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The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

Biosafety and Health 2024年第2期6卷 101-115页

作者： Yanan Wang Mengqi Qu Yuhai Bi william j.liu Sufang Ma Bo Wan Yongfei Hu Baoli Zhu Gaiping Zhang George F.Gao International joint Research Center of National Animal Immunology College of Veterinary MedicineHenan Agricultural UniversityZhengzhou 450046China CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CAS)Beijing 100101China Longhu Laboratory Zhengzhou 450046China University of Chinese Academy of Sciences Beijing 100049China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs.Despite recent significant advances in gut microbiome studies,a comprehensive study of chicken gut bacterial,archaeal,and viral genomes remains unavailable.In this study,we constructed a chicken multi-kingdom microbiome catalog(CMKMC),including 18,201 bacterial,225 archaeal,and 33,411 viral genomes,and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes(MAGs)from ten countries.We found that 812 and 240 MAGs in our dataset were putative novel species and genera,respectively,far beyond what was previously reported.The newly unclassified MAGs were predominant in Phyla Firmicutes_A(n=263),followed by Firmicutes(n=126),Bacteroidota(n=121),and Proteobacteria(n=87).Most of the classified species-level viral oper-ational taxonomic units belong to Caudovirales.Approximately,63.24%of chicken gut viromes are predicted to infect two or more hosts,including complete circular viruses.Moreover,we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses.Together,our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date,functional insights into the chicken gastrointestinal tract microbiota,and paves the way for microbial interventions for better chicken health and productivity.

关键词： Chicken Microbiome Metagenome assembled genomes Archaeome Virome Antibiotic resistance gene

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A COVID-19 T-Cell Response Detection Method Based on a Newly Identified Human CD8+T Cell Epitope from SARS-CoV-2—Hubei Province,China,2021

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China CDC weekly 2022年第5期4卷 83-87,I0005页

作者： jie Zhang Dan Lu Min Li Maoshun liu Sijia Yao jianbo Zhan william j.liu George F.Gao NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Savaid Medical School University of Chinese Academy of SciencesBeijingChina College of Laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhouZhejiangChina Hubei Provincial Center for Disease Control and Prevention WuhanHubeiChina

Introduction:Similar to antibody detection,severe acute respiratory syndrome coronavirus type 2(SARSCoV-2)-specific T-cell response evaluation is also pivotal among the coronavirus disease 2019(COVID-19)convalescents and the vaccinated populations.Nucleocapsid(N)protein is one of the main structural proteins of SARS-CoV-2 and can trigger T-cell responses in humans.Methods:An overlapping peptide pool covering the full length of the N protein was designed,peptides with positive T-cell activating potency in COVID-19 convalescents were screened,and CD8^(+)T cell epitopes were further identified.The epitope was used to detect the SARS-CoV-2-specific CD8^(+)T cell responses in COVID-19 convalescents based in intracellular cytokine staining and tetramer staining in flow cytometry.Results:A human leukocyte antigen A(HLAA)*1101-restricted CD8^(+)T cell epitope,which could stimulate the production of IFN-γvia peripheral blood mononuclear cells(PBMCs)of the convalescents was defined,and the tetramer generated with this epitope could detect SARS-CoV-2-specific T cells in the PBMCs of the convalescents.The structural investigation eliminated that the epitope was a typical HLA-A^(*)1101-restricted T-cell epitope which was conserved among all the sarbecoviruses.Discussion:The newly identified SARS-CoV-2-derived T-cell epitope was helpful to detect the cellular immunity against different sarbecoviruses including SARS-CoV and SARS-CoV-2.This study provided an evaluation method and also a peptide candidate for the research and development of T-cell based vaccine for the virus.

关键词： restricted immunity Human

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A Tale of Two Cities:From Influenza HxNy to SARS-CoV-z

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China CDC weekly 2021年第49期3卷 1052-1056页

作者： william j.liu Shelan liu Chinese National Influenza Center(CNIC) National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina Department of Infectious Diseases Zhejiang Provincial Center for Disease Control and PreventionHangzhouZhejiangChina Key Laboratory of Vaccine Prevention and Control of Infectious Disease of Zhejiang ProvinceHangzhouZhejiangChina.

