35 results on '"Yafang Zhu"'
Search Results
2. MERS–Related Betacoronavirus in Vespertilio superans Bats, China
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Li Yang, Zhiqiang Wu, Xianwen Ren, Fan Yang, Junpeng Zhang, Guimei He, Jie Dong, Lilian Sun, Yafang Zhu, Shuyi Zhang, and Qi Jin
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coronavirus ,Middle East respiratory syndrome coronavirus ,MERS-CoV ,Vespertilio superans ,bat ,reservoir ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Published
- 2014
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3. Novel Henipa-like Virus, Mojiang Paramyxovirus, in Rats, China, 2012
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Zhiqiang Wu, Li Yang, Fan Yang, Xianwen Ren, Jinyong Jiang, Jie Dong, Lilian Sun, Yafang Zhu, Hongning Zhou, and Qi Jin
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novel virus ,henipa-like virus ,henipavirus ,paramyxovirus ,Mojiang paramyxovirus ,China ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Published
- 2014
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4. Novel SARS-like Betacoronaviruses in Bats, China, 2011
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Li Yang, Zhiqiang Wu, Xianwen Ren, Fan Yang, Guimei He, Junpeng Zhang, Jie Dong, Lilian Sun, Yafang Zhu, Jiang Du, Shuyi Zhang, and Qi Jin
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Coronavirus ,Chiroptera ,SARS virus ,China ,viruses ,bats ,Medicine ,Infectious and parasitic diseases ,RC109-216 - Abstract
To clarify the evolutionary relationships among betavoronaviruses that infect bats, we analyzed samples collected during 2010–2011 from 14 insectivorous bat species in China. We identified complete genomes of 2 novel betacoronaviruses in Rhinolophus pusillus and Chaerephon plicata bats, which showed close genetic relationships with severe acute respiratory syndrome coronaviruses.
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- 2013
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5. Common changes in global gene expression induced by RNA polymerase inhibitors in Shigella flexneri.
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Hua Fu, Liguo Liu, Xiaobing Zhang, Yafang Zhu, Lina Zhao, Junping Peng, Hongxuan He, and Qi Jin
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Medicine ,Science - Abstract
Characterization of expression profile of organisms in response to antimicrobials provides important information on the potential mechanism of action of the drugs. The special expression signature can be used to predict whether other drugs act on the same target. Here, the common response of Shigella flexneri to two inhibitors of RNA polymerase was examined using gene expression profiling. Consistent with similar effects of the two drugs, the gene expression profiles indicated that responses of the bacteria to these drugs were roughly the same, with 225 genes affected commonly. Of them, 88 were induced and 137 were repressed. Real-time PCR was performed for selected genes to verify the microarray results. Analysis of the expression data revealed that more than 30% of the plasmid-encoded genes on the array were up-regulated by the antibiotics including virF regulon, other virulence-related genes, and genes responsible for plasmid replication, maintenance, and transfer. In addition, some chromosome-encoded genes involved in virulence and genes acquired from horizontal transfer were also significantly up-regulated. However, the expression of genes encoding the beta-subunit of RNA polymerase was increased moderately. The repressed genes include those that code for products associated with the ribosome, citrate cycle, glycolysis, thiamine biosynthesis, purine metabolism, fructose metabolism, mannose metabolism, and cold shock proteins. This study demonstrates that the two antibiotics induce rapid cessation of RNA synthesis resulting in inhibition of translation components. It also indicates that the production of virulence factors involved in intercellular dissemination, tissue invasion and inflammatory destruction may be enhanced through derepressing horizontal transfer genes by the drugs.
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- 2012
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6. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.
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Xianwen Ren, Tao Liu, Jie Dong, Lilian Sun, Jian Yang, Yafang Zhu, and Qi Jin
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Medicine ,Science - Abstract
Next generation sequencing (NGS) technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.
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- 2012
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7. Does prolonged emergency department length of stay(EDLOS) affect the outcomes of acute ischemic stroke patients?
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Chun-Feng Liu, Xia Zhang, Yan Qin, Yongjun Cao, Yongrong Sun, Yafang Zhu, Yan Wu, Xuechun Wu, Rongfang Shi, and Hong Pan
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Male ,medicine.medical_specialty ,Poor prognosis ,Stroke care ,Affect (psychology) ,Severity of Illness Index ,03 medical and health sciences ,0302 clinical medicine ,Risk Factors ,Modified Rankin Scale ,medicine ,Humans ,Glasgow Coma Scale ,Prospective Studies ,cardiovascular diseases ,Acute ischemic stroke ,Stroke ,Aged ,Ischemic Stroke ,business.industry ,030208 emergency & critical care medicine ,Recovery of Function ,General Medicine ,Emergency department ,Length of Stay ,Prognosis ,medicine.disease ,Increased risk ,Emergency medicine ,Disease Progression ,Emergency Medicine ,Female ,Emergency Service, Hospital ,business - Abstract
The effect of emergency department length of stay (EDLOS) on outcomes of patients with acute ischemic stroke (AIS) remains largely unexamined. We aimed to investigate the association between EDLOS and outcomes in AIS patients.618 AIS patients were enrolled. Baseline demographics, vascular risk factors, ED admission information, hyperacute treatment of AIS and stroke severity were collected. Stroke progression was defined as any new neurological symptoms/signs or any neurological worsening within 7 days after stroke onset and poor prognosis was defined as modified Rankin Scale(mRS) scores2 at 30 day. The effect of EDLOS on stroke progression and prognosis was assessed.The median EDLOS was 2.5 h (1.4-6.9 h). On multivariable linear regression, presentation month between Apr. and Jun., admission at the ED between 7 am to 3 pm(P = 0.036), transferring to stroke unit, receiving endovascular interventional treatment, onset on holidays, and progressive stroke were associated with shorter EDLOS(all P 0.05). A shorter EDLOS was significantly associated with an increased risk of stroke progression (P = 0.007). Patients with the lowest EDLOS (≤1.35 h) were 2-3 fold more likely to have stroke progression, compared with those with the highest EDLOS (6.93 h) (OR, 2.52; 95% CI, 1.29-4.93; P = 0.043). However, no significant association between EDLOS and stroke prognosis was revealed.In AIS patients, shorter EDLOS was associated with the increased risk of stroke progression, possibly reflecting prioritized admission of more severely affected patients at high risk of stroke progression. EDLOS alone might be an insufficient indicator of stroke care in the ED.
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- 2021
8. Gut microbiota associated with pulmonary tuberculosis and dysbiosis caused by anti-tuberculosis drugs
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Jian Yang, Lilian Sun, Yafang Zhu, Yongfeng Hu, Jie Dong, Fan Yang, Qi Jin, Bo Liu, Qianting Yang, Xinchun Chen, and Haoxiang Su
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Adult ,Male ,0301 basic medicine ,Microbiology (medical) ,Tuberculosis ,030106 microbiology ,Antitubercular Agents ,Biology ,Gut flora ,digestive system ,Microbiology ,Mycobacterium tuberculosis ,Feces ,03 medical and health sciences ,0302 clinical medicine ,Pulmonary tuberculosis ,RNA, Ribosomal, 16S ,medicine ,Humans ,030212 general & internal medicine ,Tuberculosis, Pulmonary ,Bacteria ,Clostridiales ,Middle Aged ,biology.organism_classification ,medicine.disease ,Gastrointestinal Microbiome ,Infectious Diseases ,Dysbiosis ,Female ,Bacteroides fragilis ,Bacteroides - Abstract
Summary Background: An improved understanding of the gut microbiota could lead to better strategies for the diagnosis, therapy and prophylaxis of tuberculosis (TB). The impact of both Mycobacterium tuberculosis (Mtb) infection and anti-TB treatment on the gut microbiota has rarely been studied. Methods: We characterized the diversity and composition of the gut microbiota in pulmonary TB patients as well as the effects of anti-TB drugs on the gut microbiota. Results: Pulmonary Mtb infection led to a minor decrease in the α diversity of the gut microbiota when compared to healthy controls, which mainly resulted from changes in the relative abundance of the members of genus Bacteroides. Anti-TB therapy caused a rapid, significant alteration in the community structure. The relative abundance of members of genus Clostridiales of the phylum Firmicutes significantly decreased during anti-TB treatment, while many members of genus Bacteroides, including Bacteroides OTU230 and Bacteroides fragilis, were among the taxa that increased. OTU8 and OTU2972 assigned to family Erysipelotrichaceae of the phylum Firmicutes showed a dramatic increase 1 week after the start of therapy, while the other members of this family decreased. Conclusions: Pulmonary TB and anti-TB treatment caused a distinct dysbiosis of the gut microbiota. Our study contributes valuable information implying potential links between the gut microbiota and TB.
