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TMB相关免疫浸润调控评分(MOTIF)预测免疫治疗响应并指导联合增效

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Science Bulletin 2024年第6期69卷 803-822页

作者：钱政宇潘艺芊李薛鑫陈衍行吴灏祥刘泽先 martin Kosar Jiri Bartek 王梓贤徐瑞华 Department of Medical Oncology Sun Yat-sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Provincial Clinical Research Center for CancerResearch Unit of Precision Diagnosis and Treatment for Gastrointestinal CancerChinese Academy of Medical SciencesGuangzhou 510060China Science for Life Laboratory Division of Genome BiologyDepartment of Medical Biochemistry and BiophysicsKarolinska InstituteStockholm S-17121Sweden Department of General Surgery The Fourth Affiliated HospitalChina Medical UniversityShenyang 110032China Bioinformatics Platform Sun Yat-sen University Cancer CenterGuangzhou 510060China Zhejiang University-University of Edinburgh Institute Zhejiang University School of MedicineHaining 314400China Edinburgh Medical School Biomedical SciencesCollege of Medicine and Veterinary MedicineThe University of EdinburghEdinburgh EH11LTUK Danish Cancer Society Research Center Copenhagen DK-2100Denmark Laboratory of Artificial Intelligence and Data Science Sun Yat-sen University Cancer CenterGuangzhou 510060China

Patients with high tumor mutational burden(TMB)levels do not consistently respond to immune checkpoint inhibitors(ICIs),possibly because a high TMB level does not necessarily result in adequate infiltration of CD8^(+)T *** bulk ribonucleic acid sequencing(RNA-seq)data from 9311 tumor samples across 30 cancer types,we developed a novel tool called the modulator of TMB-associated immune infiltration(MOTIF),which comprises genes that can determine the extent of CD8^(+)T cell infiltration prompted by a certain TMB *** confirmed that MOTIF can accurately reflect the integrity and defects of the cancer-immunity *** analyzing 84 human single-cell RNA-seq datasets from 32 types of solid tumors,we revealed that MOTIF can provide insights into the diverse roles of various cell types in the modulation of CD8^(+)T cell *** pretreatment RNA-seq data from 13 ICI-treated cohorts,we validated the use of MOTIF in predicting CD8^(+)T cell infiltration and ICI *** the components of MOTIF,we identified EMC3 as a negative regulator of CD8^(+)T cell infiltration,which was validated via in vivo ***,MOTIF provided guidance for the potential combinations of programmed death 1 blockade with certain immunostimulatory drugs to facilitate CD8^(+)T cell infiltration and improve ICI efficacy.

关键词： Tumor mutational burden Immunotherapy Cancer-immunity cycle Treatment efficacy prediction CD8^(+)T cell infiltration Combination therapy

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Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process

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Plant Communications 2024年第8期5卷 69-91页

作者： Sergio Alan Cervantes-Perez Prince Zogli Sahand Amini Sandra Thibivilliers Sutton Tennant Md Sabbir Hossain Hengping Xu Ian Meyer Akash Nooka Pengchong Ma Qiuming Yao Michael J.Naldrett Andrew Farmer Olivier martin Samik Bhattacharya Jasper Klaver Marc Libault Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68503USA Division of Plant Science and Technology College of AgricultureFoodand Natural ResourcesUniversity of Missouri-ColumbiaColumbiaMO 65211USA Interdisciplinary Plant Group of Missouri-Columbia ColumbiaMO 65211USA School of Computing University of Nebraska-LincolnLincolnNE 68503USA Proteomics and Metabolomics Facility Center for BiotechnologyUniversity of Nebraska-LincolnLincolnNE 68588USA National Center for Genome Resources Santa FeNM 87505USA INRAE UniversiteParis-SaclayInstitut des Sciences des Plantes de Paris SaclayIPS2Batiment 630 Plateau du MoulonRue Noetzlin91192 Gif sur Yvette CedexFrance Resolve Biosciences Monheim am RheinGermany Present address:The School of Plant Sciences University of ArizonaTucsonAZ 85721USA Present address:GALY Co. 100 Hood Park Dr.BostonMA 02126USA