THE COMMON FEATURES OF VIRUSES WITH PANDEMIC POTENTIAL In the past hundred years,human population expansion and globalization have changed the pattern of human-nature interactions and accelerated the emergence and spread of novel infectious diseases(1).Humans have experienced a long list of microbial threats to health,of which,70%are believed to be from animal reservoirs(2),such as severe acute respiratory syndrome coronavirus(SARS-CoV).

关键词： acute diseases respiratory

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Powassan virus:A tick borne flavivirus infecting humans

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Biosafety and Health 2022年第1期4卷 30-37页

作者： Xu Yang George F.Gao william j.liu CAS Key Laboratory of Pathogen Microbiology and Immunology Institute of MicrobiologyChinese Academy of Sciences(CAS)Beijing 100101China State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical BiologySchool of Pharmaceutical SciencesPeking UniversityBeijing 100191China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention(China CDC)Beijing 102206China

Infection of humans by Powassan virus(POWV)occurs rarely but is potentially life‐threatening.First isolated in Ontario,Canada in 1958,the presence of POWV has been confirmed in three countries:Canada,the USA,and Russia.Although a limited number of human cases has been reported thus far,the infection rate has shown signs of increasing during the 21^(st) century.Interestingly,POWV and a genetically close variant,deer tick virus(DTV),are the only member of the tick‐borne flaviviruses known to be endemic in North America and maintain in respective tick‐host cycles.In this review,we briefly summarize current knowledge involving the epidemiology and etiology,pathogenesis and immunity,molecular evolution,and protein functions of POWV,aiming to increase our understanding of the virus and unlock the potential to control this lethal pathogen.These data may also provide tools to minimize the future threat of other emerging and re‐emerging viruses.

关键词： Powassan virus(POWV) Deer tick virus(DTV) Tick‐borne flavivirus(TBFV) Tick Zoonotic disease Encephalitis

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An adjusted ELISpot-based immunoassay for evaluation of SARS-CoV-2-specific T-cell responses

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Biosafety and Health 2022年第3期4卷 179-185页

作者： Hao Lin jie Zhang Shaobo Dong Yaning liu Peipei liu George F.Gao william j.liu Guizhen Wu National Health Commission Key Laboratory of Biosafety Research Units of Adaptive Evolution and Control of Emerging VirusesChinese Academy of Medical SciencesNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and Prevention(China CDC)Beijing 102206China Macheng Center for Disease Control and Prevention Huanggang 438300China Center for Biosafety Mega-Science Chinese Academy of SciencesWuhan 430071China

Like antibody evaluation,using an effective antigen‐specific T‐cell immunity assessment method in coronavirus disease 2019(COVID‐19)patients,survivors and vaccinees is crucial for understanding the immune persistence,prognosis assessment,and vaccine development for COVID‐19.This study evaluated an empirically adjusted enzyme‐linked immunospot assay for detecting severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)‐specific T‐cell immunity in 175 peripheral blood samples from COVID‐19 convalescents and healthy individuals.Results of viral nucleic acid were used as the gold standard of infection confirmation.The SARS‐CoV‐2M peptide pool had higher sensitivity of 85%and specificity of 71%for the single peptide pool.For combined peptide pools,the parallel evaluation(at least one of the peptide pools is positive)of total peptide pools(S1&S2&M&N)had higher sensitivity(up to 93%),and the serial evaluation(all peptide pools are positive)of total peptide pools had higher specificity(up to 100%).The result of the serial evaluation was better than that of the parallel evaluation as a whole.The detection efficiency of M and N peptide pool serial evaluation appeared the highest,with a sensitivity of 80%and specificity of 93%.This T‐cell immunity detection assay introduced in this report can achieve high operability and applicability.Therefore,it can be an effective SARS‐CoV‐2‐specific cellular immune function evaluation method.

