2024

Herder, V. et al. (2024) Correlates of disease severity in bluetongue as a model of acute arbovirus infection. PLoS Pathogens, 20(8), e1012466. (doi: 10.1371/journal.ppat.1012466) (PMID:39150989) (Early Online Publication)

Ahovègbé, L. et al. (2024) Hepatitis C virus diversity and treatment outcomes in Benin; a prospective cohort study. Lancet Microbe, 5(7), pp. 697-706. (doi: 10.1016/S2666-5247(24)00041-7) (PMID:38889738)

Ranum, J. N. et al. (2024) Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Research, 52(6), pp. 3199-3212. (doi: 10.1093/nar/gkae133) (PMID:38407436) (PMCID:PMC11014358)

Spinard, E. et al. (2024) Near-complete genome sequences of multiple genotype 1 African swine fever virus isolates from 2016 to 2018 in Cameroon. Microbiology Resource Announcements, 13(4), e00978-23. (doi: 10.1128/mra.00978-23) (PMID:38477459) (PMCID:PMC11008206)

Namuwulya, P. et al. (2024) Viruses associated with measles-like illnesses in Uganda. Journal of Infection, (doi: 10.1016/j.jinf.2024.106148) (PMID:38588959) (In Press)

Herder, V. et al. (2024) A machine learning framework to identify the correlates of disease severity in acute arbovirus infection. bioRxiv, (doi: 10.1101/2024.02.23.581333)

Gonzalo Nadal, V. et al. (2024) Suspected tick-borne flavivirus meningoencephalomyelitis in dogs from the UK: six cases (2021). Journal of Small Animal Practice, 65(2), pp. 132-143. (doi: 10.1111/jsap.13682) (PMID:37956993)

2023

Meehan, G. R. et al. (2023) Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning. PLoS Pathogens, 19(11), e1011589. (doi: 10.1371/journal.ppat.1011589) (PMID:37934791) (PMCID:PMC10656012)

Jones, S. et al. (2023) SARS-CoV-2 in domestic UK cats from Alpha to Omicron: Swab surveillance and case reports. Viruses, 15(8), 1769. (doi: 10.3390/v15081769) (PMID:37632111) (PMCID:PMC10459977)

Pascall, D. J. et al. (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. Journal of Infection, 87(2), pp. 128-135. (doi: 10.1016/j.jinf.2023.05.019) (PMID:37270070) (PMCID:PMC10234362)

Hardy, A. et al. (2023) The timing and magnitude of the type I interferon response are correlated with disease tolerance in arbovirus infection. mBio, 14(3), e0010123. (doi: 10.1128/mbio.00101-23) (PMID:37097030) (PMCID:PMC10294695)

Ho, A. et al. (2023) Adeno-associated virus 2 infection in children with non-A-E hepatitis. Nature, 617(7961), pp. 555-563. (doi: 10.1038/s41586-023-05948-2) (PMID:36996873)

Pascall, D. J. et al. (2023) The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. PLoS ONE, 18(4), e0284187. (doi: 10.1371/journal.pone.0284187) (PMID:37053201) (PMCID:PMC10101505)

Viana, M. et al. (2023) Effects of culling vampire bats on the spatial spread and spillover of rabies virus. Science Advances, 9(10), eadd7437. (doi: 10.1126/sciadv.add7437) (PMID:36897949) (PMCID:PMC10005164)

Gallacher, J., Taha Y, Y., Da Silva Filipe, A. , Ijaz, S. and McPherson, S. (2023) Ledipasvir/sofosbuvir and ribavirin for the treatment of ribavirin-refractory persistent hepatitis E virus infection. ID Cases, 32, e01741. (doi: 10.1016/j.idcr.2023.e01741) (PMID:36942308) (PMCID:PMC10023993)

2022

Martinez, J. , Ross, P. A., Gu, X., Ant, T. H., Murdochy, S. M., Tong, L., da Silva Filipe, A. , Hoffmann, A. A. and Sinkins, S. P. (2022) Genomic and phenotypic comparisons reveal distinct variants of Wolbachia strain wAlbB. Applied and Environmental Microbiology, 88(22), e0141222. (doi: 10.1128/aem.01412-22) (PMID:36318064) (PMCID:PMC9680635)

