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A novel bat coronavirus with a polybasic furin-like cleavage site

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Virologica Sinica 2023年第3期38卷 344-350页

作者： Wentao Zhu Yuyuan Huang Jian Gong Lingzhi Dong Xiaojie Yu Haiyun Chen Dandan Li Libo Zhou Jing Yang Shan Lu Department of Infectious Diseases and Clinical Microbiology Beijing Institute of Respiratory Medicine and Beijing Chao-Yang HospitalCapital Medical UniversityBeijing100020China State Key Laboratory of Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing102206China Hainan Provincial Center for Disease Control and Prevention Haikou570203China research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing100730China

The current pandemic of COVID-19 caused by a novel coronavirus,severe acute respiratory syndrome coronavirus-2(SARS-CoV-2),threatens human health around the *** particular concern is that bats are recognized as one of the most potential natural hosts of SARS-CoV-2;however,coronavirus ecology in bats is still ***,we performed a degenerate primer screening and next-generation sequencing analysis of 112 bats,collected from Hainan Province,*** coronaviruses,namely bat betacoronavirus(Bat CoV)CD35,Bat CoV CD36 and bat alpha-coronavirus CD30 were *** CoV CD35 genome had 99.5%identity with Bat CoV CD36,both sharing the highest nucleotide identity with Bat Hp-betacoronavirus Zhejiang2013(71.4%),followed by SARS-CoV-2(54.0%).Phylogenetic analysis indicated that Bat CoV CD35 formed a distinct clade,and together with Bat Hp-betacoronavirus Zhejiang2013,was basal to the lineage of SARS-CoV-1 and ***,Bat CoV CD35 harbored a canonical furin-like S1/S2 cleavage site that resembles the corresponding sites of *** furin cleavage sites between CD35 and CD36 are *** addition,the receptor-binding domain of Bat CoV CD35 showed a highly similar structure to that of SARS-CoV-1 and SARS-CoV-2,especially in one binding *** conclusion,this study deepens our understanding of the diversity of coronaviruses and provides clues about the natural origin of the furin cleavage site of SARS-CoV-2.

关键词： Bat Coronavirus SARS-CoV-2 Betacoronavirus Furin Cleavage site

Species-level Microbiota of Biting Midges and Ticks from Poyang Lake

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Biomedical and Environmental Sciences 2024年第3期37卷 266-277,I0001-I0003页

作者： GONG Jian WANG Fei Fei LIU Yang Qing PU Ji DONG Ling Zhi ZHANG Si Hui HUANG Zhen Zhou HUANG Yu Yuan LI Ya Ben YANG Cai Xin TAO Yuan Meihui ZHAO Li Jun JIN Dong LIU Li Yun YANG Jing LU Shan Department of Epidemiology School of Public HealthShanxi Medical UniversityTaiyuan 030001ShanxiChina National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Jiangxi Provincial Key Laboratory of Animal-Origin and Vector-Borne Diseases Nanchang Center for Disease Control and PreventionNanchang 330038JiangxiChina research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing 100730China

Objective The purpose of this study was to investigate the bacterial communities of biting midges and ticks collected from three sites in the Poyang Lake area,namely,Qunlu Practice Base,Peach Blossom Garden,and Huangtong Animal Husbandry,and whether vectors carry any bacterial pathogens that may cause diseases to humans,to provide scientific basis for prospective pathogen discovery and disease prevention and *** Using a metataxonomics approach in concert with full-length 16S rRNA gene sequencing and operational phylogenetic unit(OPU)analysis,we characterized the species-level microbial community structure of two important vector species,biting midges and ticks,including 33 arthropod samples comprising 3,885 individuals,collected around Poyang *** A total of 662 OPUs were classified in biting midges,including 195 known species and 373 potentially new species,and 618 OPUs were classified in ticks,including 217 known species and 326 potentially new ***,OPUs with potentially pathogenicity were detected in both arthropod vectors,with 66 known species of biting midges reported to carry potential pathogens,including Asaia lannensis and Rickettsia bellii,compared to 50 in ticks,such as Acinetobacter lwoffii and Staphylococcus *** found that Proteobacteria was the most dominant group in both midges and ***,the outcomes demonstrated that the microbiota of midges and ticks tend to be governed by a few highly abundant *** sp7 was predominant in biting midges,while Coxiella sp1 was enriched in ***,Coxiella spp.,which may be essential for the survival of Haemaphysalis longicornis Neumann,were detected in all tick *** identification of dominant species and pathogens of biting midges and ticks in this study serves to broaden our knowledge associated to microbes of arthropod *** Biting midges and ticks carry large numbers of known and potentially novel bacteria,and carry a wide

关键词： Biting midge Tick Microbiota Pantoea Coxiella

functions of nuclear factor Y in nervous system development,function and health

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Neural Regeneration research 2025年第10期20卷 2887-2894页

作者： Pedro Moreira Roger Pocock Development and Stem Cells Program Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityMelbourneVICAustralia

Nuclear factor Y is a ubiquitous heterotrimeric transcription factor complex conserved across eukaryotes that binds to CCAAT boxes,one of the most common motifs found in gene promoters and *** the last 30 years,research has revealed that the nuclear factor Y complex controls many aspects of brain development,including differentiation,axon guidance,homeostasis,disease,and most recently ***,a complete understanding of transcriptional regulatory networks,including how the nuclear factor Y complex binds to specific CCAAT boxes to perform its function remains *** this review,we explore the nuclear factor Y complex’s role and mode of action during brain development,as well as how genomic technologies may expand understanding of this key regulator of gene expression.

