All Outputs (44)

‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2 (2025)
Journal Article
McClure, C. P., Tsoleridis, T., Hill, J. D., Holmes, N., Chappell, J. G., Byaruhanga, T., Duncan, J., Tofan, M., Berry, L., Clark, G., Irving, W. L., Tarr, A. W., Ball, J. K., Astbury, S., & Loose, M. (2025). ‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2. Microbial Genomics, 11(7), Article 001451. https://doi.org/10.1099/mgen.0.001451

Prior to the emergence of SARS-CoV-2 in 2019, alphacoronaviruses 229E and NL63 and betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbi... Read More about ‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2.

Wisteria floribunda agglutinin enhances Zaire ebolavirus entry through interactions at specific N-linked glycosylation sites on the virus glycoprotein complex (2025)
Journal Article
Duncan, J., Pathak, M., King, B., Bamber, H., Radford, P., Dey, J., Richardson, C., Astbury, S., McClure, P., Ball, J. K., Urbanowicz, R. A., & Tarr, A. (2025). Wisteria floribunda agglutinin enhances Zaire ebolavirus entry through interactions at specific N-linked glycosylation sites on the virus glycoprotein complex. Journal of General Virology, 106(6), Article 002120. https://doi.org/10.1099/jgv.0.002120

Entry of Zaire ebolavirus (EBOV) into a host cell is a complex process requiring interactions between the viral glycoproteins (GPs) and cellular factors. These entry factors are cell-specific and can include cell surface lectins and phosphatidylserin... Read More about Wisteria floribunda agglutinin enhances Zaire ebolavirus entry through interactions at specific N-linked glycosylation sites on the virus glycoprotein complex.

An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses (2025)
Preprint / Working Paper
Tsoleridis, T., Fan, C., Park, E. J., Duncan, J. D., Sharma, P., Wartnaby, S., Chappell, J. G., Kipar, A., Bentley, E. G., Kirby, A., Han, X., Coleman, C. M., Flyak, A. I., McClure, C. P., Rho, S., Johansson, D. X., Persson, M. A., Tarr, A. W., Haig, D., Stewart, J. P., …Ball, J. K. (2025). An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses

The threat of emergence of further SARS-CoV-2 variants, and the future spillover potential of other sarbecoviruses has prompted continued efforts to isolate broadly reactive monoclonal antibodies for therapeutic use. In this study, we generated monoc... Read More about An ultra-long heavy chain bovine antibody neutralizes SARS-CoV-2 and reacts broadly with sarbecoviruses.

Reconstruction of the historic time course of blood‐borne virus contamination of clotting factor concentrates, 1974–1992 (2024)
Journal Article
McClure, C. P., Kean, K., Reid, K., Mayne, R., Fu, M. X., Rajendra, P., Gates, S., Breuer, J., Harvala, H., Golubchik, T., Tarr, A. W., Irving, W. L., Makris, M., & Simmonds, P. (2024). Reconstruction of the historic time course of blood‐borne virus contamination of clotting factor concentrates, 1974–1992. Journal of Medical Virology, 96(7), Article e29774. https://doi.org/10.1002/jmv.29774

Factor VIII and IX clotting factor concentrates manufactured from pooled plasma have been identified as potent sources of virus infection in persons with hemophilia (PWHs) in the 1970s and 1980s. To investigate the range and diversity of viruses over... Read More about Reconstruction of the historic time course of blood‐borne virus contamination of clotting factor concentrates, 1974–1992.

Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2 (2024)
Preprint / Working Paper
McClure, C. P., Tsoleridis, T., Holmes, N., Chappell, J. G., Byaruhanga, T., Duncan, J., Tofan, M., Khater, A., Berry, L., Clark, G., Irving, W. L., Tarr, A. W., Ball, J. K., Astbury, S., & Loose, M. Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2

Prior to the emergence of SARS-CoV-2 in 2019, Alphacoronaviruses 229E and NL63 and Betacoronaviruses OC43 and HKU1 were already established endemic ‘common cold’ viral infections. Despite their collective contribution towards global respiratory morbi... Read More about Vivaldi: An amplicon-based whole genome sequencing method for the four seasonal human coronaviruses 229E, NL63, OC43 & HKU1, alongside SARS-CoV-2.

Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave (2024)
Journal Article
Acheampong, E., Husain, A. A., Dudani, H., Nayak, A. R., Nag, A., Meena, E., Shrivastava, S. K., McClure, P., Tarr, A. W., Crooks, C., Lade, R., Gomes, R. L., Singer, A., Kumar, S., Bhatnagar, T., Arora, S., Kashyap, R. S., & Monaghan, T. M. (2024). Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave. PLoS ONE, 19(5), Article e0303529. https://doi.org/10.1371/journal.pone.0303529

Wastewater-based epidemiology (WBE) has emerged as an effective environmental surveillance tool for predicting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease outbreaks in high-income countries (HICs) with centralized sewage infr... Read More about Population infection estimation from wastewater surveillance for SARS-CoV-2 in Nagpur, India during the second pandemic wave.

RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance (2023)
Journal Article
Stockdale, S. R., Blanchard, A. M., Nayak, A., Husain, A., Nashine, R., Dudani, H., McClure, C. P., Tarr, A. W., Nag, A., Meena, E., Sinha, V., Shrivastava, S. K., Hill, C., Singer, A. C., Gomes, R. L., Acheampong, E., Chidambaram, S. B., Bhatnagar, T., Vetrivel, U., Arora, S., …Monaghan, T. M. (2023). RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. The Lancet Regional Health – Southeast Asia, 14, Article 100205. https://doi.org/10.1016/j.lansea.2023.100205

Background: The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectio... Read More about RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance.

Arbovirus circulation, epidemiology and spatiotemporal distribution in Uganda (2023)
Journal Article
Byaruhanga, T., Kayiwa, J. T., Nankya, A. M., Ataliba, I. J., McClure, C. P., Ball, J. K., & Lutwama, J. J. (2023). Arbovirus circulation, epidemiology and spatiotemporal distribution in Uganda. IJID Regions, 6, 171-176. https://doi.org/10.1016/j.ijregi.2023.01.013

Background: Arboviruses are endemic in Uganda; however, little is known about their epidemiology, seasonality and spatiotemporal distribution. Our study sought to provide information on arbovirus outbreaks from acute clinical presentations. Methods:... Read More about Arbovirus circulation, epidemiology and spatiotemporal distribution in Uganda.

Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study (2022)
Journal Article
Colton, H., Parker, M. D., Stirrup, O., Blackstone, J., Loose, M., McClure, C. P., Roy, S., Williams, C., McLeod, J., Smith, D., Taha, Y., Zhang, P., Hsu, S. N., Kele, B., Harris, K., Mapp, F., Williams, R., COG-UK HOCI Investigators, COVID-19 Genomics UK (COG-UK) Consortium, Flowers, P., Breuer, J., …de Silva, T. I. (2023). Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. Journal of Hospital Infection, 131, 34-42. https://doi.org/10.1016/j.jhin.2022.09.022

Background
Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.

Aim
To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a ra... Read More about Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study.

Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination (2022)
Journal Article
Adeboyejo, K., King, B., Tsoleridis, T., Tarr, A. W., McLauchlan, J., Irving, W. L., Ball, J. K., & McClure, C. P. (2023). Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination. Journal of Medical Virology, 95(1), Article e28178. https://doi.org/10.1002/jmv.28178

Background andAims: The newly developed direct-acting antivirals have revolutionized the treatment of chronic hepatitis C virus (HCV), with cure rates as high as 98% in some cohorts. Although genome sequencing has demonstrated that some subtypes of H... Read More about Hepatitis C subtyping assay failure in UK patients born in sub-Saharan Africa: Implications for global treatment and elimination.

Human parainfluenza 2 & 4: Clinical and genetic epidemiology in the UK, 2013–2017, reveals distinct disease features and co‐circulating genomic subtypes (2022)
Journal Article
Chellapuri, A., Smitheman, M., Chappell, J. G., Clark, G., Howson-Wells, H. C., Berry, L., Ball, J. K., Irving, W. L., Tarr, A. W., & McClure, C. P. (2022). Human parainfluenza 2 & 4: Clinical and genetic epidemiology in the UK, 2013–2017, reveals distinct disease features and co‐circulating genomic subtypes. Influenza and Other Respiratory Viruses, 16(6), 1122-1132. https://doi.org/10.1111/irv.13012

Background: Human Parainfluenza viruses (HPIV) comprise of four members of the genetically distinct genera of Respirovirus (HPIV1&3) and Orthorubulavirus (HPIV2&4), causing significant upper and lower respiratory tract infections worldwide, particula... Read More about Human parainfluenza 2 & 4: Clinical and genetic epidemiology in the UK, 2013–2017, reveals distinct disease features and co‐circulating genomic subtypes.

Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity (2022)
Journal Article
Howson-Wells, H. C., Tsoleridis, T., Zainuddin, I., Tarr, A. W., Irving, W. L., Ball, J. K., Berry, L., Clark, G., & McClure, C. P. (2022). Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity. Microbial Genomics, 8(5), https://doi.org/10.1099/mgen.0.000825

Enterovirus D68 (EV-D68) has recently been identified in biennial epidemics coinciding with diagnoses of non-polio acute flaccid paralysis/myelitis (AFP/AFM). We investigated the prevalence, genetic relatedness and associated clinical features of EV-... Read More about Enterovirus D68 epidemic, UK, 2018, was caused by subclades B3 and D1, predominantly in children and adults, respectively, with both subclades exhibiting extensive genetic diversity.

Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil (2022)
Journal Article
Adeboyejo, K., Riquena Grosche, V., Pandeló José, D., Magalhães Ferreira, G., Farinha Shimizu, J., King, B. J., Tarr, A. W., Costa Nunes Soares, M. M., Ball, J. K., McClure, C. P., & Gomes Jardim, A. C. (2022). Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil. Access Microbiology, 4(3), Article 000326. https://doi.org/10.1099/acmi.0.000326

Hepatitis C virus (HCV) is responsible for more than 180 million infections worldwide, and about 80 % of infections are reported in Low and Middle-income countries (LMICs). Therapy is based on the administration of interferon (INF), ribavirin (RBV) o... Read More about Simultaneous determination of HCV genotype and NS5B resistance associated substitutions using dried serum spots from São Paulo state, Brazil.

