My research focuses on the evolution, transmission and genomic epidemiology of infectious diseases, with a particular interest in understanding how viruses evolve within individuals and spread through populations. I combine viral genomics, evolutionary biology, phylogenetics, epidemiology and computational approaches to investigate the processes that generate viral diversity, drive adaptation and emergence, and shape patterns of transmission. A central theme of my work is translating advances in pathogen genomomics into approaches that can improve infectious disease surveillance and public health, particularly through the development and application of scalable sequencing and analytical methods.

My current research spans a range of important human viruses, including HIV-1, hepatitis C virus (HCV), norovirus and SARS-CoV-2, and ranges from studying within-host viral evolution and transmission bottlenecks to reconstructing regional and global patterns of viral emergence.

Norovirus evolution and emergence

My norovirus research seeks to understand why new epidemic and pandemic lineages emerge, what determines their evolutionary success, and how genomic surveillance can be used to identify emerging variants. I have contributed to NOROPATROL, a programme investigating the drivers of norovirus epidemics and approaches for their control. This work has included phylodynamic reconstruction of GII.4 norovirus outbreaks across the UK and investigation of the evolutionary processes underlying the emergence and replacement of major norovirus lineages. In collaboration with the US Centers for Disease Control and Prevention (CDC), we identified a rare GII.4 variant containing an unusual amino-acid insertion at the beginning of antigenic site A of the major capsid protein. More recently, we characterised the emergence of a genetically distinct GII.4[P31] lineage associated with outbreaks in the UK during the COVID-19 pandemic. Our latest work has expanded beyond GII.4 to investigate the global evolutionary history of GII.17 noroviruses, showing how differences in viral fitness have contributed to the emergence, persistence and replacement of major lineages. I have also discussed norovirus evolution, outbreaks and prevention for a wider audience on the LSHTM Viral podcast: Norovirus uncovered: Why this year is worse.

Representative publications:
Tully DC, Roy S, Tutill H, Williams R, Celma C, Lindesmith L, Baric R, Breuer J. Fitness-driven emergence and lineage replacement underpin the global resurgence of GII.17 noroviruses. Nature Communications 2026. Under review: available from Research Square preprint.

Chhabra P†, Tully DC†, Mans J, Niendorf S, Barclay L, Cannon JL, Montmayeur AM, Hue S, Breuer J, Vinjé J. Emergence of Novel Norovirus GII.4 Variant. Emerging Infectious Diseases. 2024;30(1). doi:10.3201/eid3001.231003.
†Contributed equally.

HIV genomics and drug resistance

A major focus of my current research is the development and application of viral genomic approaches for HIV-1 drug resistance surveillance, particularly in settings where access to conventional sequencing and resistance testing remains limited. Working with collaborators at the MRC/UVRI & LSHTM Uganda Research Unit, we are developing approaches that use Oxford Nanopore sequencing to provide accessible, scalable and cost-effective HIV drug resistance genotyping. A key aim of this work is to understand how nanopore sequencing can be translated from a research technology into a practical tool for HIV clinical and public-health surveillance in resource-limited settings. Our research has examined the performance of nanopore sequencing for identifying clinically important HIV-1 drug resistance mutations, including direct comparison with conventional Sanger sequencing. We are also investigating the sequencing depth required to generate reliable resistance profiles and accurately recover minority variants, with the aim of defining evidence-based sequencing thresholds that maximise accuracy while reducing sequencing costs and computational requirements. Beyond consensus-level resistance testing, we are using the long-read capabilities of nanopore sequencing to investigate within-host HIV diversity and the genetic linkage of drug resistance mutations. By reconstructing viral haplotypes, this work aims to determine whether resistance-associated mutations occur together within individual viral genomes and to better understand the evolutionary pathways through which multidrug resistance emerges. A further strand of this research focuses on improving HIV genomic surveillance in samples that are difficult to analyse using conventional approaches. We have shown that nanopore sequencing can recover clinically informative HIV drug resistance profiles from samples that fail conventional PCR-based quality assessment, highlighting its potential to increase the proportion of samples that can contribute to resistance surveillance. Collectively, this work seeks to integrate genomics, bioinformatics and evolutionary analysis to develop practical approaches for monitoring HIV drug resistance and understanding the evolutionary processes that generate and maintain resistance within individuals and populations.