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- 2019
9. A Whole-genome Sequencing Analysis of Neisseria gonorrhoeae Isolates in China: An Observational Study
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Xiu-Qin Dai, Zhong-Jie Zheng, Bang-Yong Zhu, Lilian Sun, Jian Yang, Gang Yong, Junping Peng, Wen-Ling Cao, Jie Dong, Xiang-Sheng Chen, Qi Jin, Qi Zhi, Yue-Ping Yin, Bo Liu, Na Zhong, Yafang Zhu, Shao-Chun Chen, Leshan Xiu, Li-Hua Hu, Heping Zheng, Chi Zhang, Wei-Ming Gu, and Feng Wang
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Gonorrhea ,Population ,medicine.disease_cause ,01 natural sciences ,Genome ,03 medical and health sciences ,0302 clinical medicine ,Antibiotic resistance ,medicine ,030212 general & internal medicine ,0101 mathematics ,education ,Genetics ,Whole genome sequencing ,lcsh:R5-920 ,education.field_of_study ,business.industry ,010102 general mathematics ,General Medicine ,medicine.disease ,GenBank ,Neisseria gonorrhoeae ,Multilocus sequence typing ,lcsh:Medicine (General) ,business ,Research Paper - Abstract
Background: Tracking the spread of the Neisseria gonorrhoeae strains with decreased susceptibility or resistance to cephalosporins is a major priority for global surveillance programmes. Whole-genome sequencing (WGS) has been widely used by increasing countries in North America, Europe, and Pacific to determine the decreased susceptible or resistance determinants of Neisseria gonorrhoeae, track the spread of these determinants throughout the gonococcal population at national or regional level. However, no studies to date have examined the genomic epidemiology of gonorrhea in Asia where the antimicrobial resistant strains of Neisseria gonorrhoeae appears to have emerged before disseminating the strains globally. Methods: We obtained clinical isolates and data from the China Gonococcal Resistance Surveillance Programme (China-GRSP) from 2012 to 2013. We sequenced the genomes of 435 clinical isolates of Neisseria gonorrhoeae, including 112 (25.6%) isolates with decreased susceptibility to ceftriaxone (Cfx-DS). We assessed the association between antimicrobial resistance genotype and phenotype. We also compared our data with the whole genome data of the isolates from the USA and the UK in the GenBank. Findings: The most prevalent MLST STs in our gonococcal population were MLST ST7827 (n = 74), followed by ST7365 (n = 58), ST1600 (n = 38), ST7367 (n = 35), and ST7363 (n = 29). MLST ST1901 which was reported as the predominant ST in the US was not found in our population. A total of 2512 strains, including additional 2077 published NG strains, were further included for phylogenetic analysis. It generated two distinct lineages - lineage 1 and lineage 2. Analysis of MLST ST1901 in the database indicate that most of MLST ST1901 isolates in the lineage2.6 were Cfx-DS isolates while all isolates in the lineage 2.1 were sensitive to ceftriaxone (77/110 vs. 0/13; p
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- 2019
10. Proteogenomic Analysis and Discovery of Immune Antigens in Mycobacterium vaccae
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Jie Dong, Jianhua Zheng, Qi Jin, Li Haifeng, Liguo Liu, Lihong Chen, Lilian Sun, Tao Liu, Jian Yang, Dandan Zheng, Yafang Zhu, Xiaobing Zhang, and Bo Liu
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0301 basic medicine ,Tuberculosis ,medicine.medical_treatment ,030106 microbiology ,Computational biology ,Biochemistry ,Genome ,Mycobacterium ,Analytical Chemistry ,03 medical and health sciences ,Immune system ,Bacterial Proteins ,Western blot ,Antigen ,medicine ,Humans ,Electrophoresis, Gel, Two-Dimensional ,Amino Acid Sequence ,Isoelectric Point ,Molecular Biology ,Proteogenomics ,Antigens, Bacterial ,biology ,medicine.diagnostic_test ,Research ,Chromosome Mapping ,Reproducibility of Results ,Immunotherapy ,Genome project ,biology.organism_classification ,medicine.disease ,Molecular Weight ,030104 developmental biology ,Protein Biosynthesis ,Mycobacterium vaccae ,Genome, Bacterial ,Subcellular Fractions - Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, especially in developing countries. Neonatal BCG vaccination occurs in various regions, but the level of protection varies in different populations. Recently, Mycobacterium vaccae is found to be an immunomodulating therapeutic agent that could confer a significant level of protection against TB. It is the only vaccine in a phase III trial from WHO to assess its efficacy and safety in preventing TB disease in people with latent TB infection. However, the mechanism of immunotherapy of M. vaccae remains poorly understood. In this study, the full genome of M. vaccae was obtained by next-generation sequencing technology, and a proteogenomic approach was successfully applied to further perform genome annotation using high resolution and high accuracy MS data. A total of 3,387 proteins (22,508 unique peptides) were identified, and 581 proteins annotated as hypothetical proteins in the genome database were confirmed. Furthermore, 38 novel protein products not annotated at the genome level were detected and validated. Additionally, the translational start sites of 445 proteins were confirmed, and 98 proteins were validated through extension of their translational start sites based on N terminus-derived peptides. The physicochemical characteristics of the identified proteins were determined. Thirty-five immunogenic proteins of M. vaccae were identified by immunoproteomic analysis, and 20 of them were selected to be expressed and validated by Western blot for immunoreactivity to serum from patients infected with M. tuberculosis. The results revealed that eight of them showed strong specific reactive signals on the immunoblots. Furthermore, cellular immune response was further examined and one protein displayed a higher cellular immune level in pulmonary TB patients. Twelve identified immunogenic proteins have orthologous in H37Rv and BCG. This is the first study to obtain the full genome and annotation of M. vaccae using a proteogenomic approach, and some immunogenic proteins that were validated by immunoproteomic analysis could contribute to the understanding of the mechanism of M. vaccae immunotherapy.
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- 2017
11. An elaborate landscape of the human antibody repertoire against enterovirus 71 infection is revealed by phage display screening and deep sequencing
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Qi Jin, Yafang Zhu, Jian Yang, Xianwen Ren, Ying Xue, Jie Dong, Lilian Sun, and Zhe Chen
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Male ,0301 basic medicine ,Phage display ,030106 microbiology ,Immunology ,Biology ,Antibodies, Viral ,Deep sequencing ,03 medical and health sciences ,Antibody Repertoire ,Report ,Enterovirus 71 ,medicine ,Humans ,Immunology and Allergy ,Child ,Foot-and-mouth disease ,Outbreak ,biology.organism_classification ,medicine.disease ,Antibodies, Neutralizing ,Virology ,In vitro ,Enterovirus A, Human ,High-Throughput Screening Assays ,030104 developmental biology ,biology.protein ,Female ,Antibody ,Cell Surface Display Techniques ,Hand, Foot and Mouth Disease - Abstract
Enterovirus 71 (EV71) causes outbreaks of hand, foot and mouth disease (HFMD), primarily in the Asia-Pacific area, that are often associated with complications of severe to fatal neurological symptoms. There are currently no anti-viral therapies or vaccines available for the treatment of EV71 infection. Illustrating human antibody responses neutralizing EV71 infection could potentially provide valuable information for the development of effective therapies and vaccines. Here, we constructed a comprehensive phage display library based on peripheral blood of eight EV71-infected donors and identified 27 EV71-specific human antibodies, of which four have neutralizing activity in in vitro experiments. Deep sequencing analysis of the antibody heavy chains at the transcript level of another three independent EV71-infected donors and three controls demonstrates that heavy chains of the EV71-specific antibodies are conserved among EV71-infected individuals but absent in controls, suggesting convergent evolution of human antibodies against EV71.
