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Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing

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Virologica Sinica 2024年第1期39卷 134-143页

作者： Changcheng Wu Ruhan A Sheng Ye Fei Ye Weibang Huo Roujian Lu Yue Tang Jianwei Yang Xuehong Meng Yun Tang Shuang chen Li Zhao Baoying Huang Zhongxian Zhang yuda chen Dongfang Li Wenling Wang Ke-jia Shan Jian Lu Wenjie Tan NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing100052China Chongqing Municipal Key Laboratory for High Pathogenic Microbes Chongqing Center for Disease Control and PreventionChongqing400042China MGI BGI-ShenzhenShenzhen518083China Thermo Fisher Scientific Beijing100013China School of Public Health Baotou Medical CollegeBaotou014030China BGI PathoGenesis Pharmaceutical Technology Shenzhen518000China State Key Laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing100871China College of Life Sciences University of Chinese Academy of SciencesBeijing100049China

The monkeypox virus(MPXV)has triggered a current outbreak *** sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and *** is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads,as it is one of the DNA viruses with the largest genome and the most AT-biased,and has a significant number of tandem *** we evaluated the performance of metagenomic and amplicon sequencing techniques,and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese *** rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical *** sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV ***-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published ***,several intra-host single nucleotide variations were identified in the first imported mpox *** study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical *** findings of this study will significantly enhance the surveillance of MPXV.

关键词： Monkeypox virus(MPXV) Metagenomic Next generation sequencing Amplicon Third-generation sequencing

Perspective on the application of genome sequencing for monkeypox virus surveillance

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Virologica Sinica 2023年第2期38卷 327-333页

作者： yuda chen Changcheng Wu Ruhan A Li Zhao Zhongxian Zhang Wenjie Tan School of Public Health Baotou Medical CollegeBaotou014040China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing100052China

Monkeypox virus(MPXV),a DNA virus belonging to the Orthopoxvirus genus,causes a self-limiting zoonotic disease known as *** human monkeypox infection was first recorded in a 9-month-old child in the Republic of Congo in the 1970s(Ladnyj et al.,1972).For a long time,mpox was mainly prevalent in the humid forests of Central Africa and parts of West Africa(Kabugae and El Zowalaty,2019).In recent years,MPXV has been spread to other countries through trade and *** 2003,a group of rare pets carrying MPXV was exported from Africa to the United States,and an outbreak of animal-to-human transmission occurred(Di Giulio and Eckburg,2004).In 2018,two cases of mpox were confirmed in travelers from Nigeria to the United Kingdom and one case was confirmed in Israel(Vaughan et al.,2018;Erez et al.,2019).Then,in 2019,one case was confirmed in Singapore(Ng et al.,2019).The outbreak of mpox in multiple non-endemic countries in North America and Europe started in May 2022(WHO,2022b).On July 23,2022,the WHO declared MPXV a Public Health Emergency of International Concern(PHEIC)(WHO,2022a).As of March 5,2023,86,309 confirmed mpox cases have been reported from 107 countries/regions worldwide(WHO,2023).In the mainland of China,the first imported case was confirmed by the Chinese Center for Disease Control and Prevention(Zhao et al.,2022),making this the fifth confirmed mpox infection in *** zoonotic mpox has been restricted in Africa but now it is back in the spotlight worldwide(Tan and Gao,2022).

关键词： fir mainland Israel

Development of two multiplex real-time PCR assays for simultaneous detection and differentiation of monkeypox virus IIa,IIb,and I clades and the B.1 lineage

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Biosafety and Health 2022年第6期4卷 392-398页

作者： Shuting Huo yuda chen Roujian Lu Zhongxian Zhang Gaoqian Zhang Li Zhao Yao Deng Changcheng Wu Wenjie Tan NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100052China School of Public Health Baotou Medical CollegeBaotou 014030China Department of Microbiology Basic Medical CollegeInner Mongolia Medical UniversityHohhot 010010China

An ongoing multi-country outbreak of monkeypox was reported in May 2022 with several deaths,affecting 107 countries of all six World Health Organization(WHO)*** WHO has declared the current monkeypox outbreak to be a Public Health Emergency of International *** is,thus,necessary to rapidly and accurately detect and distinguish different monkeypox virus(MPXV)*** designed primers and probes based on the alignment of 138 complete genomes of *** Panel 1,we mixed one pair of primers and three probes to detect and differentiate the MPXV Western Africa(IIa,IIb clade)and Congo Basin(I clade)and other *** Panel 2,we mixed one pair of primers and two probes to detect the 2022 MPXV(B.1 lineage and its descendant lineages).In addition,we tested the specificity and sensitivity of the assay using real-time *** Panel 1,the assay reproducibly identified various concentrations of two plasmids of the monkeypox virus,whereas other orthopoxviruses did not *** Panel 2,the probe annealed well to MPXV B.1 and showed the expected *** two multiple real-time assays are inclusive and highly specific for identifying different clades of MPXV.

