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Influenza A bioinformatics

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https://www.readbyqxmd.com/read/30462955/-genetic-characteristics-of-hemagglutinin-and-neuraminidase-of-avian-influenza-a-h7n9-virus-in-guizhou-province-2014-2017
#1
Y H Wan, L Zhuang, Q N Zheng, L J Ren, L Fu, W J Jiang, G P Tang, D Z Zhang, S J Li
Objective: To understand the molecular characteristics of hemagglutinin (HA) and neuraminidase (NA) as well as the disease risk of influenza virus A H7N9 in Guizhou province. Methods: RNAs were extracted and sequenced from HA and NA genes of H7N9 virus strains obtained from 18 cases of human infection with H7N9 virus and 6 environmental swabs in Guizhou province during 2014-2017. Then the variation and the genetic evolution of the virus were analyzed by using a series of bioinformatics software package. Results: Homology analysis of HA and NA genes revealed that 2 strains detected during 2014-2015 shared 98...
November 10, 2018: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/30427878/an-open-source-k-mer-based-machine-learning-tool-for-fast-and-accurate-subtyping-of-hiv-1-genomes
#2
Stephen Solis-Reyes, Mariano Avino, Art Poon, Lila Kari
For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers...
2018: PloS One
https://www.readbyqxmd.com/read/30402160/distinguishing-the-dominant-species-of-pathogen-in-ethmoidal-sinusitis-by-sequencing-dna-dataset-analysis
#3
Junyi Zhang, Shuai He, Yunchuan Li, Minggang Lv, Hongzheng Wei, Bin Qu, Yani Zheng, Chunhua Hu
Identifying the predominant microbial species in patients with ethmoidal sinusitis is conducive to its successful treatment. The aim of the present study was to determine the microbial composition and the predominant fungal and bacterial species in patients with ethmoidal sinusitis. A sample was obtained from 3 patients with ethmoidal sinusitis and from the ethmoid sinus of 2 healthy volunteers. Those samples were sequenced using an Illumina/Solexa sequencing platform for mapping to human, fungal, and bacterial genomes...
November 2018: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/30391557/insights-into-the-population-structure-and-pan-genome-of-haemophilus-influenzae
#4
M Pinto, A González-Díaz, M P Machado, S Duarte, L Vieira, J A Carriço, S Marti, M P Bajanca-Lavado, J P Gomes
The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies...
October 31, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/30382564/chimeric-protein-consisting-of-3m2e-and-hsp-as-a-universal-influenza-vaccine-candidate-from-in-silico-analysis-to-preliminary-evaluation
#5
Behrokh Farahmand, Najmeh Taheri, Hadiseh Shokouhi, Hoorieh Soleimanjahi, Fatemeh Fotouhi
The 23-amino acid ectodomain of influenza virus M2 protein (M2e) is highly conserved among human influenza virus variants and represents an attractive target for developing a universal vaccine. Although this peptide has limited potency and low immunogenicity, the degree of M2e density has been shown to be a critical factor influencing the magnitude of epitope-specific responses. The aim of this study was to design a chimer protein consisting of three tandem repeats of M2e peptide sequence fused to the Leishmania major HSP70 gene and evaluate its characteristics and immunogenicity...
October 31, 2018: Virus Genes
https://www.readbyqxmd.com/read/30169745/robust-prediction-of-clinical-outcomes-using-cytometry-data
#6
Zicheng Hu, Benjamin S Glicksberg, Atul J Butte
Motivation: Flow cytometry and mass cytometry are widely used to diagnose diseases and to predict clinical outcomes. When associating clinical features with cytometry data, traditional analysis methods require cell gating as an intermediate step, leading to information loss and susceptibility to batch effects. Here, we wish to explore an alternative approach that predicts clinical features from cytometry data without the cell-gating step. We also wish to test if such a gating-free approach increases the accuracy and robustness of the prediction...