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- 2016
12. Distinct lung microbial community states in patients with pulmonary tuberculosis
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Xinchun Chen, Fan Yang, Yongfeng Hu, Xianwen Ren, Ying Kang, Qi Jin, Qianting Yang, Xi Liu, Yafang Zhu, Jie Dong, Min Cheng, and Lilian Sun
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0301 basic medicine ,Adult ,Male ,Lung microbiome ,Tuberculosis ,Veillonella ,Antitubercular Agents ,General Biochemistry, Genetics and Molecular Biology ,Microbiology ,03 medical and health sciences ,0302 clinical medicine ,RNA, Ribosomal, 16S ,Prevotella ,Medicine ,Humans ,Lung ,Tuberculosis, Pulmonary ,General Environmental Science ,medicine.diagnostic_test ,biology ,Bacteria ,business.industry ,Microbiota ,Mycobacterium tuberculosis ,respiratory system ,Middle Aged ,bacterial infections and mycoses ,biology.organism_classification ,medicine.disease ,respiratory tract diseases ,030104 developmental biology ,Bronchoalveolar lavage ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Gemella ,Female ,General Agricultural and Biological Sciences ,business ,Bronchoalveolar Lavage Fluid ,Mycobacterium - Abstract
An improved understanding of the lung microbiome may lead to better strategies to diagnose, treat, and prevent pulmonary tuberculosis (PTB). However, the characteristics of the lung microbiomes of patients with TB remain largely undefined. In this study, 163 bronchoalveolar lavage (BAL) samples were collected from 163 sputum-negative suspected PTB patients. Furthermore, 12 paired BAL samples were obtained from 12 Mycobacterium tuberculosis-positive (MTB+) patients before and after negative conversion following a two-month anti-TB treatment. The V3-V4 region of the 16S ribosomal RNA (rRNA) gene was used to characterize the microbial composition of the lungs. The results showed that the prevalence of MTB in the BAL samples was 42.9% (70/163) among the sputum-negative patients. The α-diversity of lung microbiota was significantly less diverse in MTB+ patients compared with Mycobacterium tuberculosis-negative (MTB-) patients. There was a significant difference in β-diversity between MTB+ and MTB- patients. MTB+ patients were enriched with Anoxybacillus, while MTB- patients were enriched with Prevotella, Alloprevotella, Veillonella, and Gemella. There was no significant difference between the Anoxybacillus detection rates of MTB+ and MTB- patients. The paired comparison between the BAL samples from MTB+ patients and their negative conversion showed that BAL negative-conversion microbiota had a higher α-diversity. In conclusion, distinct features of airway microbiota could be identified between samples from patients with and without MTB. Our results imply links between lung microbiota and different clinical groups of active PTB.
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- 2019
13. The impact of combined gene mutations in inhA and ahpC genes on high levels of isoniazid resistance amongst katG non-315 in multidrug-resistant tuberculosis isolates from China
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Jian Yang, Jie Dong, Xiaobing Zhang, Fengting Jiang, Qi Jin, Yanlin Zhao, Yang Zhou, Liguo Liu, Lihong Chen, Bing Zhao, Lilian Sun, Bo Liu, and Yafang Zhu
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0301 basic medicine ,DNA, Bacterial ,China ,Epidemiology ,030106 microbiology ,Immunology ,lcsh:QR1-502 ,Antitubercular Agents ,Drug resistance ,Microbial Sensitivity Tests ,Gene mutation ,Biology ,medicine.disease_cause ,Microbiology ,lcsh:Microbiology ,Article ,lcsh:Infectious and parasitic diseases ,Mycobacterium tuberculosis ,03 medical and health sciences ,Bacterial Proteins ,Virology ,Drug Resistance, Multiple, Bacterial ,Drug Discovery ,Tuberculosis, Multidrug-Resistant ,medicine ,Isoniazid ,Humans ,lcsh:RC109-216 ,Promoter Regions, Genetic ,Gene ,Genetics ,Mutation ,Whole Genome Sequencing ,INHA ,Structural gene ,General Medicine ,Peroxiredoxins ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,bacterial infections and mycoses ,Catalase ,Multiple drug resistance ,Infectious Diseases ,Genes, Bacterial ,Parasitology ,Oxidoreductases - Abstract
Whole-genome sequencing was used to analyze the profiles of isoniazid (INH) resistance-related mutations among 188 multidrug-resistant strains of Mycobacterium tuberculosis (MDR-TB) and mono-INH-resistant isolates collected in a recent Chinese national survey. Mutations were detected in 18 structural genes and two promoter regions in 96.8% of 188 resistant isolates. There were high mutation frequencies in katG, the inhA promoter, and ahpC-oxyR regulator regions in INH-resistant isolates with frequencies of 86.2%, 19.6%, and 18.6%, respectively. Moreover, a high diversity of mutations was identified as 102 mutants contained various types of single or combined gene mutations in the INH-resistant group of isolates. The cumulative frequencies of katG 315 or inhA-P/inhA mutations was 68.1% (128/188) for the INH-resistant isolates. Of these isolates, 46 isolates (24.5% of 188) exhibited a high level of resistance. A high level of resistance was also observed in 21 isolates (11.2% of 188) with single ahpC-oxyR mutations or a combination of ahpC-oxyR and katG non-315 mutations. The remaining 17 mutations occurred sporadically and emerged in isolates with combined katG mutations. Such development of INH resistance is likely due to an accumulation of mutations under the pressure of drug selection. Thus, these findings provided insights on the levels of INH resistance and its correlation with the combinatorial mutation effect resulting from less frequent genes (inhA and/or ahpC). Such knowledge of other genes (apart from katG) in high-level resistance will aid in developing better strategies for the diagnosis and management of TB.
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- 2018
14. Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases
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Liang Lu, Peter Daszak, Fan Yang, Yuhui Li, Hongning Zhou, Guangjian Zhu, Yu-ting Zheng, Hongying Li, Jiang Du, Li Yang, Yafang Zhu, Jie Dong, Aleksei A. Chmura, Haoxiang Su, Lilian Sun, Qi Jin, Qiyong Liu, Dandan Zheng, Bo Liu, Xianwen Ren, Zhiqiang Wu, Jinyong Jiang, Jian Yang, Jianwei Wang, and Chi Zhang
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0301 basic medicine ,Microbiology (medical) ,Emerging infectious diseases ,medicine.medical_specialty ,China ,Rodent ,viruses ,Rodentia ,Biology ,Soricomorpha ,Microbiology ,Rodents ,Communicable Diseases, Emerging ,lcsh:Microbial ecology ,03 medical and health sciences ,Medical microbiology ,biology.animal ,medicine ,Encephalitis Viruses ,Small mammals ,Animals ,Human virome ,Viral evolution ,Virome ,Research ,Shrew ,High-Throughput Nucleotide Sequencing ,Lagomorpha ,biology.organism_classification ,3. Good health ,030104 developmental biology ,Evolutionary biology ,Metagenomics ,Virus Diseases ,Viruses ,lcsh:QR100-130 ,Metagenome - Abstract
Background Rodents represent around 43% of all mammalian species, are widely distributed, and are the natural reservoirs of a diverse group of zoonotic viruses, including hantaviruses, Lassa viruses, and tick-borne encephalitis viruses. Thus, analyzing the viral diversity harbored by rodents could assist efforts to predict and reduce the risk of future emergence of zoonotic viral diseases. Results We used next-generation sequencing metagenomic analysis to survey for a range of mammalian viral families in rodents and other small animals of the orders Rodentia, Lagomorpha, and Soricomorpha in China. We sampled 3,055 small animals from 20 provinces and then outlined the spectra of mammalian viruses within these individuals and the basic ecological and genetic characteristics of novel rodent and shrew viruses among the viral spectra. Further analysis revealed that host taxonomy plays a primary role and geographical location plays a secondary role in determining viral diversity. Many viruses were reported for the first time with distinct evolutionary lineages, and viruses related to known human or animal pathogens were identified. Phylogram comparison between viruses and hosts indicated that host shifts commonly happened in many different species during viral evolutionary history. Conclusions These results expand our understanding of the viromes of rodents and insectivores in China and suggest that there is high diversity of viruses awaiting discovery in these species in Asia. These findings, combined with our previous bat virome data, greatly increase our knowledge of the viral community in wildlife in a densely populated country in an emerging disease hotspot. Electronic supplementary material The online version of this article (10.1186/s40168-018-0554-9) contains supplementary material, which is available to authorized users.
