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Rapid Acquisition of High-Quality SARS-CoV-2 Genome via Amplicon-Oxford Nanopore Sequencing

Virologica Sinica 2021年第6期36卷 901-912页

作者： Yi Yan Ke Wu Jun Chen Haizhou Liu Yi Huang Yong Zhang Jin Xiong Weipeng Quan Xin Wu Yu Liang Kunlun He Zhilong Jia Depeng Wang Di Liu Hongping Wei Jianjun Chen CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyCenter for Biosafety MegaScienceChinese Academy of SciencesWuhan 430071China National Virus Resource Center 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 101409China Wuhan Pulmonary Hospital Wuhan Tuberculosis Prevention and Treatment InstituteWuhan 430030China National Biosafety Laboratory Chinese Academy of SciencesWuhan 430071China GrandOmics Biosciences Wuhan 430000China GrandOmics Biosciences Beijing 102200China GrandOmics Diagnostics Wuhan 430000China Key Laboratory of Biomedical Engineering and Translational Medicine Ministry of Industry and Information TechnologyChinese PLA General HospitalBeijing 100039China Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure Chinese PLA General HospitalBeijing 100039China First Affiliated Hospital of Xinjiang Medical University Urumqi 830054China

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary *** the rapid acquisition of SARS-Co V-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid *** address this issue,we modified and evaluated an approach by utilizing SARS-Co V-2-specific amplicon amplification and Oxford Nanopore Prometh ION *** workflow started with the throat swab of the COVID-19 patient,combined reverse transcript PCR,and multi-amplification in one-step to shorten the experiment time,then can quickly and steadily obtain high-quality SARS-Co V-2 genome within 24 h.A comprehensive evaluation of the method was conducted in 42 samples:the sequencing quality of the method was correlated well with the viral load of the samples;high-quality SARS-Co V-2 genome could be obtained stably in the samples with Ct value up to 39.14;data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20;variation analysis indicated that the method can detect the existing and emerging genomic mutations as well;Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing,making it as low as 0.4/10,000 *** summary,high-quality SARS-Co V-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARSCo V-2.

关键词： SARS-CoV-2 Genome Amplicon Nanopore sequencing

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Virome identification in wheat in the Czech Republic using small RNA deep sequencing

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Journal of Integrative Agriculture 2020年第7期19卷 1825-1833页

作者： Khushwant SINGH Jana JAROSOVA Jan FOUSEK CHEN Huan Jiban Kumar KUNDU Plant Virus and Vector Interactions group Division of Crop Protection and Plant HeatthCrop Research InstitutePrague 16106Czech Republic Zhejiang Tianke High-Technology Development Co. Ltd.Hangzhou 310012P.R.China

High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA(sRNA)population isolated from plants allows universal virus detection and complete virome reconstruction for a given *** the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic,samples were firstly tested for barley yellow dwarf viruses(BYDVs),wheat streak mosaic virus(WSMV)and wheat dwarf virus(WDV)using ELISA,RT-PCR and *** sRNA sequencing of these samples yielded more than^60 million single-end 50-bp reads with high confidence for nine field samples of ***,16.5%of reads were virus-specific and 83.5%were mapped to the *** 21-nt reads(-7.7E+06 reads)were found than 24-nt(~6.20E+06 reads)or 22-nt(-4.30E+06 reads)*** novo assembly of the high-quality contigs revealed the presence of three earlier repoted viruses in the Czech Republic:BYDVs(31.48%),WSMV(24.23%)and WDV(2666%).We also showed the presence of cereal yellow dwarf virus(14.33%;two species CYDV-RPS and CYDV-RPV family Luteoviridae/Polerovirus)and wheat yellow dwarf virus(WYDV,3.30%;Luteoviridae).Phylogenetic analysis showed CYDV and WYDV grouped separately from ***,several recombination breakpoints were found among the groups of yellow dwarf viruses(BYDVs,CYDV,and WYDV).Using RNA deep sequencing,we confirmed the presence of the three known viruses(BYDVs,WSMV,and WDV)and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.

