Interactome networks between the human respiratory syncytial virus (HRSV), the human metapneumovirus (ΗMPV), and their host: In silico investigation and comparative functional enrichment analysis

2020 ◽  
Vol 141 ◽  
pp. 104000
Author(s):  
Erasmia Rouka ◽  
Chrissi Hatzoglou ◽  
Konstantinos I. Gourgoulianis ◽  
Sotirios G. Zarogiannis
Keyword(s):  
Respiratory Syncytial Virus ◽  
In Silico ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Human Metapneumovirus ◽  
Human Respiratory Syncytial Virus ◽  
Functional Enrichment ◽  
Syncytial Virus

scholarly journals Early Onset Ataxia with Comorbid Dystonia: Clinical, Anatomical and Biological Pathway Analysis Expose Shared Pathophysiology

Diagnostics ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 997
Author(s):  
Deborah A. Sival ◽  
Martinica Garofalo ◽  
Rick Brandsma ◽  
Tom A. Bokkers ◽  
Marloes van den Berg ◽  
...  
Keyword(s):  
Signal Transduction ◽  
In Silico ◽  
Krebs Cycle ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Genetic Network ◽  
Functional Enrichment ◽  
Biological Pathway ◽  
Adult Onset ◽  
Gene Panels

In degenerative adult onset ataxia (AOA), dystonic comorbidity is attributed to one disease continuum. However, in early adult onset ataxia (EOA), the prevalence and pathogenesis of dystonic comorbidity (EOAD+), are still unclear. In 80 EOA-patients, we determined the EOAD+-prevalence in association with MRI-abnormalities. Subsequently, we explored underlying biological pathways by genetic network and functional enrichment analysis. We checked pathway-outcomes in specific EOAD+-genotypes by comparing results with non-specifically (in-silico-determined) shared genes in up-to-date EOA, AOA and dystonia gene panels (that could concurrently cause ataxia and dystonia). In the majority (65%) of EOA-patients, mild EOAD+-features concurred with extra-cerebellar MRI abnormalities (at pons and/or basal-ganglia and/or thalamus (p = 0.001)). Genetic network and functional enrichment analysis in EOAD+-genotypes indicated an association with organelle- and cellular-component organization (important for energy production and signal transduction). In non-specifically, in-silico-determined shared EOA, AOA and dystonia genes, pathways were enriched for Krebs-cycle and fatty acid/lipid-metabolic processes. In frequently occurring EOAD+-phenotypes, clinical, anatomical and biological pathway analyses reveal shared pathophysiology between ataxia and dystonia, associated with cellular energy metabolism and network signal transduction. Insight in the underlying pathophysiology of heterogeneous EOAD+-phenotype-genotype relationships supports the rationale for testing with complete, up-to-date movement disorder gene lists, instead of single EOA gene-panels.

scholarly journals Comparison of 11 respiratory pathogens among hospitalized children before and during the COVID-19 epidemic in Shenzhen, China

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Li Li ◽  
Heping Wang ◽  
Ailiang Liu ◽  
Rongjun Wang ◽  
Tingting Zhi ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Multiplex Pcr ◽  
Detection Rate ◽  
Human Metapneumovirus ◽  
Human Respiratory Syncytial Virus ◽  
Hospitalized Children ◽  
Respiratory Pathogens ◽  
Detection Rates ◽  
Syncytial Virus ◽  
The Impact

Abstract Background The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. Methods This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children’s Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. Results A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p < 0.0001). Conclusions Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.

scholarly journals A Meta-Analysis of Multiple Whole Blood Gene Expression Data Unveils a Diagnostic Host-Response Transcript Signature for Respiratory Syncytial Virus

2020 ◽  
Vol 21 (5) ◽  
pp. 1831 ◽  
Author(s):  
Ruth Barral-Arca ◽  
Alberto Gómez-Carballa ◽  
Miriam Cebey-López ◽  
Xabier Bello ◽  
Federico Martinón-Torres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Respiratory Syncytial Virus ◽  
Drug Targets ◽  
Cohort Analysis ◽  
Enrichment Analysis ◽  
Functional Enrichment ◽  
Healthy Controls ◽  
Infection Pattern ◽  
Rsv Infection ◽  
Syncytial Virus

