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


Update: Sun Oct 25 07:18:47 2020 (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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Bangladesh

Number of isolates sequences available: 372

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_445244
EPI_ISL_447904
EPI_ISL_470801
EPI_ISL_477125
EPI_ISL_477126
EPI_ISL_477127
EPI_ISL_477128
EPI_ISL_477129
EPI_ISL_477130
EPI_ISL_477131
EPI_ISL_477132
EPI_ISL_477133
EPI_ISL_477134
EPI_ISL_477135
EPI_ISL_477136
EPI_ISL_477137
EPI_ISL_477138
EPI_ISL_477139
EPI_ISL_477140
EPI_ISL_478671The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_482742The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_492028
EPI_ISL_492029
EPI_ISL_492030
EPI_ISL_492031
EPI_ISL_487362Barisal
EPI_ISL_487363Barisal
EPI_ISL_487364Barisal
EPI_ISL_487366Barisal
EPI_ISL_487367Barisal
EPI_ISL_487368Barisal
EPI_ISL_487371Barisal
EPI_ISL_487372Barisal
EPI_ISL_487373Barisal
EPI_ISL_487375Barisal
EPI_ISL_487376Barisal
EPI_ISL_487378Barisal
EPI_ISL_487380Barisal
EPI_ISL_487382Barisal
EPI_ISL_487383Barisal
EPI_ISL_487384Barisal
EPI_ISL_487385Barisal
EPI_ISL_487386Barisal
EPI_ISL_487392Barisal
EPI_ISL_487393Barisal
EPI_ISL_487394Barisal
EPI_ISL_487395Barisal
EPI_ISL_487396Barisal
EPI_ISL_450339Chittagong
EPI_ISL_450340Chittagong
EPI_ISL_450341Chittagong
EPI_ISL_450342Chittagong
EPI_ISL_450343Chittagong
EPI_ISL_450344Chittagong
EPI_ISL_450345Chittagong
EPI_ISL_464164Chittagong
EPI_ISL_466637Chittagong
EPI_ISL_466638Chittagong
EPI_ISL_466639Chittagong
EPI_ISL_466687Chittagong
EPI_ISL_466692Chittagong
EPI_ISL_468074Chittagong
EPI_ISL_483632Chittagong
EPI_ISL_483633Chittagong
EPI_ISL_483634Chittagong
EPI_ISL_483635Chittagong
EPI_ISL_483636Chittagong
EPI_ISL_483641Chittagong
EPI_ISL_483642Chittagong
EPI_ISL_483643Chittagong
EPI_ISL_483644Chittagong
EPI_ISL_483686Chittagong
EPI_ISL_483687Chittagong
EPI_ISL_483688Chittagong
EPI_ISL_483689Chittagong
EPI_ISL_483690Chittagong
EPI_ISL_483694Chittagong
EPI_ISL_483695Chittagong
EPI_ISL_483699Chittagong
EPI_ISL_483700Chittagong
EPI_ISL_498268Chittagong
EPI_ISL_498272Chittagong
EPI_ISL_498273Chittagong
EPI_ISL_498274Chittagong
EPI_ISL_498417Chittagong
EPI_ISL_498418Chittagong
EPI_ISL_498419Chittagong
EPI_ISL_498466Chittagong
EPI_ISL_498467Chittagong
EPI_ISL_498809Chittagong
EPI_ISL_498811Chittagong
EPI_ISL_498814Chittagong
EPI_ISL_498815Chittagong
EPI_ISL_504137Chittagong
EPI_ISL_504176Chittagong
EPI_ISL_514129Chittagong
EPI_ISL_514130Chittagong
EPI_ISL_514233Chittagong
EPI_ISL_514234Chittagong
EPI_ISL_514235Chittagong
EPI_ISL_514236Chittagong
EPI_ISL_514237Chittagong
EPI_ISL_514238Chittagong
EPI_ISL_514239Chittagong
EPI_ISL_514240Chittagong
EPI_ISL_514241Chittagong
EPI_ISL_514242Chittagong
EPI_ISL_514243Chittagong
EPI_ISL_514244Chittagong
EPI_ISL_514245Chittagong
EPI_ISL_514246Chittagong
EPI_ISL_514247Chittagong
EPI_ISL_514251Chittagong
EPI_ISL_514252Chittagong
EPI_ISL_514434Chittagong
EPI_ISL_514440Chittagong
EPI_ISL_514441Chittagong
EPI_ISL_514442ChittagongThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514580Chittagong
EPI_ISL_514613Chittagong
EPI_ISL_514614Chittagong
EPI_ISL_514615Chittagong
EPI_ISL_437912Dhaka
EPI_ISL_445213Dhaka
EPI_ISL_445214Dhaka
EPI_ISL_445215Dhaka
EPI_ISL_445216Dhaka
EPI_ISL_445217Dhaka
EPI_ISL_450839Dhaka
EPI_ISL_450840Dhaka
EPI_ISL_450841Dhaka
EPI_ISL_450842Dhaka
EPI_ISL_450843Dhaka
EPI_ISL_455420Dhaka
EPI_ISL_455458Dhaka
EPI_ISL_455459Dhaka
EPI_ISL_458133Dhaka
