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Prevalence,variation,and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei,China during 2020–2021

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Virologica Sinica 2023年第3期38卷 363-372页

作者： Yi Yan Decheng Wang Ying Li Zhiyong Wu haizhou liu Yue Shi Xiaoxia Lu Di liu CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhan430071China National Virus Resource Center Chinese Academy of SciencesWuhan Institute of VirologyCenter for Biosafety Mega-ScienceWuhan430071China Computational Virology Group Center for Bacteria and Viruses Resources and BioinformationWuhan Institute of VirologyChinese Academy of SciencesWuhan430071China University of Chinese Academy of Sciences Beijing101408China Department of Respiratory Medicine Wuhan Children'HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430014China Pediatric Respiratory Disease Laboratory Institute of Maternal and Child HealthWuhan Children's HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan430014China

Human respiratory syncytial virus(RSV)is a severe threat to children and a main cause of acute lower respiratory tract infections.Nevertheless,the intra-host evolution and inter-regional diffusion of RSV are little known.In this study,we performed a systematic surveillance in hospitalized children in Hubei during 2020–2021,in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing(mNGS).RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant.About 46 high-quality genomes were used for further analyses.A total of 163 intra-host nucleotide variation(iSNV)sites distributed in 34 samples were detected,and glycoprotein(G)gene was the most enriched gene for iSNVs,with non-synonymous substitutions more than synonymous substitutions.Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher,and the population size of RSV groups changed over time.We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B,respectively.This study highlighted the intra-host and inter-host evolution of RSV,and provided some evi-dences for understanding the evolution of RSV.

关键词： Respiratory syncytial virus(RSV) Intra-host single nucleotide variation(iSNV) Evolutionary dynamic Inter-regional diffusion

Comparison of microbial composition and diversity in the upper respiratory tract between SARS-CoV-2 and influenza virus infections

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Science China(Life Sciences) 2022年第7期65卷 1469-1472页

作者： Lijia Jia Meng Xu Mengchan Hao Di liu haizhou liu Xin Zheng Jianjun Chen CAS Key Laboratory of Special Pathogens Wuhan Institute of VirologyCenter for Biosafety Mega-ScienceChinese Academy of SciencesWuhan 430071China Department of Infectious Diseases Union HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhan 430022China University of Chinese Academy of Sciences Beijing 100049China

Dear Editor,Coronavirus disease 2019(COVID-19)is still the most emerging infectious disease plaguing human society,and secondary bacterial infection is one of the major causes of its progression to severe illness and death.In this study,pharyngeal swabs were collected from patients with COVID-19 and influenza,and the microbiome landscape of the upper respiratory tract(URT)of both patients was compared,revealing disease-specific associated microorganisms.

关键词： respiratory influenza patients

Hexavalent chromium in drinking water: Chemistry,challenges and future outlook on Sn(Ⅱ)-and photocatalyst-based treatment

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Frontiers of Environmental Science & Engineering 2020年第5期14卷 137-145页

作者： haizhou liu Xuejun Yu Department of Chemical and Environmental Engineering University of California at RiversideRiversideCA 92521USA

Chromium(Cr)typically exists in either trivalent and hexavalent oxidation states in drinking water,i.e.,Cr(Ⅲ)and Cr(Ⅵ),with Cr(Ⅵ)of particular concern in recent years due to its high toxicity and new regulatory standards.This Account presented a critical analysis of the sources and occurrence of Cr(Ⅵ)in drinking water in the United States,analyzed the equilibrium chemistry of Cr(Ⅵ)species,summarized important redox reaction relevant to the fate of Cr(Ⅵ)in drinking water,and critically reviewed emerging Cr(Ⅵ)treatment technologies.There is a wide occurrence of Cr(Ⅵ)in US source drinking water,with a strong dependence on groundwater sources,mainly due to naturally weathering of chromium-containing aquifers.Challenges regarding traditional Cr(Ⅵ)treatment include chemical cost,generation of secondary waste and inadvertent re-generation of Cr(Ⅵ)after treatment.To overcome these challenges,reductive Cr(Ⅵ)treatment technologies based on the application of stannous tin or electron-releasing titanium dioxide photocatalyst hold extreme promise in the future.To moving forward in the right direction,three key questions need further exploration for the technology implementation,including effective management of residual waste,minimizing the risks of Cr(Ⅵ)re-occurrence downstream of drinking water treatment plant,and promote the socioeconomic drivers for Cr(Ⅵ)control in the future.