Sugrue, E. et al. (2022) The apparent interferon resistance of transmitted HIV-1 is possibly a consequence of enhanced replicative fitness. PLoS Pathogens, 18(11), e1010973. (doi: 10.1371/journal.ppat.1010973) (PMID:36399512) (PMCID:PMC9718408)

Willett, B. J. et al. (2022) Publisher Correction: SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7, 1709. (doi: 10.1038/s41564-022-01241-6) (PMID:36114232) (PMCID:PMC9483304)

Aranday-Cortes, E. et al. (2022) Real-world outcomes of direct-acting antiviral treatment and retreatment in United Kingdom–based patients infected with hepatitis C virus genotypes/subtypes endemic in Africa. Journal of Infectious Diseases, 226(6), pp. 995-1004. (doi: 10.1093/infdis/jiab110) (PMID:33668068) (PMCID:PMC9492310)

Martinez, J. , Ant, T. H., Murdochy, S. M., Tong, L., da Silva Filipe, A. and Sinkins, S. P. (2022) Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genetics, 18(9), e1010406. (doi: 10.1371/journal.pgen.1010406) (PMID:36121852) (PMCID:PMC9560607)

Shah, R. et al. (2022) Characterisation of a hepatitis C virus subtype 2a cluster in Scottish PWID with a suboptimal response to glecaprevir/pibrentasvir treatment. Viruses, 14(8), 1678. (doi: 10.3390/v14081678) (PMID:36016300) (PMCID:PMC9416734)

Willett, B. J. et al. (2022) SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(8), pp. 1161-1179. (doi: 10.1038/s41564-022-01143-7) (PMID:35798890) (PMCID:PMC9352574)

Nickbakhsh, S. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12, 11735. (doi: 10.1038/s41598-022-15661-1) (PMID:35853960) (PMCID:PMC9296497)

Vucak, M. et al. (2022) Genome sequences of five arenaviruses from pygmy mice (Mus minutoides) in Sierra Leone. Microbiology Resource Announcements, 11(5), e0009522. (doi: 10.1128/mra.00095-22) (PMID:35389260) (PMCID:PMC9119099)

Griffiths, M. E. , Broos, A. , Bergner, L. M. , Meza, D. K., Suarez, N. M., Da Silva Filipe, A. , Tello, C., Becker, D. J. and Streicker, D. G. (2022) Longitudinal deep sequencing informs vector selection and future deployment strategies for transmissible vaccines. PLoS Biology, 20(4), e3001580. (doi: 10.1371/journal.pbio.3001580) (PMID:35439242) (PMCID:PMC9017877)

Stockdale, A. J. et al. (2022) A clinical and molecular epidemiological survey of hepatitis C in Blantyre, Malawi suggests an historic mechanism of transmission. Journal of Viral Hepatitis, 29(4), pp. 252-262. (doi: 10.1111/jvh.13646) (PMID:35075742) (PMCID:PMC9305194)

Aggarwal, D. et al. (2022) Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13, 1012. (doi: 10.1038/s41467-022-28371-z) (PMID:35197443) (PMCID:PMC8866425)

Aggarwal, D. et al. (2022) Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13, 751. (doi: 10.1038/s41467-021-27942-w) (PMID:35136068) (PMCID:PMC8826310)

Twohig, K. A. et al. (2022) Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infectious Diseases, 22(1), pp. 35-42. (doi: 10.1016/S1473-3099(21)00475-8) (PMID:34461056) (PMCID:PMC8397301)

Xu, R. et al. (2022) The evolutionary dynamics and epidemiological history of hepatitis C virus genotype 6, including unique strains from the Li community of Hainan Island, China. Virus Evolution, 8(1), veac012. (doi: 10.1093/ve/veac012) (PMID:35600095) (PMCID:PMC9115904)

2021

Niemi, M. E. K. et al. (2021) Mapping the human genetic architecture of COVID-19. Nature, 600(7889), pp. 472-477. (doi: 10.1038/s41586-021-03767-x) (PMID:34237774) (PMCID:PMC8674144)