The soybean root system is *** addition to being composed of various cell types,the soybean root system includes the primary root,the lateral roots,and the nodule,an organ in which mutualistic symbiosis with N-fixing rhizobia occurs.A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont,resulting from the close cooperation between the plant cell and the *** date,the transcriptome of individual cells isolated from developing soybean nodules has been established,but the transcriptomic signatures of cells from the mature soybean nodule have not yet been *** single-nucleus RNA-seq and Molecular Cartography technologies,we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of ***-infected cells in the mature soybean nodule,including those actively involved in nitrogen fixation and those engaged in *** of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation *** instance,we functionally characterized the role of GmFWL3,a plasma membrane microdomain-associated protein that controls rhizobial *** study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.

关键词： soybean root nodule single-cell RNA-seq nanodomains

Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

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Oil Crop Science 2024年第2期9卷 132-141页

作者： Fentanesh Chekole Kassie Gilles Chaix Hermine Bille Ngalle Maguette Seye Coura Fall Hodo-Abalo Tossim Aissatou Sambou Olivier Gibert Fabrice Davrieux Joseph martin Bell Jean-Francois Rami Daniel Fonceka Joel Romaric Nguepjop Department of Plant Biology and Physiology Faculty of SciencesUniversity of Yaounde IYaoundeP.O.Box 337Cameroon Department of Plant Science College of AgricultureWolaita Sodo UniversitySodoP.O.Box 138Ethiopia CIRAD UMR AGAP InstitutMontpellierFrance AGAP Institut Univ MontpellierCIRADINRAEInstitut AgroMontpellierFrance ChemHouse Research Group MontpellierFrance Centre D’Etudes Regional Pour L’Amelioration de L’Adaptation a La Secheresse(CERAAS/ISRA) Route de KhomboleThiesBP 3320Senegal Dispositif de Recherche et de Formation en Partenariat Innovation et Amelioration Varietale en Afrique de L’Ouest(IAVAO)CERAASRoute de KhomboleThiesBP 3320Senegal CIRAD UMR QUALISUDSaint PierreFrance

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional *** this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed *** elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 *** were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between *** magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid *** yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples *** pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the ***,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment *** confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different f

关键词： Groundnut Oilseed Near infrared spectroscopy Germplasm analysis Environment Nutritional Breeding

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Exclusive breastfeeding greater than 50%, success of education in a university hospital in Bogotá: Case-control study

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World Journal of Clinical Pediatrics 2024年第1期13卷 23-30页

作者： Marcela Murillo Galvis Sofia Ortegon Ochoa Clara Eugenia Plata García Maria Paula Valderrama Junca Dayanna Alejandra Inga Ceballos Daniel Mauricio Mora Gómez Claudia M Granados martin Rondón Department of Pediatrics Hospital Universitario San IgnacioBogotá110111Colombia Department of Clinical Epidemiology and Biostatistics Pontifica Universidad JaverianaBogotá110111Colombia

BACKGROUND Maintenance rates of exclusive breastfeeding(EBF)worldwide are low,thus,one of the objectives of the summary of policies on breastfeeding(BF)in world nutrition goals for 2025 are that at least 50%of infants under six months of age receive EBF that *** Objective of this study is to document the rates of EBF in children born in San Ignacio University Hospital(HUSI)and identify factors associated with *** To document the percentages of EBF in those that were born at HUSI and identify factors associated to their *** This is a study of cases and controls in an analytic,retrospective cohort that took children born alive between January 2016 and January 2019 at HUSI located in the city of Bogotá,*** Receiving information about BF at HUSI was able to maintain EBF up until 4 mo(OR=1.65;95%CI:1.02-2.66).The presence of gynecologic and obstetric comorbidities(OR=0.32;95%CI:0.12-0.83),having mastitis(OR=0.56;95%CI:0.33-0.94),and receiving information from mass media(OR=0.52;95%CI:0.31-0.84)are factors associated with not maintaining *** Receiving education at a Women-and Child-Friendly Institution was the only significant factor to achieve EBF until 4 mo,with a frequency greater than the one reported in the country,which matches multiple studies where counseling and individualized support on BF achieve this *** about BF and early detection of obstetric/gynecologic complications must be strengthened among the healthcare staff in charge of mothers during ***,strategies must be promoted to continue BF such as creating milk banks with the objective of increasing BF rates even when mothers return to work.