Sero-reactivity to three distinct regions within the hepatitis C virus alternative reading frame protein (ARFP/core+1) in patients with chronic HCV genotype-3 infection (2022)
Journal Article
Elsheikh, M. E. A., Patrick McClure, C., Tarr, A. W., & Irving, W. L. (2022). Sero-reactivity to three distinct regions within the hepatitis C virus alternative reading frame protein (ARFP/core+1) in patients with chronic HCV genotype-3 infection. Journal of General Virology, 103(3), Article 001727. https://doi.org/10.1099/jgv.0.001727

Hepatitis C virus (HCV) infection affects more than 71 million people worldwide. The disease slowly progresses to chronic, long-term liver injury which leads to hepatocellular carcinoma (HCC) in 5 % of infections. The alternative reading frame protei... Read More about Sero-reactivity to three distinct regions within the hepatitis C virus alternative reading frame protein (ARFP/core+1) in patients with chronic HCV genotype-3 infection.

Human Parainfluenza 2 & 4: clinical and genetic epidemiology in the UK, 2013-2017, reveals distinct disease features and co-circulating genomic subtypes (2022)
Preprint / Working Paper
Chellapuri, A., Smitheman, M., Chappell, J. G., Clark, G., Howson-Wells, H. C., Berry, L., Ball, J. K., Irving, W. L., Tarr, A. W., & McClure, C. P. Human Parainfluenza 2 & 4: clinical and genetic epidemiology in the UK, 2013-2017, reveals distinct disease features and co-circulating genomic subtypes

Human Parainfluenza viruses (HPIV) are constituted by four members of the genetically distinct genera of Respirovirus (type 1 and 3) and Orthorubulavirus (type 2 and 4), causing significant upper and lower respiratory tract infections in both childre... Read More about Human Parainfluenza 2 & 4: clinical and genetic epidemiology in the UK, 2013-2017, reveals distinct disease features and co-circulating genomic subtypes.

Saliva for COVID-19 testing: Simple but useless or an undervalued resource? (2021)
Journal Article
Pijuan-Galito, S., Tarantini, F. S., Tomlin, H., Jenkins, H., Thompson, J. L., Scales, D., Stroud, A., Tellechea Lopez, A., Hassall, J., McTernan, P., Coultas, A., Arendt-Tranholm, A., Reffin, C., Hill, I., Lee, I.-N., Wu, S., Porte, J., Chappell, J., Lis-Slimak, K., Kaneko, K., …Denning, C. (2021). Saliva for COVID-19 testing: Simple but useless or an undervalued resource?. Frontiers in Virology, 1, Article 778790. https://doi.org/10.3389/fviro.2021.778790

During the COVID-19 pandemic, countries with robust population-based asymptomatic testing were generally successful in controlling virus spread, hence reducing hospitalizations and deaths. This effectiveness inspired widespread asymptomatic surveilla... Read More about Saliva for COVID-19 testing: Simple but useless or an undervalued resource?.

The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks (2021)
Journal Article
Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., Mahida, N., Irving, W. L., Moore, C., Holmes, N., Ball, J. K., Loose, M., & McClure, C. P. (2022). The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. Journal of Infectious Diseases, 225(1), 10-18. https://doi.org/10.1093/infdis/jiab483

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and interve... Read More about The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.

Gold–Oligonucleotide Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences (2021)
Journal Article
Chauhan, V. M., Elsutohy, M. M., McClure, C. P., Irving, W. L., Roddis, N., & Aylott, J. W. (2021). Gold–Oligonucleotide Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences. Biosensors, 11(7), Article 238. https://doi.org/10.3390/bios11070238

Enteroviruses are ubiquitous mammalian pathogens that can produce mild to life-threatening disease. We developed a multimodal, rapid, accurate and economical point-of-care biosensor that can detect nucleic acid sequences conserved amongst 96% of all... Read More about Gold–Oligonucleotide Nanoconstructs Engineered to Detect Conserved Enteroviral Nucleic Acid Sequences.

Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study (2021)
Presentation / Conference Contribution
Briggs, L., Blake, H., Cirelli, C., Corner, J., Hassard, J., Daly, J., Chappell, J., Bennett, M., Fairclough, L., McClure, C., Tarr, A., Tighe, P., Favier, A., Irving, W., & Ball, J. (2021, March). Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study. Poster presented at RSM National Conference 2021, Online

Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study (2021)
Presentation / Conference Contribution
Briggs, L., Blake, H., Hassard, J., Cirelli, C., Daly, J., Corner, J., Bennett, M., Chappell, J., Fairclough, L., McClure, C., Tarr, A., Tighe, P., Favier, A., Irving, W., & Ball, J. (2021, March). Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study. Poster presented at MedAll International Virtual Medical Conference, Online