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- 2018
15. Factors Associated with Pre-Hospital Delay and Intravenous Thrombolysis in China
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Wenjie Gong, Rongfang Shi, Xia Zhang, Cao Xiaowei, Shoujiang You, Yongjun Cao, Xiaojun Huang, Yafang Zhu, Yan Qin, and Xuan Wang
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Male ,China ,medicine.medical_specialty ,Time Factors ,Referral ,medicine.medical_treatment ,Logistic regression ,Risk Assessment ,Time-to-Treatment ,03 medical and health sciences ,0302 clinical medicine ,Fibrinolytic Agents ,Risk Factors ,medicine ,Humans ,Thrombolytic Therapy ,Prospective Studies ,Acute ischemic stroke ,Univariate analysis ,business.industry ,Rehabilitation ,Atrial fibrillation ,Thrombolysis ,Emergency department ,Middle Aged ,medicine.disease ,Service model ,Stroke ,Early Diagnosis ,Transportation of Patients ,Treatment Outcome ,Emergency medicine ,Administration, Intravenous ,Female ,Surgery ,Neurology (clinical) ,Emergency Service, Hospital ,Cardiology and Cardiovascular Medicine ,business ,030217 neurology & neurosurgery - Abstract
Background Pre-hospital delay was a critical factor affecting stroke patients receiving intravenous thrombolytic therapy. The aim of this study was to explore the factors associated with pre-hospital delay and thrombolysis in China. Methods Patient data were obtained from emergency department (ED), and the factors of patient pre-hospital delay were recorded through a well-designed form. Results A total of 630 patients were eventually included in the study. 317 patients were admitted to the ED during the thrombolysis time window, and only 105 patients received intravenous thrombolytic therapy. In the univariate analysis, transportation (OR: 0.15; 95% CI: 0.44 - 0.518; p = 0.001), atrial fibrillation (OR: 0.555; 95% CI: 0.372-0.828; p = 0.004) and response of symptoms (OR: 0.002; 95% CI: 0.000-0.013; p = 0.000) were associated with early arrival. Speech disturbances (OR: 2.095; 95% CI: 1.294-3.391; p = 0.002), smoking (OR: 2.563; 95% CI: 1.527-4.304; p = 0.000), alcohol consumption (OR: 2.155; 95% CI: 1.159-4.005; p = 0.014) and referral presentation (OR: 2.837; 95% CI: 1.584-5.082; p = 0.000) were associated with thrombolysis. In the logistic regression analysis, direct visiting to the hospital after onset and rushing to emergency after onset were independent predictor of early arrival of AIS and intravenous thrombolytic. Conclusions The pre-hospital delay of acute ischemic stroke in China was still serious. Strengthening the ability to identify stroke-related symptoms and establishing a mutual referral medical support service model between lower and upper hospitals may effectively shorten the pre-hospital delay of stroke patients.
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- 2020
16. Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance
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Xiaobing Zhang, Qi Jin, Lilian Sun, Yafang Zhu, Sarah M. Fortune, Yonatan H. Grad, Zhili Chang, Yanlin Zhao, Jie Dong, Jian Yang, Bing Zhao, Yang Zhou, Nathan D. Hicks, Shengfen Wang, Liguo Liu, Hui Xia, and Xichao Ou
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0301 basic medicine ,Microbiology (medical) ,China ,Tuberculosis ,Multidrug tolerance ,medicine.drug_class ,Immunology ,Antibiotics ,Antitubercular Agents ,Genome-wide association study ,Drug resistance ,Applied Microbiology and Biotechnology ,Microbiology ,Mycobacterium tuberculosis ,03 medical and health sciences ,Antibiotic resistance ,Bacterial Proteins ,Drug tolerance ,Drug Resistance, Multiple, Bacterial ,Tuberculosis, Multidrug-Resistant ,Genetics ,medicine ,Isoniazid ,Humans ,biology ,Macrophages ,Cell Biology ,biology.organism_classification ,medicine.disease ,3. Good health ,030104 developmental biology ,Mutation ,Acyl Coenzyme A ,Propionates ,Genome-Wide Association Study - Abstract
The global epidemic of drug-resistant tuberculosis is a catastrophic example of how antimicrobial resistance is undermining the public health gains made possible by combination drug therapy. Recent evidence points to unappreciated bacterial factors that accelerate the emergence of drug resistance. In a genome-wide association study of Mycobacterium tuberculosis isolates from China, we find mutations in the gene encoding the transcription factor prpR enriched in drug-resistant strains. prpR mutations confer conditional drug tolerance to three of the most effective classes of antibiotics by altering propionyl-CoA metabolism. prpR-mediated drug tolerance is carbon-source dependent, and while readily detectable during infection of human macrophages, is not captured by standard susceptibility testing. These data define a previously unrecognized and clinically prevalent class of M. tuberculosis variants that undermine antibiotic efficacy and drive drug resistance.
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- 2018
17. Effectiveness of different targeted temperature management methods for fever in patients with acute cerebral infarction
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Deng Taosheng, Yafang Zhu, Meng Cao, Qindi Zhang, Chunlan Zhou, Xiaomei Zhang, and Pan Suyue
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business.industry ,medicine.medical_treatment ,Significant difference ,Rectal temperature ,Targeted temperature management ,Ibuprofen ,Group B ,Anesthesia ,Acute cerebral infarction ,Medicine ,In patient ,business ,Human body temperature ,medicine.drug - Abstract
Objectives: To observe the effectiveness of different targeted temperature management (TTM) methods in patients with acute cerebral infarction (ACI) and explore the most feasible cooling strategies for ACI. Methods: We retrospectively analyzed the effectiveness of different TTM strategies for ACI patients treated in the Neuointensive Care Unit of South Hospital of Southern Medical University from June 1, 2012 to May 31, 2015. Patients were divided into four groups according to the presence or absence of fever and the cooling method: control group (n=63, normal body temperature), group A (ibuprofen alone, n=53), group B (ice bag alone, n=49), and group AB (ibuprofen + ice bag, n=62). We measured rectal temperature at admission and 1 h, 2 h, 4 h, 6 h, 12 h, 48 h and 72 h after admission in the control group. In groups A, B, and AB, we measured rectal temperature immediately after cooling and 1 h, 2 h, 4 h, 6 h, 12 h, 48 h, and 72 h after cooling. Results: Body temperature showed no significant difference immediately after cooling among groups A, B, and AB (P>0.05); however, cooling effectiveness was significantly different at multiple time points after cooling (P
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- 2017
18. Co-occurrence of amikacin-resistant and -susceptible Mycobacterium tuberculosis isolates in clinical samples from Beijing, China
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Guanglu Jiang, Junping Peng, Xiaobing Zhang, Qi Jin, Yanlin Zhao, Bing Zhao, Yafang Zhu, Liguo Liu, Hairong Huang, and Guangming Dai
- Subjects
Microbiology (medical) ,China ,Tuberculosis ,Genotype ,Capreomycin ,medicine.drug_class ,Antibiotics ,Antitubercular Agents ,Microbiology ,Mycobacterium tuberculosis ,Beijing ,Drug Resistance, Bacterial ,medicine ,Humans ,Pharmacology (medical) ,Amikacin ,Pharmacology ,biology ,business.industry ,Aminoglycoside ,Kanamycin ,medicine.disease ,biology.organism_classification ,Virology ,Molecular Typing ,Phenotype ,Infectious Diseases ,business ,medicine.drug - Abstract
Received 10 August 2012; returned 4 October 2012; revised 6 February 2013; accepted 11 February 2013Objectives: This study examined the phenomenon of heteroresistance in Mycobacterium tuberculosis clinicalisolates obtained from retreated patients in Beijing, China between 2006 and 2011.Methods: The iPLEX Gold assay platform was used to determine the prevalence of heteroresistance to inject-able second-line drugs (amikacin, kanamycin and capreomycin) in resistant isolates.Results: Heteroresistance was identified in 10.9% of 220 phenotypic amikacin-resistant isolates.Conclusions: Heteroresistance was related mainly to the short duration and repeated use of amikacin andcapreomycin during retreatment. These findings further our understanding of the evolution of resistance to in-jectable drugs used for tuberculosis treatment and help guide the rational use of injectable drugs duringtherapy.Keywords: heteroresistance, MDR-TB, aminoglycoside antibiotics, molecular typing
- Published
- 2013
19. Distribution and characteristics of rodent picornaviruses in China
- Author
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Qiyong Liu, Jiang Du, Haoxiang Su, Fan Yang, Yafang Zhu, Liang Lu, Fei Guo, Lilian Sun, Feng Liu, Xianwen Ren, Zhiqiang Wu, Qi Jin, and Jie Dong
- Subjects
0301 basic medicine ,Multidisciplinary ,food.ingredient ,Phylogenetic tree ,Rodent ,biology ,viruses ,Zoology ,medicine.disease_cause ,Genome ,Homology (biology) ,Article ,03 medical and health sciences ,030104 developmental biology ,food ,Genus ,biology.animal ,medicine ,Enterovirus ,Feces ,Hunnivirus - Abstract
Rodents are important reservoir hosts of many important zoonotic viruses. The family Picornaviridae contains clinically important pathogens that infect humans and animals, and increasing numbers of rodent picornaviruses have recently been associated with zoonoses. We collected 574 pharyngeal and anal swab specimens from 287 rodents of 10 different species from eight representative regions of China from October 2013 to July 2015. Seven representative sequences identified from six rodent species were amplified as full genomes and classified into four lineages. Three lineage 1 viruses belonged to a novel genus of picornaviruses and was more closely related to Hepatovirus than to others genera of picornaviruses based on aa homology. Lineage 2, lineage 3, and lineage 4 viruses belonged to the genera Rosavirus, Hunnivirus, and Enterovirus, respectively, representing new species. According to both phylogenetic and identity analyses, Lineage 2 viruses had a close relationship with rosavirus 2 which was recovered from the feces of a child in Gambia and Lineage 3 viruses had a close relationship with domestic animal Hunnivirus. Lineage 4 viruses provide the first evidence of these enteroviruses and their evolution in rodent hosts in China.
