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Identification and Phylogenetic analysis of two canine coronavirus strains

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Animal Diseases 2021年第2期1卷 133-139页

作者： Junji Gan Ye Tang Haifeng Lv Wenbin Xiong Xiaoyan Tian Animal Infectious Disease Laboratory School of Veterinary MedicineYangzhou UniversityYangzhouChina Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis Yangzhou UniversityYangzhouChina Jiangsu Key Laboratory of Zoonosis Yangzhou UniversityYangzhouChina

Canine coronavirus(CCoV),a member of the genus Alphocoronavirus,is an enveloped,single-stranded positive-sense RNA virus that responsible for gastroenteritis in dogs.In this study,two CCoV isolates were successfully propagated from 53 CCoV-positive clinical specimens by serial passaging in A-72 cells.These two strains,CCoV JS1706 and CCoV JS1712,caused cytopathic effects in A-72 cells.The sizes of virus plaque formed by them differed in early passages.Electron microscopy revealed a large quantity of typical coronavirus particles with 80-120 nm in diameter in cell culture media and cytoplasm of infected cells,in which they appeared as inclusion bodies.RT-PCR analysis of 5 gene indicated that these two isolates were belonged to CCoV lla subtype.Homology of RdRp,S,M and N proteins between the two strains were 100,99.6,99.2 and 100.0%,respectively,whereas they were 99.4-100%,83.1-95.2%,88.5-99.2% and 91.9-99.7%identity compared to CCoV II reference strains.Phylogenetic analysis of RdRp,S,M and N protein showed that they were closely related to CCoV II strains.These two subtype lla isolates will be useful for evaluating the pathogenesis and evolution of CCoV and for developing diagnostic reagents and vaccines.

关键词： Canine coronavirus Characterization lla subtype Isolation Phylogenetic analysis

Sequence and Phylogenetic analysis of hemagglutinin genes of H9N2 influenza viruses isolated from chicken in China from 2013 to 2015

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Journal of Integrative Agriculture 2016年第11期15卷 2604-2612页

作者： SU Xiao-na XIE Qing-mei LIAO Chang-tao YAN Zhuan-qiang CHEN Wei-guo BI Ying-zuo CHEN Feng College of Animal Science South China Agricultural University/Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding Guangzhou 510642 P.R. China Guangdong Provincial Key Laboratory of Animal Health Aquaculture and Environmental Control Guangzhou 510642 P.R. China Key Laboratory of Chicken Genetics Breeding and Reproduction Ministry of Agriculture Guangzhou 510642 P.R. China Guangdong Wen's Foodstuffs Group Co. Ltd. Yunfu 527439 P.R. China

H9N2 avian influenza virus（AIV） infection is a major problem in poultry industry worldwide. In this study, molecular characterizations and phylogenetic relationships of hemagglutinin（HA） gene sequences of H9N2 AIV of 5 Chinese isolates in 2014 recently available in Gen Bank, 3 widely used vaccine strains, and 52 novel isolates in China from 2013 to 2015 were analyzed. The homology analysis showed that the nucleotide sequences of HA gene of these recent Chinese H9N2 AIV isolates shared homologies from 94.1 to 99.9%. Phylogenetic analysis showed that all isolates belonged to AIV lineage h9.***.2.5. Fifty-six out of the 57 recent Chinese H9N2 AIV isolates had the motifs PSRSSR↓GLF at the cleavage sites within the HA protein, while one isolate PWH01 harbored LSRSSR↓GLF. Remarkably, all of the recent Chinese H9N2 AIV strains had the Q216 L substitution in the receptor binding site, which indicated that they had potential to infect humans. Most of recent Chinese H9N2 AIV isolates lost the potential N-linked glycosylation site at residues 200–202 compared with vaccine strains. This present study demonstrated that AIV lineage h9.***.2.5 was more predominant in China than other lineages as it harbored all the H9N2 AIV isolated between 2013 and 2015. Also we showed the importance of continuous surveillance of emerging H9N2 AIV in China and update of vaccine formulation accordingly in order to prevent and control H9N2 AIV.

