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Wastewater surveillance and an automated robot:effectively tracking SARS-CoV-2 transmission in the post-epidemic era

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National Science Review 2023年第6期10卷 86-95页

作者： Guanyong Ou Yuxuan Tang Shiyu Niu Liwen Wu Shaxi Li Yang Yang Jun Wang Yun Peng Chuanfu Huang Wei Hu Qinghua Hu Yinghui Li Yang Ping Chao Lin Boping Yu Qi Han Yabin Hao Zhiguang Luo Wende Tian Han Zhang Yingxia Liu School of Civil and Environmental Engineering Harbin Institute of Technology (Shenzhen) 1Institute of Solid Wastes and Physical Environment Research Shenzhen Academy of Environmental Sciences Shenzhen Metasensing Technology Co. Ltd. 13. Zhongmin (Shenzhen) intelligent ecology Co. Ltd. Research Centre for Eco-Environmental Sciences Chinese Academy of Sciences National Clinical Research Center for Infectious Disease State Key Discipline of Infectious Disease The Third People's Hospital of Shenzhen Second Hospital Affiliated to Southern University of Science and Technology School of Medicine Southern University of Science and Technology International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics College of Physics and Optoelectronic Engineering Shenzhen University Shenzhen Longhua Drainage Co. Ltd. Shenzhen Center for Disease Control and Prevention Microbiology Laboratory Shenzhen Center for Disease Control and Prevention Power China Eco-Environmental Group Co. Ltd. Shenzhen Water Planning & Design Institute Co. Ltd. Shenzhen Academy of Environmental Sciences

Wastewater-based epidemiology(WBE) has exhibited great utility in the early and rapid identification of sars-C oV-2.However,the efficacy of wastewater surveillance under China’ s previous strict epidemic prevention policy remains to be described.We collected the WBE data of wastewater treatment plants(WWTPs) in the Third People’s Hospital of Shenzhen and several communities to determine the significant effectiveness of routine wastewater surveillance in monitoring the local spread of sars-C oV-2under tight containment of the epidemic.The results of 1 month of continuous wastewater surveillance showed that positive signals for sars-C oV-2 RNA were detected in the wastewater samples,and a significant positive correlation was observed between the virus concentration and the number of daily cases.In addition,the community’ s domestic wastewater surveillance results were confirmed even 3 days before,or simultaneously with,the infected patient being confirmed as having the virus.Meanwhile,an automated sewage virus detection robot,ShenNong No.l robot,was developed,showing a high degree of agreement with experimental data,offering the possibility of large-scale multi-point surveillance.Overall,our results illustrated the clear indicative role of wastewater surveillance in combating covID-19 and provided a practical basis for rapidly expanding the feasibility and value of routine wastewater surveillance for future emerging infectious diseases.

关键词： SARS-CoV-2 wastewater surveillance wastewater-based epidemiology WWTP automated robot

covID-19 vaccination produces exercise-responsive SARS-CoV-2 specific T-cells regardless of infection history

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Journal of Sport and Health Science 2024年第1期13卷 99-107页

作者： Kyle A.Smith Tiffany M.Zúñiga Forrest L.Baker Helena Batatinha Charles R.Pedlar Shane C.Burgess Michael P.Gustafson Emmanuel Katsanis Richard J.Simpson School of Nutritional Sciences and Wellness The University of ArizonaTucsonAZ 85721USA Department of Pediatrics The University of ArizonaTucsonAZ 85724USA Faculty of Sport Allied Health and Performance ScienceSt.Mary's UniversityTwickenham TW14SXUK Institute of Sport Exercise and Health University College LondonLondon WC1E 7HUUK Department of Animal and Comparative Biomedical Sciences The University of ArizonaTucsonAZ 85721USA The University of Arizona Cancer Center The University of ArizonaTucsonAZ 85719USA Laboratory Medicine and Pathology Mayo Clinic ArizonaPhoenixAZ 85054USA Department of Immunobiology The University of ArizonaTucsonAZ 85724USA Department of Medicine The University of ArizonaTucsonAZ 85724USA Department of Pathology The University of ArizonaTucsonAZ 85724USA

