keyword
https://read.qxmd.com/read/38127927/shotgun-metagenomics-to-investigate-unknown-viral-etiologies-of-pediatric-meningoencephalitis
#21
JOURNAL ARTICLE
Andrea Castellot, Juan Camacho, María Dolores Fernández-García, David Tarragó
INTRODUCTION: Meningoencephalitis in children poses a diagnostic challenge, as etiology remains unknown for most of patients. Viral metagenomics by shotgun sequencing represents a powerful tool for investigating unknown viral infections related to these cases. PATIENTS AND METHODS: In a two-year, reference-centre, retrospective study, we investigated the usefulness of viral metagenomics of cerebrospinal fluid (CSF) for the diagnosis of viral infectious meningoencephalitis in forty seven pediatric patients, forty of them previously tested negative with a routine neurologic panel of viral targets that included herpesvirus 1-3 and enterovirus...
2023: PloS One
https://read.qxmd.com/read/38103645/phosphorylation-of-pb2-at-serine-181-restricts-viral-replication-and-virulence-of-the-highly-pathogenic-h5n1-avian-influenza-virus-in-mice
#22
JOURNAL ARTICLE
Jiao Hu, Zixiong Zeng, Xia Chen, Manyu Zhang, Zenglei Hu, Min Gu, Xiaoquan Wang, Ruyi Gao, Shunlin Hu, Yu Chen, Xiaowen Liu, Daxin Peng, Xiufan Liu
Influenza A virus (IAV) still poses a pandemic threat to public health, causing a high mortality rate annually and during pandemic years. Posttranslational modification of the viral protein plays a substantial role in regulating IAV infection. Here, based on immunoprecipitation (IP)-based mass spectrometry (MS) and purified virus-coupled MS, a total of 89 phosphorylation sites distributed among 10 encoded viral proteins of IAV were identified, including 60 novel phosphorylation sites. Additionally, for the first time, we provide evidence that PB2 can also be acetylated and the site is K187...
December 14, 2023: Virologica Sinica
https://read.qxmd.com/read/38077337/the-two-stage-molecular-scenery-of-sars-cov-2-infection-with-implications-to-disease-severity-an-in-silico-quest
#23
JOURNAL ARTICLE
George Potamias, Polymnia Gkoublia, Alexandros Kanterakis
INTRODUCTION: The two-stage molecular profile of the progression of SARS-CoV-2 (SCOV2) infection is explored in terms of five key biological/clinical questions: (a) does SCOV2 exhibits a two-stage infection profile? (b) SARS-CoV-1 (SCOV1) vs. SCOV2: do they differ? (c) does and how SCOV2 differs from Influenza/INFL infection? (d) does low viral-load and (e) does COVID-19 early host response relate to the two-stage SCOV2 infection profile? We provide positive answers to the above questions by analyzing the time-series gene-expression profiles of preserved cell-lines infected with SCOV1/2 or, the gene-expression profiles of infected individuals with different viral-loads levels and different host-response phenotypes...
2023: Frontiers in Immunology
https://read.qxmd.com/read/38044872/one-ha-stalk-topping-multiple-heads-as-a-novel-influenza-vaccine
#24
JOURNAL ARTICLE
Ping Zhou, Tianyi Qiu, Xiang Wang, Xi Yang, Hongyang Shi, Caihong Zhu, Weiqian Dai, Man Xing, Xiaoyan Zhang, Jianqing Xu, Dongming Zhou
ABSTRACT Classic chimeric hemagglutinin (cHA) was designed to induce immune responses against the conserved stalk domain of HA. However, it is unclear whether combining more than one HA head domain onto one stalk domain is immunogenic and further induce immune responses against influenza viruses. Here, we constructed numerous novel cHAs comprising two or three fused head domains from different subtypes grafted onto one stalk domain, designated as cH1-H3, cH1-H7, cH1-H3-H7, and cH1-H7-H3. The three-dimensional structures of these novel cHAs were modeled using bioinformatics simulations...