关键词： avian influenza virus H9N2 subtype Phylogenetic analysis hemagglutinin gene

Gene characterization and Phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

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Acta Oceanologica Sinica 2024年第2期43卷 137-150页

作者： Jiangyong Qu Wanqi Yang Xindong Teng Li Xu Dachuan Zhang Zhikai Xing Shuang Wang Xiumei Liu Lijun Wang Xumin Wang College of Life Science Yantai UniversityYantai 264005China Qingdao International Travel Healthcare Center Qingdao 266071China Qingdao Dagang Customs Qingdao 266071China

Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

关键词： mitochondrial genome Phylogenetic analysis Caenogastropoda

Application of Human Adenovirus Genotyping by Phylogenetic analysis in an Outbreak to Identify Nosocomial Infection

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Virologica Sinica 2021年第3期36卷 393-401页

作者： Chuanyu Yang Chunmei Zhu Yuan Qian Jie Deng Baoyuan Zhang Runan Zhu Fang Wang Yu Sun Dongmei Chen Qi Guo Yutong Zhou Lei Yu Ling Cao Linqing Zhao Laboratory of Virology Beijing Key Laboratory of Etiology of Viral Diseases in ChildrenCapital Institute of PediatricsBeijing 100020China Department of Respiratory Medicine Affiliated Children's HospitalCapital Institute of PediatricsBeijing 100020China Hospital Infection-Control Department Affiliated Children’s HospitalCapital Institute of PediatricsBeijing 100020China

Nosocomial infections are common in pediatric patients and can be fatal in infants and immunocompromised patients. In September 2018, a high positive rate of human adenovirus HAdV was occurred among hospitalized children in the Children's Hospital Affiliated to the Capital Institute of Paediatrics in Beijing. To investigate whether this outbreak of HAdV was related to nosocomial infections or the result of community infections, we collected respiratory specimens from patients with acute respiratory infections in a respiratory ward during June to December 2018, and screened for respiratory viruses. Among 1,840 cases included, 95(5.2%, 95/1840) were positive for HAdV and 81 were genotyped based on Phylogenetic analysis, including seven as HAdV-1(8.6%), 30 HAdV-3(37.0%), two HAdV-6(2.5%), and 42 HAdV-7(51.9%). More HAdV-positive samples were collected in August(4.7%, 12/255), September(15.0%, 41/274) and October(6.9%, 17/247), with a peak in September 2018. By combining the results of HAdV Phylogenetic analysis with clinical data of patients, there were 77 cases(4.2%, 77/1840;81.1%, 77/95) excluded from nosocomial infections, eight cases representing possible infections transmitted by visitors or attending parents, three cases without sequences that might have been due to infection transmitted by roommates positive for HAdV, one case of a roommate without an HAdV sequence, and six cases that shared highly homologous sequences with those of their roommates, for which nosocomial infections might be considered. In conclusion, genotyping of HAdVs based on Phylogenetic analysis combined with clinical information provides a powerful method to distinguish nosocomial infections from community acquired infection, especially when tracing the origins of nosocomial infections.

关键词： Acute respiratory tract infection Human adenovirus(HAdV) Phylogenetic analysis Nosocomial infection

Phylogenetic analysis and arsenate reduction effect of the arsenic-reducing bacteria enriched from contaminated soils at an abandoned smelter site

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Journal of Environmental Sciences 2008年第12期20卷 1501-1507页

作者： ZHANG, Xuexia JIA, Yongfeng WANG, Xin XU, Liying Institute of Applied Ecology Chinese Academy of Sciences Shenyang 110016 China Graduate University Chinese Academy of Sciences Beijing 100039 China

Microbial reduction of As(V)(i.e.,arsenate)plays an important role in arsenic(As)mobilization in aqueous environment.In this study,we investigated As(V)reduction characteristics of the bacteria enriched from the arsenic-contaminated soil at an abandoned smelter site.It was found that As(V)was completely reduced to As(III)(i.e.,arsenite)in 21 h.After 3-d incubation,a yellow solid was precipitated and the concentration of As(III)decreased sharply.After 150 h incubation,ca.65%of soluble arsenic was removed fro...

