Publications
2024
Can self-testing be enhanced to hasten safe return of healthcare workers in pandemics? Random order, open label trial using two manufacturers' SARS-CoV-2 lateral flow devices concurrently and nested viral culture study.
Zhang, X., Cheyne, C. P., Jones, C., Humann, M., Leeming, G., Smith, C., . . . Buchan, I. E. (2024). Can self-testing be enhanced to hasten safe return of healthcare workers in pandemics? Random order, open label trial using two manufacturers' SARS-CoV-2 lateral flow devices concurrently and nested viral culture study.. BMC infectious diseases, 24(1), 1276. doi:10.1186/s12879-024-10155-z
Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches.
Dandachi, I., Alrezaihi, A., Amin, D., AlRagi, N., Alhatlani, B., Binjomah, A., . . . Aljabr, W. (2024). Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches.. Microbiology spectrum, 12(8), e0066524. doi:10.1128/spectrum.00665-24
SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.
Goldswain, H., Penrice-Randal, R., Donovan-Banfield, I., Duffy, C. W., Dong, X., Randle, N., . . . Emmett, S. R. (2024). SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection.. Genome medicine, 16(1), 89. doi:10.1186/s13073-024-01360-1
Can self-testing be enhanced to hasten safe return of healthcare workers in pandemics? Random order, open label trial using two manufacturers’ SARS-CoV-2 lateral flow devices concurrently
Sequential Infection with Influenza A Virus Followed by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Leads to More Severe Disease and Encephalitis in a Mouse Model of COVID-19.
Clark, J. J., Penrice-Randal, R., Sharma, P., Dong, X., Pennington, S. H., Marriott, A. E., . . . Stewart, J. P. (2024). Sequential Infection with Influenza A Virus Followed by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Leads to More Severe Disease and Encephalitis in a Mouse Model of COVID-19.. Viruses, 16(6), 863. doi:10.3390/v16060863
2023
Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome
Alrezaihi, A., Penrice-Randal, R., Dong, X., Prince, T., Randle, N., Semple, M. G., . . . Hiscox, J. A. (2023). Enrichment of SARS-CoV-2 sequence from nasopharyngeal swabs whilst identifying the nasal microbiome. Journal of Clinical Virology, 105620. doi:10.1016/j.jcv.2023.105620
Analysis of SARS-CoV-2 Population Genetics from Samples Associated with Huanan Market and Early Cases Identifies Substitutions Associated with Future Variants of Concern.
Dong, X., & Hiscox, J. A. (2023). Analysis of SARS-CoV-2 Population Genetics from Samples Associated with Huanan Market and Early Cases Identifies Substitutions Associated with Future Variants of Concern.. Viruses, 15(8), 1728. doi:10.3390/v15081728
Recombinant SARS-CoV-2 lacking initiating and internal methionine codons within ORF10 is attenuated<i>in vivo</i>
Enrichment of Sars-Cov-2 and Seasonal Coronavirus Sequence from Nasopharyngeal Swabs Whilst Maintaining the Background Context of the Microbiome
Alrezaihi, A., Penrice-Randal, R., Dong, X., Prince, T., Randle, N., Semple, M., . . . Hiscox, J. (2023). Enrichment of Sars-Cov-2 and Seasonal Coronavirus Sequence from Nasopharyngeal Swabs Whilst Maintaining the Background Context of the Microbiome. doi:10.2139/ssrn.4484216
Linked Mutations in the Ebola Virus Polymerase Are Associated with Organ Specific Phenotypes
Dong, X., Tree, J., Banadyga, L., He, S., Zhu, W., Tipton, T., . . . Hiscox, J. A. A. (2023). Linked Mutations in the Ebola Virus Polymerase Are Associated with Organ Specific Phenotypes. MICROBIOLOGY SPECTRUM, 11(2). doi:10.1128/spectrum.04154-22
The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.