关键词： NGS sRNA BYDVs CYDV WSMV WYDV WDV

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THE FIRST CASE OF GEMINIVIRUS IN CHINA——TOBACCO LEAF CURL VIRUS

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Chinese Science Bulletin 1983年第9期28卷 1249-1252页

作者：龚祖埙沈菊英郑巧兮陈作义曹天钦陈瑞泰韩晓东张文丽 Shanghai Institute of Biochemistry Academia Sinica Institute of Tobacco Chinese Academy of Agricultural Sciences Yidu Shandong Province Institute of Tobacco Chinese Academy of Agricultural Sciences Yidu Shandong Provinceeminivirus is a group of new plant virus the single-strandedness of the smallest DNA genome and geminate morphology of which are different from those of all other groups of viruses described so far. Since the discovery of geminivirus in the beet curly top disease and the maize streak disease less than ten years ago over ten other

Geminivirus is a group of new plant virus, the single-strandedness of the smallest DNA genome and geminate morphology of which are different from those of all other groups of viruses described so far. Since the discov... 详细信息

关键词： maize streak FIRST smallest CASE DNA pathogen Pellet diseased dwarf

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Antibiotic Resistance in the Uropathogenic Enterobacteria Isolated from Patients Attending General Reference Hospital (GRH) of Niamey, Niger

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Open Journal of Medical Microbiology 2023年第1期13卷 78-90页

作者： Alassane Halawen Mohamed René Dembélé Chaibou Salaou Alix Bénédicte Kagambèga Hiliassa Coulibaly Frédéric François Bado Alio Mahamadou Fody Laouali Boubou Alkassoum Ibrahim Eric Adehossi Omar Mauricio Arcos Holzinger Nicolas Barro Microbiology Laboratory of the General Reference Hospital (GRH) Niamey Niger Laboratory of Molecular Biology Epidemiology and Surveillance of Foodborne Bacteria and Viruses (LaBESTA) University Joseph KI-ZERBO of Ouagadougou Ouagadougou Burkina Faso Training and Research Unit in Applied Sciences and Technologies University of Dedougou Dedougou Burkina Faso Superior Normal School University Abdou Moumouni of Niamey Niamey Niger Bacteriology Laboratory of the Niamey National Hospital (NNH) Niamey Niger Direction of Surveillance and Response to Epidemics Ministry of Public Health Niamey Niger Faculty of Health Sciences University Abdou Moumouni of Niamey Niamey Niger Center for Medical and Health Research Niamey Niger Instituto de Ciencias Médicas Las Tablas Panama

Background: Urinary tract infections (UTIs) are a frequent reason for consultation and lead to a significant and sometimes inappropriate prescription of antibiotics. The latter favors antibiotic resistance and an increase in mortality as well as the cost of treatment. The present study aims to contribute to the fight against antibiotic resistance of enterobacteria. Methods: This is a prospective study from January to December, 2021 in the Microbiology laboratory of the General Reference Hospital (GRH) of Niamey including 3369 urine samples. The antibiotic resistance of enterobacteria was determined using the Viteck-2 method. Results: At least 280 strains of Enterobacteriaceae were isolated from the patient’s urine. Among these strains, Escherichia coli was the most predominant (74.64%), followed by Klebsiella pneumoniae (16.07%) and Enterobacter cloacae (7.14%) and other enterobacteria 2.15%. These Enterobacteriaceae are more common in community patients than in hospitalized patients. The average age of patients is 52 years and the age group most affected by these enterobacteria is 46 - 60 years (23.33%). The female sex is the most affected sex with (51.07%) against (48.97%) for the male sex with 1.04 as sex ratio. The hospitalization departments most affected by these enterobacteria are Nephrology (29.23%) and Endocrinology (21.54%). Up to 75% of the Enterobacteriaceae isolates show high resistance to ampicillin, amoxicillin-clavulanic acid, ticarcillin, piperacillin-tazobactam, cefoxitin, cefixime, ceftazidime, ceftriaxone, cotrimoxazole, nalidixic acid and ofloxacin. Conclusion: The high rate of antibiotic resistance among enterobacteria in urine is of concern. Only a few Enterobacteriaceae show low resistance to ertapenem, imipenem, amikacin, gentamicin, fosfomycin and nitrofurantoin. Therefore, these antibiotics are recommended as first line treatment for urinary tract infections.

