GUKORA GENOME YOSE
Gukurikirana genomics ya SARS-CoV-2 ivumbuye uburyo bwo gusiba Nsp1 ihindura ubwoko bwa I interferon igisubizo
Nanopore |Illumina |Imiterere ya genome yose |metagenomics |RNA-Seq |Sanger
Biomarker Technologies yatanze ubufasha bwa tekiniki kurugero rukurikirana muri ubu bushakashatsi.
Ingingo z'ingenzi
1.SARS-CoV-2 ikurikirana rya genome hamwe nisesengura rya phylognetike byerekana ihinduka 35 ryisubiramo harimo 31 SNPs na 4 Indels.
2.Gufatanya na fenotipiki 117 yubuvuzi irerekana bishoboka
ihinduka rikomeye.
00500-532 mukarere ka Nsp1 kode ifitanye isano na virusi yo hasi
3.kuramo na serumu IFN-β.
4.Virusi itandukanya ∆500-532 mutation itera IFN-I yo hasi
igisubizo muri selile zanduye.
Igishushanyo mbonera
Ibyagezweho
1. COVID-19 epidemiologi na genomic gukurikirana
Amakuru y’amavuriro yakusanyirijwe mu ntara ya Sichuan, mu Bushinwa mu gihe cy’icyorezo kuva ku ya 22 Mutarama 2020 kugeza ku ya 20 Gashyantare 2020. Indwara 538 COVID-19 zemejwe n’ibizamini bya qPCR muri Sichuan, 28.8% muri zo zikaba ari iz'intara. umurwa mukuru.Imanza zemejwe muri Sichuan ziyongereye ku buryo bugaragara, ku ya 30 Mutarama.Na none, amakuru yashyigikiye ko intera mbonezamubano ishobora kuba ikintu cyingenzi mukurinda virusi.
Igicapo 1. Ubushakashatsi bwibyorezo bya COVID-19 mu ntara ya Sichuan, mu Bushinwa
2. SARS-CoV-2 kubaka genome no kumenyekanisha ibintu
Hamwe na multiplex ya PCR yongerewe imbaraga ikurikirwa na nanopore ikurikirana, yose hamwe 310 hafi ya hafi cyangwa igice-cyuzuye cyuzuye kubarwayi 248 byakozwe hafi.80% ya genome itwikiriwe nisomwa 10 (Bivuze ubujyakuzimu: 0.39 M isoma kuri sample).
Igishushanyo 2. Inshuro ya buri variants muri cohort ya Sichuan
Hafi ya SNPs 104 na Indels 18 zamenyekanye muri genoside ya SARS-CoV-2, aho 31 SNPs na 4 Indels byagaragaye ko ari ubwoko bwisubiramo.Mugereranije na 169 by'icyitegererezo cya Wuhan hamwe na 81,391 zo mu rwego rwohejuru za genoside zikurikirana muri GISAID, 29 muri 35 zahinduwe zabonetse muyindi migabane.Ikigaragara ni uko ibintu bine birimo ∆500-532, ACC18108AT, ∆729-737 na T13243C, wasangaga gusa bigaragara muri Sichuan na Wuhan kandi bidahari mu makuru ya GISAID, byerekana ko izo variants zishobora kuba zaranditswe muri Wuhan, zihura na ingendo zurugendo rwabarwayi.
Isesengura ry’ubwihindurize hamwe n’uburyo bushoboka (ML) hamwe n’uburyo bwa molekuline ya Bayesian bwakorewe kuri virusi nshya 88 ziva muri Sichuan na genoside 250 zahinduwe ziva mu tundi turere.Genome zifite ∆500-532 (Gusiba mu karere ka Nsp1 coding) wasangaga zikwirakwizwa gake mugiti cya phylogeneque.Isesengura rya Haplotype kuri Nsp1 ryagaragaje 5 muri yo kuva mumijyi myinshi.Ibisubizo byavugaga ko 500-532 byabereye mumijyi myinshi kandi bishobora gutumizwa inshuro nyinshi muri Wuhan.