December 4, 2023: Emerging Microbes & Infections
https://read.qxmd.com/read/38025700/in-silico-study-of-antisense-oligonucleotide-antibiotics
#25
JOURNAL ARTICLE
Erica S Chen, Eric S Ho
BACKGROUND: The rapid emergence of antibiotic-resistant bacteria directly contributes to a wave of untreatable infections. The lack of new drug development is an important driver of this crisis. Most antibiotics today are small molecules that block vital processes in bacteria. To optimize such effects, the three-dimensional structure of targeted bacterial proteins is imperative, although such a task is time-consuming and tedious, impeding the development of antibiotics. The development of RNA-based therapeutics has catalyzed a new platform of antibiotics-antisense oligonucleotides (ASOs)...
2023: PeerJ
https://read.qxmd.com/read/37981214/5-copyback-defective-viral-genomes-are-major-component-in-clinical-and-non-clinical-influenza-samples
#26
JOURNAL ARTICLE
Xing Li, Zhiping Ye, Ewan P Plant
Clinical samples from people with influenza disease have been analyzed to assess the presence and abundance of Defective Viral Genomes (DVGs), but these have not been assessed using the same bioinformatic pipeline. The type of DVG most described for influenza infections (deletion DVGs) differs from the most commonly described DVGs from non-segmented negative stranded viruses (5' copyback). This could be attributed to either differences between viruses or the tools used to detect and characterize DVGs. Here we analyze several NGS datasets from people infected with different types of influenza virus using the same bioinformatic pipeline...
November 21, 2023: Virus Research
https://read.qxmd.com/read/37977084/molecular-detection-and-characterization-of-highly-pathogenic-h5n1-clade-2-3-4-4b-avian-influenza-viruses-among-hunter-harvested-wild-birds-provides-evidence-for-three-independent-introductions-into-alaska
#27
JOURNAL ARTICLE
Andrew M Ramey, Laura C Scott, Christina A Ahlstrom, Evan J Buck, Alison R Williams, Mia Kim Torchetti, David E Stallknecht, Rebecca L Poulson
We detected and characterized highly pathogenic avian influenza viruses among hunter-harvested wild waterfowl inhabiting western Alaska during September-October 2022 using a molecular sequencing pipeline applied to RNA extracts derived directly from original swab samples. Genomic characterization of 10 H5 clade 2.3.4.4b avian influenza viruses detected with high confidence provided evidence for three independent viral introductions into Alaska. Our results highlight the utility and some potential limits of applying molecular processing approaches directly to RNA extracts from original swab samples for viral research and monitoring...
November 10, 2023: Virology
https://read.qxmd.com/read/37967595/in-silico-design-of-a-broad-spectrum-multiepitope-vaccine-against-influenza-virus
#28
JOURNAL ARTICLE
Lifang Yuan, Xu Li, Minchao Li, Rongjun Bi, Yingrui Li, Jiaping Song, Wei Li, Mingchen Yan, Huanle Luo, Caijun Sun, Yuelong Shu
Influenza remains a global health concern due to its potential to cause pandemics as a result of rapidly mutating influenza virus strains. Existing vaccines often struggle to keep up with these rapidly mutating flu viruses. Therefore, the development of a broad-spectrum peptide vaccine that can stimulate an optimal antibody response has emerged as an innovative approach to addressing the influenza threat. In this study, an immunoinformatic approach was employed to rapidly predict immunodominant epitopes from different antigens, aiming to develop an effective multiepitope influenza vaccine (MEV)...
