Genomics - Next Generation Sequencing


Dr Ana Da Silva Filipe

  • NGS Facility Manager (Research Fellow) (Centre for Virus Research)

telephone: 01413306257
email: Ana.daSilvaFilipe@glasgow.ac.uk

Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1qh

ORCID iDhttps://orcid.org/0000-0002-9442-2903

Biography

Since joining the University of Glasgow in 2008 as a molecular virologist, I have accumulated extensive experience leading research in viral genomics and transcriptomics. I am passionate about innovation and implementation of sequencing solutions applied to viral systems, while maintaining a focus on quality.

Previously, I worked on gene therapy applied to vascular diseases, where I developed targeted nanovesicles containing viral vectors, for the delivery of therapeutic genes.

Currently lead the CVR Genomics team.

Google scholar: https://scholar.google.co.uk/citations?user=tcZyY6MAAAAJ

Research interests

CVR logo  Virus image CVR Supporting COVID-19 Research Response 

 

I lead the CVR Genomics team, which provides the CVR community and collaborators with expertise in high-throughput sequencing, aiming to contribute to the understanding of viruses.

My current research focuses on viral hepatitis and respiratory viruses; I am also driving the development of sequencing solutions for viral emergence and discovery.

Twitter: https://twitter.com/CVR_Genomics

Publications

List by: Type | Date

Jump to: 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2012
Number of items: 35.

2021

Hosie, M. J. et al. (2021) Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Veterinary Record, (Accepted for Publication)

Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831)

Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, (doi: 10.1016/j.cell.2021.01.037) (PMCID:PMC7843029) (Early Online Publication)

Gallo, G. et al. (2021) Interactions of viral proteins from pathogenic and low or non-pathogenic orthohantaviruses with human type I interferon signaling. Viruses, 13(1), 140. (doi: 10.3390/v13010140)

Gupta, R. K. et al. (2021) Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. Lancet Respiratory Medicine, (doi: 10.1016/S2213-2600(20)30559-2) (PMID:33444539) (PMCID:PMC7832571) (Early Online Publication)

Schultz, V. et al. (2021) Zika virus infection leads to demyelination and axonal injury in mature CNS cultures. Viruses, 13(1), 91. (doi: 10.3390/v13010091)

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)

Aranday-Cortes, E. et al. (2021) Real-world outcomes of DAA treatment and retreatment in UK-based patients infected with HCV genotypes/subtypes endemic in Africa. Journal of Infectious Diseases, (Accepted for Publication)

2020

Griffiths, M. E., Bergner, L. M. , Broos, A. , Meza, D. K., Da Silva Filipe, A. , Davison, A. , Tello, C., Becker, D. J. and Streicker, D. G. (2020) Epidemiology and biology of a herpesvirus in rabies endemic vampire bat populations. Nature Communications, 11, 5951. (doi: 10.1038/s41467-020-19832-4) (PMID:33230120) (PMCID:PMC7683562)

Clark, J. J., Gilray, J., Orton, R. J. , Baird, M., Wilkie, G., da Silva Filipe, A. , Johnson, N., McInnes, C. J., Kohl, A. and Biek, R. (2020) Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Neglected Tropical Diseases, 14(9), e0008133. (doi: 10.1371/journal.pntd.0008133) (PMID:32925939) (PMCID:PMC7515184)

Murcia, P. , Streiker, D. , Da Silva Filipe, A. , Robertson, D. , Jarrett, R. , Willett, B. , Hosie, M. , Biek, R. , Allan, K. and Weir, W. (2020) Send cat and dog samples to test for SARS-CoV-2. Veterinary Record, 186(17), p. 571. (doi: 10.1136/vr.m2019) (PMID:32451348)

Pascall, D. J. et al. (2020) "Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence. PLoS Biology, 18(4), e3000673. (doi: 10.1371/journal.pbio.3000673) (PMID:32343693) (PMCID:PMC7188197)

