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Status of SARS-CoV-2 detection systems (RT-PCR)
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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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Lithuania

Number of isolates sequences available: 213

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_450496
EPI_ISL_450497
EPI_ISL_541848Alytaus apskritis
EPI_ISL_541852Alytaus apskritis
EPI_ISL_541853Alytaus apskritis
EPI_ISL_603082Alytaus apskritis
EPI_ISL_603083Alytaus apskritis
EPI_ISL_770513Alytaus apskritis
EPI_ISL_770533Jonavos apskritis
EPI_ISL_770534Jonavos apskritis
EPI_ISL_770535Jonavos apskritis
EPI_ISL_770536Jonavos apskritis
EPI_ISL_770537Jonavos apskritis
EPI_ISL_770538Jonavos apskritis
EPI_ISL_770539Jonavos apskritis
EPI_ISL_770540Jonavos apskritis
EPI_ISL_770541Jonavos apskritis
EPI_ISL_770542Jonavos apskritis
EPI_ISL_770543Jonavos apskritis
EPI_ISL_770544Jonavos apskritis
EPI_ISL_770545Jonavos apskritis
EPI_ISL_770546Jonavos apskritis
EPI_ISL_770547Jonavos apskritis
EPI_ISL_770548Jonavos apskritis
EPI_ISL_770549Jonavos apskritis
EPI_ISL_541864Kauno apskritis
EPI_ISL_541870Kauno apskritis
EPI_ISL_541873Kauno apskritis
EPI_ISL_603084Kauno apskritis
EPI_ISL_603085Kauno apskritis
EPI_ISL_603088Kauno apskritis
EPI_ISL_603089Kauno apskritis
EPI_ISL_603096Kauno apskritis
EPI_ISL_603112Kauno apskritis
EPI_ISL_603115Kauno apskritis
EPI_ISL_603116Kauno apskritis
EPI_ISL_603118Kauno apskritis
EPI_ISL_636842Kauno apskritis
EPI_ISL_636843Kauno apskritis
EPI_ISL_636844Kauno apskritis
EPI_ISL_636845Kauno apskritis
EPI_ISL_636846Kauno apskritis
EPI_ISL_636847Kauno apskritis
EPI_ISL_636848Kauno apskritis
EPI_ISL_636849Kauno apskritis
EPI_ISL_636850Kauno apskritis
EPI_ISL_636851Kauno apskritis
EPI_ISL_636852Kauno apskritis
EPI_ISL_636853Kauno apskritis
EPI_ISL_636854Kauno apskritis
EPI_ISL_636855Kauno apskritis
EPI_ISL_636856Kauno apskritis
EPI_ISL_636857Kauno apskritis
EPI_ISL_636858Kauno apskritis
EPI_ISL_636859Kauno apskritis
EPI_ISL_636860Kauno apskritis
EPI_ISL_636861Kauno apskritis
EPI_ISL_636862Kauno apskritis
EPI_ISL_636864Kauno apskritis
EPI_ISL_636865Kauno apskritis
EPI_ISL_636868Kauno apskritis
EPI_ISL_636869Kauno apskritis
EPI_ISL_636870Kauno apskritis
EPI_ISL_636871Kauno apskritis
EPI_ISL_636875Kauno apskritis
EPI_ISL_636876Kauno apskritis
EPI_ISL_636877Kauno apskritis
EPI_ISL_636878Kauno apskritis
EPI_ISL_636879Kauno apskritis
EPI_ISL_636880Kauno apskritis
EPI_ISL_636881Kauno apskritis
EPI_ISL_636882Kauno apskritis
EPI_ISL_636883Kauno apskritis
EPI_ISL_636884Kauno apskritis
EPI_ISL_636885Kauno apskritis
EPI_ISL_636886Kauno apskritis
EPI_ISL_636888Kauno apskritis
EPI_ISL_636889Kauno apskritis
EPI_ISL_636890Kauno apskritis
EPI_ISL_636891Kauno apskritis
EPI_ISL_636892Kauno apskritis
EPI_ISL_636893Kauno apskritis
EPI_ISL_636894Kauno apskritis
EPI_ISL_636895Kauno apskritis
EPI_ISL_636896Kauno apskritis
EPI_ISL_636897Kauno apskritis
EPI_ISL_636898Kauno apskritis
EPI_ISL_636899Kauno apskritis
EPI_ISL_636900Kauno apskritis
EPI_ISL_636901Kauno apskritis
EPI_ISL_636902Kauno apskritis
EPI_ISL_636903Kauno apskritis
EPI_ISL_636904Kauno apskritis
EPI_ISL_636905Kauno apskritis
EPI_ISL_636906Kauno apskritis
EPI_ISL_770498Kauno apskritis
EPI_ISL_770499Kauno apskritis
EPI_ISL_770501Kauno apskritis
EPI_ISL_770502Kauno apskritis
EPI_ISL_770504Kauno apskritis
EPI_ISL_770505Kauno apskritis
EPI_ISL_770506Kauno apskritis
EPI_ISL_770507Kauno apskritis
EPI_ISL_770508Kauno apskritis
EPI_ISL_770509Kauno apskritis
EPI_ISL_770510Kauno apskritis
EPI_ISL_770511Kauno apskritis