Goldswain, H., Dong, X., Penrice-Randal, R., Alruwaili, M., Shawli, G. T., Prince, T., . . . Hiscox, J. A. (2023). The P323L substitution in the SARS-CoV-2 polymerase (NSP12) confers a selective advantage during infection.. Genome biology, 24(1), 47. doi:10.1186/s13059-023-02881-5
2022
Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial
Donovan-Banfield, I., Penrice-Randal, R., Goldswain, H., Rzeszutek, A. M., Pilgrim, J., Bullock, K., . . . Fletcher, T. (2022). Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial. NATURE COMMUNICATIONS, 13(1). doi:10.1038/s41467-022-34839-9
New Cell Lines Derived from Laboratory Colony Triatoma infestans and Rhodnius prolixus, Vectors of Trypanosoma cruzi, Do Not Harbour Triatoma Virus
Penrice-Randal, R., Hartley, C., Beliavskaia, A., Dong, X., Brandner-Garrod, L., Whitten, M., & Bell-Sakyi, L. (2022). New Cell Lines Derived from Laboratory Colony Triatoma infestans and Rhodnius prolixus, Vectors of Trypanosoma cruzi, Do Not Harbour Triatoma Virus. INSECTS, 13(10). doi:10.3390/insects13100906
Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.
Penrice-Randal, R., Dong, X., Shapanis, A. G., Gardner, A., Harding, N., Legebeke, J., . . . Baralle, D. (2022). Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.. Frontiers in immunology, 13, 988685. doi:10.3389/fimmu.2022.988685
Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages
Prince, T., Dong, X., Penrice-Randal, R., Randle, N., Hartley, C., Goldswain, H., . . . Hiscox, J. A. (2022). Analysis of SARS-CoV-2 in Nasopharyngeal Samples from Patients with COVID-19 Illustrates Population Variation and Diverse Phenotypes, Placing the Growth Properties of Variants of Concern in Context with Other Lineages. MSPHERE, 7(3). doi:10.1128/msphere.00913-21
SARS-CoV-2 minor variant genomes at the start of the pandemic contained markers of VoCs
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Donovan-Banfield, I., . . . Hiscox, J. A. (2022). Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. GIGASCIENCE, 11. doi:10.1093/gigascience/giac045
Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19
Legebeke, J., Lord, J., Penrice-Randal, R., Vallejo, A. F., Poole, S., Brendish, N. J., . . . Baralle, D. (2022). Evaluating the Immune Response in Treatment-Naive Hospitalised Patients With Influenza and COVID-19. FRONTIERS IN IMMUNOLOGY, 13. doi:10.3389/fimmu.2022.853265
Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway
Zhou, J., Peacock, T. P., Brown, J. C., Goldhill, D. H., Elrefaey, A. M. E., Penrice-Randal, R., . . . Barclay, W. S. (2022). Mutations that adapt SARS-CoV-2 to mink or ferret do not increase fitness in the human airway. Cell Reports, 110344. doi:10.1016/j.celrep.2022.110344
Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway.
Zhou, J., Peacock, T., Brown, J., Goldhill, D., Elrefaey, A., Penrice-Randal, R., . . . Barclay, W. (2021). Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway.. doi:10.21203/rs.3.rs-829214/v1
2021
Dose-Dependent Response to Infection with Ebola Virus in the Ferret Model and Evidence of Viral Evolution in the Eye
Watson, R. J., Tree, J., Fotheringham, S. A., Hall, Y., Dong, X., Steeds, K., . . . Funnell, S. G. P. (2021). Dose-Dependent Response to Infection with Ebola Virus in the Ferret Model and Evidence of Viral Evolution in the Eye. JOURNAL OF VIROLOGY, 95(24). doi:10.1128/JVI.00833-21
Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.
