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Influenza A bioinformatics

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https://www.readbyqxmd.com/read/30087171/heterosubtypic-protections-against-human-infecting-avian-influenza-viruses-correlate-to-biased-cross-t-cell-responses
#1
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
#2
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...
July 20, 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
#3
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
#4
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
#5
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
#6
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
#7
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...
May 30, 2018: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/29774014/oral-microbiota-community-dynamics-associated-with-oral-squamous-cell-carcinoma-staging
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/29558968/baldr-a-computational-pipeline-for-paired-heavy-and-light-chain-immunoglobulin-reconstruction-in-single-cell-rna-seq-data
#14
Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells...
March 20, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29473023/basic-characterization-of-natural-transformation-in-a-highly-transformable-haemophilus-parasuis-strain-sc1401
#15
Ke Dai, Lvqin He, Yung-Fu Chang, Sanjie Cao, Qin Zhao, Xiaobo Huang, Rui Wu, Yong Huang, Qigui Yan, Xinfeng Han, Xiaoping Ma, Xintian Wen, Yiping Wen
Haemophilus parasuis causes Glässer's disease and pneumonia, incurring serious economic losses in the porcine industry. In this study, natural competence was investigated in H. parasuis . We found competence genes in H. parasuis homologous to ones in Haemophilus influenzae and a high consensus battery of Sxy-dependent cyclic AMP (cAMP) receptor protein (CRP-S) regulons using bioinformatics. High rates of natural competence were found from the onset of stationary-phase growth condition to mid-stationary phase (OD600 from 0...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29447223/virome-and-bacteriome-characterization-of-children-with-pneumonia-and-asthma-in-mexico-city-during-winter-seasons-2014-and-2015
#16
Jose A Romero-Espinoza, Yazmin Moreno-Valencia, Rodrigo H Coronel-Tellez, Manuel Castillejos-Lopez, Andres Hernandez, Aaron Dominguez, Angel Miliar-Garcia, Arturo Barbachano-Guerrero, Rogelio Perez-Padilla, Alejandro Alejandre-Garcia, Joel A Vazquez-Perez
BACKGROUND: Acute asthma exacerbations and pneumonia are important causes of morbidity and mortality in children and may coexist in the same children, although symptom overlap may lead to difficulties in diagnosis. Microbial and viral diversity and differential abundance of either may play an important role in infection susceptibility and the development of acute and chronic respiratory diseases. OBJECTIVES: To describe the virome and bacteriome present in the upper respiratory tract of hospitalized children with a clinical diagnosis of asthma and pneumonia during an acute exacerbation and an acute respiratory illness ARI episode respectively...
2018: PloS One
https://www.readbyqxmd.com/read/29433425/antigenic-cartography-of-h1n1-influenza-viruses-using-sequence-based-antigenic-distance-calculation
#17
Christopher S Anderson, Patrick R McCall, Harry A Stern, Hongmei Yang, David J Topham
BACKGROUND: The ease at which influenza virus sequence data can be used to estimate antigenic relationships between strains and the existence of databases containing sequence data for hundreds of thousands influenza strains make sequence-based antigenic distance estimates an attractive approach to researchers. Antigenic mismatch between circulating strains and vaccine strains results in significantly decreased vaccine effectiveness. Furthermore, antigenic relatedness between the vaccine strain and the strains an individual was originally primed with can affect the cross-reactivity of the antibody response...
February 12, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29363430/a-comprehensive-study-on-cellular-rna-editing-activity-in-response-to-infections-with-different-subtypes-of-influenza-a-viruses
#18
Yingying Cao, Ruiyuan Cao, Yaowei Huang, Hongxia Zhou, Yuanhua Liu, Xuan Li, Wu Zhong, Pei Hao
BACKGROUND: RNA editing is an important mechanism that expands the diversity and complexity of genetic codes. The conversions of adenosine (A) to inosine (I) and cytosine (C) to uridine (U) are two prominent types of RNA editing in animals. The roles of RNA editing events have been implicated in important biological pathways. Cellular RNA editing activity in response to influenza A virus infection has not been fully characterized in human and avian hosts. This study was designed as a big data analysis to investigate the role and response of RNA editing in epithelial cells during the course of infection with various subtypes of influenza A viruses...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29348625/universal-type-subtype-specific-antibodies-for-quantitative-analyses-of-neuraminidase-in-trivalent-influenza-vaccines
#19
Kangwei Xu, Changgui Li, Caroline Gravel, Zheng Jiang, Bozena Jaentschke, Gary Van Domselaar, Xuguang Li, Junzhi Wang
Both influenza viral hemagglutinin and neuraminidase can induce protective immune responses in humans. Although the viral hemagglutinin antigens have been quantified in influenza vaccines, the amounts of neuraminidase remain undetermined. Using comprehensive bioinformatics analyses of all neuraminidase sequences, we identified highly conserved and subtype-specific peptide epitopes within each of N1, N2 and type B neuraminidase groups. Mono-specific antibodies generated against these peptides bound to their respective subtype/type only while demonstrating remarkable specificity against the viral neuraminidase sequences without any cross-reactivity with allantoic and cellular proteins...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322922/analysis-of-viral-diversity-for-vaccine-target-discovery
#20
Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August
BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples...
December 21, 2017: BMC Medical Genomics
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