564
EPI_ISL_884565
EPI_ISL_884566
EPI_ISL_884567
EPI_ISL_884568
EPI_ISL_884569
EPI_ISL_884570
EPI_ISL_884571
EPI_ISL_884572
EPI_ISL_884573
EPI_ISL_884574
EPI_ISL_884575
EPI_ISL_884576
EPI_ISL_884577
EPI_ISL_884578
EPI_ISL_884579
EPI_ISL_887763
EPI_ISL_887877
EPI_ISL_887895
EPI_ISL_887976
EPI_ISL_887990
EPI_ISL_888064
EPI_ISL_888099
EPI_ISL_888343
EPI_ISL_888362
EPI_ISL_888366
EPI_ISL_888527
EPI_ISL_888554
EPI_ISL_888569
EPI_ISL_890236
EPI_ISL_450624Alabama
EPI_ISL_494504Alabama
EPI_ISL_498695Alabama
EPI_ISL_498696Alabama
EPI_ISL_500522Alabama
EPI_ISL_501072Alabama
EPI_ISL_509424Alabama
EPI_ISL_509425Alabama
EPI_ISL_509426Alabama
EPI_ISL_509427Alabama
EPI_ISL_509428Alabama
EPI_ISL_509429Alabama
EPI_ISL_509688Alabama
EPI_ISL_571016Alabama
EPI_ISL_571017Alabama
EPI_ISL_571155Alabama
EPI_ISL_571572Alabama
EPI_ISL_747044Alabama
EPI_ISL_747045Alabama
EPI_ISL_747046Alabama
EPI_ISL_747047Alabama
EPI_ISL_747048Alabama
EPI_ISL_751647Alabama
EPI_ISL_751668Alabama
EPI_ISL_751753Alabama
EPI_ISL_751755Alabama
EPI_ISL_751756Alabama
EPI_ISL_751791Alabama
EPI_ISL_751792Alabama
EPI_ISL_778867Alabama
EPI_ISL_802654Alabama
EPI_ISL_812560Alabama
EPI_ISL_812561Alabama
EPI_ISL_812597Alabama
EPI_ISL_812598Alabama
EPI_ISL_812613Alabama
EPI_ISL_812638Alabama
EPI_ISL_850576Alabama
EPI_ISL_850580Alabama
EPI_ISL_850757Alabama
EPI_ISL_850856Alabama
EPI_ISL_850899Alabama
EPI_ISL_850964Alabama
EPI_ISL_871817Alabama
EPI_ISL_872395Alabama
EPI_ISL_872396Alabama
EPI_ISL_872397Alabama
EPI_ISL_872398Alabama
EPI_ISL_872399Alabama
EPI_ISL_872400Alabama
EPI_ISL_872401Alabama
EPI_ISL_872402Alabama
EPI_ISL_872403Alabama
EPI_ISL_872404Alabama
EPI_ISL_872405Alabama
EPI_ISL_872406Alabama
EPI_ISL_872407Alabama
EPI_ISL_872408Alabama
EPI_ISL_872409Alabama
EPI_ISL_872410Alabama
EPI_ISL_872411Alabama
EPI_ISL_872412Alabama
EPI_ISL_872413Alabama
EPI_ISL_872414Alabama
EPI_ISL_872415Alabama
EPI_ISL_872416Alabama
EPI_ISL_872417Alabama
EPI_ISL_872418Alabama
EPI_ISL_872419Alabama
EPI_ISL_872420Alabama
EPI_ISL_872421Alabama
EPI_ISL_872422Alabama
EPI_ISL_872423Alabama
EPI_ISL_872424Alabama
EPI_ISL_872425Alabama
EPI_ISL_872426Alabama
EPI_ISL_872427Alabama
EPI_ISL_872428Alabama
EPI_ISL_872429Alabama
EPI_ISL_872430Alabama
EPI_ISL_872431Alabama
EPI_ISL_872432Alabama
EPI_ISL_872433Alabama
EPI_ISL_872434Alabama
EPI_ISL_872435Alabama
EPI_ISL_872436Alabama
EPI_ISL_872437Alabama
EPI_ISL_872438Alabama
EPI_ISL_872439Alabama
EPI_ISL_872440Alabama
EPI_ISL_872441Alabama
EPI_ISL_872442Alabama
EPI_ISL_872443Alabama
EPI_ISL_872444Alabama
EPI_ISL_872445Alabama
EPI_ISL_872446Alabama
EPI_ISL_872447Alabama
EPI_ISL_872448Alabama
EPI_ISL_872449Alabama
EPI_ISL_872450Alabama
EPI_ISL_872451Alabama
EPI_ISL_872452Alabama
EPI_ISL_872453Alabama
EPI_ISL_872454Alabama
EPI_ISL_872455Alabama
EPI_ISL_872456Alabama
EPI_ISL_872457Alabama
EPI_ISL_872458Alabama
EPI_ISL_872459Alabama
EPI_ISL_872460Alabama
EPI_ISL_872461Alabama
EPI_ISL_872462Alabama
EPI_ISL_872463Alabama
EPI_ISL_872464Alabama
EPI_ISL_872465Alabama
EPI_ISL_872466Alabama
EPI_ISL_872467Alabama
EPI_ISL_872468Alabama
EPI_ISL_872469Alabama
EPI_ISL_872470Alabama
EPI_ISL_872471Alabama
EPI_ISL_872472Alabama
EPI_ISL_872473Alabama
EPI_ISL_872474Alabama
EPI_ISL_872475Alabama
