TAG NRHO GENOME RESEQUENING
Genomics soj ntsuam ntawm SARS-CoV-2 uncovers Nsp1 deletion variant uas modulates hom I interferon teb
Nanopor |Illumina |Tag nrho genome resequencing |metagenomics |RNA-Seq |Sanger
Biomarker Technologies tau muab kev txhawb nqa rau cov qauv ua ntu zus hauv txoj kev tshawb no.
Qhov tseem ceeb
1.SARS-CoV-2 genome sequencing and phylognetic analysis detect 35 recurrent mutations including 31 SNPs and 4 Indels.
2.Kev koom tes nrog 117 qhov chaw kho mob phenotypes nthuav tawm qhov muaj peev xwm
kev hloov pauv tseem ceeb.
∆500-532 hauv Nsp1 coding cheeb tsam cuam tshuam nrog cov kab mob qis dua
3.load thiab serum IFN-β.
4.Viral cais nrog ∆500-532 kev hloov pauv induce qis IFN-I
teb nyob rau hauv cov kab mob.
Kev sim tsim
Kev ua tiav
1. COVID-19 kev kis kab mob thiab kev soj ntsuam genomic
Cov ntaub ntawv kho mob tau sau tseg hauv xeev Sichuan, Suav teb thoob plaws lub sijhawm muaj tus kabmob kis txij lub Ib Hlis 22, 2020 txog Lub Ob Hlis 20, 2020. Tag nrho ntawm 538 tus neeg mob COVID-19 tau lees paub los ntawm qPCR kev sim hauv Sichuan, 28.8% ntawm cov uas yog los ntawm lub xeev. peev.Cov ntaub ntawv lees paub hauv Sichuan tau nce ntxiv, nce siab thaum Lub Ib Hlis 30th.Tsis tas li, cov ntaub ntawv txhawb nqa tias kev nyob sib nrug deb tuaj yeem yog qhov tseem ceeb hauv kev tiv thaiv tus kabmob kis.
Daim duab 1. Kev tshawb fawb txog kev sib kis ntawm COVID-19 hauv xeev Sichuan, Suav
2. SARS-CoV-2 genome construction and variants identification
Nrog multiplex PCR amplification ua raws li nanopore sequencing, tag nrho ntawm 310 ze- lossis ib nrab-ua tiav genomes los ntawm 248 tus neeg mob tau tsim nrog kwv yees.80% ntawm genomes them los ntawm 10 nyeem (Lub ntsiab lus tob: 0.39 M nyeem ib qho qauv).
Daim duab 2. Ntau zaus ntawm txhua qhov sib txawv hauv Sichuan pawg
Tag nrho ntawm 104 SNPs thiab 18 Indels tau txheeb xyuas los ntawm SARS-CoV-2 genomes, nyob rau hauv uas 31 SNPs thiab 4 Indels tau txheeb xyuas tias yog cov caj ces rov tshwm sim.Los ntawm kev sib piv lawv nrog 169 tus qauv los ntawm Wuhan thiab nrog 81,391 cov khoom lag luam zoo tshaj plaws hauv GISAID, 29 ntawm 35 qhov sib txawv pom tau nthuav tawm hauv lwm lub tebchaws.Qhov tseem ceeb, plaub qhov sib txawv suav nrog ∆500-532, ACC18108AT, ∆729-737 thiab T13243C, tsuas yog pom muaj nyob rau hauv Sichuan thiab Wuhan thiab tsis nyob hauv GISAID cov ntaub ntawv, qhia tias cov kev hloov pauv no feem ntau yuav raug hloov kho los ntawm Wuhan, uas ua tau raws li cov ntaub ntawv GISAID. cov ntaub ntawv taug kev ntawm cov neeg mob.
Evolutionary tsom xam nrog qhov muaj feem ntau (ML) txoj kev thiab Bayesian molecular moos mus kom ze tau ua tiav ntawm 88 tus kab mob tshiab los ntawm Sichuan thiab 250 curated genomes los ntawm lwm cheeb tsam.Genomes nrog ∆500-532 (Kev tshem tawm hauv cheeb tsam Nsp1 coding) tau pom muaj faib me me hauv tsob ntoo phylogenetic.Kev tshuaj xyuas Haplotype ntawm Nsp1 variants tau txheeb xyuas 5 ntawm lawv los ntawm ntau lub nroog.Cov txiaj ntsig no tau qhia tias ∆500-532 tau tshwm sim hauv ntau lub nroog thiab tuaj yeem raug xa tawm ntau zaus los ntawm Wuhan.