关键词： Breastfeeding Women-and Child-Friendly Institutional Strategy Strategies Adherence Education

Carbocysteine as Adjuvant Therapy in Acute Respiratory Tract Infections in Patients without Underlying Chronic Conditions: Systematic Review and Meta-Analysis

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Open Journal of Respiratory Diseases 2024年第2期14卷 39-50页

作者： Myriam Calle Rubio Olga de la Serna Blazquez José Luis R. martin Manuel Ruiz Cuetos Pulmonology Department Hospital Clínico San Carlos Madrid Spain Department of Medicine School of Medicine Universidad Complutense de Madrid Madrid Spain Instituto de Investigacion Sanitaria del Hospital Clínico San Carlos (IdISSC) Madrid Spain Pediatric Pulmonology Unit Pediatrics Department Hospital Universitario La Paz Madrid Spain Simplifying Research Institute Layos Spain Medical department in ITF Research Pharma S.L.U. Alcobendas Spain

Objective: This study aims to systematically examine the existing evidence regarding the clinical benefits of carbocysteine as an adjunctive treatment in acute bronchopulmonary and otorhinological processes. Design: Systematic review and meta-analysis. Data sources: An electronic search was conducted across PubMed, Cochrane Library, ***, and the European Clinical Trial Register, with the search dated to May 2023. Bibliographic references from other literature reviews and meta-analyses were also reviewed. The search was limited to randomized clinical trials published in any language and year. It was completed by cross-checking the references of the located articles. Methods: Inclusion criteria covered studies assessing systemic or inhaled carbocysteine, regardless of dosing regimen. Concomitant medication use was acceptable if balanced between intervention and control groups. Authors independently extracted data, resolving disagreements through consensus. Methodological quality assessment relied on critical reading of each study. Dichotomous variables were analyzed using odds ratio (OR), and a final effect size was calculated. Statistical significance was established when confidence intervals did not cross the neutral value. Heterogeneity was assessed via the X2 test and I2 index. Results: Out of 318 initially identified studies, 4 met inclusion criteria. The meta-analysis for poor general condition yielded an OR of 0.45 in favor of intervention, p = 0.013, with non-significant heterogeneity. Cough events showed a percentage of 15.8% for carbocysteine vs. 27.2% for placebo. On the seventh day, expectoration rates were 18.37% for carbocysteinevs 33.3% for placebo. Conclusions: The observed clinical benefits align with carbocysteine’s mucoactive and muco-regulatory properties, complemented by anti-inflammatory and antioxidant actions. Carbocysteine stands out among mucolytic agents. In the context of persistent infectious diseases,

关键词： Acute Respiratory Infections Carbocystenine Systematic Review Meta-Analysis

Functionally graded structure of a nitride-strengthened Mg_(2)Si-based hybrid composite

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Journal of Magnesium and Alloys 2024年第3期12卷 1239-1256页