Respiratory syncytial virus (RSV) is one of the major causes of acute lower respiratory tract infection worldwide. The absence of a commercial vaccine and the limited success of current therapeutic strategies against RSV make further research necessary. We used a multi-cohort analysis approach to investigate host transcriptomic biomarkers and shed further light on the molecular mechanism underlying RSV-host interactions. We meta-analyzed seven transcriptome microarray studies from the public Gene Expression Omnibus (GEO) repository containing a total of 922 samples, including RSV, healthy controls, coronaviruses, enteroviruses, influenzas, rhinoviruses, and coinfections, from both adult and pediatric patients. We identified > 1500 genes differentially expressed when comparing the transcriptomes of RSV-infected patients against healthy controls. Functional enrichment analysis showed several pathways significantly altered, including immunologic response mediated by RSV infection, pattern recognition receptors, cell cycle, and olfactory signaling. In addition, we identified a minimal 17-transcript host signature specific for RSV infection by comparing transcriptomic profiles against other respiratory viruses. These multi-genic signatures might help to investigate future drug targets against RSV infection.

scholarly journals Desenho e Validação de Primers In Silico para Detecção do Vírus Sincicial Respiratório Humano

REVISTA FIMCA ◽  
2017 ◽  
Vol 4 (1) ◽  
pp. 17-30
Author(s):  
Jackson Alves da Silva Queiroz ◽  
Luciane Soares Alves ◽  
Deusilene Souza Vieira Dall’acqua ◽  
Luan Felipo Botelho Souza
Keyword(s):  
Respiratory Syncytial Virus ◽  
In Silico ◽  
Human Respiratory Syncytial Virus ◽  
Base Pairs ◽  
Gene Encoding ◽  
Target Region ◽  
Glycoprotein G ◽  
Syncytial Virus ◽  
Delta G

Introdução: O desenvolvimento de primers é extremamente importante para pesquisas moleculares. Objetivos: O presente estudo objetivou desenhar e validar primers in silico para detecção do vírus sincicial respiratório humano (RSVH). Materiais e Métodos: Foi construído um banco de 100 sequências de genoma completo do Vírus Sincicial Respiratório Humano (RSVH) depositadas no Genbank (NCBI). Realizado um alinhamento múltiplo global utilizando o algoritimo Clustal W, mapeadas as regiões conservadas e selecionado os primers. Posteriormente submetidos a análise dos parâmetros especificidade, pela ferramenta BLAST, concentração de GC%, TMelting, comprimento, formação de dímeros e hairpin utilizando o software Oligo Analyser, validando-os para uso in vitro. Para discussão dos resultados, foram selecionados 14 primers de estudos realizados, submetidos à metodologia proposta neste estudo, comparando os dados obtidos. A região alvo escolhida foi o gene da Glicoproteína G, pela presença de sítios conservados. Resultados: Os primers amplificam um fragmento de 381pb, que submetido a uma segunda PCR, resulta em 109 pb correspondente ao tipo A do vírus e 168 pb para o tipo B, permitindo a detecção viral e a distinção de genótipos. Os primers possuem tamanho de 21 a 24 pb, com uma temperatura de melting entre 48,9 oC e 55,3 oC. A concentração de GC% varia de 33,3% a 52,4%. O número de bases complementares na análise de dímeros e hairpin manteve-se abaixo de 5 bases. A Energia Livre de Gibbs (Delta G) acima de -9 kcal.moles(-1) como desejado. Conclusão: Os valores obtidos na validação dos primers estão em concordância com os já utilizados em estudos de referência, validando assim o seu uso in vitro. Introduction: Developing primers is extremely important to molecular researches. Objectives: This study aims to drawing and validate in silico primers for detection of Human Respiratory Syncytial Virus (RSVH). Materials and Methods: It was built a database of 100 complete genome sequences of Human Respiratory Syncytial Virus (RSVH) deposited in the Genbank (NCBI), carried out a global multiple alignment using the algoritm Clustal W, thus mapping the conserved regions, and selecting primers, subsequently submitted to analysis of parameters such as specificity, by the BLAST tool, concentration of GC% TMelting, length, and formation of dimers and hairpins using the software Oligo Analyser, validating them to use in vitro. For discussion of the results, we selected 14 primers of studies already carried out and submitted the methodology proposed in this study, comparing the data obtained. The selected target region was the gene encoding the Glycoprotein G, by the presence of conserved sites. Results: The primers selected amplifies a fragment of 381 bp in the 1st PCR, which subjected to a second PCR results in 109 bp corresponding to the type A of the virus and 168 base pairs for the type Bwhat allows not only viral detection, as the distinction of the type to which it belongs. The primers have size from 21 to 24 base pairs, having a melting temperature (Tmelting) between 48,9o C and 55,3o C and GC% concentration ranging from 33.3% to 52.4%. The number of complementary bases in the dimers and hairpins analysis was maintained below 5 bases, while the Gibbs free energy (Delta G) was kept above kcal.mole -9(-1) as desired. Conclusion: All values obtained in the validation of the primers are in agreement with the ones already used in the reference studies, thereby validating its use in vitro.

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