IGENOME IPHINDE I-RESEQUENING
Uhlolo lweGenomics lwe-SARS-CoV-2 lutyhila ukwahluka kokususwa kwe-Nsp1 emodareyitha impendulo yohlobo lwe-interferon
Nanopore |Ilumina |Ulandelelwano lwegenome yonke |Imetagenomics |I-RNA-Seq |Sanger
I-Biomarker Technologies ibonelele ngenkxaso yobugcisa kulandelelwano lwesampulu kolu phononongo.
Iimbalasane
I-1.SARS-CoV-2 i-genome sequencing kunye nohlalutyo lwe-phylognetic ichonga ukuguqulwa kwe-35 okuphindaphindiweyo kuquka i-31 ye-SNP kunye ne-Indels ezi-4.
I-2.Ukudibanisa kunye ne-117 ye-phenotypes yeklinikhi ibonisa ukuba kunokwenzeka
utshintsho olubalulekileyo.
∆500-532 kwindawo yekhowudi ye-Nsp1 ihambelana nentsholongwane esezantsi
3.umthwalo kunye ne-serum IFN-β.
I-4.I-Viral isolate ene-∆500-532 yokuguqulwa kwenguqu ibangela i-IFN-I ephantsi
impendulo kwiiseli ezosulelekileyo.
Uyilo loMfuniselo
Impumelelo
1. COVID-19 epidemiological and genomic surveillance
Idatha yezonyango yaqokelelwa kwiphondo laseSichuan, eChina kulo lonke ixesha lokuqhambuka ukusuka nge-22 kaJan, 2020 ukuya kwi-20 kaFebruwari, 2020. Itotali yamatyala angama-538 e-COVID-19 aqinisekiswa luvavanyo lwe-qPCR eSichuan, i-28.8% yawo ibisuka kwiphondo. inkunzi.Amatyala aqinisekisiweyo eSichuan anyuke ngokukhawuleza, afikelela kwi-30 kaJan.Kwakhona, idatha exhaswayo ukuba ukungenelela ekuhlaleni kunokuba yinto ephambili ekuthinteleni ukusasazeka kwentsholongwane.
Umfanekiso 1. Uphononongo lwe-Epidemiological ye-COVID-19 kwiphondo laseSichuan, eTshayina
2. Ukwakhiwa kwegenome ye-SARS-CoV-2 kunye nokuchongwa kwezinto ezahlukeneyo
Ngokwandisa i-PCR ye-multiplex elandelwa yi-nanopore sequencing, i-310 iyonke i-genomes esondeleyo okanye inxalenye-epheleleyo evela kwizigulane ze-248 yenziwe malunga ne-approx.I-80% yeegenomes ezigutyungelwe ngofundo olu-10(Ubunzulu obuphakathi: 0.39 M ufundo ngesampulu nganye).
Umzobo 2. Ukuphindaphinda kwezinto ezahlukeneyo kwiqela leSichuan
Zizonke ii-SNP ezili-104 kunye nee-Indels ezili-18 zachongwa kwiigenomes ze-SARS-CoV-2, apho ii-SNP ezingama-31 kunye nee-Indels ezi-4 zachongwa njengeenguqu zemfuzo eziqhubekayo.Ngokuzithelekisa kunye neesampulu ze-169 ezivela e-Wuhan kunye ne-81,391 yomgangatho ophezulu wokulandelelana kwe-genome yoluntu kwi-GISAID, i-29 ye-35 eyahlukileyo efunyenwe kwamanye amazwekazi.Ngokucacileyo, iintlobo ezine ezibandakanya i-∆500-532, ACC18108AT, ∆729-737 kunye ne-T13243C, zifunyenwe kuphela eSichuan nase-Wuhan kwaye zingekho kwidatha ye-GISAID, ebonisa ukuba olu lwantlukwano lunokwenzeka kakhulu ukuba lungeniswe e-Wuhan, oludibana ne-. iirekhodi zokuhamba zezigulane.
Uhlalutyo lwendaleko olunamathuba aphezulu (ML) indlela kunye neendlela ze-Bayesian zewotshi yeemolekyuli zacutshungulwa kwintsholongwane entsha engama-88 ukusuka eSichuan kunye nama-250 eejenomes eziculiweyo ezisuka kweminye imimandla.IiGenomes ezine-∆500-532 (Ukususwa kwindawo yekhowudi ye-Nsp1) zifunyenwe zisasazwe kancinci kumthi we-phylogenetic.Uhlalutyo lweHaplotype kukwahluka kwe-Nsp1 ichonge ezi-5 kuzo kwizixeko ezininzi.Ezi ziphumo zicebise ukuba i-∆500-532 yenzeka kwizixeko ezininzi kwaye ingangeniswa ngaphandle amaxesha amaninzi isuka eWuhan.