- Published
- 2016
20. Subpopulation Analysis of Heteroresistance to Fluoroquinolone in Mycobacterium tuberculosis Isolates from Beijing, China
- Author
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Xiaobing Zhang, Yafang Zhu, Bing Zhao, Liguo Liu, Yanlin Zhao, and Qi Jin
- Subjects
Microbiology (medical) ,China ,Tuberculosis ,Genotype ,Epidemiology ,Antitubercular Agents ,Mutation, Missense ,Drug resistance ,Biology ,DNA gyrase ,Microbiology ,Mycobacterium tuberculosis ,Molecular typing ,Bacterial Proteins ,Beijing ,Drug Resistance, Bacterial ,Tuberculosis, Multidrug-Resistant ,medicine ,Humans ,In patient ,Tuberculosis, Pulmonary ,Sequence Analysis, DNA ,medicine.disease ,biology.organism_classification ,Virology ,Molecular Typing ,Phenotype ,DNA Gyrase ,Fluoroquinolones - Abstract
The presence of heteroresistance was represented by 23% of 235 fluoroquinolone (FQ)-resistant Mycobacterium tuberculosis isolates in Beijing, China, from 2008 to 2010. The main mechanism of FQ heteroresistance is due to the segregation of a single M. tuberculosis strain in patients; the majority of isolates with multidrug-resistant tuberculosis contained a mixture of bacterial subpopulations consisting of various mutant types, suggesting that the improper use of FQ is the major cause of FQ resistance.
- Published
- 2012
21. Rapid genome sequencing and characterization of novel avian-origin influenza A H7N9 virus directly from clinical sample by semiconductor sequencing
- Author
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Yongfeng Hu, Xi Zhang, Fan Yang, Lilian Sun, Yan Xiao, Jie Dong, Yafang Zhu, Qi Jin, Xianwen Ren, and Li Li
- Subjects
Genetics ,Cancer genome sequencing ,Male ,Sequence Analysis, RNA ,Sequence assembly ,High-Throughput Nucleotide Sequencing ,Ion semiconductor sequencing ,Genome, Viral ,Biology ,medicine.disease_cause ,Influenza A Virus, H7N9 Subtype ,DNA sequencing ,Deep sequencing ,Infectious Diseases ,Virology ,Novel virus ,Influenza, Human ,Influenza A virus ,medicine ,Humans ,RNA, Viral ,Exome sequencing ,Phylogeny ,Aged - Abstract
Background Recent outbreaks of severe pneumonia or acute respiratory distress syndrome have attracted much public interest. Rapid and accurate diagnosis of the causative agent is key for an adequate response to suspected outbreaks. Objectives We report a case that highlights the potential of semiconductor sequencing to rapidly determine the novel virus genome sequences. Study design We have developed a method for rapid de novo assembly of the novel influenza A H7N9 virus genome directly from the tracheal aspirate of a patient using semiconductor sequencer without culture and prior sequence information. Further, characteristic amino acids were analyzed and phylogenetic analysis were done for key genes of the influenza A virus. Results Deep sequencing yielded 435,239 reads assigned to H7N9 viruses, with an average length of 172 bp, accounting for 18.6% of total reads (2,339,680). Complete genome of the virus was obtained by de novo assembly method within 2 days. Genomic average depth of coverage of the Ion Torrent PGM was up to 5679 fold. Selected characteristic amino acids were observed, and phylogenetic analyses showed that the novel H7 virus was genetically close to 2011 duck H7N3 viruses in Zhejiang. The novel N9 sequences were most closely related to gene sequences of N9 derived from ducks H11N9 in 2011 in Jiangxi and H2N9 sequences from Hong Kong in 2010, in China, and therefore they may share a common ancestor. Conclusions The sequence-independent semiconductor sequencing is a powerful tool to investigate outbreak of a novel pathogen.
- Published
- 2015
22. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery
- Author
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Shuxia Chen, Boqin Qiang, Huan Nie, Xiaobing Zhang, Qi Jin, Jun Yu, Junping Peng, Fan Yang, Yu-Mei Wen, Yan Jiang, Zhijian Yao, Lilian Sun, Yan Shen, Yafang Zhu, Xingye Xu, Jian Yang, Xudong Tang, Jie Dong, Yongliang Yan, Zhenghong Yuan, Ying Xue, Jianguo Xu, Zhaohui Xiong, Lihong Chen, Yunde Hou, Yu Wang, and Jing Wang
- Subjects
Shigella dysenteriae ,Virulence ,medicine.disease_cause ,Article ,Microbiology ,03 medical and health sciences ,Shigella flexneri ,Genetics ,medicine ,Shigella ,Shigella sonnei ,Enteroinvasive Escherichia coli ,030304 developmental biology ,Shigella boydii ,Dysentery, Bacillary ,Comparative genomics ,0303 health sciences ,biology ,030306 microbiology ,Genetic Variation ,biology.organism_classification ,3. Good health ,DNA Transposable Elements ,Gene Deletion ,Genome, Bacterial ,Pseudogenes - Abstract
The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.
- Published
- 2005
23. Novel SARS-like Betacoronaviruses in Bats, China, 2011
- Author
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Junpeng Zhang, Jie Dong, Qi Jin, Shuyi Zhang, Yafang Zhu, Xianwen Ren, Lilian Sun, Zhiqiang Wu, Li Yang, Jiang Du, Fan Yang, and Guimei He
- Subjects
Microbiology (medical) ,China ,animal structures ,Genes, Viral ,Epidemiology ,Expedited ,Molecular Sequence Data ,bats ,Zoology ,lcsh:Medicine ,SARS virus ,Genome, Viral ,Biology ,medicine.disease_cause ,Genome ,lcsh:Infectious and parasitic diseases ,Sars virus ,Rhinolophus pusillus ,Phylogenetics ,Chiroptera ,medicine ,Animals ,Humans ,viruses ,lcsh:RC109-216 ,Phylogeny ,Coronavirus ,lcsh:R ,Dispatch ,High-Throughput Nucleotide Sequencing ,Insectivore ,Chaerephon plicata ,biology.organism_classification ,Infectious Diseases - Abstract
To clarify the evolutionary relationships among betavoronaviruses that infect bats, we analyzed samples collected during 2010–2011 from 14 insectivorous bat species in China. We identified complete genomes of 2 novel betacoronaviruses in Rhinolophus pusillus and Chaerephon plicata bats, which showed close genetic relationships with severe acute respiratory syndrome coronaviruses.
- Published
- 2013
24. Complete Genome Sequence of Neisseria meningitidis Serogroup A Strain NMA510612, Isolated from a Patient with Bacterial Meningitis in China
- Author
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Yafang Zhu, Qi Jin, Yan Zhang, Li Xu, Bo Liu, Xiaobing Zhang, Zhujun Shao, and Jian Yang
- Subjects
Whole genome sequencing ,Neisseria meningitidis serogroup ,Strain (biology) ,Neisseria meningitidis ,Biology ,biology.organism_classification ,medicine.disease_cause ,Genome ,Microbiology ,Pandemic ,Genotype ,Genetics ,medicine ,Prokaryotes ,Molecular Biology ,Bacteria - Abstract
Serogroup A meningococcal strains have been involved in several pandemics and a series of epidemics worldwide in the past. Determination of the genome sequence of the prevalent genotype strain will help us understand the genetic background of the evolutionary and epidemiological properties of these bacteria. We sequenced the complete genome of Neisseria meningitidis NMA510612, a clinical isolate from a patient with meningococcal meningitis.