November 13, 2023: International Journal of Biological Macromolecules
https://read.qxmd.com/read/37916972/informed-interpretation-of-metagenomic-data-by-strainphlan-enables-strain-retention-analyses-of-the-upper-airway-microbiome
#29
JOURNAL ARTICLE
Nadja Mostacci, Tsering Monika Wüthrich, Léa Siegwald, Silas Kieser, Ruth Steinberg, Olga Sakwinska, Philipp Latzin, Insa Korten, Markus Hilty
Shotgun metagenomic sequencing has the potential to provide bacterial strain-level resolution which is of key importance to tackle a host of clinical questions. While bioinformatic tools that achieve strain-level resolution are available, thorough benchmarking is needed to validate their use for less investigated and low biomass microbiomes like those from the upper respiratory tract. We analyzed a previously published data set of longitudinally collected nasopharyngeal samples from Bangladeshi infants (Microbiota and Health study) and a novel data set of oropharyngeal samples from Swiss children with cystic fibrosis...
November 2, 2023: MSystems
https://read.qxmd.com/read/37903415/visn-virus-instance-segmentation-network-for-tem-images-using-deep-attention-transformer
#30
JOURNAL ARTICLE
Chi Xiao, Jun Wang, Shenrong Yang, Minxin Heng, Junyi Su, Hao Xiao, Jingdong Song, Weifu Li
The identification of viruses from negative staining transmission electron microscopy (TEM) images has mainly depended on experienced experts. Recent advances in artificial intelligence have enabled virus recognition using deep learning techniques. However, most of the existing methods only perform virus classification or semantic segmentation, and few studies have addressed the challenge of virus instance segmentation in TEM images. In this paper, we focus on the instance segmentation of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and other respiratory viruses and provide experts with more effective information about viruses...
September 22, 2023: Briefings in Bioinformatics
https://read.qxmd.com/read/37896808/sequence-based-antigenic-analyses-of-h1-swine-influenza-a-viruses-from-colombia-2008-2021-reveals-temporal-and-geographical-antigenic-variations
#31
JOURNAL ARTICLE
Andres F Ospina-Jimenez, Arlen P Gomez, Maria A Rincon-Monroy, Lucia Ortiz, Daniel R Perez, Mario Peña, Gloria Ramirez-Nieto
Swine influenza is a respiratory disease that affects the pork industry and is a public health threat. It is caused by type A influenza virus (FLUAV), which continuously undergoes genetic and antigenic variations. A large amount of information regarding FLUAV in pigs is available worldwide, but it is limited in Latin America. The HA sequences of H1 subtype FLUAV-positive samples obtained from pigs in Colombia between 2008-2021 were analyzed using sequence-based antigenic cartography and N-Glycosylation analyses...
September 30, 2023: Viruses
https://read.qxmd.com/read/37895321/sequence-analysis-of-the-malaysian-low-pathogenic-avian-influenza-virus-strain-h5n2-from-duck
#32
JOURNAL ARTICLE
Fatin Ahmad Rizal, Kok Lian Ho, Abdul Rahman Omar, Wen Siang Tan, Abdul Razak Mariatulqabtiah, Munir Iqbal
The avian influenza viruses (AIV) of the H5 subtype have the ability to mutate from low pathogenic (LPAI) to highly pathogenic (HPAI), which can cause high mortality in poultry. Little is known about the pathogenic switching apart from the mutations at the haemagglutinin cleavage site, which significantly contributes to the virus virulence switching phenomenon. Therefore, this study aimed to compare the molecular markers in the haemagglutinin ( HA ), neuraminidase ( NA ), and matrix ( M ) genes of a locally isolated LPAI AIV strain H5N2 from Malaysia with the reference HPAI strains using bioinformatics approaches, emphasising the pathogenic properties of the viral genes...