Umzobo 2. Ukwahluka kofuzo okuphindaphindiweyo kunye nohlalutyo lwephylogenetic kwi-SARS-CoV-2 genomes.
3. Umbutho wokwahluka kofuzo oluphindaphindiweyo kunye neziphumo zonyango
Iiphenotypes zeklinikhi ezili-117 zaye zanxulunyaniswa nobungqongqo be-COVID-19, apho iiphenotypes ezinxulumene nobungqongqo ezili-19 zahlelwa zaba ziimpawu ezibukhali nezingamandundu.Ubudlelwane phakathi kwezi mpawu kunye ne-35 yokwahluka kwemfuzo ephindaphindiweyo yabonwa kwi-bi-cluster heatmap.Uhlalutyo lokutyebisa olufana ne-GSEA lubonakaliswe ukuba i-∆500-532 ihambelana kakubi ne-ESR, i-serum IFN-β kunye ne-CD3 + CD8 + i-cell counts egazini.Ngaphezu koko, iimvavanyo ze-qPCR zibonise ukuba izigulana ezosulelwe yintsholongwane egcina ∆500-532 zinelona xabiso liphezulu le-Ct, oko kukuthi, umthamo wentsholongwane egazini usezantsi.
Umzobo 3. Imibutho ye-35 ephindaphindiweyo yezofuzo ezahlukeneyo kunye ne-phenotypes yeklinikhi
4. Ukuqinisekiswa kwintsholongwane yentsholongwane ehambelana ne-phenotypes yeklinikhi
Ukuze uqonde iimpembelelo ze-∆500-532 kwimisebenzi ye-Nsp1, iiseli ze-HEK239T zatshintshwa ngeeplasmids ezibonisa ubude obugcweleyo, i-WT Nsp1 kunye neefom eziguqukayo ngokucinywa.Iiprofayili ze-Transcriptome zeeseli ze-HEK239T nganye eziphathwayo zaqhutyelwa kuhlalutyo lwe-PCA, ebonisa ukuba iinguqu eziguquguqukayo zokucima zidibene ngokusondeleyo kwaye zahluke kakhulu kwi-WT Nsp1.Iijini eziye zanyanzeliswa kakhulu kwiinguqu eziguquguqukayo zaye zatyetyiswa kakhulu "kwi-peptide biosynthetic / metabolic process", "ribonucleoprotein complex biogenesis", "iprotheyini ejoliswe kwi-membrane / ER", njl.
Umzobo 4. Uhlalutyo lwe-Transcriptome kwiiseli ze-HEK239T ezosulelwa yi-WT Nsp1 kwaye ngokucinywa.
Iimpembelelo zokususwa kwimpendulo ye-IFN-1 nayo yavavanywa kwisifundo esigqithisiweyo.Konke ukucinywa okuvavanywayo kuboniswe ukunciphisa i-IFN-1 i-repsonse kwi-HEK239T kunye neeseli ze-A549 ezitshintshiweyo kwinqanaba le-transcriptome kunye nenqanaba leprotheni.Okubangel 'umdla kukuba, i-genes ephantsi kakhulu ekucinyweni kwayo iphuculwe "kwimpendulo yokukhusela kwintsholongwane", "i-viral genome replication", "ukulawulwa kokubhalwa kwe-RNA polymerase II" kunye "nempendulo yohlobo lwe-interferon".
Umzobo 5. Ulawulo oluphantsi lweendlela zokubonisa i-interferon kwi-∆500-532 eguquguqukayo
Kolu phononongo, impembelelo yoku kucinywa kwintsholongwane yaqinisekiswa ngakumbi ngophononongo losulelo lwentsholongwane.Iintsholongwane ezineentsholongwane ezithile ziye zahlukaniswa kwiisampulu zeklinikhi kwaye zosulelwa kwiiseli zeCalu-3.Iziphumo ezineenkcukacha kuphononongo losulelo lwentsholongwane zingafundwa kwiphepha.
doi:10.1016/j.chom.2021.01.015
Isalathiso
ULin J, uTang C, u-Wei H, nabanye.Uhlolo lweGenomic lwe-SARS-CoV-2 lutyhila ukwahluka kocimo lwe-Nsp1 olumodareyitha impendulo yohlobo lwe-interferon[J].Umamkeli weeseli & microbe, 2021.
Iindaba neembalasane ijolise ekwabelaneni ngamatyala aphumeleleyo amva nje kunye ne-Biomarker Technologies, ukubamba impumelelo yesayensi enoveli kunye nobuchule obubalaseleyo obusetyenzisiweyo ngexesha lokufunda.
Ixesha lokuposa: Jan-06-2022