Vöhringer, H. S. et al. (2021) Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600(7889), pp. 506-511. (doi: 10.1038/s41586-021-04069-y) (PMID:34649268) (PMCID:PMC8674138)

Boshier, F. A.T. et al. (2021) The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83(6), pp. 693-700. (doi: 10.1016/j.jinf.2021.09.022) (PMID:34610391) (PMCID:PMC8487101)

Herder, V. et al. (2021) Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of IFN-mediated innate immune defences. PLoS Biology, 19(12), e3001065. (doi: 10.1371/journal.pbio.3001065) (PMID:34932557) (PMCID:PMC8765667)

Shaw, A. E. et al. (2021) The antiviral state has shaped the CpG composition of the vertebrate interferome to avoid self-targeting. PLoS Biology, 19(9), e3001352. (doi: 10.1371/journal.pbio.3001352) (PMID:34491982) (PMCID:PMC8423302)

Baksmeier, C. et al. (2021) Modified recombinant human IgG1-Fc is superior to natural intravenous immunoglobulin at inhibiting immune-mediated demyelination. Immunology, 164(1), pp. 90-105. (doi: 10.1111/imm.13341) (PMID:33880776) (PMCID:PMC8358725)

Smith, D. A. et al. (2021) Real world SOF/VEL/VOX retreatment outcomes and viral resistance analysis for HCV patients with prior failure to DAA therapy. Journal of Viral Hepatitis, 28(9), pp. 1256-1264. (doi: 10.1111/jvh.13549) (PMID:34003556)

Szemiel, A. M. et al. (2021) In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. PLoS Pathogens, 17(9), e1009929. (doi: 10.1371/journal.ppat.1009929) (PMID:34534263) (PMCID:PMC8496873)

Russell, C. D. et al. (2021) Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe, 2(8), e354-e365. (doi: 10.1016/S2666-5247(21)00090-2) (PMID:34100002) (PMCID:PMC8172149)

Drake, T. M. et al. (2021) Characterisation of in-hospital complications associated with COVID-19 using the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, multicentre cohort study. Lancet, 398(10296), pp. 223-237. (doi: 10.1016/S0140-6736(21)00799-6) (PMID:34274064) (PMCID:PMC8285118)

Li, K. K. et al. (2021) Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - a high risk community-hospital interface. Journal of Infection, 83(1), pp. 96-103. (doi: 10.1016/j.jinf.2021.04.020) (PMID:33895226) (PMCID:PMC8061788)

Davis, C. A. et al. (2021) Hepatitis E virus: whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes. Journal of Clinical Virology, 139, 104738. (doi: 10.1016/j.jcv.2021.104738) (PMID:33933822)

Graham, M. S. et al. (2021) Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. Lancet Public Health, 6(5), e335-e345. (doi: 10.1016/S2468-2667(21)00055-4)

Volz, E. et al. (2021) Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), pp. 266-269. (doi: 10.1038/s41586-021-03470-x) (PMID:33767447)

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, 188(8), e247. (doi: 10.1002/vetr.247) (PMID:33890314) (PMCID:PMC8251078)

Lythgoe, K. A. et al. (2021) SARS-CoV-2 within-host diversity and transmission. Science, 372(6539), eabg0821. (doi: 10.1126/science.abg0821) (PMID:33688063) (PMCID:PMC8128293)

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, 9(4), pp. 349-359. (doi: 10.1016/S2213-2600(20)30559-2) (PMID:33444539) (PMCID:PMC7832571)

Thomson, E. C. et al. (2021) Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(5), 1171-1187.e20. (doi: 10.1016/j.cell.2021.01.037) (PMID:33621484) (PMCID:PMC7843029)

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) (PMCID:PMC7906417)

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) (PMID:33478127) (PMCID:PMC7835746)

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) (PMID:33440758) (PMCID:PMC7827345)

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)

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)

Parker, M. D. et al. (2021) Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31, pp. 645-658. (doi: 10.1101/gr.268110.120) (PMID:33722935) (PMCID:PMC8015849)

Stirrup, O. et al. (2021) SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8, e001029. (doi: 10.1136/bmjresp-2021-001029) (PMID:34544733) (PMCID:PMC8453594)

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)

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) (PMID:31478835) (PMCID:PMC6721795)

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)

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)