关键词： Antibiotic Resistance Urinary Tract Infections Enterobacteriaceae Viteck-2 Niger

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Severe human infection with a novel avian-origin influenza A(H7N4) virus

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Science Bulletin 2018年第16期63卷 1043-1050页

作者： Xiang Huo Lun-biao Cui Cong Chen Dayan Wang Xian Qi Ming-hao Zhou Xiling Guo Fengming Wang William J. Liu Weirong Kong Daxin Ni Ying Chi Yiyue Ge Haodi Huang Feifei Hu Chao Li Xiang Zhao Ruiqi Ren Chang-jun Bao George F. Gao Feng-Cai Zhu Key Laboratories of enteric Pathogenic Microbiology (Ministry of Health) Jiangsu Provincial Center for Disease Control and Prevention. Nanjing 210009 China Chinese Center for Disease Control and Prevention (China CDC) Beijing 102206 China National Institute for Viral Disease Control and Prevention China CDC Beijing 102206 China Changzhou Center for Disease Control and Prevention Changzhou 213022 China Liyang Center for Disease Control and Prevention Liyang 213300 China CAS Key Laboratory of Pathogenic Microbiology and Immunology Institute of Microbiology Chinese Academy of Sciences (CA5) Beijing 100101 China Center for Influenza Research and Early-Warning (CASCIRE) Chinese Academy of Sciences Beijing 100101 China Key Laboratory of Infectious Diseases School of Public Health Nanjing Medical University Nanjing 211166 China

Human infections with influenza H7 subtypes, such as H7N9, have raised concerns worldwide. Here, we report a human infection with a novel influenza A(H7N4) virus. A 68 years-old woman with cardiovascular and cholecystic comorbidities developed rapidly progressed pneumonia with influenza-like-illness as initial symptom, recovered after 23 days-hospitalization including 8 days in ICU. Laboratory indicators for liver and blood coagulation dysfunction were observed. Oseltamivir phosphate, glucocorticoids and antibiotics were jointly implemented, with nasal catheterization of oxygen inhalation for this *** obtained the medical records and collected serial respiratory and blood specimens from her. We collected throat, cloacal and/or feces samples of poultry and wild birds from the patient's backyard, neighborhood, local live poultry markets(LPMs) and the nearest lake. All close contacts of the patient were followed up and sampled with throat swabs and sera. Influenza viruses and other respiratory pathogens were tested by real-time RT-PCR, viral culturing and/or sequencing for human respiratory and bird samples. Micro-neutralizing assay was performed for sera. A novel reassortant wild bird-origin H7N4 virus is identified from the patient and her backyard poultry(chickens and ducks) by sequencing, which is distinct from previously-reported avian H7N4 and H7N9 viruses. At least four folds increase of neutralizing antibodies to H7N4 was detected in her convalescent sera. No samples from close contacts, wild birds or other poultry were tested positive for H7N4 by real-time RT-PCR.

关键词：流行性感冒病毒野鸟感染起源 RT-PCR 家禽市场世界范围机能障碍

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Emerging HIV Epidemic in the North-Eastern State of Assam, India: An Exploratory Study Using Mixed-Methods Approach

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World Journal of AIDS 2018年第1期8卷 21-36页

作者： Chiranjeev Bhattacharjya Giridhar Pathak Tulika Goswami Mahanta Y. Manihar Singh Ranjanjyoti Deka Mitali Sen Alok Kr. Deb Assam State AIDS Control Society (SACS) Guwahati India Silchar Medical College & Hospital Silchar India Assam Medical College & Hospital Dibrugarh India Regional Institute of Medical Sciences Imphal India Part-Time Project Consultant Kolkata India ICMR-National Institute of Cholera & enteric Diseases Kolkata India

