ZINTHU ZONSE ZA GENOME RESEQUENING
Kuwunika kwa Genomics kwa SARS-CoV-2 kumavumbulutsa mtundu wa Nsp1 wochotsa womwe umasinthira kuyankha kwamtundu wa I interferon
Nanopore |Ilumina |Kubwereza kwamtundu wonse |Metagenomics |RNA-Seq |Sanger
Biomarker Technologies idapereka chithandizo chaukadaulo pakutsatizana kwa zitsanzo mu kafukufukuyu.
Mfundo zazikuluzikulu
1.SARS-CoV-2 genome sequencing ndi phylognetic kusanthula kumazindikira masinthidwe 35 obwereza kuphatikiza 31 SNPs ndi 4 Indels.
2.Kugwirizana ndi 117 zachipatala phenotypes zimawulula zotheka
masinthidwe ofunikira.
∆500-532 m'dera la Nsp1 coding correlates ndi ma virus otsika
3.load ndi seramu IFN-β.
4.Viral isolates ndi ∆500-532 mutation imapangitsa kuti IFN-I ikhale yotsika
kuyankha m'maselo omwe ali ndi kachilomboka.
Mapangidwe Oyesera
Zopambana
1. COVID-19 epidemiological and genomic surveillance
Zambiri zachipatala zidasonkhanitsidwa m'chigawo cha Sichuan, China nthawi yonseyi kuyambira Januware 22, 2020 mpaka Feb. 20, 2020. Milandu 538 ya COVID-19 idatsimikiziridwa ndi mayeso a qPCR ku Sichuan, 28.8% omwe anali ochokera m'chigawochi. likulu.Milandu yotsimikizika ku Sichuan idakwera kwambiri, kufika pachimake pa Januware 30.Komanso, zidziwitso zimatsimikizira kuti kusamvana kumatha kukhala chinthu chofunikira kwambiri popewa kufalikira kwa ma virus.
Chithunzi 1. Kafukufuku wa Epidemiological wa COVID-19 m'chigawo cha Sichuan, China
2. SARS-CoV-2 genome kupanga ndi mitundu yosiyanasiyana
Ndi multiplex PCR amplification yotsatiridwa ndi nanopore sequencing, ma genomes okwana 310 pafupi kapena pang'ono kuchokera kwa odwala 248 anapangidwa ndi pafupifupi.80% ya ma genome omwe amawerengedwa ndi 10 (Kuzama kwake: 0.39 M amawerengedwa pa chitsanzo).
Chithunzi 2. Kachulukidwe kamitundu iliyonse mugulu la Sichuan
Ma SNP 104 ndi ma Indels 18 adadziwika kuchokera ku ma SARS-CoV-2 genomes, momwe ma SNP 31 ndi ma Indels 4 adazindikiritsidwa ngati mitundu yobwerezabwereza.Powayerekeza ndi zitsanzo 169 zochokera ku Wuhan komanso zotsatizana 81,391 zapamwamba za publich genome mu GISAID, 29 mwa mitundu 35 yomwe yapezeka m'makontinenti ena.Makamaka, mitundu inayi kuphatikiza ∆500-532, ACC18108AT, ∆729-737 ndi T13243C, idapezeka kuti ikupezeka ku Sichuan ndi Wuhan komanso kulibe mu data ya GISAID, kuwonetsa kuti izi zitha kupangidwa kuchokera ku Wuhan, zomwe zimakwaniritsa zolemba zapaulendo za odwala.
Kusanthula kwachisinthiko kokhala ndi kuthekera kwakukulu (ML) njira ndi njira za mawotchi a Bayesian molekyulu zidakonzedwa pa ma virus 88 atsopano ochokera ku Sichuan ndi ma genome 250 osungidwa kuchokera kumadera ena.Ma genome okhala ndi ∆500-532 (Kuchotsa m'dera la Nsp1 coding) adapezeka atagawidwa mochepa mumtengo wa phylogenetic.Kusanthula kwa Haplotype pamitundu ya Nsp1 kudazindikira 5 mwa iwo kuchokera kumizinda ingapo.Zotsatirazi zikuwonetsa kuti ∆500-532 idachitika m'mizinda ingapo ndipo itha kutumizidwa kangapo kuchokera ku Wuhan.