- Published
- 2014
25. MERS-related betacoronavirus in Vespertilio superans bats, China
- Author
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Jie Dong, Shuyi Zhang, Qi Jin, Junpeng Zhang, Guimei He, Xianwen Ren, Zhiqiang Wu, Fan Yang, Yafang Zhu, Lilian Sun, and Li Yang
- Subjects
Microbiology (medical) ,China ,reservoir ,Letter ,Vespertilio superans ,MERS–related betacoronavirus ,Epidemiology ,Middle East respiratory syndrome coronavirus ,coronavirus ,lcsh:Medicine ,bat ,Genome, Viral ,Biology ,medicine.disease_cause ,lcsh:Infectious and parasitic diseases ,MERS-CoV ,lineage C betacoronavirus ,Phylogenetics ,Chiroptera ,medicine ,Animals ,lcsh:RC109-216 ,viruses ,Letters to the Editor ,Phylogeny ,Genetics ,Whole genome sequencing ,Phylogenetic tree ,lcsh:R ,sequencing ,betacoronaviruses ,medicine.disease ,biology.organism_classification ,Virology ,Infectious Diseases ,GenBank ,Novel virus ,Middle East Respiratory Syndrome Coronavirus ,Middle East respiratory syndrome ,Middle East respiratory syndrome coronavirus–related betacoronavirus ,Coronavirus Infections ,Betacoronavirus ,lineage - Abstract
To the Editor: Middle East respiratory syndrome coronavirus (MERS-CoV), a novel lineage C betacoronavirus, was first described in September 2012, and by April 16, 2014, the virus had caused 238 infections and 92 deaths in humans worldwide (1). Antibodies against MERS-CoV in dromedary camels were recently reported (2), as was the full genome of MERS-CoV from dromedary camels (3). Finding the natural reservoir of MERS-CoV is fundamental to our ability to control transmission of this virus to humans (4). We report a novel lineage C betacoronavirus identified from Vespertilio superans bats in China. The full-length genome of this betacoronavirus showed close genetic relationship with MERS-CoV. Together with other evidence of MERS-CoV–related viruses in bats (5–8), our findings suggest that bats might be the natural reservoirs of MERS-related CoVs. In June 2013, we collected anal swab samples from 32 V. superans bats from southwestern China. A small proportion of each sample was pooled (without barcoding) and processed by using virus particle–protected nucleic acid purification and sequence-independent PCR for next-generation sequencing analysis with the Illumina (Solexa) Genome Analyzer II (Illumina, San Diego, CA, USA). Redundant reads were filtered, as described (9), from the raw sequencing reads generated by the genome analyzer and then aligned with the nonredundant protein database of the National Center for Biotechnology Information (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) by using BLAST (http://blast.ncbi.nlm.nih.gov). The taxonomy of these aligned reads was parsed by using MEGAN 4 (http://ab.inf.uni-tuebingen.de/software/megan/). On the basis of the BLAST results, 8,751,354 sequence reads 81 nt in length were aligned with the protein sequences of the nonredundant protein database: 72,084 of the reads were uniquely matched with virus proteins. Of these 72,084 reads, 32,365 were assigned to the family Coronaviridae, primarily to lineage C of the genus Betacoronavirus, and found to share 60%–97% aa identity with MERS-CoV. The MERS-CoV–related reads were extracted and assembled by using SeqMan software from the Lasergene 7.1.0 program (DNASTAR, Madison, WI, USA), resulting in a draft CoV genome. Reverse transcription PCR selective for the partial RNA-dependent RNA polymerase (RdRp) gene of this novel lineage C betacoronavirus suggested that 5 of the 32 samples (≈16%) were positive for the novel betacoronavirus, and the PCR amplicons shared >98% nt identity with each other. Using a set of overlapped nested PCRs and the rapid amplification of cDNA ends method, we determined the full-length genome of 1 strain of this V. superans bat–derived betacoronavirus (referred to as BtVs-BetaCoV/SC2013, GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"KJ473821","term_id":"627792518","term_text":"KJ473821"}}KJ473821). The betacoronavirus strain had a genome length of 30,413 nt, excluding the 3′ poly (A) tails, and a G+C content of 43.1%. Pairwise genome sequence alignment, conducted by the EMBOSS Needle software (http://www.ebi.ac.uk/Tools/psa/emboss_needle/) with default parameters, suggested that the genome sequence of BtVs-BetaCoV/SC2013 showed 75.7% nt identity with that of human MERS-CoV (hCoV-MERS); this shared identity is higher than that for other lineage C betacoronaviruses (from bats and hedgehogs) with full genomes available. hCoV-MERS showed 69.9% nt identity with bat CoV (BtCoV) HKU4-1, 70.1% nt identity with BtCoV-HKU5-1, and 69.6% nt identity with hedgehog CoV EriCoV-2012–174. Compared with those lineage C betacoronaviruses, which had an 816-bp partial RdRp sequence fragment available, BtVs-BetaCoV/SC2013 shared 96.7 % aa identity with hCoV-MERS. Pipistrellus BtCoVs found in Europe (BtCoV-8-724, BtCoV-8-691, BtCoV-UKR-G17) shared 98.2 % aa identity with hCoV-MERS, and Eptesicus BtCoV found in Italy (BtCoV-ITA26/384/2012) and other lineage C betacoronaviruses shared 96.3 % aa and
- Published
- 2014
26. Full Genome of Influenza A (H7N9) Virus Derived by Direct Sequencing without Culture
- Author
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Jian Yang, Jie Dong, Li Li, Yongfeng Hu, Qi Jin, Yan Xiao, Jianwei Wang, Lilian Sun, Xianwen Ren, Fan Yang, Ting Zhang, Yafang Zhu, and Liguo Liu
- Subjects
Microbiology (medical) ,China ,Epidemiology ,viruses ,Molecular Sequence Data ,lcsh:Medicine ,culture-free ,Hemagglutinin Glycoproteins, Influenza Virus ,Chick Embryo ,Genome, Viral ,Biology ,Influenza A Virus, H7N9 Subtype ,medicine.disease_cause ,Genome ,avian-origin ,Virus ,Deep sequencing ,lcsh:Infectious and parasitic diseases ,H7N9 ,deep sequencing ,Phylogenetics ,Influenza, Human ,Influenza A virus ,medicine ,Animals ,Humans ,influenza A virus ,lcsh:RC109-216 ,Phylogeny ,Genetics ,Viral culture ,lcsh:R ,Sputum ,Dispatch ,Embryonated ,High-Throughput Nucleotide Sequencing ,Sequence Analysis, DNA ,direct sequencing ,Middle Aged ,Virology ,Infectious Diseases ,Female ,medicine.symptom ,influenza - Abstract
An epidemic caused by influenza A (H7N9) virus was recently reported in China. Deep sequencing revealed the full genome of the virus obtained directly from a patient’s sputum without virus culture. The full genome showed substantial sequence heterogeneity and large differences compared with that from embryonated chicken eggs.
- Published
- 2013
27. Genotypic analysis of serogroups other than A, B or C of Neisseria meningitidis in China
- Author
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Xingye Xu, Xiaobing Zhang, Yafang Zhu, Yu Wang, Machao Li, Xiaofeng Liang, Jie Yang, Zhujun Shao, Qi Jin, Jianguo Xu, Lei Xu, and Li Yang
- Subjects
Microbiology (medical) ,China ,Genotype ,Neisseria meningitidis ,Meningococcal disease ,medicine.disease_cause ,Microbiology ,Neisseria meningitidis, Serogroup W-135 ,medicine ,Humans ,Statistical analysis ,Typing ,General Immunology and Microbiology ,biology ,General Medicine ,Sequence types ,bacterial infections and mycoses ,biology.organism_classification ,medicine.disease ,Meningococcal Infections ,Infectious Diseases ,Multilocus sequence typing ,Neisseriaceae ,Neisseria meningitidis, Serogroup Y - Abstract
To serologically and genetically characterize other serogroups (except A, B, and C) of Neisseria meningitidis isolates in China, we collected 56 strains of other serogroups, identified by serogroup typing and multilocus sequence typing (MLST). All of them are non-invasive isolates. The serogroups of the 56 Chinese isolates were W135 (11 isolates), Y (4), X (15), 29E (15), D (1), H (4), I (3), K (2), and non-groupable (1). By MLST, 34 different sequence types (STs) were identified, 28 of which were not found in the MLST database as of July 2006 and seemed to be unique to China. Statistical analysis of the MLST results revealed that, although the Chinese isolates seemed to be genetically divergent, they could be classified into 5 major clonal groups and other minor groups. Among these isolates, none of the well-documented ST complexes found worldwide was present.