关键词： Monkeypox virus Monkeypox virus B.1 lineage Real-time PCR Diagnostic accuracy

Genomic Recombination of SARS-CoV-2 Subvariants BA.5.2.48 and BF.7.14—China,2023

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China CDC weekly 2023年第14期5卷 318-320页

作者： Zhongxian Zhang Han Li Hongxia Ma Wenling Wang Dawei Gao Fei Ye Weibang Huo yuda chen Changcheng Wu Wenjie Tan National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and PreventionBeijingChina School of Public Health Baotou Medical CollegeBaotou CityInner Mongolia Autonomous RegionChina Henan Provincial Center for Disease Control and Prevention Zhengzhou CityHenan ProvinceChina Lu’an Municipal Center for Disease Control and Prevention Lu’an CityAnhui ProvinceChina

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),a single-stranded positive RNA virus,exhibits a high rate of genome mutation and recombination(1–2).Recombinant strains of this virus could potentially affect their binding ability to the ACE2 receptor,which may in turn diminish the protection offered by vaccines and neutralizing ***,the Delta and Omicron recombinations have been collectively referred to as Deltacron(3).Furthermore,XBB.1.5,a recombinant strain resulting from the combination of the BA.2 sublineages BA.2.10.1 and BA.2.75,has demonstrated enhanced transmissibility(4).As such,it is imperative to monitor the genome recombination of SARS-CoV-2 in order to provide valuable insights regarding epidemic and transmission trends.

关键词： acute respiratory collective

Detecting SARS-CoV-2 BA.2,BA.4,and BA.5 Variants Utilizing a Robust RT-RPA-CRISPR/Cas12a-Based Method-China,2023

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China CDC weekly 2023年第26期5卷 584-591页

作者： Meihui Luo Yang Pan Yaqing He Ruhan A Changcheng Wu Baoying Huang Roujian Lu Li Zhao Bo Peng Fei Ye Huijuan Wang yuda chen Zhen Li Daitao Zhang Wenling Wang Wenjie Tan MHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChina CDCBeijingChina Beijing Center for Disease Prevention and Control BeijingChina Microbiology Laboratory Shenzhen Center for Disease Control and PreventionShenzhen CityGuangdong ProvinceChina School of Public Health Baotou Medical CollegeBaotou CityInner Mongolia Autonomous RegionChina Collaborative Innovation Centre for Regenerative Medicine and Medical BioResourse Development and Application Co-constructed by the Province and Ministry Guangxi Medical UniversityGuangxi Zhuang Autonomous RegionChina

Introduction:Since 2019,numerous variants of concern for severe acute respiratory syndrome virus 2(SARS-CoV-2)have emerged,leading to significant *** development of novel,highly accurate,and rapid detection techniques for these new SARSCoV-2 variants remains a primary focus in the ongoing efforts to control and prevent the coronavirus disease 2019(COVID-19)***:Reverse transcription-recombinase polymerase amplification combined with the clustered regularly interspaced short palindromic repeatsassociated protein 12a(CRISPR/Cas12a)system was used to validate the detection of the Omicron BA.2,BA.4,and BA.5 variants of ***:Our results demonstrate that the CRISPR/Cas12a assay is capable of effectively detecting the SARS-CoV-2 BA.2,BA.4,and BA.5 variants with a limit of detection of 10,1,and 10 copies/μL,***,our assay successfully differentiated the three SARS-CoV-2 Omicron strains from one ***,we evaluated 46 SARS-CoV-2 positive clinical samples consisting of BA.2(n=20),BA.4(n=6),and BA.5(n=20)variants,and the sensitivity of our assay ranged from 90%to 100%,while the specificity was 100%.Discussion:This research presents a swift and reliable CRISPR-based method that may be employed to track the emergence of novel SARS-CoV-2 variants.

关键词： CRISPR/Cas limit specificity

SEVAR: a stereo event camera dataset for virtual and augmented reality

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Frontiers of Information Technology & Electronic Engineering 2024年第5期25卷 755-762页

作者： yuda DONG Zetao chen Xin HE Lijun LI Zichao SHU Yinong CAOl Junchi FENG Shijie LIU Chunlai LI Jianyu WANG Hangzhou Institute for Advanced Study University of Chinese Academy of SciencesHangzhou 310024China Shanghai Institute of Technical Physics Chinese Academy of SciencesShanghai 200083China University of Chinese Academy of Sciences Bejing 100049China Yongjiang Laboratory Ningbo 130021China

Event cameras,characterized by their low latency,large dynamic range,and extremely high temporal resolution,have recently received increasing *** features make them particularly well-suited for virtual/augmented reality(VR/AR)*** facilitate the development of three-dimensional(3D)perception and navigation algorithms in VR/AR applications using event cameras,we introduce the Stereo Event camera dataset for Virtual and Augmented Reality(SEVAR),which comprises a wide variety of head-mounted indoor sequences,including scenarios with rapid motion and a large dynamic range.