作者： Jeongho Yang Woongbeom Heogh Hogi Ju Sukhyun Kang Tae-Sik Jang Hyun-Do Jung Mohammad Jahazi Seung Chul Han Seong Je Park Hyoung Seop Kim Susmita Bose Amit Bandyopadhyay martin Byung-Guk Jun Young Won Kim Dae-kyeom Kim Rigoberto CAdvincula Clodualdo Aranas Jr Sang Hoon Kim School of Mechanical Engineering Pusan National UniversityBusan 46241Republic of Korea Department of Mechanical Design Engineering Hanyang UniversitySeoul 04763Republic of Korea Process Research 3 Team LG Display Co.Ltd.PajuGyeonggi-do 10845Republic of Korea Department of Materials Science and Engineering Chosun UniversityGwangju 61452Republic of Korea Institute of Well-Aging Medicare&Chosun University LAMP Center Chosun UniversityGwangju 61452Republic of Korea Division of Materials Science and Engineering Hanyang UniversitySeoul 04763Republic of Korea Department of Mechanical Engineering École de Technologie SupérieureMontrealQuebec H3C 1K3Canada Material&Component Convergence R&D Center Korea Construction Equipment Technology InstituteGunsanJeollabuk-do 54002Republic of Korea School of Mechanical and Aerospace Engineering Nanyang Technological UniversitySingapore 639798Singapore Graduate Institute of Ferrous&Eco Materials Technology Pohang University of Science and TechnologyPohangGyeongsangbuk-do 37673Republic of Korea Advanced Institute for Materials Research Tohoku UniversitySendai 980-8577Japan Institute for Convergence Research and Education in Advanced Technology Yonsei UniversitySeoul 03722Republic of Korea School of Mechanical and Materials Engineering Washington State UniversityPullmanWashington 99164USA School of Mechanical Engineering Purdue UniversityWest LafayetteIndiana 47907USA Research Institute of Advanced Manufacturing Technology Korea Institute of Industrial TechnologyIncheon 21999Republic of Korea Department of Macromolecular Science and Engineering Case Western Reserve UniversityClevelandOhio 44106USA Department of Chemical and Biomolecular Engineering and Joint Institute for Advanced Materials University of TennesseeKnoxvilleTennessee 37996USA Center for Nanophase Materials and Sciences Oak Ridge National LaboratoryOak RidgeTennessee 37830USA Department of Mechanical Engineering University of New BrunswickFrederictonNew Brunswick E3B 5A3Cana

The ex-situ incorporation of the secondary SiC reinforcement,along with the in-situ incorporation of the tertiary and quaternary Mg_(3)N_(2) and Si_(3)N_(4) phases,in the primary matrix of Mg_(2)Si is employed in order to provide ultimate wear resistance based on the laser-irradiation-induced inclusion of N_(2) gas during laser powder bed *** is substantialized based on both the thermal diffusion-and chemical reactionbased metallurgy of the Mg_(2)Si–SiC/nitride hybrid *** study also proposes a functional platform for systematically modulating a functionally graded structure and modeling build-direction-dependent architectonics during additive *** strategy enables the development of a compositional gradient from the center to the edge of each melt pool of the Mg_(2)Si–SiC/nitride hybrid ***,the coefficient of friction of the hybrid composite exhibits a 309.3%decrease to–1.67 compared to–0.54 for the conventional nonreinforced Mg_(2)Si structure,while the tensile strength exhibits a 171.3%increase to 831.5 MPa compared to 485.3 MPa for the conventional *** outstanding mechanical behavior is due to the(1)the complementary and synergistic reinforcement effects of the SiC and nitride compounds,each of which possesses an intrinsically high hardness,and(2)the strong adhesion of these compounds to the Mg_(2)Si matrix despite their small sizes and low concentrations.

关键词： Laser powder bed fusion Mg_(2)Si-SiC/nitride hybrid composite Both the thermal diffusion-and chemical reaction-based metallurgy Functionally graded structure Compositional gradient Wear resistance.

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Preparation and Characterisation of Corncob-Based Biosorbents in Côte d’Ivoire

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Advances in Materials Physics and Chemistry 2024年第8期14卷 178-195页

作者： Miezan Gnoan Ghislaine De Bouanzi Patrick Grah Atheba Serge Kouassi Gbamélé martin Alla Aka Albert Trokourey Laboratory of Constitution and Reaction of Matter (LCRM) Flix Houphout-Boigny University Abidjan Cte dIvoire Laboratory of Environmental Sciences (LSE) Nangui Abrogoua University Abidjan Cte dIvoire

