Status of SARS-CoV-2 detection systems (RT-PCR)
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Update: Sun Jan 31 07:00:30 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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Indonesia

Number of isolates sequences available: 334

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 ID	Region	Collection date	2019-nCoV_N1	2019-nCoV_N2	2019-nCoV_N3	E-Sarbeco	RdRP
EPI_ISL_757287	Aceh
EPI_ISL_791981	Aceh
EPI_ISL_538503	Bali
EPI_ISL_775596	Bali
EPI_ISL_747237	Bangka Belitung Islands
EPI_ISL_438546	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_438547	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_438548	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_438549	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_518819	Banten
EPI_ISL_574611	Banten
EPI_ISL_707692	Banten
EPI_ISL_707696	Banten
EPI_ISL_707778	Banten
EPI_ISL_707890	Banten
EPI_ISL_708652	Banten
EPI_ISL_766034	Banten
EPI_ISL_766036	Banten
EPI_ISL_766042	Banten
EPI_ISL_779383	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779384	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779385	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779386	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779387	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779388	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779389	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779390	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779391	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779392	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779393	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779394	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_779395	Banten		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_833388	Banten
EPI_ISL_833389	Banten
EPI_ISL_833390	Banten
EPI_ISL_833391	Banten
EPI_ISL_833499	Banten
EPI_ISL_882645	Banten
EPI_ISL_882646	Banten
EPI_ISL_882656	Banten
EPI_ISL_883957	Banten
EPI_ISL_888985	Banten
EPI_ISL_888988	Banten
EPI_ISL_888989	Banten
EPI_ISL_888990	Banten
EPI_ISL_888991	Banten
EPI_ISL_888992	Banten
EPI_ISL_889003	Banten
EPI_ISL_889004	Banten
EPI_ISL_889009	Banten
EPI_ISL_889016	Banten
EPI_ISL_889017	Banten
EPI_ISL_791979	Bengkulu
EPI_ISL_525492	Central Java
EPI_ISL_568686	Central Java
EPI_ISL_576383	Central Java
EPI_ISL_610155	Central Java
EPI_ISL_610161	Central Java
EPI_ISL_610162	Central Java
EPI_ISL_759701	Central Java
EPI_ISL_759702	Central Java
EPI_ISL_759703	Central Java
EPI_ISL_759705	Central Java
EPI_ISL_759842	Central Java
EPI_ISL_763063	Central Java
EPI_ISL_763064	Central Java
EPI_ISL_763066	Central Java
EPI_ISL_763068	Central Java
EPI_ISL_763070	Central Java
EPI_ISL_791982	Central Java
EPI_ISL_791987	Central Java
EPI_ISL_791988	Central Java
EPI_ISL_538502	Central Kalimantan
EPI_ISL_437187	East Java
EPI_ISL_437188	East Java
EPI_ISL_458079	East Java
EPI_ISL_458081	East Java
EPI_ISL_458082	East Java
EPI_ISL_458083	East Java
EPI_ISL_529138	East Java
EPI_ISL_529961	East Java
EPI_ISL_529962	East Java
EPI_ISL_529963	East Java
EPI_ISL_529964	East Java
EPI_ISL_529965	East Java
EPI_ISL_529966	East Java
EPI_ISL_529967	East Java
EPI_ISL_538498	East Java
EPI_ISL_538499	East Java
EPI_ISL_538511	East Java
EPI_ISL_560991	East Java
EPI_ISL_759955	East Java
EPI_ISL_759956	East Java
EPI_ISL_759957	East Java
EPI_ISL_759958	East Java
EPI_ISL_759959	East Java
EPI_ISL_759960	East Java
EPI_ISL_759961	East Java
EPI_ISL_759962	East Java
EPI_ISL_759963	East Java