October 22, 2023: Genes
https://read.qxmd.com/read/37876532/reducing-cell-intrinsic-immunity-to-mrna-vaccine-alters-adaptive-immune-responses-in-mice
#33
JOURNAL ARTICLE
Ziyin Wang, Egon J Jacobus, David C Stirling, Stefanie Krumm, Katie E Flight, Robert F Cunliffe, Jonathan Mottl, Charanjit Singh, Lucy G Mosscrop, Leticia Aragão Santiago, Annette B Vogel, Katalin Kariko, Ugur Sahin, Stephanie Erbar, John S Tregoning
The response to mRNA vaccines needs to be sufficient for immune cell activation and recruitment, but moderate enough to ensure efficacious antigen expression. The choice of the cap structure and use of N1-methylpseudouridine (m1Ψ) instead of uridine, which have been shown to reduce RNA sensing by the cellular innate immune system, has led to improved efficacy of mRNA vaccine platforms. Understanding how RNA modifications influence the cell intrinsic immune response may help in the development of more effective mRNA vaccines...
December 12, 2023: Molecular Therapy. Nucleic Acids
https://read.qxmd.com/read/37859974/key-aspects-defining-the-development-and-implementation-of-a-regional-genomic-surveillance-strategy-for-the-eastern-mediterranean-region
#34
JOURNAL ARTICLE
Luke W Meredith, Mustafa Aboualy, Rachel Ochola, Patrick Okwarah, Mehmet Ozel, Abdinasir Abubakar, Amal Barakat
The COVID-19 pandemic highlighted the critical role of pathogen sequencing in making informed public health decisions. Initially, the Eastern Mediterranean Region faced limitations in sequencing capacity. However, with robust WHO and stakeholder support, the situation significantly improved. By 2022, COVID-19 sequencing was underway in 22 out of 23 regional countries, with varying throughput and capacity. Notably, three genomic hubs were established in Oman, UAE, and Morocco, playing a key role in providing expanded genomics training and support across the region...
October 2023: Influenza and Other Respiratory Viruses
https://read.qxmd.com/read/37842064/multi-omics-data-integration-reveals-the-complexity-and-diversity-of-host-factors-associated-with-influenza-virus-infection
#35
JOURNAL ARTICLE
Zhaozhong Zhu, Ruina You, Huiru Li, Shuidong Feng, Huan Ma, Chaohao Tuo, Xiangxian Meng, Song Feng, Yousong Peng
Influenza viruses pose a significant and ongoing threat to human health. Many host factors have been identified to be associated with influenza virus infection. However, there is currently a lack of an integrated resource for these host factors. This study integrated human genes and proteins associated with influenza virus infections for 14 subtypes of influenza A viruses, as well as influenza B and C viruses, and built a database named H2Flu to store and organize these genes or proteins. The database includes 28,639 differentially expressed genes (DEGs), 1,850 differentially expressed proteins, and 442 proteins with differential posttranslational modifications after influenza virus infection, as well as 3,040 human proteins that interact with influenza virus proteins and 57 human susceptibility genes...
2023: PeerJ
https://read.qxmd.com/read/37811997/integration-of-sars-cov-2-testing-and-genomic-sequencing-into-influenza-sentinel-surveillance-in-uganda-january-to-december-2022
#36
JOURNAL ARTICLE
John T Kayiwa, Charity Nassuna, Sophia Mulei, Gladys Kiggundu, Joweria Nakaseegu, Maria Nabbuto, Esther Amwine, Bridget Nakamoga, Sarah Nankinga, Phiona Atuhaire, Pheobe Nabiryo, Pixy Alunzi, Tony Mbaziira, Paul Isabirye, Noel Ayuro, Nicholas Owor, Jocelyn Kiconco, Barnabas Bakamutumaho, Earl Austin Middlebrook, Pontiano Kaleebu, Julius J Lutwama, Andrew William Bartlow
The Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 polymerase chain reaction testing and genomic sequencing into the influenza surveillance program that was established in 2007. A total of 7,698 nasopharyngeal/oropharyngeal (NP/OP) swab samples were collected and analyzed from ILI/SARI sentinel sites across the country from January to December 2022. All samples were tested for influenza and SARS-CoV-2. Of these, 252 (3.3%), 162 (2.1%), and 589 (7.7%) were positive for influenza A, influenza B, and SARS-CoV-2, respectively...