- Published
- 2007
28. The outer membrane phospholipase A is essential for membrane integrity and type III secretion in Shigella flexneri
- Author
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Jian Yang, Bo Liu, Jie Dong, Feng Jiang, Xia Wang, Lilian Sun, Qi Jin, Lihong Chen, Jianhua Zheng, Yafang Zhu, and Guowei Yang
- Subjects
0301 basic medicine ,030106 microbiology ,Immunology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Type three secretion system ,Microbiology ,03 medical and health sciences ,Shigella flexneri ,shigella flexneri ,medicine ,Secretion ,lcsh:QH301-705.5 ,Escherichia coli ,host cell invasion ,cell membranes ,biology ,Research ,General Neuroscience ,Periplasmic space ,biology.organism_classification ,Cell biology ,lcsh:Biology (General) ,Membrane protein ,Cell envelope ,Bacterial outer membrane ,phospholipase a ,Research Article - Abstract
Outer membrane phospholipase A (OMPLA) is an enzyme located in the outer membrane of Gram-negative bacteria. OMPLA exhibits broad substrate specificity, and some of its substrates are located in the cellular envelope. Generally, the enzymatic activity can only be induced by perturbation of the cell envelope integrity through diverse methods. Although OMPLA has been thoroughly studied as a membrane protein in Escherichia coli and is constitutively expressed in many other bacterial pathogens, little is known regarding the functions of OMPLA during the process of bacterial infection. In this study, the proteomic and transcriptomic data indicated that OMPLA in Shigella flexneri , termed PldA, both stabilizes the bacterial membrane and is involved in bacterial infection under ordinary culture conditions. A series of physiological assays substantiated the disorganization of the bacterial outer membrane and the periplasmic space in the ΔpldA mutant strain. Furthermore, the ΔpldA mutant strain showed decreased levels of type III secretion system expression, contributing to the reduced internalization efficiency in host cells. The results of this study support that PldA, which is widespread across Gram-negative bacteria, is an important factor for the bacterial life cycle, particularly in human pathogens.
- Published
- 2016
29. Common changes in global gene expression induced by RNA polymerase inhibitors in Shigella flexneri
- Author
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Xiaobing Zhang, Hongxuan He, Hua Fu, Lina Zhao, Junping Peng, Liguo Liu, Qi Jin, and Yafang Zhu
- Subjects
Drugs and Devices ,Drug Research and Development ,lcsh:Medicine ,Biology ,Real-Time Polymerase Chain Reaction ,Biochemistry ,Microbiology ,Shigella flexneri ,Molecular Genetics ,chemistry.chemical_compound ,Plasmid ,Bacterial Proteins ,RNA polymerase ,Gene expression ,Molecular Cell Biology ,Genetics ,lcsh:Science ,Gene ,Regulation of gene expression ,Multidisciplinary ,Virulence ,Gene Expression Profiling ,lcsh:R ,Computational Biology ,DNA-Directed RNA Polymerases ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Microarray Analysis ,Anti-Bacterial Agents ,Gene expression profiling ,Regulon ,chemistry ,Protein Biosynthesis ,Medicine ,lcsh:Q ,Research Article ,Biotechnology - Abstract
Characterization of expression profile of organisms in response to antimicrobials provides important information on the potential mechanism of action of the drugs. The special expression signature can be used to predict whether other drugs act on the same target. Here, the common response of Shigella flexneri to two inhibitors of RNA polymerase was examined using gene expression profiling. Consistent with similar effects of the two drugs, the gene expression profiles indicated that responses of the bacteria to these drugs were roughly the same, with 225 genes affected commonly. Of them, 88 were induced and 137 were repressed. Real-time PCR was performed for selected genes to verify the microarray results. Analysis of the expression data revealed that more than 30% of the plasmid-encoded genes on the array were up-regulated by the antibiotics including virF regulon, other virulence-related genes, and genes responsible for plasmid replication, maintenance, and transfer. In addition, some chromosome-encoded genes involved in virulence and genes acquired from horizontal transfer were also significantly up-regulated. However, the expression of genes encoding the beta-subunit of RNA polymerase was increased moderately. The repressed genes include those that code for products associated with the ribosome, citrate cycle, glycolysis, thiamine biosynthesis, purine metabolism, fructose metabolism, mannose metabolism, and cold shock proteins. This study demonstrates that the two antibiotics induce rapid cessation of RNA synthesis resulting in inhibition of translation components. It also indicates that the production of virulence factors involved in intercellular dissemination, tissue invasion and inflammatory destruction may be enhanced through derepressing horizontal transfer genes by the drugs.
- Published
- 2012
30. Diagnosis of pulmonary disease caused by Mycobacterium abscessus: a case report
- Author
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Yafang Zhu, Yanping Zhang, Yonghong Li, P Zhao, and Kanglin Wan
- Subjects
Male ,medicine.drug_class ,Antitubercular Agents ,Disease ,Mycobacterium abscessus ,Antimycobacterial ,Biochemistry ,Polymerase Chain Reaction ,Microbiology ,law.invention ,Mycobacterium ,law ,medicine ,Humans ,Polymerase chain reaction ,DNA Primers ,Mycobacterium Infections ,Bronchiectasis ,biology ,Base Sequence ,business.industry ,Biochemistry (medical) ,Cell Biology ,General Medicine ,Middle Aged ,bacterial infections and mycoses ,biology.organism_classification ,rpoB ,medicine.disease ,Radiography ,bacteria ,Differential diagnosis ,business ,Polymorphism, Restriction Fragment Length - Abstract
Mycobacterium abscessus ( M. abscessus) is a non-tuberculous mycobacterium and an important emerging pathogen causing skin, soft tissue and pulmonary infections. The case of a 59-year-old man with a history of pulmonary tuberculosis (TB) and current pulmonary infection due to M. abscessus, complicated with pneumocardial disease and bronchiectasis, is described. Zhiel—Neelsen stain and acid Lowenstein—Jensen culture were both positive for acid-fast bacillus. The patient was initially misdiagnosed and ineffectively treated for pulmonary TB. Antimycobacterial susceptibility tests found the isolate to be resistant to four first-line and seven second-line antituberculosis drugs. The isolate was finally identified as M. abscessus using 16S ribosomal RNA and hsp65 and rpoB gene sequence analysis. Species of mycobacterium should be included in the differential diagnosis when patients do not respond to standard antituberculosis therapy. Molecular methods are useful for rapid and species-specific identification.
- Published
- 2011
31. Distribution of surface-protein variants of hyperinvasive meningococci in China
- Author
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Junping Peng, Jianguo Xu, Yafang Zhu, Li Yang, Jie Dong, Qi Jin, and Xiaobing Zhang
- Subjects
Microbiology (medical) ,clone (Java method) ,DNA, Bacterial ,China ,Molecular Sequence Data ,Porins ,Biology ,Meningitis, Meningococcal ,Neisseria meningitidis ,medicine.disease_cause ,Meningococcal disease ,Genetic analysis ,Microbiology ,Genotype ,medicine ,Antigenic variation ,Humans ,Genetics ,Molecular epidemiology ,Membrane Proteins ,Sequence Analysis, DNA ,medicine.disease ,Antigenic Variation ,Infectious Diseases ,Surface protein ,Bacterial Outer Membrane Proteins - Abstract
Summary Objective Information regarding the different types of FetA and PorB meningococci that circulate in various regions of the world is still scarce. The present study investigated the distribution of FetA and PorB variable region (VR) types among meningococci belonging to hyperinvasive lineages circulating in China. Methods The approach consisted of genotypic analysis of 201 Neisseria meningitidis strains belonging to hyperinvasive lineages isolated in China during the period 1956–2006. Results Sixteen different PorB types were found, 8 of which were newly identified. Of the 24 different FetA VR types, 3 were determined to be novel. Particular combinations of FetA and PorB types associated with distinct clonal complexes were also observed. Most cases of invasive disease were caused by five individual clones: A: P1.7-1,10: F5-5: ST-3 (cc1) with P3.6,11,10,7 (class 3 PorB protein; VR1-6, VR2-11, VR3-10, and VR4-7); A: P1.20,9: F3-1: ST-5 (cc5) with P3.4,11,10,7; A: P1.20,9: F3-1: ST-5 (cc5) with P3.9,11,10,7; A: P1.20,9: F3-1: ST-7 (cc5) with P3.4,11,10,7; and C: P1.7-2,14: F3-3: ST-4821 (cc4821) with P3.9,15,6,7. Conclusion A number of antigen–gene variants and combinations exhibited broad temporal and geographic distributions, although several invasive clones were mainly associated with a specified timeframe. The changes that are increasingly emerging in circulating strains and the prevalent clone replacement describe the molecular epidemiology of meningococcal disease in China. Our findings have implications for both public-health monitoring and further study of this organism.