Daim duab 2. Recurrent genetic variants and phylogenetic analysis in the SARS-CoV-2 genomes
3. Kev sib koom ua ke ntawm cov noob caj noob ces rov tshwm sim nrog kev cuam tshuam rau kev kho mob
117 qhov chaw kho mob phenotypes tau cuam tshuam nrog COVID-19 qhov hnyav, qhov twg 19 qhov xwm txheej cuam tshuam txog qhov hnyav tau muab faib ua qhov hnyav thiab tsis hnyav.Kev sib raug zoo ntawm cov cwj pwm no thiab 35 qhov kev hloov pauv caj ces rov tshwm sim tau raug viualized nyob rau hauv ob-cluster heatmap.GSEA-zoo li qeb duas kev txheeb xyuas pom tau tias ∆500-532 tsis zoo cuam tshuam nrog ESR, ntshav IFN-β thiab CD3 + CD8 + T cell suav hauv cov ntshav.Ntxiv mus, qPCR cov kev ntsuam xyuas pom tau hais tias cov neeg mob kis tus kab mob harboring ∆500-532 muaj tus nqi Ct siab tshaj plaws, piv txwv li cov kab mob qis tshaj.
Daim duab 3. Cov koom haum ntawm 35 recurrent genetic variants nrog kev kho mob phenotypes
4. Kev lees paub ntawm tus kab mob hloov pauv cuam tshuam nrog kev kho mob phenotypes
Yuav kom nkag siab txog qhov cuam tshuam ntawm ∆500-532 ntawm Nsp1 kev ua haujlwm, HEK239T hlwb tau hloov nrog plasmids qhia tag nrho ntev, WT Nsp1 thiab mutant cov ntaub ntawv nrog kev tshem tawm.Transcriptome profiles ntawm txhua cov kho HEK239T hlwb tau ua tiav rau PCA tsom xam, qhia tias kev tshem tawm cov mutants pawg tau ze dua thiab txawv txawv ntawm WT Nsp1.Cov noob uas tau hloov pauv ntau hauv cov mutants feem ntau yog enriched nyob rau hauv "peptide biosynthetic / metabolic txheej txheem", "ribonucleoprotein complex biogenesis", "protein targeting rau membrane / ER", thiab lwm yam. Ntxiv mus, ob deletions qhia ib tug txawv expssion qauv los ntawm WT.
Daim duab 4. Kev txheeb xyuas cov ntaub ntawv pov thawj ntawm HEK239T cov hlwb hloov los ntawm WT Nsp1 thiab nrog kev tshem tawm
Qhov cuam tshuam ntawm kev tshem tawm ntawm IFN-1 cov lus teb kuj tau sim hauv kev tshawb fawb ntau dhau.Txhua qhov kev sim tshem tawm tau pom tias yuav txo tau IFN-1 repsonse nyob rau hauv transfected HEK239T thiab A549 hlwb ntawm ob theem transcriptome thiab qib protein.Interestingly, cov noob caj noob ces txo qis hauv kev tshem tawm tau ntxiv rau "kev tiv thaiv teb rau tus kab mob", "viral genome replication", "txoj cai ntawm kev sau los ntawm RNA polymerase II" thiab " teb rau hom I interferon".
Daim duab 5. Kev tswj hwm ntawm interferon signaling pathways hauv ∆500-532 mutant
Hauv txoj kev tshawb no, qhov cuam tshuam ntawm cov kev tshem tawm ntawm tus kab mob no tau lees paub ntxiv los ntawm kev tshawb fawb txog kab mob kis.Cov kab mob uas muaj qee yam mutants raug cais tawm ntawm cov qauv kuaj mob thiab kis mus rau Calu-3 hlwb.Cov ntsiab lus ntxaws ntxaws ntawm kev tshawb nrhiav kab mob kis tau tuaj yeem nyeem hauv daim ntawv.
doi:10.1016/j.chom.2021.01.015
Kev siv
Lin J, Tang C, Wei H, et al.Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response[J].Cell host & microbe, 2021.
Xov xwm thiab qhov tseem ceeb Lub hom phiaj ntawm kev sib koom cov xwm txheej ua tiav tshiab nrog Biomarker Technologies, khaws cov kev tshawb fawb tshiab thiab cov txuj ci tseem ceeb siv thaum kawm.
Post lub sij hawm: Jan-06-2022