关键词： axon guidance CCAAT boxes neuronal degeneration neuronal differentiation neuronal regeneration nuclear factor Y complex transcription factor transcriptional regulation

“Mutation blacklist”and “mutation whitelist”of SARS-CoV-2

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Journal of Biosafety and Biosecurity 2022年第2期4卷 114-120页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu research Institute of Public Health Nankai UniversityTianjinPR China research Center for functional Genomics and Biochip TianjinPR China State Key Laboratory for Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 202206PR China TEDA Institute of Biological Sciences and Biotechnology Nankai UniversityPR China research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing 100730PR China

Over the past two years,scientists throughout the world have completed more than 6 million SARS-CoV-2 genome ***,the number of SARS-CoV-2 genomes exceeds the total number of all other viral *** genomes are a record of the evolution of SARS-CoV-2 in the human host,and provide information on the emergence of *** this study,analysis of these sequenced genomes identified 296,728 de novo mutations(DNMs),and found that six types of base substitutions reached saturation in the sequenced genome *** on this analysis,a“mutation blacklist”of SARS-CoV-2 was *** loci on the“mutation blacklist”are highly conserved,and these mutations likely have detrimental effects on virus survival,replication,and *** information is valuable for SARS-CoV-2 research on gene function,vaccine design,and drug *** association analysis of DNMs and viral transmission rates,we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate,and these DNMs where classified as the“mutation whitelist”of *** mutations on the“mutation whitelist”are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new *** occurrence of mutations and the evolution of viruses are dynamic *** more effectively monitor the mutations and variants of SARS-CoV-2,we built a SARS-CoV-2 mutation and variant monitoring and pre-warning system(MVMPS),which can monitor the occurrence and development of mutations and variants of SARSCoV-2,as well as provide pre-warning for the prevention and control of SARS-CoV-2(https://***/).Additionally,this system could be used in real-time to update the“mutation whitelist”and“mutation blacklist”of SARS-CoV-2.

关键词： SARS-CoV-2 Mutation saturation De novo mutations Transmission

Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

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mLife 2022年第3期1卷 311-322页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu research Institute of Public Health Nankai UniversityTianjinChina TEDA Institute of Biological Sciences and Biotechnology Nankai UniversityTianjinChina Engineering and research Center for Microbial functional Genomics and Detection Ministry of EducationNankai UniversityTianjinChina State Key Laboratory for Infectious Disease Prevention and Control Chinese Center for Disease Control and PreventionNational Institute for Communicable Disease Control and PreventionBeijingChina research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijingChina

The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal ***,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 *** this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 *** possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation *** a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation ***,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons *** addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐***,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.

关键词： de novo mutation evolutionary trends mutation characteristics mutation frequency SARS‐CoV‐2

Beta-and Novel Delta-Coronaviruses Are Identified from Wild Animals in the Qinghai-Tibetan Plateau, China

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Virologica Sinica 2021年第3期36卷 402-411页

作者： Wentao Zhu Jing Yang Shan Lu Ruiting Lan Dong Jin Xue-lian Luo Ji Pu Shusheng Wu Jianguo Xu State Key Laboratory of Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Shanghai Public Health Clinical Center Fudan UniversityShanghai 201508China research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing 100730China School of Biotechnology and Biomolecular Sciences University of New South WalesSydneyNSW 2052Australia Yushu Prefecture Center for Disease Control and Prevention Yushu 815000China Department of Laboratorial Science and Technology&Vaccine research Center School of Public HealthPeking UniversityBeijing 100191China

Outbreaks of severe virus infections with the potential to cause global pandemics are increasingly concerning. One type of those commonly emerging and re-emerging pathogens are coronaviruses(SARS-Co V, MERS-Co V and SARS-Co V-2).Wild animals are hosts of different coronaviruses with the potential risk of cross-species transmission. However, little is known about the reservoir and host of coronaviruses in wild animals in Qinghai Province, where has the greatest biodiversity among the world's high-altitude regions. Here, from the next-generation sequencing data, we obtained a known beta-coronavirus(beta-Co V) genome and a novel delta-coronavirus(delta-Co V) genome from faecal samples of 29 marmots, 50 rats and 25 birds in Yushu Tibetan Autonomous Prefecture, Qinghai Province, China in July 2019. According to the phylogenetic analysis, the beta-Co V shared high nucleotide identity with Coronavirus HKU24. Although the novel delta-Co V(Mt Co V) was closely related to Sparrow deltacoronavirus ISU42824, the protein spike of the novel delta-Co V showed highest amino acid identity to Sparrow coronavirus HKU17(73.1%). Interestingly, our results identified a novel host(Montifringilla taczanowskii) for the novel delta-Co V and the potential cross-species transmission. The most recent common ancestor(t MRCA) of Mt Co Vs along with other closest members of the species of Coronavirus HKU15 was estimated to be 289 years ago. Thus, this study increases our understanding of the genetic diversity of beta-Co Vs and deltaCo Vs, and also provides a new perspective of the coronavirus hosts.