Aljabr, W., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A., Harrison, A. J., Ryan, Y., . . . Hiscox, J. A. (2021). Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.. mSphere, e0021921. doi:10.1128/msphere.00219-21
Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans
Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Salguero, J., . . . Hiscox, J. (2021). Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans. doi:10.1101/2021.03.03.433753
Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19
Salguero, F. J., White, A. D., Slack, G. S., Fotheringham, S. A., Bewley, K. R., Gooch, K. E., . . . Carroll, M. W. (2021). Comparison of rhesus and cynomolgus macaques as an infection model for COVID-19. NATURE COMMUNICATIONS, 12(1). doi:10.1038/s41467-021-21389-9
Tissue-Specific Immunopathology in Fatal COVID-19
Dorward, D. A., Russell, C. D., Um, I. H., Elshani, M., Armstrong, S. D., Penrice-Randal, R., . . . Lucas, C. D. (2021). Tissue-Specific Immunopathology in Fatal COVID-19. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 203(2), 192-201. doi:10.1164/rccm.202008-3265OC
Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care
Bosworth, A., Rickett, N. Y., Dong, X., Ng, L. F. P., Garcia-Dorival, I., Matthews, D. A., . . . Hiscox, J. A. (2021). Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care. GENOME MEDICINE, 13(1). doi:10.1186/s13073-020-00811-9
2020
Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)
Aljabr, W., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A., Harrison, A. J., Ryan, Y., . . . Hiscox, J. (2020). Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS). doi:10.1101/2020.11.28.400671
Sequential infection with influenza A virus followed by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to more severe disease and encephalitis in a mouse model of COVID-19
Clark, J., Penrice-Randal, R., Sharma, P., Kipar, A., Dong, X., Pennington, S., . . . Stewart, J. (2020). Sequential infection with influenza A virus followed by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to more severe disease and encephalitis in a mouse model of COVID-19. doi:10.1101/2020.10.13.334532
Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism
Moore, S. C., Penrice-Randal, R., Alruwaili, M., Randle, N., Armstrong, S., Hartley, C., . . . Hiscox, J. A. (2020). Amplicon-Based Detection and Sequencing of SARS-CoV-2 in Nasopharyngeal Swabs from Patients With COVID-19 and Identification of Deletions in the Viral Genome That Encode Proteins Involved in Interferon Antagonism. VIRUSES-BASEL, 12(10). doi:10.3390/v12101164
Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease
Dong, X., Munoz-Basagoiti, J., Rickett, N. Y., Pollakis, G., Paxton, W. A., Guenther, S., . . . Hiscox, J. A. (2020). Variation around the dominant viral genome sequence contributes to viral load and outcome in patients with Ebola virus disease. GENOME BIOLOGY, 21(1). doi:10.1186/s13059-020-02148-3
Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19
Moore, S., Penrice-Randal, R., Alruwaili, M., Dong, X., Pullan, S., Carter, D., . . . Hiscox, J. (2020). Amplicon based MinION sequencing of SARS-CoV-2 and metagenomic characterisation of nasopharyngeal swabs from patients with COVID-19. doi:10.1101/2020.03.05.20032011
2019
Investigating the Cellular Transcriptomic Response Induced by the Makona Variant of Ebola Virus in Differentiated THP-1 Cells
Bosworth, A., Dowall, S. D., Armstrong, S., Liu, X., Dong, X., Bruce, C. B., . . . Hiscox, J. A. (2019). Investigating the Cellular Transcriptomic Response Induced by the Makona Variant of Ebola Virus in Differentiated THP-1 Cells. VIRUSES-BASEL, 11(11). doi:10.3390/v11111023
Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <em>Mycobacterium ulcerans</em> and Multiple <em>Wolbachia</em> Sequence Types Revealed by Metagenomics
A systematic comparison of eight new plastome sequences from <i>Ipomoea</i> L.
