University of Turin logo DBIOS logo


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).

Go to home

Lithuania

Number of isolates sequences available: 50

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_541864Kauno apskritis
EPI_ISL_541870Kauno apskritis
EPI_ISL_541873Kauno 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_541868Taurages 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.

Download all results


GISAID data provided on this website is subject to GISAID’s Terms and Conditions | Privacy policy of University of Turin.