Alexander, A. J.T. et al. (2020) Development of a reverse genetics system for Toscana virus (lineage A). Viruses, 12(4), 411. (doi: 10.3390/v12040411)

2019

Childs, K. et al. (2019) Suboptimal SVR rates in African patients with atypical Genotype 1 subtypes: implications for global elimination of Hepatitis C. Journal of Hepatology, 71(6), pp. 1099-1105. (doi: 10.1016/j.jhep.2019.07.025) (PMID:31400349)

Jerome, H. et al. (2019) Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. Journal of Infection, 79(4), pp. 383-388. (doi: 10.1016/j.jinf.2019.08.003) (PMID:31398374) (PMCID:PMC6859916)

Wing, P. A.C. et al. (2019) Amino acid substitutions in genotype 3a hepatitis C virus polymerase protein affect responses to sofosbuvir. Gastroenterology, 157(3), 692-704.e9. (doi: 10.1053/j.gastro.2019.05.007) (PMID:31078622)

Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi: 10.1016/j.jhep.2019.04.008) (PMID:31075322)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi: 10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)

Bergner, L. M. , Orton, R. J. , da Silva Filipe, A. , Shaw, A. E., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Using noninvasive metagenomics to characterize viral communities from wildlife. Molecular Ecology Resources, 19(1), pp. 128-143. (doi: 10.1111/1755-0998.12946) (PMID:30240114) (PMCID:PMC6378809)

Ansari, M. A. et al. (2019) Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife, 8, e42463. (doi: 10.7554/eLife.42463.001) (PMID:31478835) (PMCID:PMC6721795)

2018

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi: 10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Bamford, C. G.G. et al. (2018) A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. PLoS Pathogens, 14(10), e1007307. (doi: 10.1371/journal.ppat.1007307) (PMID:30308076) (PMCID:PMC6181419)

Masembe, C. , Sreenu, V. B. , Da Silva Filipe, A. , Wilkie, G. S., Ogweng, P., Mayega, F. J., Muwanika, V. B., Biek, R. , Palmarini, M. and Davison, A. J. (2018) Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda. Microbiology Resource Announcements, 7(13), e01018-18. (doi: 10.1128/mra.01018-18) (PMID:30533685) (PMCID:PMC6256554)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi: 10.1016/j.jhep.2017.11.044) (PMID:29339112)

2017

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi: 10.1016/j.jhep.2017.06.035) (PMID:28789880)

Çevik, R. E., Cesarec, M., Da Silva Filipe, A. , Licastro, D., McLauchlan, J. and Marcello, A. (2017) Hepatitis C virus NS5A targets the nucleosome assembly protein NAP1L1 to control the innate cellular response. Journal of Virology, 91(18), e00880-17. (doi: 10.1128/JVI.00880-17) (PMID:28659470)

2016

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi: 10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Thomson, E. et al. (2016) Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes. Journal of Clinical Microbiology, 54(10), pp. 2470-2484. (doi: 10.1128/JCM.00330-16) (PMID:27385709) (PMCID:PMC5035407)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

2015

Robinson, M. W. et al. (2015) Viral genotype correlates with distinct liver gene transcription signatures in chronic hepatitis C virus infection. Liver International, 35(10), pp. 2256-2264. (doi: 10.1111/liv.12830) (PMID:25800823) (PMCID:PMC4949513)

Filipe, A. and McLauchlan, J. (2015) Hepatitis C virus and lipid droplets: finding a niche. Trends in Molecular Medicine, 21(1), pp. 34-42. (doi: 10.1016/j.molmed.2014.11.003)

2012

Oehler, V., Filipe, A. , Montserret, R., da Costa, D., Brown, G., Penin, F. and McLauchlan, J. (2012) Structural analysis of Hepatitis C virus core-E1 signal peptide and requirements for cleavage of the genotype 3a signal sequence by signal peptide peptidase. Journal of Virology, 86(15), pp. 7818-7828. (doi: 10.1128/JVI.00457-12) (PMID:22593157) (PMCID:PMC3421639)

This list was generated on Mon Mar 1 12:26:07 2021 GMT.
Jump to: Articles
Number of items: 35.

