Notable Recent Publications

These are some recent publications which give a flavour of the research from the Barclay lab. For a complete list of publications, please see below.


Species difference in ANP32A underlies influenza A virus polymerase host restriction. Nature (2016).
Jason S. Long, Efstathios S. Giotis, Olivier Moncorgé, Rebecca Frise, Bhakti Mistry, Joe James, Mireille Morisson, Munir Iqbal, Alain Vignal, Michael A. Skinner & Wendy S. Barclay

This paper identified a key factor that explained why the polymerases from avian influenza viruses are restricted in humans.  For more, please see the associated New and Views.

See our latest ANP32 papers here: eLIFE, Journal of Virology, Journal of Virology.


The mechanism of resistance to favipiravir in influenza. PNAS (2018).
Daniel H. GoldhillAartjan J. W. te VelthuisRobert A. FletcherPinky LangatMaria ZambonAngie Lackenby & Wendy S. Barclay

This paper showed how influenza could evolve resistance to favipiravir, an antiviral that may be used to treat influenza. The residue that mutated to give resistance was highly conserved suggesting that the mechanism of resistance may be applicable to other RNA viruses.


Internal genes of a highly pathogenic H5N1 influenza virus determine high viral replication in myeloid cells and severe outcome of infection in mice. Plos Path. (2018).
Hui Li*, Konrad C. Bradley*, Jason S. Long, Rebecca Frise, Jonathan W. Ashcroft, Lorian C. Hartgroves, Holly Shelton, Spyridon Makris, Cecilia Johansson, Bin Cao & Wendy S. Barclay

Why do avian influenza viruses like H5N1 cause such severe disease in humans? This paper demonstrated that H5N1 viruses replicate better than human viruses in myeloid cells from mice leading to a cytokine storm and more severe disease.


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  • Journal article
    Lesch M, Luckner M, Meyer M, Weege F, Gravenstein I, Raftery M, Sieben C, Martin-Sancho L, Imai-Matsushima A, Welke R-W, Frise R, Barclay W, Schoenrich G, Herrmann A, Meyer TF, Karlas Aet al., 2019,

    RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals

    , PLoS Pathogens, Vol: 15, Pages: 1-34, ISSN: 1553-7366

    Influenza viruses (IVs) tend to rapidly develop resistance to virus-directed vaccines and common antivirals targeting pathogen determinants, but novel host-directed approaches might preclude resistance development. To identify the most promising cellular targets for a host-directed approach against influenza, we performed a comparative small interfering RNA (siRNA) loss-of-function screen of IV replication in A549 cells. Analysis of four different IV strains including a highly pathogenic avian H5N1 strain, an influenza B virus (IBV) and two human influenza A viruses (IAVs) revealed 133 genes required by all four IV strains. According to gene enrichment analyses, these strain-independent host genes were particularly enriched for nucleocytoplasmic trafficking. In addition, 360 strain-specific genes were identified with distinct patterns of usage for IAVs versus IBV and human versus avian IVs. The strain-independent host genes served to define 43 experimental and otherwise clinically approved drugs, targeting reportedly fourteen of the encoded host factors. Amongst the approved drugs, the urea-based kinase inhibitors (UBKIs) regorafenib and sorafenib exhibited a superior therapeutic window of high IV antiviral activity and low cytotoxicity. Both UBKIs appeared to block a cell signaling pathway involved in IV replication after internalization, yet prior to vRNP uncoating. Interestingly, both compounds were active also against unrelated viruses including cowpox virus (CPXV), hantavirus (HTV), herpes simplex virus 1 (HSV1) and vesicular stomatitis virus (VSV) and showed antiviral efficacy in human primary respiratory cells. An in vitro resistance development analysis for regorafenib failed to detect IV resistance development against this drug. Taken together, the otherwise clinically approved UBKIs regorafenib and sorafenib possess high and broad-spectrum antiviral activity along with substantial robustness against resistance development and thus constitute attractive hos

  • Journal article
    Lindsey BB, Singanayagam A, Tregoning JS, De Silva T, Barclay Wet al.,

    The impact of an updated pandemic H1N1 strain on shedding and immunogenicity to Russian-backbone live attenuated influenza vaccine among children in The Gambia: an open-label, observational, phase 4 study

    , Lancet Respiratory Medicine, ISSN: 2213-2600

    Background: Poor efficacy and effectiveness of thepandemic H1N1 (pH1N1) component inlive attenuated influenza vaccine (LAIV)has been demonstrated in several studies.The reasons for this are unclear, butmay be due toimpairedreplicative fitness of pH1N1 A/California/07/2009-like (Cal09) strains. The aim of this study was to establish whether an updated pH1N1 strain in the Russian-backbone trivalent LAIV resulted in greater shedding and immunogenicitycompared to Cal09.Methods: In an open-label, prospective,observational,phase 4study, we evaluated the impact of updating the pH1N1 component in the WHO prequalified Russian-backbone trivalent LAIV from Cal09in 2016-17(n=118) to an A/Michigan/45/2015-like strain (A/17/New York/15/5364, NY15) in 2017-18(n=126),on shedding and immunogenicity in Gambian children aged 2-4 years old.The study was nested within a randomised controlled trial investigating LAIV-microbiome interactions (ClinicalTrials.gov NCT02972957). Findings: Cal09 showed impairednasopharyngeal shedding(13.6%children shedding at day 2 post-LAIV)compared to H3N2(45.8%)and influenza B(80.5%), along with sub-optimal serum antibody(5.1%seroconversion)and T-cell responses(40.5% CD4+IFN-g+ and/or CD4+IL-2+responders). Following the switch to NY15, a significant increase in pH1N1 shedding(63.5%)was seen, along with improvements in seroconversion(19.1%)and influenza-specific CD4+ T-3cell responses(65.7%). The improvement in pH1N1 seroconversion with NY15 was even greater in children seronegative at baseline(37.5% vs. 7.6%). Persistent shedding today 7was independently associated with both seroconversionand CD4+ T cell responsein multivariable logistic regression. Interpretation:The pH1N1 component switch may have overcome problems in prior LAIV formulations.LAIV effectiveness against pH1N1 shouldtherefore improve in upcoming influenza seasons. Our dataalso highlightthe importance of evaluat

  • Journal article
    Dunning J, Blankley S, Hoang LT, Cox M, Graham CM, James PL, Bloom CI, Chaussabel D, Banchereau J, Brett SJ, MOSAIC Investigators, Moffatt MF, O'Garra A, Openshaw PJMet al., 2019,

    Author Correction: Progression of whole-blood transcriptional signatures from interferon-induced to neutrophil-associated patterns in severe influenza.

    , Nature Immunology, Vol: 20, Pages: 373-373, ISSN: 1529-2908

    In the version of this article initially published, a source of funding was not included in the Acknowledgements section. That section should include the following: P.J.M.O. was supported by EU FP7 PREPARE project 602525. The error has been corrected in the HTML and PDF version of the article.

  • Journal article
    James J, Smith N, Ross C, Iqbal M, Goodbourn S, Digard P, Barclay WS, Shelton Het al., 2019,

    The cellular localization of avian influenza virus PB1-F2 protein alters the magnitude of IFN2 promoter and NFκB-dependent promoter antagonism in chicken cells.

    , J Gen Virol, Vol: 100, Pages: 414-430

    The accessory protein, PB1-F2, of influenza A virus (IAV) functions in a chicken host to prolong infectious virus shedding and thus the transmission window. Here we show that this delay in virus clearance by PB1-F2 in chickens is accompanied by reduced transcript levels of type 1 interferon (IFN)-induced genes and NFκB-activated pro-inflammation cytokines. In vitro, two avian influenza isolate-derived PB1-F2 proteins, H9N2 UDL01 and H5N1 5092, exhibited the same antagonism of the IFN and pro-inflammation induction pathways seen in vivo, but to different extents. The two PB1-F2 proteins had different cellular localization in chicken cells, with H5N1 5092 being predominantly mitochondrial-associated and H9N2 UDL being cytoplasmic but not mitochondrial-localized. We hypothesized that PB1-F2 localization might influence the functionality of the protein during infection and that the protein sequence could alter cellular localization. We demonstrated that the sequence of the C-terminus of PB1-F2 determined cytoplasmic localization in chicken cells and this was linked with protein instability. Mitochondrial localization of PB1-F2 resulted in reduced antagonism of an NFκB-dependent promoter. In parallel, mitochondrial localization of PB1-F2 increased the potency of chicken IFN 2 induction antagonism. We suggest that mitochondrial localization of PB1-F2 restricts interaction with cytoplasmic-located IKKβ, reducing NFκB-responsive promoter antagonism, but enhances antagonism of the IFN2 promoter through interaction with the mitochondrial adaptor MAVS. Our study highlights the differential mechanisms by which IAV PB1-F2 protein can dampen the avian host innate signalling response.

  • Journal article
    Barclay WS, 2019,

    Receptor for bat influenza virus uncovers potential risk to humans

    , Nature, Vol: 567, Pages: 35-36, ISSN: 0028-0836

    How bat influenza viruses infect cells has been unclear. The discovery that they bind to a cell receptor that is present in many different species raises concerns about their potential risk to humans.

  • Journal article
    Long JS, Mistry B, Haslam SM, Barclay WSet al., 2019,

    Host and viral determinants of influenza A virus species specificity (vol 17, pg 67, 2018)

    , NATURE REVIEWS MICROBIOLOGY, Vol: 17, Pages: 124-124, ISSN: 1740-1526
  • Journal article
    Goldhill DH, Langat P, Xie H, Galiano M, Miah S, Kellam P, Zambon M, Lackenby A, Barclay Wet al., 2019,

    Determining the mutation bias of favipiravir in influenza using next-generation sequencing

    , Journal of Virology, Vol: 93, ISSN: 1098-5514

    Favipiravir is a broad-spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.IMPORTANCE New antiviral drugs are needed as a first line of defence in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.

  • Journal article
    Long JS, Mistry B, Haslam SM, Barclay WSet al., 2018,

    Host and viral determinants of influenza A virus species specificity

    , NATURE REVIEWS MICROBIOLOGY, Vol: 17, Pages: 67-81, ISSN: 1740-1526
  • Journal article
    Goldhill DH, te Velthuis AJW, Fletcher RA, Langat P, Zambon M, Lackenby A, Barclay WSet al., 2018,

    The mechanism of resistance to favipiravir in influenza

    , Proceedings of the National Academy of Sciences of the United States of America, Vol: 115, Pages: 11613-11618, ISSN: 0027-8424

    Favipiravir is a broad-spectrum antiviral that has shown promise in treatment of influenza virus infections. While emergence of resistance has been observed for many antiinfluenza drugs, to date, clinical trials and laboratory studies of favipiravir have not yielded resistant viruses. Here we show evolution of resistance to favipiravir in the pandemic H1N1 influenza A virus in a laboratory setting. We found that two mutations were required for robust resistance to favipiravir. We demonstrate that a K229R mutation in motif F of the PB1 subunit of the influenza virus RNA-dependent RNA polymerase (RdRP) confers resistance to favipiravir in vitro and in cell culture. This mutation has a cost to viral fitness, but fitness can be restored by a P653L mutation in the PA subunit of the polymerase. K229R also conferred favipiravir resistance to RNA polymerases of other influenza A virus strains, and its location within a highly conserved structural feature of the RdRP suggests that other RNA viruses might also acquire resistance through mutations in motif F. The mutations identified here could be used to screen influenza virus-infected patients treated with favipiravir for the emergence of resistance.

  • Journal article
    Barclay W, Openshaw P, 2018,

    The 1918 Influenza Pandemic: one hundred years of progress, but where now?

    , Lancet Respiratory Medicine, Vol: 6, ISSN: 2213-2600

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