关键词： Chromium Chemistry Treatment Future outlook

Transcriptome Analyses Implicate Endogenous Retroviruses Involved in the Host Antiviral Immune System through the Interferon Pathway

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Virologica Sinica 2021年第6期36卷 1315-1326页

作者： Miao Wang Liying Wang haizhou liu Jianjun Chen Di liu CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Computational Virology Group Center for Bacteria and Viruses Resources and BioinformationWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China First Affiliated Hospital of Xinjiang Medical University Urumqi 830054China

Human endogenous retroviruses(HERVs) are the remains of ancient retroviruses that invaded our ancestors’ germline cell and were integrated into the genome. The expression of HERVs has always been a cause for concern because of its association with various cancers and diseases. However, few previous studies have focused on specific activation of HERVs by viral infections. Our previous study has shown that dengue virus type 2(DENV-2) infection induces the transcription of a large number of abnormal HERVs loci;therefore, the purpose of this study was to explore the relationship between exogenous viral infection and HERV activation further. In this study, we retrieved and reanalyzed published data on 21 transcriptomes of human cells infected with various viruses. We found that infection with different viruses could induce transcriptional activation of HERV loci. Through the comparative analysis of all viral datasets, we identified 43 key HERV loci that were up-regulated by DENV-2, influenza A virus, influenza B virus, Zika virus, measles virus, and West Nile virus infections. Furthermore, the neighboring genes of these HERVs were simultaneously up-regulated, and almost all such neighboring genes were interferon-stimulated genes(ISGs), which are enriched in the host’s antiviral immune response pathways. Our data supported the hypothesis that activation of HERVs, probably via an interferon-mediated mechanism, plays an important role in innate immunity against viral infections.

关键词： Human endogenous retrovirus(HERV) RNA-seq Virus infection Interferon-stimulated genes(ISGs)

Nanopore sequencing: a rapid solution for infectious disease epidemics

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Science China(Life Sciences) 2019年第8期62卷 1101-1103页

作者： Ying Cao Jing Li Xin Chu haizhou liu Wenjun liu Di liu Center for Emerging Infectious Diseases Wuhan Institute of VirologyChinese Academy of SciencesWuhan430071China Research Group of Computer Virology Center for Bacteria and Virus Resources and ApplicationWuhan Institute of VirologyChineseAcademy of SciencesWuhan430071China Institute of Microbiology Chinese Academy of SciencesBeijing100101China Bureau of Major R&D Programs Chinese Academy of SciencesBeijing100864China University of Chinese Academy of Sciences Beijing100049China

Emerging and re-emerging infectious diseases have given rise to a large number of human infections,morbidity,and heavy economic burden,including the Middle East respiratory syndrome caused by a coronavirus in 2012,global influenza pandemic caused by the H7N9 influenza A virus in2013,Ebola epidemic in West Africa in 2014,and Lassa fever epidemic in Nigeria in 2019.The healthcare war against viruses deserves constant surveillance due to the continuous emergence of new viruses and rapid evolution of existing viruses(liu and liu,2017).

关键词： pro RNA Nanopore sequencing a rapid solution for infectious disease epidemics

Pan-Genomic Analysis of African Swine Fever Virus

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Virologica Sinica 2020年第5期35卷 662-665页

作者： Ziming Wang Lijia Jia Jing Li haizhou liu Di liu CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Computational Virology Group Center for Bacteria and Virus Resources and BioinformationWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China African Swine Fever Regional Laboratory of China Wuhan 430071China Center for Biosafety Mega-Science Chinese Academy of SciencesWuhan 430071China

Dear Editor,African swine fever(ASF)is a severe haemorrhagic fever in domestic pigs and wild boar with extremely high mortality rate.It is cataloged as a notifiable disease by the World Organization for Animal Health(OIE).The etiological agent that causes the highly lethal disease is the African swine fever virus(ASFV)(Sanchez-Vizcaino) et al.