Background:The mobilization and redistribution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)specific T-cells and neutralizing antibodies(nAbs)during exercise is purported to increase immune surveillance and protect against severe coronavirus disease 2019(covID-19).We sought to determine if covID-19 vaccination would elicit exercise-responsive SARS-CoV-2 T-cells and transiently alter nAb titers.Methods:Eighteen healthy participants completed a 20-min bout of graded cycling exercise before and/or after receiving a covID-19 vaccine.All major leukocyte subtypes were enumerated before,during,and after exercise by flow cytometry,and immune responses to SARS-CoV-2 were determined using whole blood peptide stimulation assays,T-cell receptor(TCR)-βsequencing,and SARS-CoV-2 nAb serology.Results:covID-19 vaccination had no effect on the mobilization or egress of major leukocyte subsets in response to intensity-controlled graded exercise.However,non-infected participants had a significantly reduced mobilization of CD4+and CD8+naive T-cells,as well as CD4+central memory T-cells,after vaccination(synthetic immunity group);this was not seen after vaccination in those with prior SARS-CoV-2 infection(hybrid immunity group).Acute exercise after vaccination robustly mobilized SARS-CoV-2 specific T-cells to blood in an intensity-dependent manner.Both groups mobilized T-cells that reacted to spike protein;however,only the hybrid immunity group mobilized T-cells that reacted to membrane and nucleocapsid antigens.nAbs increased significantly during exercise only in the hybrid immunity group.Conclusion:These data indicate that acute exercise mobilizes SARS-CoV-2 specific T-cells that recognize spike protein and increases the redistribution of nAbs in individuals with hybrid immunity.

关键词： Anti-viral covID-19 Exercise immunology SARS-CoV-2 T-Cells Vaccine

A comprehensive survey of bat sarbecoviruses across China in relation to the origins of sars-cov and SARS-CoV-2

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National Science Review 2023年第6期10卷 117-130页

作者： Zhiqiang Wu Yelin Han Yuyang Wang Bo Liu Lamei Zhao Junpeng Zhang Haoxiang Su Wenliang Zhao Liguo Liu Shibin Bai Jie Dong Lilian Sun Yafang Zhu Siyu Zhou Yiping Song Hongtao Sui Jian Yang Jianwei Wang Shuyi Zhang Zhaohui Qian Qi Jin NHC Key Laboratory of Systems Biology of Pathogens Institute of Pathogen Biology Chinese Academy of Medical Sciences and Peking Union Medical College Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical College College of Animal Science and Veterinary Medicine Shenyang Agricultural University

sars-C oV and sars-C oV-2 have been thought to originate from bats.In this study,we screened pharyngeal and anal swabs from 13 064 bats collected between 2016 and 2021 at 703 locations across China for sarbecoviruses,covering almost all known southern hotspots,and found 146 new bat sarbecoviruses.Phylogenetic analyses of all available sarbecoviruses show that there are three different lineages—L1 as sars-cov-related covs(sarsr-covs),L2 as SARS-CoV-2-related covs(SC2r-covs) and novel L-R(recombinants of L1 and L2)—present in Rhinolophus pusillus bats,in the mainland of China.Among the146 sequences,only four are L-Rs.Importantly,none belong in the L2 lineage,indicating that circulation of SC2r-C oVs in China might be very limited.All remaining 142 sequences belong in the L1 lineage,of which YN2020B-G shares the highest overall se quence identity with sars-C oV(95.8 %).The observation suggests endemic circulations of sarsr-covs,but not SC2r-covs,in bats in China.Geographic analysis of the collection sites in this study,together with all published reports,indicates that SC2r-C oVs maybe mainly present in bats of Southeast Asia,including the southern border of Yunnan province,but absent in all other regions within China.In contrast,sarsr-covs appear to have broader geographic distribution,with the highest genetic diversity and sequence identity to human sarbecoviruses along the southwest border of China.Our data provide the rationale for further extensive surveys in broader geographical regions within,and beyond,Southeast Asia in order to find the most recent ancestors of human sarbecoviruses.

