University of Turin logo DBIOS logo


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


Update: Sun Nov 29 12:36:20 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

Palestine

Number of isolates sequences available: 70

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_596502Bethlehem
EPI_ISL_596503Bethlehem
EPI_ISL_596504Bethlehem
EPI_ISL_596505Bethlehem
EPI_ISL_596506Bethlehem
EPI_ISL_596509Bethlehem
EPI_ISL_596513Bethlehem
EPI_ISL_596515Bethlehem
EPI_ISL_596521Hebron
EPI_ISL_596557Hebron
EPI_ISL_596558Hebron
EPI_ISL_596559Hebron
EPI_ISL_596560Hebron
EPI_ISL_596561Hebron
EPI_ISL_596563Hebron
EPI_ISL_596540Jenin
EPI_ISL_596541Jenin
EPI_ISL_596524Jericho
EPI_ISL_596531Jericho
EPI_ISL_596532Jericho
EPI_ISL_596534Jericho
EPI_ISL_596500Jerusalem
EPI_ISL_596501Jerusalem
EPI_ISL_596516Jerusalem
EPI_ISL_596518Jerusalem
EPI_ISL_596522Jerusalem
EPI_ISL_596523Jerusalem
EPI_ISL_596525Jerusalem
EPI_ISL_596526Jerusalem
EPI_ISL_596527Jerusalem
EPI_ISL_596528Jerusalem
EPI_ISL_596529Jerusalem
EPI_ISL_596530Jerusalem
EPI_ISL_596533Jerusalem
EPI_ISL_596535Jerusalem
EPI_ISL_596538Jerusalem
EPI_ISL_596555Jerusalem
EPI_ISL_596567Jerusalem
EPI_ISL_596542Nablus
EPI_ISL_596543Nablus
EPI_ISL_596544Nablus
EPI_ISL_596545Nablus
EPI_ISL_596546Nablus
EPI_ISL_596547Nablus
EPI_ISL_596548Nablus
EPI_ISL_596549Nablus
EPI_ISL_596550Nablus
EPI_ISL_596551Nablus
EPI_ISL_596552Nablus
EPI_ISL_596553Nablus
EPI_ISL_596554Nablus
EPI_ISL_596556Nablus
EPI_ISL_596562Nablus
EPI_ISL_596564Nablus
EPI_ISL_596565Nablus
EPI_ISL_596507Ramallah
EPI_ISL_596508Ramallah
EPI_ISL_596510Ramallah
EPI_ISL_596511Ramallah
EPI_ISL_596512Ramallah
EPI_ISL_596514Ramallah
EPI_ISL_596517Ramallah
EPI_ISL_596520Ramallah
EPI_ISL_596536Ramallah
EPI_ISL_596537Ramallah
EPI_ISL_596539Ramallah
EPI_ISL_596566Ramallah
EPI_ISL_596519Tulkarem
EPI_ISL_596568Tulkarem
EPI_ISL_649153West Bank

Download all results


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