关键词： Swine swine OIE

High-intensity spatial-mode steerable frequency up-converter toward on-chip integration

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Opto-Electronic Science 2024年第4期3卷 12-20页

作者： haizhou Huang Huaixi Chen Huagang liu Zhi Zhang Xinkai Feng Jiaying Chen Hongchun Wu Jing Deng Wanguo Liang Wenxiong Lin Key Laboratory of Optoelectronic Materials Chemistry and Physics Fujian Institute of Research on the Structure of MatterChinese Academy of ScienceFuzhou 350002China Key Laboratory of Opto-Electronic Science and Technology for Medicine of Ministry of Education Fujian Provincial Key Laboratory of Photonics TechnologyCollege of Photonic and Electronic EngineeringFujian Normal UniversityFuzhou 350117China Fujian Science&Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou 350108China College of Digital Economy Fujian Agriculture and Forestry UniversityFuzhou 350002China University of Chinese Academy of Sciences Beijing 100049China.

Integrated photonic devices are essential for on-chip optical communication,optical-electronic systems,and quantum information sciences.To develop a high-fidelity interface between photonics in various frequency domains without disturbing their quantum properties,nonlinear frequency conversion,typically steered with the quadratic(χ2)process,should be considered.Furthermore,another degree of freedom in steering the spatial modes during theχ2 process,with unprecedent mode intensity is proposed here by modulating the lithium niobate(LN)waveguide-based inter-mode quasi-phasematching conditions with both temperature and wavelength parameters.Under high incident light intensities(25 and 27.8 dBm for the pump and the signal lights,respectively),mode conversion at the sum-frequency wavelength with sufficient high output power(−7–8 dBm)among the TM01,TM10,and TM00 modes is realized automatically with characterized broad temperature(ΔT≥8°C)and wavelength windows(Δλ≥1 nm),avoiding the previous efforts in carefully preparing the signal or pump modes.The results prove that high-intensity spatial modes can be prepared at arbitrary transparent wavelength of theχ2 media toward on-chip integration,which facilitates the development of chip-based communication and quantum information systems because spatial correlations can be applied to generate hyperentangled states and provide additional robustness in quantum error correction with the extended Hilbert space.

关键词： integrated photonics LN waveguide sum-frequency generation spatial-mode steering on-chip integration

Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain

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Virologica Sinica 2021年第2期36卷 321-324页

作者： Lijia Jia Jianjun Chen haizhou liu Wenhui Fan Depeng Wang Jing Li Di liu CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China Computational Virology Group Center for Bacteria and Viruses Resources and BioinformationWuhan Institute of VirologyChinese Academy of SciencesWuhan 430071China African Swine Fever Regional Laboratory of China Wuhan 430071China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Next Omics Biosciences Wuhan 430074China Center for Biosafety Mega-Science Chinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China

Dear Editor,It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019).

关键词： Rural African killed

Low Pathogenic Avian Influenza A(H5N7) Virus Isolated from a Domestic Duck in Dongting Lake Wetland of China,2016

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Virologica Sinica 2019年第1期34卷 97-101页

作者： Liping Ma haizhou liu Runkun Wang Tao Jin Di liu George Fu Gao Quanjiao Chen CAS Key Laboratory of Special Pathogens and Biosafety CAS Center for Influenza Research and Early WarningWuhan Institute of VirologyChinese Academy of Sciences University of Chinese Academy of Sciences China National Genebank-Shenzhen BGI-Shenzhen Savaid Medical School University of Chinese Academy of Sciences CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences

Dear Editor,The avian influenza virus (AIV) H5N7 was first isolated from wild birds in North America in 2001 (Spackman et al.2007), and information on only 25 strains of this virus has been deposited in the Global Initiative on Sharing All Influenza Data (GISAID-http://***/epi3/frontend#493de3) database until October 30, 2018. Twenty viruses were identified in the United States from 2001 to2017.

关键词： HPAIV Virus Isolated from a Domestic Duck in Dongting Lake Wetland of China,2016 Low Pathogenic Avian Influenza A