Background: The national HIV scenario in India has improved impressively during past two decades. Contrastingly, the State-level HIV sentinel surveil-lance and routine programme data from various testing facilities indicated an increasing HIV prevalence among antenatal clinic attendees and female sex workers (FSWs) in three districts of Assam. Objectives: 1) To explore the reasons behind increasing adult HIV prevalence and 2) To understand the role of FSW and Migrants/long distance truckers as drivers of the HIV epi-demic in these districts. Methodology: Three sources of data were utilized in this concurrent mixed methods study—1) existing programme data for past three years;2) questionnaire-based data for a case-control study, where dur-ing past six months at designated testing facilities HIV(+) married women were “cases” and age-matched HIV(?) women from the same district were “controls”. Spouses of these women were also interviewed separately;and 3) a qualitative study, where focus group discussions were conducted among FSWs, outgoing male migrant labourers and long-distance truckers. Results: The study revealed high levels of unsafe sexual practices among the FSWs. Sometimes in poverty-struck areas, women, not identifying themselves as sex workers, sold sex on a part-time basis to earn extra money for financial sup-port and often remained invisible to the programme. The clients of the sex workers, male migrants and truckers also revealed various risk behaviours for contracting and transmitting HIV infection. Conclusion: Population and context specific programme strategies are required to halt the rising trend of HIV infection in the general population in Assam.

关键词： HIV Assam Mixed Methods

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Design of porous Eudragit^(■)L beads for floating drug delivery by wax removal technique

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Asian Journal of Pharmaceutical Sciences 2017年第3期12卷 227-234页

作者： Kampanart Huanbutta Tassanee Nernplod Prasert Akkaramongkolporn Pornsak Sriamornsak Faculty of Pharmaceutical Sciences Burapha UniversityChonburi 20131Thailand Pharmaceutical Biopolymer group(PBiG) Faculty of PharmacySilpakorn UniversityNakhon Pathom 73000Thailand Department of Pharmaceutical Technology Faculty of PharmacySilpakorn UniversityNakhon Pathom 73000Thailand

The aim of this study was to design porous matrix beads for floating drug delivery using enteric polymer, Eudragit~? L and various amounts of waxes(0, 0.1, 0.5, 1, 2 and 3% w/w). In this study, wax containing cetyl alcohol and white petrolatum was utilized to produce pores using a wax removal technique. To prepare the beads, Eudragit~? L, metronidazole and wax were dissolved in acetone and then extruded into dichloromethane. The effect of the amount of wax on the floating and drug release behavior of the Eudragit~? L beads was *** the extruded product was immersed in dichloromethane, wax dissolved out from the formed beads, resulting in a porous structure. The prepared beads could float in simulated gastric fluid for more than 10 hours. Different amounts of wax had an effect on the drug release. We found that when the percentage of wax increased, the drug release was higher while the beads remained floating. The results suggest that Eudragit~? L beads could be used as a carrier for an intragastric floating drug delivery system.

关键词： Porous beads Floating Wax removal Eudragit^(■)L

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Intelligent Oxygen-Enriched and “Sterilized” Underground Gyms: Background, Dilemmas and Pathways

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Health 2023年第11期15卷 1171-1190页

作者： Jianzhong Sun Lili Jin Chan Lin Lei Wang School of Physical Education Chizhou University Chizhou China Sports group Chengxi Primary School in Guichi District Chizhou China Sports Health Promotion Center Chizhou University Chizhou China Basic Teaching Department Chizhou Vocational and Technical College Chizhou China

The in-depth integration of healthy China with national fitness and the hope to achieve the long-term goal of “leading Sports Nation” by 2035, can’t be realized without gyms where people do physical exercise. The international academic community recognizes that the 21st century is the golden time for sustainable and quality development. Taking a national perspective, authors of this paper studied the feasibility of building underground gyms in China through the approach of interdisciplinary research, as well as its dilemmas and pathways, and found out that quality development of underground space can effectively address challenges for large cities in China by increasing the resilience of urban area, and give full engage to underground capacity in striving for the goal of carbon peak and carbon neutrality. Underground gyms can also be incorporated into resident’s 15-min fitness circle, satisfying people’s needs of doing exercise at any time and in an easily-accessible place. However, China’s underground area development has been hindered by unclear property rights, chaotic action and utilization, and relatively backward laws and regulations. Moreover, building underground gyms still has to solve many problems such as poor air quality, severe sweat smell, and excessive bacteria and viruses. It is suggested that the capable authorities shall first clarify laws and regulations over place compound utilization, property rights and fire protection to facilitate the process of building underground gyms;encourage fitness practitioners to explore underground areas as gyms, and transfer their ground business to underground;then produce an intelligent and systematic solution of air quality improvement featuring oxygen-enrichment and “sterilization” with integration, a variety of instruments to monitor air quality of indoor gyms in real-time, to realize automatic control and management, and truly create worry-free and oxygen-enriched underground gyms with no sweat sme