EPI_ISL_759964	East Java
EPI_ISL_759965	East Java
EPI_ISL_759966	East Java
EPI_ISL_759967	East Java
EPI_ISL_759968	East Java
EPI_ISL_791980	East Java
EPI_ISL_791989	East Java
EPI_ISL_872897	East Java		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_877419	East Java
EPI_ISL_877420	East Java
EPI_ISL_877421	East Java
EPI_ISL_877422	East Java
EPI_ISL_877423	East Java
EPI_ISL_877456	East Java
EPI_ISL_877457	East Java
EPI_ISL_877458	East Java
EPI_ISL_877459	East Java
EPI_ISL_877460	East Java
EPI_ISL_877538	East Java
EPI_ISL_882769	East Java
EPI_ISL_882770	East Java
EPI_ISL_882771	East Java
EPI_ISL_888591	East Java
EPI_ISL_888593	East Java
EPI_ISL_467374	East Kalimantan
EPI_ISL_791977	East Kalimantan
EPI_ISL_791983	East Kalimantan
EPI_ISL_766033	East Nusa Tenggara
EPI_ISL_766039	East Nusa Tenggara
EPI_ISL_766048	East Nusa Tenggara
EPI_ISL_414375	Jakarta		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_414376	Jakarta		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_414377	Jakarta		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_428207	Jakarta		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_428208	Jakarta		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_435281	Jakarta
EPI_ISL_435282	Jakarta
EPI_ISL_435283	Jakarta
EPI_ISL_437189	Jakarta
EPI_ISL_437190	Jakarta
EPI_ISL_437191	Jakarta
EPI_ISL_437192	Jakarta
EPI_ISL_467376	Jakarta
EPI_ISL_518820	Jakarta
EPI_ISL_538504	Jakarta
EPI_ISL_538505	Jakarta
EPI_ISL_538508	Jakarta
EPI_ISL_538509	Jakarta
EPI_ISL_568687	Jakarta
EPI_ISL_568688	Jakarta
EPI_ISL_568689	Jakarta
EPI_ISL_568690	Jakarta
EPI_ISL_568691	Jakarta
EPI_ISL_568692	Jakarta
EPI_ISL_574433	Jakarta
EPI_ISL_574607	Jakarta
EPI_ISL_574608	Jakarta
EPI_ISL_574609	Jakarta
EPI_ISL_574610	Jakarta
EPI_ISL_574613	Jakarta
EPI_ISL_574614	Jakarta
EPI_ISL_574615	Jakarta
EPI_ISL_574616	Jakarta
EPI_ISL_574617	Jakarta
EPI_ISL_574618	Jakarta
EPI_ISL_576386	Jakarta
EPI_ISL_576387	Jakarta
EPI_ISL_747194	Jakarta
EPI_ISL_747233	Jakarta
EPI_ISL_747234	Jakarta
EPI_ISL_766037	Jakarta
EPI_ISL_766038	Jakarta
EPI_ISL_766040	Jakarta
EPI_ISL_766041	Jakarta
EPI_ISL_766043	Jakarta
EPI_ISL_766044	Jakarta
EPI_ISL_766045	Jakarta
EPI_ISL_766046	Jakarta
EPI_ISL_766047	Jakarta
EPI_ISL_833130	Jakarta
EPI_ISL_833393	Jakarta
EPI_ISL_833492	Jakarta
EPI_ISL_833495	Jakarta
EPI_ISL_833497	Jakarta
EPI_ISL_833498	Jakarta
EPI_ISL_833500	Jakarta
EPI_ISL_833503	Jakarta
EPI_ISL_833504	Jakarta
EPI_ISL_833505	Jakarta
EPI_ISL_833507	Jakarta
EPI_ISL_833508	Jakarta
EPI_ISL_888979	Jakarta
EPI_ISL_888981	Jakarta
EPI_ISL_888982	Jakarta
EPI_ISL_888983	Jakarta
EPI_ISL_888994	Jakarta
EPI_ISL_888995	Jakarta
EPI_ISL_889002	Jakarta
EPI_ISL_889006	Jakarta
EPI_ISL_889019	Jakarta
EPI_ISL_775594	Lampung
EPI_ISL_791978	Lampung
EPI_ISL_803876	North Kalimantan
EPI_ISL_791986	North Maluku
EPI_ISL_467375	North Sulawesi
EPI_ISL_568694	North Sulawesi
EPI_ISL_574604	North Sulawesi
EPI_ISL_574619	North Sulawesi
EPI_ISL_574620	North Sulawesi
EPI_ISL_574621	North Sulawesi
EPI_ISL_574622	North Sulawesi
EPI_ISL_574623	North Sulawesi
EPI_ISL_538500	North Sumatra
EPI_ISL_538501	North Sumatra
EPI_ISL_756401	North Sumatra
EPI_ISL_538506	Papua
EPI_ISL_538507	Papua
EPI_ISL_538512	Papua
EPI_ISL_568693	Papua
EPI_ISL_574603	Papua
EPI_ISL_791985	Riau Islands
EPI_ISL_538510	South Kalimantan
EPI_ISL_576385	South Kalimantan
EPI_ISL_753699	South Kalimantan
EPI_ISL_753698	South Sulawesi
EPI_ISL_775599	South Sulawesi
EPI_ISL_833392	South Sulawesi
EPI_ISL_833501	South Sulawesi
EPI_ISL_833502	South Sulawesi