关键词： SARS‐CoV‐2 COVID‐19 T‐cell response ELISpot assay Sensitivity Specificity

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It’s not just science: challenges for public health intervention in Ebola epidemics in the Democratic Republic of Congo

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Science China(Life Sciences) 2020年第7期63卷 1079-1081页

作者： Pengyan Wang william j.liu School of Laboratory Medicine and Life Sciences Wenzhou Medical UniversityWenzhou 325035China NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China

The Democratic Republic of Congo (DRC) is suffering from the world’s second largest and most prolonged Ebola virus disease (EVD) epidemic on record (Figure 1). The current prevalence of EVD in the DRC makes this the 10th (and largest) EVD epidemic in the DRC since the first discovery of the Zaire Ebola virus in 1976 (Ilunga Kalenga, 2019).Globally, it is the second worst outbreak in the history of Ebola epidemics.

关键词： It’s not just science challenges for public health intervention in Ebola epidemics in the Democratic Republic of Congo

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The triphibious warfare against viruses

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Science China(Life Sciences) 2017年第12期60卷 1295-1298页

作者： william j.liu Di liu Key Laboratory of Medical Virology and Viral Diseases Ministry of Health of People's Republic of China National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention CAS Key Laboratory for Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences Computational Virology Group CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology Chinese Academy of Sciences

Despite the long journey undertaken by mankind to confront the diseases caused by viruses,people were unaware of the existence of viruses until the closing years of the 19th century,when the Russian biologist Dmitri Ivanovsky demonstrated that tobacco plants could be infected by a toxin smaller than bacteria,followed by which the Dutch

关键词： The triphibious warfare against viruses

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The Arms Race in the War Between Virus and Host: Implications for Anti-Infection Immunity

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Infectious Diseases & Immunity 2022年第3期2卷 129-131页

作者： william j.liu jianqing Xu NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China Clinical Center for Biotherapy at Zhongshan Hospital&Institutes of Biomedical Sciences Fudan UniversityShanghai 201508China

Viruses are recognized as the simplest form of life on earth,whereas humans are the most complex,flattered by ourselves.Nonetheless,warfare between viruses and human immunity is never ending.Some human organs,such as the respiratory tract and liver,appear to be fertile ground for specific viruses,leading to sometimes aggressive infection.The immune system acts as the human’s army,shouldering the responsibility of defending the body.Military operations are carried out by a complex system,reflected in the intricacy of its components.

关键词： immunity organs respiratory

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Let’s Get Vaccinated for Both Flu and COVID-19:On the World Flu Day 2021

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China CDC weekly 2021年第44期3卷 915-917页

作者： George F.Gao william j.liu Chinese Center for Disease Control and Prevention BeijingChina.

This year marks the fourth World Flu Day on November 1.In 2018,on the occasion of centenary of the 1918 flu pandemic,the first World Flu Day was formally initiated and developed by leading influenza specialists in China and all over the world at a symposium in Shenzhen,China,with the theme to“Commemorate the Centenary of the 1918–19 Influenza Pandemic”(1).Scientists and representatives from different international associations and organizations.

关键词： formally initiated World

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Human T-cell immunity against the emerging and re-emerging viruses

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Science China(Life Sciences) 2017年第12期60卷 1307-1316页

作者： Min Zhao Hangjie Zhang Kefang liu George F.Gao william j.liu Research Network of lmmunity and Health(RN1H) Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing 100101China Key Laboratory of Medical Virology and Viral Diseases Ministry of Health of People's Republic of ChinaNational Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 102206China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Over the past decade, we have seen an alarming number of high-profile outbreaks of newly emerging and re-emerging viruses.Recent outbreaks of avian influenza viruses, Middle East respiratory syndrome coronaviruses, Zika virus and Ebola virus present great threats to global health. Considering the pivotal role of host T-cell immunity in the alleviation of symptoms and the clearance of viruses in patients, there are three issues to be primarily concerned about T-cell immunity when a new virus emerges: first, does the population possess pre-existing T-cells against the new virus through previous infections of genetically relevant viruses; second, does a proper immune response arise in the patients to provide protection through an immunopathogenic effect; lastly, how long can the virus-specific immune memory persist. Herein, we summarize the current updates on the characteristics of human T-cell immunological responses against recently emerged or re-emerged viruses, and emphasize the necessity for timely investigation on the T-cell features of these viral diseases, which may provide beneficial recommendations for clinical diagnosis and vaccine development.

关键词： emerging viruses avian influenza H7N9 MERS-CoV Zika Ebola human immunity T-cell cross-reactivity

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