August 31, 2018: Bioinformatics
https://www.readbyqxmd.com/read/30151591/software-for-characterizing-the-antigenic-and-genetic-evolution-of-human-influenza-viruses
#7
Susanne Reimering, Alice C McHardy
Influenza viruses are rapidly evolving pathogens causing annual epidemics and occasional pandemics. The accumulation of amino acid substitutions allows the virus to adapt to changing environments like novel host species or to escape the acquired immunity of the host population. Especially substitutions in the epitope regions of the surface protein HA lead to antigenic change, facilitating the evasion of the host's immune response by the virus and making frequent updates of the vaccine composition necessary...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30087171/heterosubtypic-protections-against-human-infecting-avian-influenza-viruses-correlate-to-biased-cross-t-cell-responses
#8
Min Zhao, Kefang Liu, Jiejian Luo, Shuguang Tan, Chuansong Quan, Shuijun Zhang, Yan Chai, Jianxun Qi, Yan Li, Yuhai Bi, Haixia Xiao, Gary Wong, Jianfang Zhou, Taijiao Jiang, Wenjun Liu, Hongjie Yu, Jinghua Yan, Yingxia Liu, Yuelong Shu, Guizhen Wu, Aiping Wu, George F Gao, William J Liu
Against a backdrop of seasonal influenza virus epidemics, emerging avian influenza viruses (AIVs) occasionally jump from birds to humans, posing a public health risk, especially with the recent sharp increase in H7N9 infections. Evaluations of cross-reactive T-cell immunity to seasonal influenza viruses and human-infecting AIVs have been reported previously. However, the roles of influenza A virus-derived epitopes in the cross-reactive T-cell responses and heterosubtypic protections are not well understood; understanding those roles is important for preventing and controlling new emerging AIVs...
August 7, 2018: MBio
https://www.readbyqxmd.com/read/30031927/molecular-epidemiological-survey-and-complete-genomic-phylogenetic-analysis-of-h6-subtype-avian-influenza-viruses-in-poultry-in-china-from-2011-to-2016
#9
Cheng Peng, Hongtao Sun, Jinping Li, Guangyu Hou, Suchun Wang, Shuo Liu, Qingye Zhuang, Shanju Cheng, Jiming Chen, Wenming Jiang
To investigate the prevalence and evolution of the H6 subtype avian influenza viruses (AIVs) circulating in poultry in China from 2011 to 2016, 11 molecular epidemiological surveys was performed in this study. In total, 893 H6 subtype viral strains were isolated from 67,639 swab samples and 360 environmental samples. From these strains, 35 representative strains were selected and their whole genomic sequences determined. According to a phylogenetic analysis and molecular characterization, all 35 viral strains belonged to the Eurasian avian lineage...
November 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29954441/insaflu-an-automated-open-web-based-bioinformatics-suite-from-reads-for-influenza-whole-genome-sequencing-based-surveillance
#10
Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes
BACKGROUND: A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data...
June 29, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29935353/a-new-method-to-cluster-genomes-based-on-cumulative-fourier-power-spectrum
#11
Rui Dong, Ziyue Zhu, Changchuan Yin, Rong L He, Stephen S-T Yau
Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences...
October 5, 2018: Gene
https://www.readbyqxmd.com/read/29888214/mir-21-3p-regulates-influenza-a-virus-replication-by-targeting-histone-deacetylase-8
#12
Binghui Xia, Jiansheng Lu, Rong Wang, Zhixin Yang, Xiaowei Zhou, Peitang Huang
Influenza A virus (IAV) is responsible for severe morbidity and mortality in animals and humans worldwide. miRNAs are a class of small noncoding single-stranded RNA molecules that can negatively regulate gene expression and play important roles in virus-host interaction. However, the roles of miRNAs in IAV infection are still not fully understood. Here, we profiled the cellular miRNAs of A549 cells infected with A/goose/Jilin/hb/2003 (H5N1) and a comparison A/Beijing/501/2009 (H1N1). miRNA microarray and quantitative PCR analysis showed that several miRNAs were differentially expressed in A549 cells during IAV infection...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29878046/graph-guided-multi-task-sparse-learning-model-a-method-for-identifying-antigenic-variants-of-influenza-a-h3n2-virus
#13
Lei Han, Lei Li, Feng Wen, Lei Zhong, Tong Zhang, Xiu-Feng Wan
Motivation: Influenza virus antigenic variants continue to emerge and cause disease outbreaks. Time-consuming, costly, and middle-throughput serologic methods using virus isolates are routinely used to identify influenza antigenic variants for vaccine strain selection. However, the resulting data are notoriously noisy and difficult to interpret and integrate because of variations in reagents, supplies, and protocol implementation. A novel method without such limitations is needed for antigenic variant identification...
June 7, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29847214/the-human-vaccines-project-towards-a-comprehensive-understanding-of-the-human-immune-response-to-immunization
#14
Stacey L Wooden, Wayne C Koff
Although the success of vaccination to date has been unprecedented, our inadequate understanding of the details of the human immune response to immunization has resulted in several recent vaccine failures and significant delays in the development of high-need vaccines for global infectious diseases and cancer. Because of the need to better understand the immense complexity of the human immune system, the Human Vaccines Project was launched in 2015 with the mission to decode the human immune response to accelerate development of vaccines and immunotherapies for major diseases...