关键词： microbial reduction arsenic Phylogenetic analysis

Comparative mitochondrial genome analysis of Sesarmidae and its phylogenetic implications

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Acta Oceanologica Sinica 2022年第8期41卷 62-73页

作者： Ying Zhang Lei Meng Liming Wei Bingjian Liu Liqin Liu Zhenming Lü Yang Gao Li Gong National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization Zhejiang Ocean UniversityZhoushan 316022China Marine Science and Technology College Zhejiang Ocean UniversityZhoushan 316022China School of Fishery Zhejiang Ocean UniversityZhoushan 316022China

Here,we sequenced the complete mitogenome of Parasesarma eumolpe(Brachyura:Grapsoidea:Sesarmidae)for the first time.The characteristics of this newly sequenced mitogenome were described and compared with other Sesarmidae species.The 15646-bp mitogenome contains 13 protein-coding genes(PCGs),two ribosomal RNA genes(r RNAs),22 transfer RNA genes(t RNAs),and an A-T rich region.All of the PCGs are initiated by the start codon ATN and terminated by the standard TAN codon or an incomplete T.The pairwise Ka/Ks ratio analysis shows that all 13 PCGs are under purifying selection,whereas the ATP8 gene is an outlier,with pairwise comparison values ranging from neutral selection(0.000)to positive selection(1.039).The gene arrangement of P.eumolpe compared with ancestral Decapoda shows the translocation of two t RNAs(t RNA-His and t RNA-Gln),which is identical to other Sesarmidae species.phylogenetic analyses show that all Sesarmidae species are placed into one group,and the polyphyly of Eriphioidea,Ocypodoidea,and Grapsoidea is well supported.The relationship between gaps in the QIM region and the phylogeny of Sesarmidae is analyzed.It is obvious that both the G5(the gap between Q and I)and G6(the gap between I and M)decrease progressively with the evolution process.These results will help to better understand the genomic evolution within Sesarmidae and provide insights into the phylogeny of Brachyura.

关键词： sesarmid crab mitogenome gene rearrangement tandem duplication/random loss Phylogenetic analysis

Identification and Phylogenetic analysis of an Orf Virus Isolated from an Outbreak in Boer Goat in Shanxi Province

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Agricultural Sciences in China 2011年第6期10卷 946-953页

作者： GU Shao-peng SHI Xin-tao SHI Zhong-yong WANG Zhong-bing ZHENG Ming-xue College of Animal Science and Veterinary Medicine Shanxi Agricultural University Taigu 030801 P.R.China Genetically Modified Testing Center Ministry of Agriculture/College of Life Science Shanxi Agricultural Universit Taigu 030801 P.R. China Center for Animal Disease Control and Prevention of Shanxi Province Taiyuan 030024 P.R.China

To identify and analyze the Orf virus in Shanxi Province, China, an Orf virus strain was successfully isolated from crust materials of boer goat with clinical sore mouth symptom from a goat farm of Shanxi Province by passaging in lamb testis （LT）. The Orf virus was identified by enzyme linked immunosorbent assay （ELISA） test, recurrent infection test, transmission electron microscopy, and PCR. The nucleotide and amino acid sequences of two genes of the Orf virus were analyzed. The results showed that under the electron microscopy the virus had a presence of typical parapoxvirus virions and there were many eosinophilic intracytoplasmic inclusions observed by hematoxylin-eosin （H＆E） stain. In ELISA test, optical density （OD） readings of the sample showed a positive result, and the rabbits infected with the virus showed a typically Orf virus-infected appearance. All these findings proved that the sample was an Orf virus. The phylogenetic studies of Orf B2L and Orf F1L genes showed that the virus clustered in different branches and were closer to the Orf virus Nantou （DQ904351） and the OV-SA00 isolates （AY386264）. Furthermore, the above results may provide some insight into the genotype of the etiological agent responsible for the Orf outbreak in Shanxi Province, and could also provide a comparative view of the B2L and F1L genes of parapoxvirus.

