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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., …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., …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., …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., …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., …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., …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)
Working Paper
Chellapuri, A., Smitheman, M., Chappell, J. G., Clark, G., Howson-Wells, H. C., Berry, L., …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., …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., …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 (2020)
Journal Article
Blake, H., Corner, J., Cirelli, C., Hassard, J., Briggs, L., Daly, J. M., …Ball, J. (2021). Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study. International Journal of Environmental Research and Public Health, 18(1), 1-26. https://doi.org/10.3390/ijerph18010188

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. We aimed to explore student and staff perceptions and experiences of a pilot SARS-CoV-2 asymptomatic testing service (P-ATS) in a UK university campus setting. This was a mixed-method study co... Read More about Perceptions and Experiences of the University of Nottingham Pilot SARS-CoV-2 Asymptomatic Testing Service: A Mixed-Methods Study.

Enterovirus subtyping in a routine UK laboratory setting between 2013 and 2017 (2020)
Journal Article
Howson-Wells, H. C., Winckles, S., Aliker, C., Tarr, A. W., Irving, W. L., Clark, G., & McClure, C. P. (2020). Enterovirus subtyping in a routine UK laboratory setting between 2013 and 2017. Journal of Clinical Virology, 132, Article 104646. https://doi.org/10.1016/j.jcv.2020.104646

© 2020 Elsevier B.V. Background: Human enteroviruses (EV) are the leading cause of viral meningitis. EV genotyping is predominantly performed through amplification and sequencing of viral capsid protein-1 (VP1), frequently by national reference labor... Read More about Enterovirus subtyping in a routine UK laboratory setting between 2013 and 2017.

Nanopore sequencing from extraction-free direct PCR of dried serum spots for portable hepatitis B virus drug-resistance typing (2020)
Journal Article
Astbury, S., Nunes Soares, M. M. D. C., Peprah, E., King, B., Jardim, A. C. G., Shimizu, J. F., …McClure, P. (2020). Nanopore sequencing from extraction-free direct PCR of dried serum spots for portable hepatitis B virus drug-resistance typing. Journal of Clinical Virology, 129, Article 104483. https://doi.org/10.1016/j.jcv.2020.104483

© 2020 Background: Effective drug regimens for the treatment of hepatitis B virus (HBV) infections are essential to achieve the World Health Organisation commitment to eliminate viral hepatitis by 2030. Lamivudine (3TC) is widely used in countries wi... Read More about Nanopore sequencing from extraction-free direct PCR of dried serum spots for portable hepatitis B virus drug-resistance typing.

Human Bocavirus infection and respiratory tract disease identified in a UK patient cohort (2020)
Journal Article
Bagasi, A. A., Howson-Wells, H. C., Clark, G., Tarr, A. W., Soo, S., Irving, W. L., & McClure, C. P. (2020). Human Bocavirus infection and respiratory tract disease identified in a UK patient cohort. Journal of Clinical Virology, 129, Article 104453. https://doi.org/10.1016/j.jcv.2020.104453

© 2020 Elsevier B.V. Background: Since its first isolation in 2005, Human Bocavirus (HBoV) has been repeatedly associated with acute respiratory tract infections, although its role in pathogenicity remains unclear due to high co-infection rates. Obje... Read More about Human Bocavirus infection and respiratory tract disease identified in a UK patient cohort.

Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species (2020)
Journal Article
Chappell, J. G., Tsoleridis, T., Onianwa, O., Drake, G., Ashpole, I., Dobbs, P., …McClure, C. P. (2020). Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species. Viruses, 12(4), Article 454. https://doi.org/10.3390/v12040454

©2020 by the authors. Licensee MDPI, Basel, Switzerland. Orthohantaviruses are globally distributed viruses, associated with rodents and other small mammals. However, data on the circulation of orthohantaviruses within the UK, particularly the UK-end... Read More about Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports Its Classification as a Novel Species.

Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits (2019)
Journal Article
Tsoleridis, T., Chappell, J. G., Monchatre-Leroy, E., Umhang, G., Shi, M., Bennett, M., …Ball, J. K. (2019). Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits. Viruses, 12(1), Article 47. https://doi.org/10.3390/v12010047

The advent of unbiased metagenomic virus discovery has revolutionized studies of virus biodiversity and evolution. Despite this, our knowledge of the virosphere, including in mammalian species, remains limited. We used unbiased metagenomic sequencing... Read More about Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits.