Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection

Dissanayake, Thrimendra Kaushika; Schäuble, Sascha; Mirhakkak, Mohammad H.; Wu, Wai-Lan; Ng, Anthony Chin-Ki; Yip, Cyril C. Y.; López, Albert García; Wolf, Thomas; Yeung, M.R.; Chan, Kwok‐Hung; Yuen, Kwok‐Yung; Panagiotou, Gianni; To, Kelvin Kai‐Wang

doi:10.3389/fmicb.2020.01580

Cited by 15 publications

(20 citation statements)

References 50 publications

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“…Viral load was measured using TB Green Premix Ex Taq (Takara Bio Inc., Shiga, Japan). Real time PCR assays were performed in LightCycler 96 system (Roche Applied Sciences, Indianapolis, USA) using primers for IAV, RV and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) described previously with modifications [26]. The expression of house-keeping gene GAPDH was quantified in parallel for RNA normalization.…”

Section: Methodsmentioning

confidence: 99%

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Differential role of sphingomyelin in influenza virus, rhinovirus and SARS-CoV-2 infection of Calu-3 cells

Dissanayake

Yan

et al. 2021

Journal of General Virology

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Host cell lipids play a pivotal role in the pathogenesis of respiratory virus infection. However, a direct comparison of the lipidomic profile of influenza virus and rhinovirus infections is lacking. In this study, we first compared the lipid profile of influenza virus and rhinovirus infection in a bronchial epithelial cell line. Most lipid features were downregulated for both influenza virus and rhinovirus, especially for the sphingomyelin features. Pathway analysis showed that sphingolipid metabolism was the most perturbed pathway. Functional study showed that bacterial sphingomyelinase suppressed influenza virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication, but promoted rhinovirus replication. These findings suggest that sphingomyelin pathway can be a potential target for antiviral therapy, but should be carefully evaluated as it has opposite effects on different respiratory viruses. Furthermore, the differential effect of sphingomyelinase on rhinovirus and influenza virus may explain the interference between rhinovirus and influenza virus infection.

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Section: Methodsmentioning

confidence: 99%

“…The viruses used in this study were all isolated from patients as we described previously, including influenza A(H1N1) virus A/HK/415742/2009 [24,25], influenza B virus B/ HK/411989/2011 [25], rhinovirus 451892/2011 (belongs to rhinovirus species A type 1A) [26], and SARS-CoV-2 HKU001a [27,28].…”

Section: Viruses and Cellsmentioning

confidence: 99%

Differential role of sphingomyelin in influenza virus, rhinovirus and SARS-CoV-2 infection of Calu-3 cells

Dissanayake

Yan

et al. 2021

Journal of General Virology

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“…Sequencing libraries were prepared using a TruSeq Stranded mRNA Sample Prep Kit and sequenced on a HiSeq 2000 (Illumina, San Diego, CA, USA). Influenza A and B, and the rhinovirus preparation methodologies are described in detail in Dissanayake et al, 2020 [ 27 ]. Viruses were isolated from patients in Hong Kong with Influenza A (H1N1) virus A/HK/415742/2009 and influenza B virus B/HK/411989/2011, and a patient with pneumonia from which rhinovirus species A type 1A was isolated.…”

Section: Methodsmentioning

confidence: 99%

“…Raw RNA sequencing data were retrieved from the sequence read archive (SRA) database under accession nos. (SARS-CoV-2: SRP253951 [ 25 ]; SARS-CoV and SARS-MERS: SRP056612 [ 26 ]; FLUA, FLUB, and RHINO: SRP251473) [ 27 ]. Data were retrieved using the SRA toolkit version 2.9.2 as previously described [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

“…However, whether the observed molecular changes in host cells were unique to SARS-CoV-2 infection are not addressed thus far. In the current study, we compared six datasets of Calu-3 human lung epithelial cells infected with different viruses: SARS-CoV-2 [ 25 ], SARS-CoV, SARS-MERS [ 26 ], FLUA, FLUB, and RHINO [ 27 ]. Previous studies showed the suitability of the Calu-3 cell model due to its susceptibility to infection by respiratory viruses, including influenza virus A, rhinovirus, and SARS-CoV.…”

Section: Introductionmentioning

confidence: 99%

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Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2

Shaath

Alajez

2020

Biology

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The continuous and rapid emergence of new viral strains calls for a better understanding of the fundamental changes occurring within the host cell upon viral infection. In this study, we analyzed RNA-seq transcriptome data from Calu-3 human lung epithelial cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared to five other viruses namely, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East Respiratory Syndrome (SARS-MERS), influenzavirus A (FLUA), influenzavirus B (FLUB), and rhinovirus (RHINO) compared to mock-infected cells and characterized their coding and noncoding RNA transcriptional portraits. The induction of interferon, inflammatory, and immune response was a hallmark of SARS-CoV-2 infection. Comprehensive bioinformatics revealed the activation of immune response and defense response to the virus as a common feature of viral infection. Interestingly however, the degree of functional categories and signaling pathways activation varied among different viruses. Ingenuity pathways analysis highlighted altered conical and casual pathways related to TNF, IL1A, and TLR7, which are seen more predominantly during SARS-CoV-2 infection. Nonetheless, the activation of chemotaxis and lipid synthesis was prominent in SARS-CoV-2-infected cells. Despite the commonality among all viruses, our data revealed the hyperactivation of chemotaxis and immune cell trafficking as well as the enhanced fatty acid synthesis as plausible mechanisms that could explain the inflammatory cytokine storms associated with severe cases of COVID-19 and the rapid spread of the virus, respectively.

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Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication

Chakraborty

Bhattacharya

Dhama

et al. 2023

Journal of Infection and Public Health

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Comparative Transcriptomic Analysis of Rhinovirus and Influenza Virus Infection

Cited by 15 publications

References 50 publications

Differential role of sphingomyelin in influenza virus, rhinovirus and SARS-CoV-2 infection of Calu-3 cells

Differential role of sphingomyelin in influenza virus, rhinovirus and SARS-CoV-2 infection of Calu-3 cells

Computational and Transcriptome Analyses Revealed Preferential Induction of Chemotaxis and Lipid Synthesis by SARS-CoV-2

Evaluation of differentially expressed genes during replication using gene expression landscape of monkeypox-infected MK2 cells: A bioinformatics and systems biology approach to understanding the genomic pattern of viral replication

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