EPI_ISL_833039	South Sumatra
EPI_ISL_516800	Special Region of Yogyakarta
EPI_ISL_516806	Special Region of Yogyakarta
EPI_ISL_516829	Special Region of Yogyakarta
EPI_ISL_574605	Special Region of Yogyakarta
EPI_ISL_575331	Special Region of Yogyakarta
EPI_ISL_576113	Special Region of Yogyakarta
EPI_ISL_576114	Special Region of Yogyakarta
EPI_ISL_576115	Special Region of Yogyakarta
EPI_ISL_576116	Special Region of Yogyakarta
EPI_ISL_576128	Special Region of Yogyakarta
EPI_ISL_576130	Special Region of Yogyakarta
EPI_ISL_576145	Special Region of Yogyakarta
EPI_ISL_610158	Special Region of Yogyakarta
EPI_ISL_632936	Special Region of Yogyakarta
EPI_ISL_632937	Special Region of Yogyakarta
EPI_ISL_766032	Special Region of Yogyakarta
EPI_ISL_862039	Special Region of Yogyakarta
EPI_ISL_862040	Special Region of Yogyakarta
EPI_ISL_862041	Special Region of Yogyakarta
EPI_ISL_872188	Special Region of Yogyakarta
EPI_ISL_872189	Special Region of Yogyakarta
EPI_ISL_872190	Special Region of Yogyakarta
EPI_ISL_877126	Special Region of Yogyakarta
EPI_ISL_877127	Special Region of Yogyakarta
EPI_ISL_877128	Special Region of Yogyakarta
EPI_ISL_877129	Special Region of Yogyakarta
EPI_ISL_877130	Special Region of Yogyakarta
EPI_ISL_877131	Special Region of Yogyakarta
EPI_ISL_885142	Special Region of Yogyakarta
EPI_ISL_890185	Special Region of Yogyakarta
EPI_ISL_890186	Special Region of Yogyakarta
EPI_ISL_890187	Special Region of Yogyakarta
EPI_ISL_891151	Special Region of Yogyakarta
EPI_ISL_902737	Special Region of Yogyakarta
EPI_ISL_902749	Special Region of Yogyakarta
EPI_ISL_413219	West Java		The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available	The sequence is not available
EPI_ISL_511878	West Java
EPI_ISL_511879	West Java
EPI_ISL_528745	West Java
EPI_ISL_528746	West Java
EPI_ISL_528747	West Java
EPI_ISL_528748	West Java
EPI_ISL_528749	West Java
EPI_ISL_528750	West Java
EPI_ISL_528751	West Java
EPI_ISL_528752	West Java
EPI_ISL_528753	West Java
EPI_ISL_528759	West Java
EPI_ISL_529718	West Java
EPI_ISL_529719	West Java
EPI_ISL_538513	West Java
EPI_ISL_574606	West Java
EPI_ISL_574612	West Java
EPI_ISL_745033	West Java
EPI_ISL_747235	West Java
EPI_ISL_747236	West Java
EPI_ISL_747238	West Java
EPI_ISL_747239	West Java
EPI_ISL_747240	West Java
EPI_ISL_747241	West Java
EPI_ISL_754239	West Java
EPI_ISL_754241	West Java
EPI_ISL_756376	West Java
EPI_ISL_766035	West Java
EPI_ISL_833493	West Java
EPI_ISL_833494	West Java
EPI_ISL_833496	West Java
EPI_ISL_833506	West Java
EPI_ISL_833509	West Java
EPI_ISL_833510	West Java
EPI_ISL_888980	West Java
EPI_ISL_888984	West Java
EPI_ISL_888986	West Java
EPI_ISL_888987	West Java
EPI_ISL_888993	West Java
EPI_ISL_888996	West Java
EPI_ISL_888997	West Java
EPI_ISL_888998	West Java
EPI_ISL_888999	West Java
EPI_ISL_889000	West Java
EPI_ISL_889001	West Java
EPI_ISL_889005	West Java
EPI_ISL_889007	West Java
EPI_ISL_889008	West Java
EPI_ISL_889010	West Java
EPI_ISL_889011	West Java
EPI_ISL_889012	West Java
EPI_ISL_889013	West Java
EPI_ISL_889014	West Java
EPI_ISL_889015	West Java
EPI_ISL_889018	West Java
EPI_ISL_889020	West Java
EPI_ISL_889021	West Java
EPI_ISL_889022	West Java
EPI_ISL_775595	West Kalimantan
EPI_ISL_833040	West Kalimantan
EPI_ISL_902917	West Kalimantan
EPI_ISL_902918	West Kalimantan
EPI_ISL_902919	West Kalimantan
EPI_ISL_902921	West Kalimantan
EPI_ISL_902922	West Kalimantan
EPI_ISL_902924	West Kalimantan
EPI_ISL_775598	West Nusa Tenggara
EPI_ISL_775597	West Papua

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