- Published
- 2008
32. Revisiting the molecular evolutionary history of Shigella spp
- Author
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Jun Yu, Yafang Zhu, Fan Yang, Huan Nie, Jian Yang, Xingye Xu, Xiaobing Zhang, Qi Jin, and Lihong Chen
- Subjects
Operon ,Biology ,medicine.disease_cause ,Genome ,Polymerase Chain Reaction ,Evolution, Molecular ,Plasmid ,Phylogenetics ,Genetics ,medicine ,Escherichia coli ,Shigella ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Phylogenetic tree ,Virulence ,Genetic Variation ,Chromosomes, Bacterial ,Housekeeping gene ,Genes, Bacterial ,Genome, Bacterial ,Plasmids - Abstract
The theory that Shigella is derived from multiple independent origins of Escherichia coli (Pupo et al. 2000) has been challenged by recent findings that the virulence plasmids (VPs) and the chromosomes share a similar evolutionary history (Escobar-Paramo et al. 2003), which suggests that an ancestral VP entered an E. coli strain only once, which gave rise to Shigella spp. In an attempt to resolve these conflicting theories, we constructed three phylogenetic trees in this study: a robust chromosomal tree using 23 housekeeping genes from 46 strains of Shigella and enteroinvasive E. coli (EIEC), a chromosomal tree using 4 housekeeping genes from 19 EcoR strains and 46 Shigella/EIEC strains, and a VP tree using 5 genes outside of the VP cell-entry region from 38 Shigella/EIEC strains. Both chromosomal trees group Shigella into three main clusters and five outliers, and strongly suggest that Shigella has multiple origins within E. coli. Most strikingly, the VP tree shows that the VPs from two main Shigella clusters, C1 and C2, are more closely related, which contradicts the chromosomal trees that place C2 and C3 next to each other but C1 at a distance. Additionally, we have identified a complete tra operon of the F-plasmid in the genome sequence of an EIEC strain and found that two other EIEC strains are also likely to possess a complete tra operon. All lines of evidence support an alternative multiorigin theory that transferable diverse ancestral VPs entered diverse origins of E. coli multiple times during a prolonged period of time, resulting in Shigella species with diverse genomes but similar pathogenic properties.
- Published
- 2006
33. Genetic characteristics of human enterovirus 71 and coxsackievirus A16 circulating from 1999 to 2004 in Shenzhen, People's Republic of China
- Author
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Yaqing He, Junping Zhu, Yafang Zhu, Linlin Li, Xingye Xu, Jie Dong, Qi Jin, and Hong Yang
- Subjects
Microbiology (medical) ,Mainland China ,Genetics ,Phylogenetic tree ,Genotype ,Reverse Transcriptase Polymerase Chain Reaction ,Lineage (evolution) ,Strain (biology) ,Sequence Analysis, DNA ,Biology ,medicine.disease_cause ,medicine.disease ,Virology ,Phylogenetics ,medicine ,Coinfection ,Enterovirus ,Humans ,Hand, Foot and Mouth Disease ,Phylogeny - Abstract
The genetic and phylogenetic characteristics of human enterovirus 71 (EV71) and coxsackievirus A16 (CA16) sampled from children with hand, foot, and mouth disease in Shenzhen, People's Republic of China, over a 6-year period (1999 to 2004) were examined with reverse transcription-PCR and DNA sequencing. Out of 147 stool specimens, 60 showed positive signals when screened with EV71- and CA16-specific primers. EV71 was identified in 19 specimens, and CA16 was identified in 41 specimens; coinfection by EV71 and CA16 was not observed. Phylogenetic analysis of all EV71 strains isolated from the mainland Chinese samples established C4 as the predominant genotype. Only one other known strain (3254-TAI-98; AF286531), isolated in Taiwan in 1998, was identified as belonging to genotype C4. Phylogenetic analysis of CA16 strains allowed us to identify three new genetic lineages (A, B, and C), with lineage C recently predominating in Asian countries, such as the People's Republic of China, Malaysia, and Japan. These new observations indicate that CA16 circulating in the People's Republic of China is genetically diverse, and additional surveillance is warranted.
- Published
- 2005
34. Complete Genome Sequence of the Neonatal-Meningitis-Associated Escherichia coli Strain CE10
- Author
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Kwang Sik Kim, Jian Yang, Shuting Lu, Yafang Zhu, Xiaobing Zhang, and Qi Jin
- Subjects
Whole genome sequencing ,Base Sequence ,Meningitis, Escherichia coli ,Strain (chemistry) ,Escherichia coli Proteins ,Molecular Sequence Data ,Infant, Newborn ,Biology ,medicine.disease ,medicine.disease_cause ,Microbiology ,Genome ,Virology ,Genome Announcements ,Neonatal meningitis ,Pathogenesis ,Escherichia coli ,medicine ,Humans ,Molecular Biology ,Meningitis ,Pathogen ,Genome, Bacterial - Abstract
Neonatal bacterial meningitis continues to be an important cause of mortality and morbidity worldwide. Escherichia coli possessing the K1 capsular polysaccharide is the most common Gram-negative pathogen causing neonatal meningitis. Here we present the complete genome sequence of neonatal meningitis-associated E. coli strain CE10, a unique K1 strain with a functional type III secretion system. Functional analysis of the genome should enhance our knowledge of the pathogenesis of neonatal E. coli K1 meningitis.
- Published
- 2011
35. Genetic diversity of coronaviruses in Miniopterus fuliginosus bats
- Author
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Xianwen Ren, Zhiqiang Wu, Yafang Zhu, Shuyi Zhang, Junpeng Zhang, Fan Yang, Jiang Du, Jie Dong, Lilian Sun, Qi Jin, Li Yang, and Plazi
- Subjects
0301 basic medicine ,Genes, Viral ,Miniopterus pusillus ,Middle East respiratory syndrome coronavirus ,Coronaviridae ,viruses ,coronavirus ,Zoology ,bat ,Miniopterus magnater ,Biology ,medicine.disease_cause ,Alphacoronavirus ,General Biochemistry, Genetics and Molecular Biology ,virus-host ,03 medical and health sciences ,co-infection ,pathogen-host ,Environmental Science(all) ,Chiroptera ,medicine ,Animals ,Viral ,biotic relations ,Viridae ,Phylogeny ,General Environmental Science ,Coronavirus ,Genetic diversity ,Agricultural and Biological Sciences(all) ,Miniopterus ,Biochemistry, Genetics and Molecular Biology(all) ,biotic associations ,corona viruses ,Genetic Variation ,covid ,pathogens ,biology.organism_classification ,biotic interaction ,recombination ,030104 developmental biology ,Miniopterus fuliginosus ,covid-19 ,Genes ,General Agricultural and Biological Sciences ,Research Paper ,CETAF-taskforce - Abstract
Coronaviruses, such as severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus, pose significant public health threats. Bats have been suggested to act as natural reservoirs for both these viruses, and periodic monitoring of coronaviruses in bats may thus provide important clues about emergent infectious viruses. The Eastern bent-wing bat Miniopterus fuliginosus is distributed extensively throughout China. We therefore analyzed the genetic diversity of coronaviruses in samples of M. fuliginosus collected from nine Chinese provinces during 2011–2013. The only coronavirus genus found was Alphacoronavirus. We established six complete and five partial genomic sequences of alphacoronaviruses, which revealed that they could be divided into two distinct lineages, with close relationships to coronaviruses in Miniopterus magnater and Miniopterus pusillus. Recombination was confirmed by detecting putative breakpoints of Lineage 1 coronaviruses in M. fuliginosus and M. pusillus (Wu et al., 2015), which supported the results of topological and phylogenetic analyses. The established alphacoronavirus genome sequences showed high similarity to other alphacoronaviruses found in other Miniopterus species, suggesting that their transmission in different Miniopterus species may provide opportunities for recombination with different alphacoronaviruses. The genetic information for these novel alphacoronaviruses will improve our understanding of the evolution and genetic diversity of coronaviruses, with potentially important implications for the transmission of human diseases.
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