Sun, J., Dong, X., Cao, Q., Xu, T., Zhu, M., Sun, J., . . . Li, Z. (2019). A systematic comparison of eight new plastome sequences from <i>Ipomoea</i> L.. PeerJ, 7, e6563. doi:10.7717/peerj.6563
Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <i>Mycobacterium ulcerans</i> and Multiple <i>Wolbachia</i> Sequence Types Revealed by Metagenomics
Esemu, S. N., Dong, X., Kfusi, A. J., Hartley, C. S., Ndip, R. N., Ndip, L. M., . . . Makepeace, B. L. (2019). Aquatic Hemiptera in Southwest Cameroon: Biodiversity of Potential Reservoirs of <i>Mycobacterium ulcerans</i> and Multiple <i>Wolbachia</i> Sequence Types Revealed by Metagenomics. DIVERSITY-BASEL, 11(12). doi:10.3390/d11120225
2018
Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism
Dong, X., Chaisiri, K., Xia, D., Armstrong, S. D., Fang, Y., Donnelly, M. J., . . . Makepeace, B. L. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. GigaScience, 7(12), 33 pages. doi:10.1093/gigascience/giy127
Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism
Dong, X., Chaisiri, K., Xia, D., Armstrong, S., Fang, Y., Donnelly, M., . . . Makepeace, B. (2018). Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism. doi:10.1101/259044
2017
Characterization of the Copy Number and Variants of Deformed Wing Virus (DWV) in the Pairs of Honey Bee Pupa and Infesting <i>Varroa destructor</i> or <i>Tropilaelaps mercedesae</i>
Wu, Y., Dong, X., & Kadowaki, T. (2017). Characterization of the Copy Number and Variants of Deformed Wing Virus (DWV) in the Pairs of Honey Bee Pupa and Infesting <i>Varroa destructor</i> or <i>Tropilaelaps mercedesae</i>. FRONTIERS IN MICROBIOLOGY, 8. doi:10.3389/fmicb.2017.01558
Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history
Dong, X., Armstrong, S., Xia, D., Makepeace, B., Darby, A. C., & Kadowaki, T. (2017). Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history. GigaScience, 6(3). doi:10.1093/gigascience/gix008
GENOMES OF TROMBIDIOID MITES UNCOVER ADAPTATIONS TO PARASITISM IN THE SCRUB TYPHUS VECTOR, <i>LEPTOTROMBIDIUM DELIENSE</i>
Dong, X., Chaisiri, K., Donnelly, M. J., McGarry, J. W., Kadowaki, T., Darby, A. C., & Makepeace, B. L. (2017). GENOMES OF TROMBIDIOID MITES UNCOVER ADAPTATIONS TO PARASITISM IN THE SCRUB TYPHUS VECTOR, <i>LEPTOTROMBIDIUM DELIENSE</i>. In AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE Vol. 97 (pp. 5). Retrieved from https://www.webofscience.com/
2016
TRPA1 Channels in <i>Drosophila</i> and Honey Bee Ectoparasitic Mites Share Heat Sensitivity and Temperature-Related Physiological Functions
Peng, G., Kashio, M., Li, T., Dong, X., Tominaga, M., & Kadowaki, T. (2016). TRPA1 Channels in <i>Drosophila</i> and Honey Bee Ectoparasitic Mites Share Heat Sensitivity and Temperature-Related Physiological Functions. FRONTIERS IN PHYSIOLOGY, 7. doi:10.3389/fphys.2016.00447
Isoform-specific modulation of the chemical sensitivity of conserved TRPA1 channel in the major honeybee ectoparasitic mite, <i>Tropilaelaps mercedesae</i>
Dong, X., Kashio, M., Peng, G., Wang, X., Tominaga, M., & Kadowaki, T. (2016). Isoform-specific modulation of the chemical sensitivity of conserved TRPA1 channel in the major honeybee ectoparasitic mite, <i>Tropilaelaps mercedesae</i>. OPEN BIOLOGY, 6(6). doi:10.1098/rsob.160042
Undated
Molecular ecological characterization of a honey bee ectoparasitic mite, Tropilaelaps mercedesae.
Dong, X. (n.d.). Molecular ecological characterization of a honey bee ectoparasitic mite,Tropilaelaps mercedesae.. (PhD Thesis, University of Liverpool).