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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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Mexico

Number of isolates sequences available: 174

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_576258Aguascalientes
EPI_ISL_576261Aguascalientes
EPI_ISL_493347Baja California
EPI_ISL_496339Baja California
EPI_ISL_496340Baja California
EPI_ISL_496341Baja California
EPI_ISL_496342Baja California
EPI_ISL_496343Baja California
EPI_ISL_496344Baja California
EPI_ISL_496345Baja California
EPI_ISL_496346Baja California
EPI_ISL_496347Baja California
EPI_ISL_496348Baja California
EPI_ISL_496349Baja California
EPI_ISL_496350Baja California
EPI_ISL_496351Baja California
EPI_ISL_496352Baja California
EPI_ISL_496353Baja California
EPI_ISL_496354Baja California
EPI_ISL_496355Baja California
EPI_ISL_496356Baja California
EPI_ISL_496357Baja California
EPI_ISL_496358Baja California
EPI_ISL_496359Baja California
EPI_ISL_496360Baja California
EPI_ISL_496361Baja California
EPI_ISL_496362Baja California
EPI_ISL_496363Baja California
EPI_ISL_496364Baja California
EPI_ISL_496365Baja California
EPI_ISL_496366Baja California
EPI_ISL_496367Baja California
EPI_ISL_496368Baja California
EPI_ISL_496369Baja California
EPI_ISL_496370Baja California
EPI_ISL_496371Baja California
EPI_ISL_496372Baja California
EPI_ISL_496373Baja California
EPI_ISL_496374Baja California
EPI_ISL_496375Baja California
EPI_ISL_496376Baja California
EPI_ISL_516608Baja California
EPI_ISL_516609Baja California
EPI_ISL_516610Baja California
EPI_ISL_516611Baja California
EPI_ISL_516612Baja California
EPI_ISL_485587Baja California SurThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493340Baja California Sur
EPI_ISL_493345Baja California Sur
EPI_ISL_493346Baja California Sur
EPI_ISL_576265Campeche
EPI_ISL_576266Campeche
EPI_ISL_576267Campeche
Mexico/Chiapas-InDRE_02/2020 EPI_ISL_424666Chiapas2020-02-29
EPI_ISL_493338Chiapas
Mexico/Chihuahua-IMSS_01/2020 EPI_ISL_424731Chihuahua2020-03-13
EPI_ISL_516613Chihuahua
EPI_ISL_516614Chihuahua
EPI_ISL_516615Chihuahua
EPI_ISL_516616Chihuahua
EPI_ISL_516617Chihuahua
EPI_ISL_516618Coahuila
EPI_ISL_516619Coahuila
EPI_ISL_516620Coahuila
EPI_ISL_516621Coahuila de Zaragoza
EPI_ISL_576278Colima
EPI_ISL_576279Colima
EPI_ISL_455432Durango
EPI_ISL_493334Guanajuato
EPI_ISL_493335Guanajuato
EPI_ISL_455434Guerrero
EPI_ISL_493339Guerrero
EPI_ISL_485591HidalgoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485592HidalgoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576257Hidalgo
EPI_ISL_576268Hidalgo
EPI_ISL_455435Jalisco
EPI_ISL_455454Jalisco
Mexico/CDMX-InDRE_01/2020 EPI_ISL_412972Mexico City2020-02-27
Mexico/CDMX-INER_01/2020 EPI_ISL_424345Mexico City2020-03-12
Mexico/CDMX-INER_02/2020 EPI_ISL_424348Mexico City2020-03-13
Mexico/CDMX-INER_03/2020 EPI_ISL_424625Mexico City2020-03-13
Mexico/CDMX-INER_04/2020 EPI_ISL_424626Mexico City2020-03-15
Mexico/CDMX-INER_05/2020 EPI_ISL_424627Mexico City2020-03-16
Mexico/CDMX-InDRE_06/2020 EPI_ISL_424673Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_01/2020 EPI_ISL_426361Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_02/2020 EPI_ISL_426362Mexico City2020-03-10
Mexico/CDMX-INCMNSZ_03/2020 EPI_ISL_426363Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_04/2020 EPI_ISL_426364Mexico City2020-03-12
Mexico/CDMX-INCMNSZ_05/2020 EPI_ISL_426365Mexico City2020-03-12
EPI_ISL_455436Mexico City
EPI_ISL_455437Mexico City
EPI_ISL_455439Mexico City
EPI_ISL_485578Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485584Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485585Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485597Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485600Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485601Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485602Mexico CityThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_522872Mexico City
EPI_ISL_522873Mexico City
EPI_ISL_522874Mexico City
EPI_ISL_522875Mexico City
EPI_ISL_522876Mexico City
EPI_ISL_522877Mexico City
EPI_ISL_522878Mexico City
EPI_ISL_522879Mexico City
EPI_ISL_522880Mexico City
EPI_ISL_522940Mexico City
EPI_ISL_522941Mexico City
EPI_ISL_522942Mexico City
EPI_ISL_522978Mexico City
EPI_ISL_522979Mexico City
EPI_ISL_522980Mexico City
EPI_ISL_522981Mexico City
EPI_ISL_522982Mexico City
EPI_ISL_522983Mexico City
EPI_ISL_522984Mexico City
EPI_ISL_522985Mexico City
EPI_ISL_522986Mexico City
EPI_ISL_523500Mexico City
EPI_ISL_485583MichoacanThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576271Michoacan
EPI_ISL_576276Michoacan
EPI_ISL_576277Michoacan
EPI_ISL_485576MorelosThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485577MorelosThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493341Morelos
EPI_ISL_493342Nayarit
EPI_ISL_493343Nayarit
EPI_ISL_576262Nuevo Leon
EPI_ISL_576263Nuevo Leon
EPI_ISL_485593OaxacaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_576264Oaxaca
Mexico/Puebla-InDRE_05/2020 EPI_ISL_424672Puebla2020-03-11
EPI_ISL_455455Puebla
EPI_ISL_485590PueblaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
Mexico/Queretaro-InDRE_04/2020 EPI_ISL_424670Queretaro2020-03-10
EPI_ISL_455456Queretaro
EPI_ISL_485580QueretaroThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_455438Quintana Roo
EPI_ISL_576272San Luis Potosi
EPI_ISL_493336Sinaloa
EPI_ISL_493344Sonora
EPI_ISL_493349Sonora
EPI_ISL_516622Sonora
EPI_ISL_516623Sonora
Mexico/EdoMex-InDRE_03/2020 EPI_ISL_424667State of Mexico2020-03-04
EPI_ISL_452139State of Mexico
EPI_ISL_452141State of Mexico
EPI_ISL_485575State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485579State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485581State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485582State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485586State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485588State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485589State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485594State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485595State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485596State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485598State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_485599State of MexicoThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_493337Tabasco
EPI_ISL_516624Tamaulipas
EPI_ISL_516625Tamaulipas
EPI_ISL_576259Tlaxcala
EPI_ISL_576260Tlaxcala
EPI_ISL_576269Veracruz
EPI_ISL_576270Veracruz
EPI_ISL_493348Yucatan
EPI_ISL_576273Zacatecas
EPI_ISL_576274Zacatecas
EPI_ISL_576275Zacatecas

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