Chithunzi 2. Kusiyanasiyana kwa majini obwerezabwereza ndi kusanthula kwa phylogenetic mu ma genome a SARS-CoV-2
3. Kugwirizana kwa mitundu yosiyanasiyana ya ma genetic ndi zotsatira zachipatala
Ma phenotypes 117 azachipatala adalumikizidwa ndi kuuma kwa COVID-19, pomwe ma phenotypes 19 okhudzana ndi kuuma adayikidwa m'magulu owopsa komanso osawopsa.Ubale pakati pa mikhalidwe iyi ndi mitundu 35 yobwerezabwereza ya majini idawonedwa mu bi-cluster heatmap.Kusanthula kolemetsa kwamtundu wa GSEA kwawonetsa kuti ∆500-532 imagwirizana molakwika ndi ESR, seramu IFN-β ndi CD3 + CD8 + T imawerengera m'magazi.Kuphatikiza apo, mayeso a qPCR adawonetsa kuti odwala omwe ali ndi kachilombo komwe amakhala ∆500-532 anali ndi mtengo wapamwamba kwambiri wa Ct, mwachitsanzo, kuchuluka kwa ma virus otsika kwambiri.
Chithunzi 3. Mayanjano a 35 obwerezabwereza ma genetic ndi ma phenotypes azachipatala
4. Kutsimikizika pa kusintha kwa ma virus kumakhudzana ndi ma phenotypes azachipatala
Kuti timvetsetse momwe ∆500-532 imakhudzira ntchito za Nsp1, ma cell a HEK239T adasinthidwa ndi ma plasmids owonetsa kutalika, WT Nsp1 ndi mawonekedwe osinthika omwe amachotsa.Mbiri ya Transcriptome ya maselo aliwonse a HEK239T omwe amathandizidwa adasinthidwa kuti awonedwe ndi PCA, kuwonetsa kuti zosintha zochotsa zidalumikizana kwambiri ndipo zinali zosiyana kwambiri ndi WT Nsp1.Ma jini omwe adasinthidwa kwambiri muzosinthazo adalimbikitsidwa makamaka mu "peptide biosynthetic / metabolic process", "ribonucleoprotein complex biogenesis", "mapuloteni omwe amayang'ana ku membrane / ER", ndi zina zambiri. Komanso, kufufutidwa kuwiri kunawonetsa njira yosiyana ya expssion kuchokera ku WT.
Chithunzi 4. Kusanthula kwa Transcriptome pa ma cell a HEK239T opatsiridwa ndi WT Nsp1 ndi omwe amachotsa.
Zotsatira za kuchotsedwa pa IFN-1 kuyankha kunayesedwanso mu kafukufuku wochuluka.Kufufutidwa konse koyesedwa kunawonetsedwa kuti kumachepetsa kubwereza kwa IFN-1 m'maselo a HEK239T ndi A549 omwe adasinthidwa pamlingo wa transcriptome ndi protein level.Chochititsa chidwi n'chakuti, majini omwe amachepetsedwa kwambiri pochotsa adalimbikitsidwa "kuyankha kwa chitetezo ku kachilomboka", "viral genome replication", "malamulo olembedwa ndi RNA polymerase II" ndi "mayankho amtundu wa I interferon".
Chithunzi 5. Kutsika kwamalamulo a interferon signing pathways mu ∆500-532 mutant
Mu kafukufukuyu, zotsatira za kufufutidwa kwa kachilomboka zidatsimikiziridwanso ndi maphunziro a matenda a virus.Ma virus omwe ali ndi masinthidwe ena adasiyanitsidwa ndi zitsanzo zachipatala ndikukhudzidwa ndi ma cell a Calu-3.Zotsatira zatsatanetsatane pa kafukufuku wa matenda a virus zitha kuwerengedwa papepala.
doi:10.1016/j.chom.2021.01.015
Buku
Lin J, Tang C, Wei H, et al.Kuyang'anira genomic kwa SARS-CoV-2 kumavumbulutsa mtundu wochotsa wa Nsp1 womwe umasinthira kuyankha kwamtundu wa I interferon[J].Ma cell host & microbe, 2021.
Nkhani ndi Mfundo Zazikulu ikufuna kugawana milandu yaposachedwa kwambiri ndi Biomarker Technologies, kujambula zomwe zakwaniritsa zasayansi komanso njira zodziwika bwino zomwe zimagwiritsidwa ntchito pophunzira.
Nthawi yotumiza: Jan-06-2022