Articles

Hosie, M. J. et al. (2021) Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission. Veterinary Record, (Accepted for Publication)

Rihn, S. J. et al. (2021) A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. PLoS Biology, 19(2), e3001091. (doi: 10.1371/journal.pbio.3001091) (PMID:33630831)

Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, (doi: 10.1016/j.cell.2021.01.037) (PMCID:PMC7843029) (Early Online Publication)

Gallo, G. et al. (2021) Interactions of viral proteins from pathogenic and low or non-pathogenic orthohantaviruses with human type I interferon signaling. Viruses, 13(1), 140. (doi: 10.3390/v13010140)

Gupta, R. K. et al. (2021) Development and validation of the ISARIC 4C Deterioration model for adults hospitalised with COVID-19: a prospective cohort study. Lancet Respiratory Medicine, (doi: 10.1016/S2213-2600(20)30559-2) (PMID:33444539) (PMCID:PMC7832571) (Early Online Publication)

Schultz, V. et al. (2021) Zika virus infection leads to demyelination and axonal injury in mature CNS cultures. Viruses, 13(1), 91. (doi: 10.3390/v13010091)

Da Silva Filipe, A. et al. (2021) Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(1), pp. 112-122. (doi: 10.1038/s41564-020-00838-z) (PMID:33349681)

Volz, E. et al. (2021) Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. Cell, 184(1), 64-75.e11. (doi: 10.1016/j.cell.2020.11.020) (PMID:33275900) (PMCID:PMC7674007)

Aranday-Cortes, E. et al. (2021) Real-world outcomes of DAA treatment and retreatment in UK-based patients infected with HCV genotypes/subtypes endemic in Africa. Journal of Infectious Diseases, (Accepted for Publication)

Griffiths, M. E., Bergner, L. M. , Broos, A. , Meza, D. K., Da Silva Filipe, A. , Davison, A. , Tello, C., Becker, D. J. and Streicker, D. G. (2020) Epidemiology and biology of a herpesvirus in rabies endemic vampire bat populations. Nature Communications, 11, 5951. (doi: 10.1038/s41467-020-19832-4) (PMID:33230120) (PMCID:PMC7683562)

Clark, J. J., Gilray, J., Orton, R. J. , Baird, M., Wilkie, G., da Silva Filipe, A. , Johnson, N., McInnes, C. J., Kohl, A. and Biek, R. (2020) Population genomics of louping ill virus provide new insights into the evolution of tick-borne flaviviruses. PLoS Neglected Tropical Diseases, 14(9), e0008133. (doi: 10.1371/journal.pntd.0008133) (PMID:32925939) (PMCID:PMC7515184)

Murcia, P. , Streiker, D. , Da Silva Filipe, A. , Robertson, D. , Jarrett, R. , Willett, B. , Hosie, M. , Biek, R. , Allan, K. and Weir, W. (2020) Send cat and dog samples to test for SARS-CoV-2. Veterinary Record, 186(17), p. 571. (doi: 10.1136/vr.m2019) (PMID:32451348)

Pascall, D. J. et al. (2020) "Frozen evolution" of an RNA virus suggests accidental release as a potential cause of arbovirus re-emergence. PLoS Biology, 18(4), e3000673. (doi: 10.1371/journal.pbio.3000673) (PMID:32343693) (PMCID:PMC7188197)

Alexander, A. J.T. et al. (2020) Development of a reverse genetics system for Toscana virus (lineage A). Viruses, 12(4), 411. (doi: 10.3390/v12040411)

Childs, K. et al. (2019) Suboptimal SVR rates in African patients with atypical Genotype 1 subtypes: implications for global elimination of Hepatitis C. Journal of Hepatology, 71(6), pp. 1099-1105. (doi: 10.1016/j.jhep.2019.07.025) (PMID:31400349)

Jerome, H. et al. (2019) Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. Journal of Infection, 79(4), pp. 383-388. (doi: 10.1016/j.jinf.2019.08.003) (PMID:31398374) (PMCID:PMC6859916)

Wing, P. A.C. et al. (2019) Amino acid substitutions in genotype 3a hepatitis C virus polymerase protein affect responses to sofosbuvir. Gastroenterology, 157(3), 692-704.e9. (doi: 10.1053/j.gastro.2019.05.007) (PMID:31078622)

Ankcorn, M. et al. (2019) Convalescent plasma therapy for persistent hepatitis E virus infection. Journal of Hepatology, 71(2), pp. 434-438. (doi: 10.1016/j.jhep.2019.04.008) (PMID:31075322)

Singer, J. B. et al. (2019) Interpreting viral deep sequencing data with GLUE. Viruses, 11(4), 323. (doi: 10.3390/v11040323) (PMID:30987147) (PMCID:PMC6520954)

Davis, C. et al. (2019) New highly diverse hepatitis C strains detected in sub‐Saharan Africa have unknown susceptibility to direct‐acting antiviral treatments. Hepatology, 69(4), pp. 1426-1441. (doi: 10.1002/hep.30342) (PMID:30387174) (PMCID:PMC6492010)

McFarlane, S. et al. (2019) The histone chaperone HIRA promotes the induction of host innate immune defences in response to HSV-1 infection. PLoS Pathogens, 15(3), e1007667. (doi: 10.1371/journal.ppat.1007667) (PMID:30901352) (PMCID:PMC6472835)

Bergner, L. M. , Orton, R. J. , da Silva Filipe, A. , Shaw, A. E., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Using noninvasive metagenomics to characterize viral communities from wildlife. Molecular Ecology Resources, 19(1), pp. 128-143. (doi: 10.1111/1755-0998.12946) (PMID:30240114) (PMCID:PMC6378809)

Ansari, M. A. et al. (2019) Interferon lambda 4 impacts the genetic diversity of hepatitis C virus. eLife, 8, e42463. (doi: 10.7554/eLife.42463.001) (PMID:31478835) (PMCID:PMC6721795)

Dunlop, J. I. et al. (2018) Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas. PLoS Neglected Tropical Diseases, 12(10), e0006884. (doi: 10.1371/journal.pntd.0006884) (PMID:30372452) (PMCID:PMC6245839)

Bamford, C. G.G. et al. (2018) A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages. PLoS Pathogens, 14(10), e1007307. (doi: 10.1371/journal.ppat.1007307) (PMID:30308076) (PMCID:PMC6181419)

Masembe, C. , Sreenu, V. B. , Da Silva Filipe, A. , Wilkie, G. S., Ogweng, P., Mayega, F. J., Muwanika, V. B., Biek, R. , Palmarini, M. and Davison, A. J. (2018) Genome sequences of five African swine fever virus genotype IX isolates from domestic pigs in Uganda. Microbiology Resource Announcements, 7(13), e01018-18. (doi: 10.1128/mra.01018-18) (PMID:30533685) (PMCID:PMC6256554)

da Silva Filipe, A. et al. (2018) Reply to: "Reply to: 'Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries'". Journal of Hepatology, 68(4), pp. 864-866. (doi: 10.1016/j.jhep.2017.11.044) (PMID:29339112)

da Silva Filipe, A. et al. (2017) Response to DAA therapy in the NHS England early access programme for rare HCV subtypes from low and middle income countries. Journal of Hepatology, 67(6), pp. 1348-1350. (doi: 10.1016/j.jhep.2017.06.035) (PMID:28789880)

Çevik, R. E., Cesarec, M., Da Silva Filipe, A. , Licastro, D., McLauchlan, J. and Marcello, A. (2017) Hepatitis C virus NS5A targets the nucleosome assembly protein NAP1L1 to control the innate cellular response. Journal of Virology, 91(18), e00880-17. (doi: 10.1128/JVI.00880-17) (PMID:28659470)