October 9, 2023: Microbiology Spectrum
https://read.qxmd.com/read/37728538/structural-dynamics-of-the-rna-dependent-rna-polymerase-of-h1n1-strain-affecting-humans-a-bioinformatics-approach
#37
JOURNAL ARTICLE
Mahesh Samantaray, Shilpa Sri Pushan, Muthukumaran Rajagopalan, Amutha Ramaswamy
The Influenza flu is a pandemic disease that renders the highest risk factor to the society due to its efficient ability of airborne transmission. Studies on the H1N1 strain gained significant focus, since its pandemic outbreak in 2009 and particularly the computational studies on its structural elements significantly aided in revealing their functional uniqueness. Among the 10 structural proteins of H1N1, the RNA-dependent RNA polymerase (RdRp) heterotrimeric protein complex, which is responsible for the synthesis of viral RNA (vRNA) from the negative-sense RNA genome of the virus, is the focus of the present study...
September 20, 2023: Journal of Biomolecular Structure & Dynamics
https://read.qxmd.com/read/37722877/identification-of-differentially-expressed-genes-and-pathways-in-beas-2b-cells-upon-long-term-exposure-to-particulate-matter-pm-2-5-from-biomass-combustion-using-bioinformatics-analysis
#38
JOURNAL ARTICLE
Qian Yuan, Haiqiao Zhang
BACKGROUND: Long-term exposure to PM2.5 from burning domestic substances has been linked to an increased risk of lung disease, but the underlying mechanisms are unclear. This study is to explore the hub genes and pathways involved in PM2.5 toxicity in human bronchial epithelial BEAS-2B cells. METHODS: The GSE158954 dataset is downloaded from the GEO database. Differentially expressed genes (DEGs) were screened using the limma package in RStudio (version 4.2.1). In addition, DEGs analysis was performed by Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis...
2023: Environmental Health and Preventive Medicine
https://read.qxmd.com/read/37684288/cross-reactive-mhc-class-i-t-cell-epitopes-may-dictate-heterologous-immune-responses-between-respiratory-viruses-and-food-allergens
#39
JOURNAL ARTICLE
Kathrin Balz, Abhinav Kaushik, Franz Cemic, Vanitha Sampath, Vanessa Heger, Harald Renz, Kari Nadeau, Chrysanthi Skevaki
Respiratory virus infections play a major role in asthma, while there is a close correlation between asthma and food allergy. We hypothesized that T cell-mediated heterologous immunity may induce asthma symptoms among sensitized individuals and used two independent in silico pipelines for the identification of cross-reactive virus- and food allergen- derived T cell epitopes, considering individual peptide sequence similarity, MHC binding affinity and immunogenicity. We assessed the proteomes of human rhinovirus (RV1b), respiratory syncytial virus (RSVA2) and influenza-strains contained in the seasonal quadrivalent influenza vaccine 2019/2020 (QIV 2019/2020), as well as SARS-CoV-2 for human HLA alleles, in addition to more than 200 most common food allergen protein sequences...
September 8, 2023: Scientific Reports
https://read.qxmd.com/read/37676707/evaluation-of-sequence-hybridization-for-respiratory-viruses-using-the-twist-bioscience-respiratory-virus-research-panel-and-the-onecodex-respiratory-virus-sequence-analysis-workflow
#40
JOURNAL ARTICLE
Natalia Kapel, Elizabeth Kalimeris, Sheila Lumley, Arun Decano, Gillian Rodger, Marcela Lopes Alves, Kate Dingle, Sarah Oakley, Lucinda Barrett, Sophie Barnett, Derrick Crook, David W Eyre, Philippa C Matthews, Teresa Street, Nicole Stoesser
Respiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic content in respiratory samples is human, and amplifying and sequencing the viral/pathogen component in an unbiased manner is challenging. PCR-based tests, including those which detect multiple pathogens, are already widely used, but do not capture information on strain-level variation; tests with larger viral repertoires are also expensive on a per-test basis...
September 2023: Microbial Genomics
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