关键词： Coronavirus Qinghai-Tibetan plateau Rat Montifringilla taczanowskii Marmot

Evolutionary analysis of Omicron variant BF.7 and BA.5.2 pandemic in China

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Journal of Biosafety and Biosecurity 2023年第1期5卷 14-20页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu research Institute of Public Health Nankai UniversityTianjinPR China research Center for functional Genomics and Biochip TianjinPR China c State Key Laboratory for Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 202206PR China TEDA Institute of Biological Sciences and Biotechnology Key Laboratory of Molecular Microbiology and TechnologyMinistry of EducationNankai UniversityTianjinPR China research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing 100730PR China

On December 7,2022,China adjusted public health control measures,there have been widespread of SARS-CoV-2 infections in Chinese *** the number of infected people increased,the mutation probability of SARS-CoV-2 is also ***,it is of great importance to monitor SARS-CoV-2 variants and its mutations in *** this current study,665 SARS-CoV-2 genomes from China deposited in the public database were used to analyze the proportion of different variants;to determine the composition of variants in China across different provinces;and analyze specific mutation frequency,focusing on 12 immune escape *** results showed that no new mutations were generated on the 12 immune escape *** evolutionary analysis of the BF.7 variant circulating in China showed that there is an independent evolutionary branch with unique mutation sites,officially named BF.7.14 by *** variant may have been imported from Russia to Inner Mongolia at the end of September 2022 and continued its spread in *** evolutionary analysis of BA.5.2 variant shows that the variant is composed of two sub-variants,named BA.5.2.48 and BA.5.2.49 by PANGO,*** variant may have been imported from abroad to Beijing at the beginning of September 2022 and formed two sub-variants after domestic ***,this study showed that current epidemic variants in China were already circulating in other countries,and there were no additional mutations on immune escape residues that could pose a threat to other countries.

关键词： SARS-CoV-2 Immune escape Evolutionary analysis

Genomic Characterization of a New Coronavirus from Migratory Birds in Jiangxi Province of China

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Virologica Sinica 2021年第6期36卷 1656-1659页

作者： Wentao Zhu Wentao Song Guoyin Fan Jing Yang Shan Lu Dong Jin Xue-lian Luo Ji Pu Haiying Chen Jianguo Xu State Key Laboratory of Infectious Disease Prevention and Control National Institute for Communicable Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China The Collaboration Unit for Field Epidemiology of State Key Laboratory of Infectious Disease Prevention and Control Jiangxi Provincial Key Laboratory of Animal-Origin and Vector-Borne DiseasesNanchang Center for Disease Control and PreventionNanchang 330038China Shanghai Public Health Clinical Center Fudan UniversityShanghai 201508China research units of discovery of unknown bacteria and function Chinese Academy of Medical SciencesBeijing 100730China

Dear Editor,The emergence of COVID-19 since December 2019 has attracted great attention around the world and reminds the powerful pathogenic potential of viruses(Zhou et al.2020).The subfamily Orthocoronavirinae of the family Coronaviridae contains four genera Alphacoronavirus,Betacoronavirus,Gammacoronavirus,and Deltacoronavirus,which are the largest group of positive-sense,non-segmented,single-stranded,enveloped RNA viruses(Woo et al.2012;Shi et al.2016).The genus Gammacoronavirus currently has five species(https://***/taxonomy/),which are primarily spread through birds(Woo et al.2012).

关键词： taxonomy Corona Jiangxi

Highly Site-selective Electrooxidation Providing Facile Entries to functionalized Aromatic Acetals

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Chemical research in Chinese Universities 2020年第4期36卷 723-724页

作者： WU Jinnan YU Yi YE Keyin Key Laboratory of Molecule Synthesis and function discovery(Fujian Province University) College of ChemistryFuzhou UniversityFuzhou 350108P.R.China

Given the fact that aldehydes are among the most fundamental and versatile building blocks in organic syn thesis,the development of highly efficient and selective methods for their preparation,especially for those delicatelk functionalized ones remains sigmificant *** address such an issue,Xu and co-workers have recently reported an elegant electrochemical approach realizing the highly regioselective oxidation of functionalized methyl aromatic hydrocarbons towards the desired aromatic acetals without the use of any chemical oxidants or transition metal catalysts These acetals can be then conveniently converted into corresponding structurally diverse aldehydes via *** addition,the synthetic practicability of current method was further highlighted as the key step in the preparation of the antihypertensive drug *** work has been published in the Nature Communications and can be reached at https://***/10.1038/s41467-020-16519-8.

关键词： aldehydes aromatic Highly