This study focuses on the preparation of corncob-based biosorbents. The chemical impregnation method was used to vary the chemical agent namely phosphoric acid H3PO4 (BA) and sodium hydroxide NaOH (BB). The physicochemical analysis of the two biosorbents indicated that under the same preparation conditions, the bio-sorbents have after activation yields lower than 50% (24.37% for BB and 49.09% for BA). In addition, the biosorbents have iodine index values between 444.17 mg/g and 418.79 mg/g and specific surfaces related to the adsorption of methylene blue ranging from 18.54 m2/g to 19.70 m2/g. The study of surface functional groups by using the Boehm test and pH zero point charge (pHPZC) confirmed the acidic nature of BA and BB biosorbents with respective values pHPZC = 4.01 and pHPZC = 4.90. The Langmuir method and BET analysis determined the specific surface areas by liquid phase adsorption of methylene blue as well as the porosity. The BET surface areas of BA and BB obtained are 72.01 m2/g and 63.10 m2/g respectively. The influence of the chemical activating agent on the formation of pores was confirmed by electron microscopy (SEM) analysis. From this study, it is found that the best activating agent for corn cobs was found to be phosphoric acid because the BA biosorbent was revealed to be the most favourable due to its surface area and good pore volume which are high compared to sodium hydroxide NaOH. Moreover, their application as adsorbent for effluent treatment could be explored.

关键词： Biosorbent Corncobs Chemical Activation Phosphoric Acid Sodium Hydroxide

Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

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Molecular Plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang martin Vingron Ralph Bock Jun Yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China Department of Computational Molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany Department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops ***,its genetic origin remains controversial,and its domestication history remains *** this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of *** diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to *** tetraploid progenitor of sweetpotato was most likely *** 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast *** most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome *** addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome *** analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of *** study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

Quantitative and qualitative subgenomic RNA profiles of SARS-CoV-2 in respiratory samples: A comparison between Omicron BA.2 and non-VOC-D614G

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Virologica Sinica 2024年第2期39卷 218-227页

作者： Zigui Chen Rita Way Yin Ng Grace Lui Lowell Ling Agnes S.Y.Leung Chit Chow Siaw Shi Boon Wendy C.S.Ho Maggie Haitian Wang Renee Wan Yi Chan Albert martin Li David Shu Cheong Hui Paul Kay Sheung Chan Department of Microbiology Faculty of MedicineThe Chinese University of Hong KongHong KongChina Department of Medicine and Therapeutics Faculty of MedicineThe Chinese University of Hong KongHong KongChina Department of Anaesthesia and Intensive Care Faculty of MedicineThe Chinese University of Hong KongHong KongChina Department of Paediatrics Faculty of MedicineThe Chinese University of Hong KongHong KongChina Department of Anatomical and Cellular Pathology Faculty of MedicineThe Chinese University of Hong KongHong KongChina Jockey Club School of Public Health and Primary Care Faculty of MedicineThe Chinese University of Hong KongHong KongChina Stanley Ho Centre for Emerging Infectious Diseases Faculty of MedicineThe Chinese University of Hong KongHong KongChina

The SARS-CoV-2 Omicron variants are notorious for their transmissibility,but little is known about their subgenomic RNA(sgRNA)*** study applied RNA-seq to delineate the quantitative and qualitative profiles of canonical sgRNA of 118 respiratory samples collected from patients infected with Omicron BA.2 and compared with 338 patients infected with non-variant of concern(non-VOC)-D614G.A unique characteristic profile depicted by the relative abundance of 9 canonical sgRNAs was reproduced by both BA.2 and non-VOCD614G regardless of host gender,age and presence of ***,such profile was lost in samples with low viral load,suggesting a potential application of sgRNA pattern to indicate viral activity of individual patient at a specific time point.A characteristic qualitative profile of canonical sgRNAs was also reproduced by both BA.2 and *** presence of a full set of canonical sgRNAs carried a coherent correlation with crude viral load(AUC¼0.91,95%CI 0.88–0.94),and sgRNA ORF7b was identified to be the best surrogate marker allowing feasible routine application in characterizing the infection status of individual *** potentials in using sgRNA as a target for vaccine and antiviral development are worth pursuing.

关键词： Coronavirus SARS-CoV-2 Omicron BA.2 Non-VOC-D614G RNA-seq Subgenomic RNA(sgRNA)