关键词： Underground Space Gyms Air Quality Intelligence “Sterilization”

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Comparative Analysis of RNAi Suppression Activity of Proteins from Two Disparate viruses

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American Journal of Plant Sciences 2014年第12期5卷 1789-1798页

作者： Sudhanshu Sekhar Das Neeti Sanan-Mishra Plant Molecular Biology group International Centre for Genetic Engineering and Biotechnology New Delhi India

RNAi is an efficient surveillance machinery that plays a robust defensive role in shielding plant and animal hosts against viral infections. In counter-defense viruses encode suppressor proteins that have the ability to restrict the RNAi machinery to ensure successful systemic invasion. The B2 protein of insect Flock House Virus (FHV-B2) and AC2 protein of Mungbean Yellow Mosaic India Virus (MYMIV-AC2) are two well-characterized suppressors of RNAi, capable of reversing reporter gene silencing. In this study, we compared the strength of the two suppressors by assaying for the degree of RNAi reversion and the duration of sustaining the reversal in planta. The suppression activity was observed by assaying for GFP fluorescence at 3 dpi, 7 dpi and 14 dpi. The phenotypic observations were corroborated with small RNA Northern Blotting and semi-quantitative RT-PCR. The results indicate that suppressor strength of FHVB2 is comparable to MYMIV-AC2, although they are encoded by virus infecting host from two different eukaryotic kingdoms. This study will provide new insights to dissect the conservation in the RNAi pathways during the host-virus interactions.

关键词： MYMIV-AC2 FHVB2 Agroinfiltration RNA Silencing Suppressor (RSS) Reversal of GFP Silencing Assay

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Inhibition of African swine fever virus in liquid and feed by medium-chain fatty acids and glycerol monolaurate

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Journal of Animal Science and Biotechnology 2021年第2期12卷 569-578页

作者： Joshua A.Jackman Astghik Hakobyan Hovakim Zakaryan Charles C.Elrod School of Chemical Engineering Sungkyunkwan UniversitySuwon 16419Republic of Korea group of Antiviral Defense Mechanisms Institute of Molecular Biology of NASYerevanArmenia Natural Biologics Inc. NewfieldNY 14867USA. Department of Animal Science Cornell UniversityIthacaNY 14853USA

Background:The ongoing African swine fever virus(ASFv)epidemic has had a major impact on pig production globally and biosecurity efforts to curb ASFv infectivity and transmission are a high *** has been recently identified that feed and feed ingredients,along with drinking water,can serve as transmission vehicles and might facilitate transboundary spread of ***,it is important to test the antiviral activity of regulatory compatible,antiviral feed additives that might inhibit ASFv infectivity in *** promising group of feed additive candidates includes medium-chain fatty acids(MCFA)and monoglyceride derivatives,which are known to disrupt the lipid membrane surrounding certain enveloped viruses and ***:The antiviral activities of selected MCFA,namely caprylic,capric,and lauric acids,and a related monoglyceride,glycerol monolaurate(GML),to inhibit ASFv in liquid and feed conditions were investigated and suitable compounds and inclusion rates were identified that might be useful for mitigating ASFv in feed *** assays showed that all tested MCFA and GML inhibit *** was more potent than MCFA because it worked at a lower concentration and inhibited ASFv due to direct virucidal activity along with one or more other antiviral ***-dependent feed experiments further showed that sufficiently high GML doses can significantly reduce ASFv infectivity in feed in a linear manner in periods as short as 30 min,as determined by infectious viral titer ***-linked immunosorbent assay(ELISA)experiments revealed that GML treatment also hinders antibody recognition of the membrane-associated ASFv p72 structural protein,which likely relates to protein conformational changes arising from viral membrane ***:Together,the findings in this study indicate that MCFA and GML inhibit ASFv in liquid conditions and that GML is also able to reduce ASFv infectivity in feed,which may help to curb disease tr

关键词： African swine fever virus Antiviral Feed pathogen mitigation MCFA Medium-chain fatty acids Monoglycerides

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