SARS-CoV2 ,uutta tietoa JATKUU (2)

SARS-CoV-2 Information

Genomic sequences for isolate
SARS-CoV-2 Wuhan-Hu-1 ( MN908947.3 / NC_045512.2),
 SARS-CoV-2_HKU-SZ-002a_2020 MN938384,
 SARS-CoV-2_HKU-SZ-005b_2020 MN975262,
SARS-CoV-2/USA-WA1/2020 MN985325,
SARS-CoV-2/USA-IL1/2020 MN988713.
More SARS-CoV-2 sequences from Genbank are available at
 https://www.ncbi.nlm.nih.gov/genbank/SARS-CoV-2-seqs/.
 NCBI information about Wuhan seafood market pneumonia virus is aggregated at Taxonomy ID:2697049.

Table 2.

 Sequence identity (Ide in percentage) of

 SARS-CoV-2 proteins from MN908947 with proteins from

•  Bat SARS-like coronavirus isolate bat-SL-CoVZC45 MG772933 (unpublished, submitted on January 5, 2018 by Hu D, Institute of Military Medicine, Nanjing, China),

•  SARS coronavirus Urbani AY278741 [41] and 

• MERS coronavirus MERS-CoV/KOR/KNIH/002_05_2015 KT029139 [42].

 The identity is calculated through NCBI Needleman-Wunsch alignment of two protein sequences. *: orf1ab polyprotein generates multiple nonstructural proteins upon protease cleavage.

Research Reagents and Instruments

CDC Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus

See the detailed instruction here
 https://www.cdc.gov/coronavirus/SARS-CoV-2/lab/rt-pcr-detection-instructions.html.
 Primers and probes for Real-time RT-PCR.

Gene	Protein	Accession	Bat SARS-like CoV		SARS-CoV		MERS-CoV
			Accession	Ide %	Accession	Ide %	Accession	Ide %
orf1ab	orf1ab*	QHD43415	AVP78030	96	AAP13442	86	AKL59399	45
S	spike protein	QHD43416	AVP78031	81	AAP13441	76	AKL59401	31
orf3a	orf3a	QHD43417	AVP78032	91	AYV99818	73
E	envelope protein	QHD43418	AVP78033	100	AYV99820	95	AKL59406	34
M	matrix protein	QHD43419	AVP78034	99	AYV99821	90	AKL59407	39
orf6	orf6	QHD43420	AVP78035	93	AYV99822	67
orf7a	orf7a	QHD43421	AVP78036	88	AYV99823	85
orf8	orf8	QHD43422	AVP78037	94
N	nucleocapsid protein	QHD43423	AVP78038	94	AYV99813	91	AKL59408	46
orf10	orf10	QHI42199

Kommentti:
Taulukko arkoittaa, että  uusi SARS2 virus muistuttaa rakenteellisilta osiltaan enemmän  lepakkojen  SARS-kaltaista (SL) koronavirusta kuin  itseään entistä ihmisen SARS1 virusta ) joka on SARBECOVIRUS) .   Vielä vähemmän uusi virus muistuttaa MERS- koronavirusta ( joka on MERBECOVIRUS-ryhmää) - Kuitenkin mainittu lepakkovirus ja uusi SARS2 oat SARBECOVIRUS- ryhmää  betakoronaviruksia.