关键词： Orf virus boer goat identification Phylogenetic analysis B2L F1L

Nucleotide sequence characterization and Phylogenetic analysis of hantaviruses isolated in Shandong Province,China

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Chinese Medical Journal 2007年第9期120卷 825-830页

作者： LI Jian ZHAO Zhong-tang WANG Zhi-qiang LIU Yun-xi HU Mao-hong Department of Epidemiology and Health Statistics School of Public Health Shandong University Jinan 250012 China Institute for Infectious Disease Control and Prevention Shandong Centre for Disease Control and Prevention Jinan 250014 China Department of Nosocomial Infection Management and Disease Control Beijing Institute of Microbiology and Epidemiology Beijing 100071 China

Background China is the most severe endemic area of hemorrhagic fever with renal syndrome （HFRS） in the world with 30 000-50 000 cases reported annually, which accounts for more than 90% of total number of cases worldwide. The incidence rate of the syndrome in Shandong Province is one of the highest in China, which has ever reached 50 per 100 000 persons per year. However, the molecular characteristics of hantaviruses （HV） epidemic in Shandong Province remain unclear. Therefore it is useful to clarify nucleotide sequence and phylogenetic characteristics of HV isolated in Shandong Province in order to provide better advices to control and prevent HFRS. Methods RNAs were extracted from sera of clinically diagnosed patients and positive rodent lungs that were detected by indirect immunofluorescent assay （IFA）. Partial M segments of HV were amplified from the RNAs with reverse transcription nested polymerase chain reactions （nested PCR） using hantavirus genotype specific primers. The nested PCR products were sequenced and compared with those from previously epidemic isolates in Shandong and with other representative HV sequences from GenBank. phylogenetic tree analyses were performed based on the sequences of the M genes. Results Thirty-four HV isolates in Shandong showed 67.1%-100% nucleotide identities. The nucleotide homologies among 6 Hantaan viruses （HTNV） isolates in Shandong were 78.1%-98.7%, while the homologies among 28 Seoul virus （SEOV） isolates in Shandong were 93.7%-100%. There were at least 3 subtypes HTNV （H2, H5, H9） and 2 subtypes SEOV （S2, S3） in Shandong Province. Conclusions In Shandong Province, the homologies of HTNV were lower and there were no predominant subtypes, while the homologies of SEOV were higher and S3 was the predominant subtype. The homologies of SEOV from rodents were higher than those from patients. The distribution of subtypes in Shandong was similar to that of the adjoining provinces. phylogenetic analyses of the sequences showed geographic clustering of HV in Shandong.

关键词： hantavirus sequence analysis Phylogenetic analysis

Phylogenetic analysis and Expression Patterns of the MAPK Gene Family in Wheat (Triticum aestivum L.)

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Journal of Integrative Agriculture 2012年第8期11卷 1227-1235页

作者： LIAN Wei-wei TANG Yi-miao GAO Shi-qing ZHANG Zhao ZHAO Xin ZHAO Chang-ping Beijing Engineering and Technique Research Center of Hybrid Wheat Beijing Academy of Agricultural and Forestry Sciences Beijing 100097 P.R.China College of Life Science Capital Normal University Beijing 100048 P.R. China

Mitogen activated protein kinases （MAPK） cascades based on protein phosphorylation play an important role in plant growth and development. In this study, we have identified 15 putative members of the wheat MAPK gene （TaMPK） family through an in silico search of wheat expressed sequence tags （EST） databases based on the presence of amino acid sequence of Arabidopsis and rice MAPKs. phylogenetic analyses of MAPKs from wheat, rice and Arabidopsis genomes have classified them into seven subgroups （A, B, C, D, E, F, and G）. Using the available EST information as a source of expression data, the MAPK family genes from Triticum aestivum were detected in diverse tissues. Further expression analysis of the MAPKs in NCBI EST database revealed that their transcripts were most abundant in callus （20%）, followed by leaf （12%） and inflorescence （12%）. Most MAPK family genes showed some tissue specificity.

关键词： wheat MAPK EST Phylogenetic analysis profile