关键词： mounted dynamic camera

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单轴压缩下岩石裂纹扩展应力阈值识别与验证

岩石力学与工程学报 2023年第S1期42卷 3121-3130页

作者：李地元陈昱达中南大学资源与安全工程学院湖南长沙410083

准确识别岩石在单轴压缩变形破坏过程中几个典型阶段的应力阈值,能更好地理解岩石渐进破坏过程中内部裂纹扩展力学行为和岩石破坏机制。通过对5种岩石开展单轴压缩试验,在裂纹体积应变法的基础上引入岩石裂纹轴向应变和裂纹径向面积应变... 详细信息

准确识别岩石在单轴压缩变形破坏过程中几个典型阶段的应力阈值,能更好地理解岩石渐进破坏过程中内部裂纹扩展力学行为和岩石破坏机制。通过对5种岩石开展单轴压缩试验,在裂纹体积应变法的基础上引入岩石裂纹轴向应变和裂纹径向面积应变2个参数,并结合声发射监测手段对5种岩石的应力阈值进行识别。依据岩石破坏时裂纹径向面积应变曲线斜率的关系,把岩石分成类型I和类型Ⅱ岩石。研究表明,对于类型I和类型Ⅱ岩石,分别利用其裂纹轴向应变和裂纹径向面积应变曲线特征点能较准确识别出岩石裂纹稳定扩展应力σ_(sd)、裂纹不稳定扩展应力σ_(usd)以及岩石裂纹相互贯通应力阈值σ_(ct),其结果与利用声发射特征现象所识别的应力阈值相近。该方法合理解释了利用体应变法、裂纹体积应变法与声发射法识别的应力阈值不匹配现象,实现了岩石压缩过程中利用应力、应变数据与声发射数据对应力阈值识别结果的一致性。

关键词：岩石力学应力阈值识别声发射裂纹体积应变体应变

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虑及谐波耦合的对转桨扇不平衡辨识方法

航空动力学报 2024年第8期39卷 272-282页

作者：龙昱达陈立芳北京化工大学发动机健康监控及网络化教育部重点实验室北京100029

对转桨扇双螺旋桨转子系统中,振动信号经中介轴承在内、外转子间相互传递,产生复杂的耦合振动,通常表现为基频、倍频的拍振形式,造成振动信号辨识困难、动平衡效率低。传统最小二乘辨识方法仅考虑了基频信号,未虑及谐波及噪声的干扰,导... 详细信息

对转桨扇双螺旋桨转子系统中,振动信号经中介轴承在内、外转子间相互传递,产生复杂的耦合振动,通常表现为基频、倍频的拍振形式,造成振动信号辨识困难、动平衡效率低。传统最小二乘辨识方法仅考虑了基频信号,未虑及谐波及噪声的干扰,导致辨识精确度低。为解决该问题,提出一种虑及谐波信号的最小二乘法(HLSM),通过仿真实验对比了多种辨识方法与HLSM的辨识效果,验证HLSM的辨识精确度更高。在搭建的同轴对转双转子实验台上应用HLSM辨识结果进行双转子动平衡,结果显示内、外转子不平衡振动分别降低70%与96%。

关键词：对转桨扇耦合振动不平衡响应信号辨识最小二乘法动平衡

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障碍物空间下分布式轨迹规划的死锁破解

航空学报 2023年第S2期44卷 426-442页

作者：董豪泽陈昱达刘丹李忠奎北京大学工学院北京100871 中国空间技术研究院通信与导航卫星总体部北京100094

基于优化的分布式轨迹规划方法因具有较强的可解释性和可扩展性而备受关注,但由于缺少中心节点和全局优先级,容易诱发集群运动陷入死锁,即若干机器人互相阻隔而无法到达终点的情形。现有的障碍物空间下死锁解决方案大多是启发式的,缺乏... 详细信息

基于优化的分布式轨迹规划方法因具有较强的可解释性和可扩展性而备受关注,但由于缺少中心节点和全局优先级,容易诱发集群运动陷入死锁,即若干机器人互相阻隔而无法到达终点的情形。现有的障碍物空间下死锁解决方案大多是启发式的,缺乏理论支撑。为此,本文针对可行域为半空间交集这一基础情形,通过构建多机器人轨迹规划的模型预测控制(MPC)问题,得到了死锁发生的必要条件,并指出该条件可以理解为机器人所受来自自身目标的吸引力、来自其他机器人的斥力和来自障碍物约束面的斥力三者的受力平衡。在此基础上,提出了一种死锁破解策略,并证明其在一定条件下可避免发生稳定的死锁现象。最后,通过密集空间下的随机对比仿真验证了算法的有效性。

关键词：多机器人系统分布式轨迹规划死锁破解模型预测控制障碍物空间