Igicapo ca 2. Guhindura ingirabuzima fatizo hamwe nisesengura rya phylogeneque muri genoside ya SARS-CoV-2
3. Ihuriro ryibinyabuzima bigenda bisubirwamo hamwe nubuvuzi
117 ivuriro rya fenotipike ryahujwe nuburemere bwa COVID-19, aho 19 fenotipike ijyanye nuburemere yashyizwe mubikorwa bikomeye kandi bidakabije.Isano iri hagati yibi biranga na 35 byagarutsweho na genetique byagaragaye mubushyuhe bwa bi-cluster.Isesengura ryitunganyirizwa rya GSEA ryerekanye ko ∆500-532 rifitanye isano ribi na ESR, serumu IFN-β na CD3 + CD8 + T ibara mu maraso.Byongeye kandi, ibizamini bya qPCR byerekanaga ko abarwayi banduye virusi ya 00500-532 bafite agaciro gakomeye ka Ct, ni ukuvuga virusi nkeya.
Igicapo 3. Amashyirahamwe yibintu 35 byisubiramo hamwe na fenotipiki yubuvuzi
4. Kwemeza kuri mutation ya virusi ifitanye isano na clinique phenotypes
Kugirango dusobanukirwe n'ingaruka za 500-532 kumikorere ya Nsp1, selile HEK239T zahinduwe hamwe na plasima zerekana uburebure bwuzuye, WT Nsp1 hamwe na mutant hamwe no gusiba.Umwirondoro wa transcriptque ya buri selile yavuwe HEK239T yatunganijwe kugirango isesengurwe rya PCA, yerekana ko gusiba kwa mutant byegeranye cyane kandi bitandukanye cyane na WT Nsp1.Ingirabuzima fatizo zagengwaga cyane na mutant zari zikungahaye cyane kuri "peptide biosynthetic / metabolic process", "ribonucleoprotein complex biogenesis", "protein yibasira membrane / ER", n'ibindi.
Igicapo 4. Isesengura ryanditse kuri selile HEK239T yandujwe na WT Nsp1 kandi hamwe no gusiba
Ingaruka zo gusiba kuri IFN-1 igisubizo nacyo cyageragejwe mubushakashatsi bukabije.Gusiba kwose kwerekanwe kwerekana kugabanya IFN-1 repsonse muri selile HEK239T na A549 zahinduwe kurwego rwa transcriptome na protein.Igishimishije, ingirabuzimafatizo zigabanuka cyane mugusiba zarakungahajwe no "kwirinda igisubizo cya virusi", "kwigana virusi ya virusi", "kugena inyandiko-mvugo ya RNA polymerase II" no "gusubiza ubwoko bwa I interferon".
Igicapo 5. Hasi amabwiriza ya interferon yerekana inzira muri ∆500-532 mutant
Muri ubu bushakashatsi, ingaruka zo gusiba kuri virusi zashimangiwe n’ubushakashatsi bwanduye virusi.Virusi zifite mutant zimwe na zimwe zitandukanijwe n’ubuvuzi kandi zanduza selile ya Calu-3.Ibisubizo birambuye kubyerekeranye no kwandura virusi murashobora kubisoma mu mpapuro.
doi:10.1016 / j.chom.2021.01.015
Reba
Lin J, Tang C, Wei H, n'abandi.Igenzura rusange rya SARS-CoV-2 rivumbura uburyo bwo gusiba Nsp1 ihindura ubwoko bwa I interferon igisubizo [J].Akagari ka selile & microbe, 2021.
Amakuru n'ibikurubikuru igamije gusangira ibibazo byatsinzwe na Biomarker Technologies, gufata ibyagezweho mu buhanga hamwe nubuhanga bukomeye bwakoreshejwe mugihe cyo kwiga.
Igihe cyo kohereza: Mutarama-06-2022