EPI_ISL_872476Alabama
EPI_ISL_872477Alabama
EPI_ISL_875570Alabama
EPI_ISL_875571Alabama
EPI_ISL_875572Alabama
EPI_ISL_875573Alabama
EPI_ISL_875574Alabama
EPI_ISL_875575Alabama
EPI_ISL_875576Alabama
EPI_ISL_875577Alabama
EPI_ISL_875578Alabama
EPI_ISL_875579Alabama
EPI_ISL_875580Alabama
EPI_ISL_875581Alabama
EPI_ISL_875582Alabama
EPI_ISL_875583Alabama
EPI_ISL_875584Alabama
EPI_ISL_875585Alabama
EPI_ISL_875586Alabama
EPI_ISL_875587Alabama
EPI_ISL_875588Alabama
EPI_ISL_875589Alabama
EPI_ISL_875590Alabama
EPI_ISL_875591Alabama
EPI_ISL_875592Alabama
EPI_ISL_875593Alabama
EPI_ISL_875594Alabama
EPI_ISL_875595Alabama
EPI_ISL_875596Alabama
EPI_ISL_875597Alabama
EPI_ISL_875598Alabama
EPI_ISL_875599Alabama
EPI_ISL_875600Alabama
EPI_ISL_875601Alabama
EPI_ISL_875602Alabama
EPI_ISL_875603Alabama
EPI_ISL_875604Alabama
EPI_ISL_875605Alabama
EPI_ISL_875606Alabama
EPI_ISL_875607Alabama
EPI_ISL_875608Alabama
EPI_ISL_875609Alabama
EPI_ISL_875610Alabama
EPI_ISL_875611Alabama
EPI_ISL_875612Alabama
EPI_ISL_875613Alabama
EPI_ISL_875614Alabama
EPI_ISL_875615Alabama
EPI_ISL_875616Alabama
EPI_ISL_875617Alabama
EPI_ISL_875618Alabama
EPI_ISL_875619Alabama
EPI_ISL_875620Alabama
EPI_ISL_875621Alabama
EPI_ISL_875622Alabama
EPI_ISL_875623Alabama
EPI_ISL_875624Alabama
EPI_ISL_875625Alabama
EPI_ISL_875626Alabama
EPI_ISL_875627Alabama
EPI_ISL_875628Alabama
EPI_ISL_875629Alabama
EPI_ISL_875630Alabama
EPI_ISL_875631Alabama
EPI_ISL_875632Alabama
EPI_ISL_875633Alabama
EPI_ISL_875634Alabama
EPI_ISL_875635Alabama
EPI_ISL_875636Alabama
EPI_ISL_875637Alabama
EPI_ISL_875638Alabama
EPI_ISL_875639Alabama
EPI_ISL_875640Alabama
EPI_ISL_875641Alabama
EPI_ISL_875642Alabama
EPI_ISL_875643Alabama
EPI_ISL_875644Alabama
EPI_ISL_875645Alabama
EPI_ISL_875646Alabama
EPI_ISL_875647Alabama
EPI_ISL_875648Alabama
EPI_ISL_875649Alabama
EPI_ISL_875650Alabama
EPI_ISL_875651Alabama
EPI_ISL_875652Alabama
EPI_ISL_875653Alabama
EPI_ISL_875654Alabama
EPI_ISL_875655Alabama
EPI_ISL_875656Alabama
EPI_ISL_875657Alabama
EPI_ISL_875658Alabama
EPI_ISL_875659Alabama
EPI_ISL_875874Alabama
EPI_ISL_875875Alabama
EPI_ISL_875876Alabama
EPI_ISL_875877Alabama
EPI_ISL_875878Alabama
EPI_ISL_875879Alabama
EPI_ISL_875880Alabama
EPI_ISL_875881Alabama
EPI_ISL_875882Alabama
EPI_ISL_875883Alabama
EPI_ISL_875884Alabama
EPI_ISL_875885Alabama
EPI_ISL_875886Alabama
EPI_ISL_875887Alabama
EPI_ISL_875888Alabama
EPI_ISL_875889Alabama
EPI_ISL_875890Alabama
EPI_ISL_875891Alabama
EPI_ISL_875892Alabama
EPI_ISL_875893Alabama
EPI_ISL_875894Alabama
EPI_ISL_875895Alabama
EPI_ISL_875896Alabama
EPI_ISL_875897Alabama
EPI_ISL_875898Alabama
EPI_ISL_875899Alabama
EPI_ISL_875900Alabama
EPI_ISL_875901Alabama
EPI_ISL_875902Alabama
EPI_ISL_875903Alabama
EPI_ISL_875904Alabama
EPI_ISL_875905Alabama
EPI_ISL_875906Alabama
EPI_ISL_875907Alabama
EPI_ISL_875908Alabama
EPI_ISL_875909Alabama
EPI_ISL_875910Alabama
EPI_ISL_875911Alabama
EPI_ISL_875912Alabama
EPI_ISL_875913Alabama
EPI_ISL_875914Alabama
EPI_ISL_875915Alabama
EPI_ISL_875916Alabama
EPI_ISL_875917Alabama
EPI_ISL_875918Alabama
EPI_ISL_875919Alabama
EPI_ISL_875920Alabama
EPI_ISL_875921Alabama
EPI_ISL_875922Alabama
EPI_ISL_875923Alabama
EPI_ISL_875924Alabama
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