2018: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/29774014/oral-microbiota-community-dynamics-associated-with-oral-squamous-cell-carcinoma-staging
#15
Chia-Yu Yang, Yuan-Ming Yeh, Hai-Ying Yu, Chia-Yin Chin, Chia-Wei Hsu, Hsuan Liu, Po-Jung Huang, Song-Nian Hu, Chun-Ta Liao, Kai-Ping Chang, Yu-Liang Chang
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29772263/comparative-analysis-of-microrna-expression-in-dog-lungs-infected-with-the-h3n2-and-h5n1-canine-influenza-viruses
#16
Yun Zheng, Xinliang Fu, Lifang Wang, Wenyan Zhang, Pei Zhou, Xin Zhang, Weijie Zeng, Jidang Chen, Zongxi Cao, Kun Jia, Shoujun Li
MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach...
August 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29751021/a-new-era-of-virus-bioinformatics
#17
REVIEW
Bashar Ibrahim, Dino P McMahon, Franziska Hufsky, Martin Beer, Li Deng, Philippe Le Mercier, Massimo Palmarini, Volker Thiel, Manja Marz
Despite the recognized excellence of virology and bioinformatics, these two communities have interacted surprisingly sporadically, aside from some pioneering work on HIV-1 and influenza. Bringing together the expertise of bioinformaticians and virologists is crucial, since very specific but fundamental computational approaches are required for virus research, particularly in an era of big data. Collaboration between virologists and bioinformaticians is necessary to improve existing analytical tools, cloud-based systems, computational resources, data sharing approaches, new diagnostic tools, and bioinformatic training...
June 2, 2018: Virus Research
https://www.readbyqxmd.com/read/29656441/a-review-on-current-status-of-antiviral-sirna
#18
REVIEW
Abid Qureshi, Vaqar Gani Tantray, Altaf Rehman Kirmani, Abdul Ghani Ahangar
Viral diseases like influenza, AIDS, hepatitis, and Ebola cause severe epidemics worldwide. Along with their resistant strains, new pathogenic viruses continue to be discovered so creating an ongoing need for new antiviral treatments. RNA interference is a cellular gene-silencing phenomenon in which sequence-specific degradation of target mRNA is achieved by means of complementary short interfering RNA (siRNA) molecules. Short interfering RNA technology affords a potential tractable strategy to combat viral pathogenesis because siRNAs are specific, easy to design, and can be directed against multiple strains of a virus by targeting their conserved gene regions...
July 2018: Reviews in Medical Virology
https://www.readbyqxmd.com/read/29651275/structural-and-functional-motifs-in-influenza-virus-rnas
#19
REVIEW
Damien Ferhadian, Maud Contrant, Anne Printz-Schweigert, Redmond P Smyth, Jean-Christophe Paillart, Roland Marquet
Influenza A viruses (IAV) are responsible for recurrent influenza epidemics and occasional devastating pandemics in humans and animals. They belong to the Orthomyxoviridae family and their genome consists of eight (-) sense viral RNA (vRNA) segments of different lengths coding for at least 11 viral proteins. A heterotrimeric polymerase complex is bound to the promoter consisting of the 13 5'-terminal and 12 3'-terminal nucleotides of each vRNA, while internal parts of the vRNAs are associated with multiple copies of the viral nucleoprotein (NP), thus forming ribonucleoproteins (vRNP)...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29574656/differences-in-type-i-interferon-response-in-human-lung-epithelial-cells-infected-by-highly-pathogenic-h5n1-and-low-pathogenic-h11n1-avian-influenza-viruses
#20
Milind M Thube, Pratip Shil, Rewati Kasbe, Avinash A Patil, Shailesh D Pawar, Jayati Mullick
Influenza A virus infection induces type I interferons (IFNs α/β) which activate host antiviral responses through a cascade of IFN signaling events. Herein, we compared highly pathogenic H5N1 and low pathogenic H11N1 avian influenza viruses isolated from India, for their replication kinetics and ability to induce IFN-β and interferon-stimulating genes (ISGs). The H5N1 virus showed a higher replication rate and induced less IFN-β and ISGs compared to the H11N1 virus when grown in the human lung epithelial A549 cells, reflecting the generation of differential innate immune responses during infection by these viruses...
June 2018: Virus Genes
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