EPI_ISL_770512Kauno apskritis
EPI_ISL_770514Kauno apskritis
EPI_ISL_770515Kauno apskritis
EPI_ISL_770516Kauno apskritis
EPI_ISL_770517Kauno apskritis
EPI_ISL_770518Kauno apskritis
EPI_ISL_770519Kauno apskritis
EPI_ISL_770520Kauno apskritis
EPI_ISL_770521Kauno apskritis
EPI_ISL_770522Kauno apskritis
EPI_ISL_770523Kauno apskritis
EPI_ISL_770524Kauno apskritis
EPI_ISL_770525Kauno apskritis
EPI_ISL_770526Kauno apskritis
EPI_ISL_770529Kauno apskritis
EPI_ISL_770530Kauno apskritis
EPI_ISL_770531Kauno apskritis
EPI_ISL_770532Kauno apskritis
EPI_ISL_770550Kauno apskritis
EPI_ISL_603095Klaipedos apskritis
EPI_ISL_603120Klaipedos apskritis
EPI_ISL_636867Marijampole apskritis
EPI_ISL_536398Marijampoles apskritis
EPI_ISL_541847Marijampoles apskritis
EPI_ISL_541849Marijampoles apskritis
EPI_ISL_541850Marijampoles apskritis
EPI_ISL_541851Marijampoles apskritis
EPI_ISL_541854Marijampoles apskritis
EPI_ISL_541855Marijampoles apskritis
EPI_ISL_541856Marijampoles apskritis
EPI_ISL_541857Marijampoles apskritis
EPI_ISL_541858Marijampoles apskritis
EPI_ISL_541859Marijampoles apskritis
EPI_ISL_541860Marijampoles apskritis
EPI_ISL_541861Marijampoles apskritis
EPI_ISL_541862Marijampoles apskritis
EPI_ISL_541863Marijampoles apskritis
EPI_ISL_541865Marijampoles apskritis
EPI_ISL_541866Marijampoles apskritis
EPI_ISL_541867Marijampoles apskritis
EPI_ISL_541869Marijampoles apskritis
EPI_ISL_541871Marijampoles apskritis
EPI_ISL_541872Marijampoles apskritis
EPI_ISL_541874Marijampoles apskritis
EPI_ISL_541875Marijampoles apskritis
EPI_ISL_541876Marijampoles apskritis
EPI_ISL_541877Marijampoles apskritis
EPI_ISL_603086Marijampoles apskritis
EPI_ISL_603087Marijampoles apskritis
EPI_ISL_603090Marijampoles apskritis
EPI_ISL_603091Marijampoles apskritis
EPI_ISL_603092Marijampoles apskritis
EPI_ISL_603093Marijampoles apskritis
EPI_ISL_603094Marijampoles apskritis
EPI_ISL_603097Marijampoles apskritis
EPI_ISL_603098Marijampoles apskritis
EPI_ISL_603099Marijampoles apskritis
EPI_ISL_603100Marijampoles apskritis
EPI_ISL_603101Marijampoles apskritis
EPI_ISL_603102Marijampoles apskritis
EPI_ISL_603103Marijampoles apskritis
EPI_ISL_603104Marijampoles apskritis
EPI_ISL_603105Marijampoles apskritis
EPI_ISL_603106Marijampoles apskritis
EPI_ISL_603107Marijampoles apskritis
EPI_ISL_603108Marijampoles apskritis
EPI_ISL_603109Marijampoles apskritis
EPI_ISL_603110Marijampoles apskritis
EPI_ISL_603111Marijampoles apskritis
EPI_ISL_603113Marijampoles apskritis
EPI_ISL_603114Marijampoles apskritis
EPI_ISL_603117Marijampoles apskritis
EPI_ISL_603119Marijampoles apskritis
EPI_ISL_603121Marijampoles apskritis
EPI_ISL_603122Marijampoles apskritis
EPI_ISL_636873Marijampoles apskritis
EPI_ISL_636874Marijampoles apskritis
EPI_ISL_770500Marijampoles apskritis
EPI_ISL_770503Marijampoles apskritis
EPI_ISL_770527Marijampoles apskritis
EPI_ISL_770528Marijampoles apskritis
EPI_ISL_541868Taurages apskritis
EPI_ISL_636604Taurages apskritis
EPI_ISL_636839Taurages apskritis
EPI_ISL_636840Taurages apskritis
EPI_ISL_636841Taurages apskritis
EPI_ISL_636863Taurages apskritis
EPI_ISL_636866Taurages apskritis
EPI_ISL_636872Taurages apskritis
EPI_ISL_636887Taurages apskritis
Lithuania/ChVir1632/2020 EPI_ISL_416741Vilnius2020-02
EPI_ISL_560392Vilnius
EPI_ISL_560394Vilnius
EPI_ISL_560395Vilnius
EPI_ISL_560396Vilnius
EPI_ISL_560397Vilnius
EPI_ISL_560400Vilnius
EPI_ISL_560402Vilnius
EPI_ISL_560404Vilnius
EPI_ISL_560405Vilnius
EPI_ISL_560391Vilnius r.
EPI_ISL_560393Vilnius r.
EPI_ISL_560398Vilnius r.
EPI_ISL_560399Vilnius r.
EPI_ISL_560401Vilnius r.
EPI_ISL_560403Vilnius r.

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