EPI_ISL_462090Dhaka
EPI_ISL_462091Dhaka
EPI_ISL_462092Dhaka
EPI_ISL_462093Dhaka
EPI_ISL_462094Dhaka
EPI_ISL_462095Dhaka
EPI_ISL_462096Dhaka
EPI_ISL_462097Dhaka
EPI_ISL_462098Dhaka
EPI_ISL_464159Dhaka
EPI_ISL_464160Dhaka
EPI_ISL_464161Dhaka
EPI_ISL_464162Dhaka
EPI_ISL_464163Dhaka
EPI_ISL_464165Dhaka
EPI_ISL_464166Dhaka
EPI_ISL_465163Dhaka
EPI_ISL_465164Dhaka
EPI_ISL_466626Dhaka
EPI_ISL_466627Dhaka
EPI_ISL_466628Dhaka
EPI_ISL_466629Dhaka
EPI_ISL_466630Dhaka
EPI_ISL_466636Dhaka
EPI_ISL_466644Dhaka
EPI_ISL_466645Dhaka
EPI_ISL_466649Dhaka
EPI_ISL_466650Dhaka
EPI_ISL_466686Dhaka
EPI_ISL_466688Dhaka
EPI_ISL_466689Dhaka
EPI_ISL_466690Dhaka
EPI_ISL_466691Dhaka
EPI_ISL_466693Dhaka
EPI_ISL_466694Dhaka
EPI_ISL_468070Dhaka
EPI_ISL_468071Dhaka
EPI_ISL_468072Dhaka
EPI_ISL_468073Dhaka
EPI_ISL_468075Dhaka
EPI_ISL_468076Dhaka
EPI_ISL_468077Dhaka
EPI_ISL_468078Dhaka
EPI_ISL_475169Dhaka
EPI_ISL_475170Dhaka
EPI_ISL_475754Dhaka
EPI_ISL_475760Dhaka
EPI_ISL_480414Dhaka
EPI_ISL_480415Dhaka
EPI_ISL_480416Dhaka
EPI_ISL_480417Dhaka
EPI_ISL_480418Dhaka
EPI_ISL_480419Dhaka
EPI_ISL_480420Dhaka
EPI_ISL_480421Dhaka
EPI_ISL_480424Dhaka
EPI_ISL_480425Dhaka
EPI_ISL_480426Dhaka
EPI_ISL_480427Dhaka
EPI_ISL_480439Dhaka
EPI_ISL_480440Dhaka
EPI_ISL_480441Dhaka
EPI_ISL_482487Dhaka
EPI_ISL_482489Dhaka
EPI_ISL_482700Dhaka
EPI_ISL_482701Dhaka
EPI_ISL_514248Dhaka
EPI_ISL_514249Dhaka
EPI_ISL_514250Dhaka
EPI_ISL_514253Dhaka
EPI_ISL_576389JashoreThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576390JashoreThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576391JashoreThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576392JashoreThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576393JashoreThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_447590KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_447897KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_475570Khulna
EPI_ISL_475571Khulna
EPI_ISL_475573Khulna
EPI_ISL_490109Khulna
EPI_ISL_490110Khulna
EPI_ISL_490111Khulna
EPI_ISL_490113Khulna
EPI_ISL_490114Khulna
EPI_ISL_490144Khulna
EPI_ISL_490164Khulna
EPI_ISL_490165Khulna
EPI_ISL_490167Khulna
EPI_ISL_490168Khulna
EPI_ISL_498253Khulna
EPI_ISL_498254Khulna
EPI_ISL_498267Khulna
EPI_ISL_498806Khulna
EPI_ISL_498808Khulna
EPI_ISL_503958Khulna
EPI_ISL_504040Khulna
EPI_ISL_512774Khulna
EPI_ISL_514228Khulna
EPI_ISL_514229Khulna
EPI_ISL_514230Khulna
EPI_ISL_514231Khulna
EPI_ISL_514232Khulna
EPI_ISL_548259KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_548260KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_548261KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_548262KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_548263KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_561375KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_561376KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_561377KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_561630KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_572319KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_572325KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_572326KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_572327KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576394KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576395KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576396KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576397KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583535KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583536KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583537KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583538KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583539KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583540KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583541KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583542KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583543KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583544KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583545KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583546KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583547KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583548KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583549KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583550KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583551KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583552KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583553KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583554KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583555KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_583556KhulnaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_498788Mymensingh
EPI_ISL_498789Mymensingh
EPI_ISL_498790Mymensingh
EPI_ISL_498791Mymensingh
EPI_ISL_498792Mymensingh
EPI_ISL_498793Mymensingh
EPI_ISL_498794Mymensingh
EPI_ISL_498795Mymensingh
EPI_ISL_498796Mymensingh
EPI_ISL_498932Mymensingh
EPI_ISL_498933Mymensingh
EPI_ISL_504180Mymensingh
EPI_ISL_504181Mymensingh
EPI_ISL_504182Mymensingh
EPI_ISL_480442Rajshahi
EPI_ISL_480443Rajshahi
EPI_ISL_480444Rajshahi
EPI_ISL_480445Rajshahi
EPI_ISL_480446Rajshahi
EPI_ISL_480447Rajshahi
EPI_ISL_480448Rajshahi
EPI_ISL_480449Rajshahi
EPI_ISL_480450Rajshahi
EPI_ISL_482485Rajshahi
EPI_ISL_482486Rajshahi
EPI_ISL_482488Rajshahi
EPI_ISL_483622Rajshahi
EPI_ISL_483623Rajshahi
EPI_ISL_483624Rajshahi
EPI_ISL_483626Rajshahi
EPI_ISL_483627Rajshahi
EPI_ISL_483628Rajshahi
EPI_ISL_483629Rajshahi
EPI_ISL_483630Rajshahi
EPI_ISL_483631Rajshahi
EPI_ISL_483693Rajshahi
EPI_ISL_498227Rajshahi
EPI_ISL_498228Rajshahi
EPI_ISL_498797Rajshahi
EPI_ISL_498800Rajshahi
EPI_ISL_498801Rajshahi
EPI_ISL_498802Rajshahi
EPI_ISL_498803Rajshahi
EPI_ISL_498804Rajshahi
EPI_ISL_498805Rajshahi
EPI_ISL_504183Rajshahi
EPI_ISL_504184Rajshahi
EPI_ISL_469285Rangpur
EPI_ISL_469286Rangpur
EPI_ISL_469297Rangpur
EPI_ISL_469298Rangpur
EPI_ISL_469299Rangpur
EPI_ISL_469300Rangpur
EPI_ISL_475083Rangpur
EPI_ISL_475084Rangpur
EPI_ISL_475165Rangpur
EPI_ISL_475166Rangpur
EPI_ISL_475167Rangpur
EPI_ISL_475168Rangpur
EPI_ISL_475171Rangpur
EPI_ISL_475172Rangpur
EPI_ISL_475173Rangpur
EPI_ISL_475238Rangpur
EPI_ISL_475755Rangpur
EPI_ISL_475756Rangpur
EPI_ISL_475757Rangpur
EPI_ISL_475758Rangpur
EPI_ISL_475759Rangpur
EPI_ISL_475761Rangpur
EPI_ISL_498549Rangpur
EPI_ISL_498816Rangpur
EPI_ISL_504177Rangpur
EPI_ISL_483645Sylhet
EPI_ISL_483646Sylhet
EPI_ISL_483647Sylhet
EPI_ISL_483691Sylhet
EPI_ISL_483692Sylhet
EPI_ISL_483703Sylhet
EPI_ISL_483705Sylhet
EPI_ISL_483707Sylhet
EPI_ISL_483710Sylhet
EPI_ISL_498550Sylhet
EPI_ISL_498783Sylhet
EPI_ISL_498784Sylhet
EPI_ISL_498785Sylhet
EPI_ISL_498786Sylhet
EPI_ISL_498787Sylhet
EPI_ISL_498817Sylhet
EPI_ISL_498818Sylhet
EPI_ISL_498830Sylhet
EPI_ISL_498892Sylhet
EPI_ISL_504178Sylhet
EPI_ISL_504179Sylhet

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