关键词： sars-cov SARS-CoV-2 bats China origin tracing

Occurrence and Decay of SARS-CoV-2 in Community Sewage Drainage Systems

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Engineering 2023年第7期26卷 214-219,I0008,I0009页

作者： Qian Dong 蔡俊雄刘艳臣凌海波 Qi Wang Luo-Jing Xiang Shao-Lin Yang Zheng-Sheng Lu Yi Liu Xia Huang 曲久辉 State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084China Hubei Provincial Academy of Eco-Environmental Sciences Wuhan 430072China Key Laboratory of Drinking Water Science and Technology Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing 100085China

The rapid spread of the coronavirus disease(covID-19)pandemic in over 200 countries poses a substantial threat to human health.Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),which causes covID-19,can be discharged with feces into the drainage system.However,a comprehensive understanding of the occurrence,presence,and potential transmission of SARS-CoV-2 in sewers,especially in community sewers,is still lacking.This study investigated the virus occurrence by viral nucleic acid testing in vent stacks,septic tanks,and the main sewer outlets of community where confirmed patients had lived during the early days of the epidemic in Wuhan,China.The results indicated that the risk of long-term emission of SARS-CoV-2 to the environment via vent stacks of buildings was low after confirmed patients were hospitalized.SARS-CoV-2 were mainly detected in the liquid phase,as opposed to being detected in aerosols,and its RNA in the sewage of septic tanks could be detected for only four days after confirmed patients were hospitalized.The surveillance of SARS-CoV-2 in sewage could be a sensitive indicator for the possible presence of asymptomatic patients in the community,though the viral concentration could be diluted more than ten times,depending on the sampling site,as indicated by the Escherichia coli test.The comprehensive investigation of the community sewage drainage system is helpful to understand the occurrence characteristics of SARS-CoV-2 in sewage after excretion with feces and the feasibility of sewage surveillance for covID-19 pandemic monitoring.

关键词： SARS-CoV-2 Transmission risk Drainage system Sewage Community

Impact of thermal stratification on airborne transmission risk of SARS-CoV-2 in various indoor environments

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Building Simulation 2023年第7期16卷 1159-1172页

作者： Fan Liu Zhiwen Luo Hua Qian School of Environment and Architecture University of Shanghai for Science and TechnologyShanghaiChina Welsh School of Architecture Cardiff UniversityCardiffUK School of Energy and Environment Southeast UniversityNanjingChina

There exist various vertical temperature gradients in different-type buildings.A holistic understanding of the impact of different temperature-stratified indoor environments on infection risk is necessary.In this work,the airborne transmission risk of SARS-CoV-2 in different thermally stratified indoor environments is assessed using our previously developed airborne infection risk model.Results show that the vertical temperature gradients in office building,hospital,classroom,etc.are within the range of−0.34 to 3.26℃/m.In large space such as coach station,airport terminal,and sport hall,the average temperature gradient ranges within 0.13–2.38℃/m in occupied zone(0–3 m);in ice rink with special requirements of indoor environment,the temperature gradient is higher than those in the above indoor spaces.The existence of temperature gradients causes multi-peaks of the transmission risk of SARS-CoV-2 with distancing,and our results show that in office,hospital ward and classroom,the second peak of the transmission risk is higher than 10^(−3)in most contact scenarios,while most being lower than 10^(−6)in large spaces like coach station and airport.The work is expected to provide some guidance on specific intervention policies in relation to the types of indoor environments.

关键词： SARS-CoV-2 temperature gradient different-type buildings transmission risk

基于RBD抗原性的五种SARS-CoV-2血清型分类

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Science Bulletin 2023年第23期68卷 3003-3012,M0005页

作者：胡世雄吴春丽吴鑫凯马雪慧舒畅陈茜郑安琪杨惠婷陆剑杜沛高福王奇慧 College of Veterinary Medicine Shanxi Agricultural UniversityJinzhong 030801China CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China School of Life Sciences Yunnan UniversityKunming 650091China School of Life Sciences Peking UniversityBeijing 100871China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Faculty of Health Sciences University of MacaoMacao 999078China

新冠病毒(SARS-CoV-2)的不断进化带来了大量的变异株,特别是Omicron变异株及其众多的亚型.这些变异株表现出越来越强的免疫逃逸能力,使现有疫苗和治疗抗体的效力不断下降.目前,众多变异株已表现出血清交叉中和作用减弱的现象,表明新冠... 详细信息