Donald, C. L. et al. (2016) Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil. PLoS Neglected Tropical Diseases, 10(10), e0005048. (doi: 10.1371/journal.pntd.0005048) (PMID:27706161) (PMCID:PMC5051680)

Thomson, E. et al. (2016) Comparison of next generation sequencing technologies for the comprehensive assessment of full-length hepatitis C viral genomes. Journal of Clinical Microbiology, 54(10), pp. 2470-2484. (doi: 10.1128/JCM.00330-16) (PMID:27385709) (PMCID:PMC5035407)

Jacobs, M. et al. (2016) Late Ebola virus relapse causing meningoencephalitis: a case report. Lancet, 388(10043), pp. 498-503. (doi: 10.1016/S0140-6736(16)30386-5) (PMID:27209148) (PMCID:PMC4967715)

Robinson, M. W. et al. (2015) Viral genotype correlates with distinct liver gene transcription signatures in chronic hepatitis C virus infection. Liver International, 35(10), pp. 2256-2264. (doi: 10.1111/liv.12830) (PMID:25800823) (PMCID:PMC4949513)

Filipe, A. and McLauchlan, J. (2015) Hepatitis C virus and lipid droplets: finding a niche. Trends in Molecular Medicine, 21(1), pp. 34-42. (doi: 10.1016/j.molmed.2014.11.003)

Oehler, V., Filipe, A. , Montserret, R., da Costa, D., Brown, G., Penin, F. and McLauchlan, J. (2012) Structural analysis of Hepatitis C virus core-E1 signal peptide and requirements for cleavage of the genotype 3a signal sequence by signal peptide peptidase. Journal of Virology, 86(15), pp. 7818-7828. (doi: 10.1128/JVI.00457-12) (PMID:22593157) (PMCID:PMC3421639)

This list was generated on Mon Mar 1 12:26:07 2021 GMT.

Grants

Grants and Awards listed are those received whilst working with the University of Glasgow.

  • SARS-CoV-2 infections in cats: assessing their zoonotic potential and role in sustaining the pandemic
    Biotechnology and Biological Sciences Research Council
    2021 - 2022
     
  • Enhancing dengue surveillance in the Philippines
    British Council
    2020 - 2023
     
  • A pilot study to establish the use of whole genome sequencing in characterising nosocomial influenza cases
    Sheffield Teaching Hospitals NHS Foundation Trust
    2019 - 2020
     
  • Exploring in-host evolution and viral determinants of enhanced replicative ability of live attenuated influenza vaccine using whole genome sequencing
    British Infection Association
    2018 - 2020
     
  • Developing innovative and sustainable approaches to prevent the spread fo African swine fever in Africa (ASF-RESIST)
    African Union
    2018 - 2021
     
  • DENV project
    Medical Research Council
    2016 - 2019
     
  • Validation of metabolomics as a technique to identify determinants of treatment response in HCV infection (ISSF Catalyst)
    Wellcome Trust
    2014 - 2015
     

Research datasets

Jump to: 2020
Number of items: 1.

2020

Schultz, V. , Cumberworth, S., Gu, N., Johnson, N., Donald, C. , McCanney, G., Barrie, J., Da Silva Filipe, A. , Linington, C. , Willison, H. , Edgar, J., Barnett, S. and Kohl, A. (2020) Zika virus infection leads to demyelination and axonal injury in mature CNS cultures. [Data Collection]

This list was generated on Mon Mar 1 04:59:02 2021 GMT.

Research group members

 

Ana da Silva Filipe
NGS Facility Manager

Stephen Carmichael

 Stephen Carmichael
 Research Associate NGS

Daniel Mair

Daniel Mair
Technician - Genomics

 

 

Jenna Nichols CVR staff profile

Jenna Nichols
Research Technician

 

 

Katherine Smollett

Katherine Smollett
Research Associate NGS

Lily Tong
Research Support - Genomics

 

 

Kyriaki Nomikou
Research Associate NGS

MRC, University of Glasgow and CVR logos