新冠病毒(SARS-CoV-2)的不断进化带来了大量的变异株,特别是Omicron变异株及其众多的亚型.这些变异株表现出越来越强的免疫逃逸能力,使现有疫苗和治疗抗体的效力不断下降.目前,众多变异株已表现出血清交叉中和作用减弱的现象,表明新冠病毒可能已进化出多种血清型.因此,我们选取新冠病毒的主要抗原,即刺突(S)蛋白的受体结合域(RBD)对其进行血清分型.我们首先选择了23个具有代表性的新冠病毒毒株,涵盖了前Omicron变异株和Omicron变异株的多种亚型.通过对RBD抗原性的系统评估,我们将23种变异株分为5种血清型,每种血清型都包含了数种基因型不同的变异株.具体而言,Ⅰ型涵盖了所有前Omicron变异株(含两种亚型),而其余四种血清型均包含处于不同进化阶段的Omicron亚型.本文中的血清分型可以为新型变异株的快速评估奠定基础,并指导未来针对新冠病毒的广谱疫苗和中和抗体的开发.

关键词： SARS-CoV-2 Serotype classification mRNA vaccine Spike(S) Receptor-binding domain(RBD)

Number of covID-19 cases required in a population to detect SARS-CoV-2 RNA in wastewater in the province of Alberta, Canada:Sensitivity assessment

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Journal of Environmental Sciences 2023年第3期125卷 843-850页

作者： Qiaozhi Li Bonita E.Lee Tiejun Gao Yuanyuan Qiu Erik Ellehoj Jiaao Yu Mathew Diggle Graham Tipples Rasha Maal-Bared Deena Hinshaw Christopher Sikora Nicholas J.Ashbolt James Talbot Steve E.Hrudey Xiaoli Pang School of Public Health University of AlbertaEdmontonAB T6G 2R3Canada Department of Pediatrics University of AlbertaEdmontonAB T6G 1C9Canada Department of Laboratory Medicine and Pathology University of AlbertaEdmontonAB T6G 2B7Canada University of Alberta Central Receiving EdmontonAlbertaT6G 2R3Canada Provincial Laboratory for Public Health EdmontonAlbertaCanada EPCOR EdmontonAB T5H 0E8Canada Department of Medicine University of AlbertaEdmontonAB T6G 2G3Canada Faculty of Science and Engineering Southern Cross UniversityEast Lismore NSW 2480Australia

With a unique and large size of testing results of 1,842 samples collected from 12 wastewater treatment plants (WWTP) for 14 months through from low to high prevalence of covID-19,the sensitivity of RT-qPCR detection of SARS-CoV-2 RNA in wastewater that correspond to the communities was computed by using Probit analysis.This study determined the number of new covID-19 cases per 100,000 population required to detect SARS-CoV-2RNA in wastewater at defined probabilities and provided an evidence-based framework of wastewater-based epidemiology surveillance (WBE).Input data were positive and negative test results of SARS-CoV-2 RNA in wastewater samples and the corresponding new covID-19 case rates per 100,000 population served by each WWTP.The analyses determined that RT-qPCR-based SARS-CoV-2 RNA detection threshold at 50%,80%and 99%probability required a median of 8 (range:4-19),18 (9-43),and 38 (17-97) of new covID-19 cases/100,000,respectively.Namely,the positive detection rate at 50%,80%and 99%probability were 0.01%,0.02%,and 0.04%averagely for new cases in the population.This study improves understanding of the performance of WBE SARS-CoV-2 RNA detection using the large datasets and prolonged study period.Estimated covID-19 burden at a community level that would result in a positive detection of SARS-CoV-2 in wastewater is critical to support WBE application as a supplementary warning/monitoring system for covID-19 prevention and control.

关键词： SARS-CoV-2 covID-19 cases Wastewater Probit analysis Probability Detection sensitivity

Ratiometric fluorescent Si-FITC nanoprobe for immunoassay of SARS-CoV-2 nucleocapsid protein

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Nano Research 2023年第2期16卷 2859-2865页

作者： Guobin Mao Silu Ye Wen Yin Yang Yang Xinghu Ji Jin He Yingxia Liu Junbiao Dai Zhike He Yingxin Ma CAS Key Laboratory of Quantitative Engineering Biology Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China State Key Laboratory of Agricultural Microbiology College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China Shenzhen Key Laboratory of Pathogen and Immunity National Clinical Research Center for Infectious DiseaseState Key Discipline of Infectious DiseaseShenzhen Third People's HospitalSecond Hospital Affiliated to Southern University of Science and TechnologyShenzhen 518112China College of Chemistry and Molecular Sciences Wuhan UniversityWuhan 430072China

Coronavirus disease 2019(covID-19)highlights the importance of rapid and reliable diagnostic assays for the management of virus transmission.Here,we developed a one-pot hydrothermal method to prepare Si-FITC nanoparticles(NPs)for the fluorescent immunoassay of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)nucleocapsid protein(N protein).The synthesis of Si-FITC NPs did not need post-modification,which addressed the issue of quantum yield reduction during the coupling reaction.Si-FITC NPs showed two distinct peaks,Si fluorescence atλem=385 nm and FITC fluorescence atλem=490 nm.In the presence of KMnO_(4),Si fluorescence was decreased and FITC fluorescence was enhanced.Briefly,in the presence of N protein,catalase(CAT)-linked secondary antibody/reporter antibody/N protein/capture antibody immunocomplexes were formed on microplates.Subsequently,hydrogen peroxide(H_(2)O_(2))and Si-FITC NPs/KMnO_(4)were injected into the microplate together.The decomposition of H_(2)O_(2)by CAT resulted in remaining of KMnO_(4),which changed the fluorescence intensity ratio of Si-FITC NPs.The fluorescence intensity ratio correlated significantly with the N protein concentration ranging from 0.02 to 50.00 ng/mL,and the detection limit was 0.003 ng/mL,which was more sensitive than the commercial ELISA kit with a detection limit of 0.057 ng/mL.The N protein concentration can be accurately determined in human serum.Furthermore,the covID-19 and non-covID-19 patients were distinguishable by this method.Therefore,the ratiometric fluorescent immunoassay can be used for SARS-CoV-2 infection diagnosis with a high sensitivity and selectivity.

关键词： Si-FITC nanoparticles ratiometric fluorescent probe SARS-CoV-2 ELISA

Multi-omics analysis of attenuated variant reveals potential evaluation marker of host damaging for SARS-CoV-2 variants

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Science China(Life Sciences) 2024年第1期67卷 83-95页

作者： Guangshan Xie Lin Zhu Siwen Liu Cun Li Xin Diao Yanhao Zhang Xiuli Su Yuanyuan Song Guodong Cao Li Zhong Pui Wang Xiaojuan Liu Bobo Wing-Yee Mok Shusheng Zhang Dong-Yan Jin Jie Zhou Honglin Chen Zongwei Cai State Key Laboratory of Environmental and Biological Analysis Hong Kong Baptist UniversityHong Kong SARChina State Key Laboratory for Emerging Infectious Diseases and Department of MicrobiologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina College of Chemistry Zhengzhou UniversityZhengzhou 450001China School of Biomedical Sciences The University of Hong KongHong Kong SARChina HKBU Shenzhen Institute of Research and Continuing Education Shenzhen 518000China

SARS-CoV-2 continues to threaten human society by generating novel variants via mutation and recombination.The high number of mutations that appeared in emerging variants not only enhanced their immune-escaping ability but also made it difficult to predict the pathogenicity and virulence based on viral nucleotide sequences.Molecular markers for evaluating the pathogenicity of new variants are therefore needed.By comparing host responses to wild-type and variants with attenuated pathogenicity at proteome and metabolome levels,six key molecules on the polyamine biosynthesis pathway including putrescine,SAM,dc-SAM,ODC1,SAMS,and SAMDC were found to be differentially upregulated and associated with pathogenicity of variants.To validate our discovery,human airway organoids were subsequently used which recapitulates SARS-CoV-2 replication in the airway epithelial cells of covID-19 patients.Using ODC1 as a proof-ofconcept,differential activation of polyamine biosynthesis was found to be modulated by the renin-angiotensin system(RAS)and positively associated with ACE2 activity.Further experiments demonstrated that ODC1 expression could be differentially activated upon a panel of SARS-CoV-2 variants of concern(VOCs)and was found to be correlated with each VOCs’pathogenic properties.Particularly,the presented study revealed the discriminative ability of key molecules on polyamine biosynthesis as a predictive marker for virulence evaluation and assessment of SARS-CoV-2 variants in cell or organoid models.Our work,therefore,presented a practical strategy that could be potentially applied as an evaluation tool for the pathogenicity of current and emerging SARS-CoV-2 variants.

关键词： SARS-CoV-2 multi-omics attenuated variant predictive pathogenic marker polyamine biosynthesis