Representative Publications:

Lule DB, Ssemwanga D, Kaleebu P, Tully DC. The utility of integrating nanopore sequencing into routine HIV-1 drug resistance surveillance. Microb Genom. 2025 Mar;11(3):001375. doi: 10.1099/mgen.0.001375. PMID: 40111248; PMCID: PMC11925199.

Lule DB, Ssemwanga D, Bbosa N, Kaleebu P, Tully DC. Optimising Nanopore Sequencing for Reliable HIV-1 Drug Resistance Profiling. 2026. Available at SSRN: https://ssrn.com/abstract=7224048 or http://dx.doi.org/10.2139/ssrn.7224048

SARS-CoV-2 Evolution & Epidemiology

My work on SARS-CoV-2 examines how genomic data can be used to understand the emergence, evolution and transmission of new viral lineages. During the COVID-19 pandemic, I contributed to research examining the emergence and epidemiological consequences of the SARS-CoV-2 Alpha variant in England. Subsequent work has used phylogenetic approaches to reconstruct the early dissemination of Alpha across Europe. A broader theme of this research is understanding both the power and the limitations of pathogen phylogenetics during rapidly developing outbreaks, particularly when genomic data are incomplete or unevenly sampled.

Representative Publications:

Evans A, Tully DC. Phylogenetic Insights into the Early Spread of the SARS-CoV-2 Alpha Variant Across Europe, Virus Evolution, 2025;, veaf030, https://doi.org/10.1093/ve/veaf030

Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CAB, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KLM, van Zandvoort K, Silverman JD; CMMID COVID-19 Working Group; COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science. 2021 Apr 9;372(6538):eabg3055. doi: 10.1126/science.abg3055.

Villabona-Arenas CJ, Hanage WP, Tully DC. Phylogenetic interpretation during outbreaks requires caution. Nature Microbiology. 2020 Jul;5(7):876-877. doi: 10.1038/s41564-020-0738-5.

Genomic epidemiology of HCV from rural US communities affected by the opioid epidemic

A major strand of my research uses pathogen genomics to understand hepatitis C virus transmission among people who use drugs, particularly in rural US communities affected by the opioid epidemic. Working with the Ragon Institute of MGH, MIT and Harvard and collaborators across the United States, we established HCV genomic surveillance capacity as part of a programme funded by the US National Institute on Drug Abuse (NIDA). This work has supported implementation of the CDC's Global Hepatitis Outbreak and Surveillance Technology (GHOST) platform. By combining viral sequencing with epidemiological data, we use genomic surveillance to identify transmission networks, investigate outbreaks and characterise patterns of HCV spread that would be difficult to detect through conventional surveillance alone. Our work across rural US communities has demonstrated substantial geographical variation in HCV transmission networks and highlighted how genomic data can help target public-health interventions. A major goal is to translate these findings into practical genomic-surveillance approaches that can support HCV prevention and elimination, particularly in communities disproportionately affected by injecting drug use.

See the rural opioid initiative for more details.

Representative Publications:

Tully DC, Bean DJ, Sarette J, Ngo TL, Power KA, Brook D, Cooper H, Feinberg J, Friedmann PD, Hochstatter KR, Havens JR, Babalonis S, Hurt C, Jenkins W, Korthuis PT, Miller W, Pho MT, Smith G, Stopka TJ, Tsui JI, Mixson S, Westergaard RP, Young AM, Allen TM. Genomic surveillance uncovers regional variation in HCV transmission networks among people who use drugs in rural U.S. communities. 2025. Genomic surveillance uncovers regional variation in HCV transmission networks in rural United States. Nat Commun. 2025 Dec 2;17(1):249. doi: 10.1038/s41467-025-66934-y

Tully DC, Power KA, Sarette J, Stopka TJ,Friedmann PD, Korthuis TP, Cooper H, Young AM, Seal DW, Westergaard RP, Allen TM. Validation of Dried Blood Spots for Capturing Hepatitis C Virus Diversity for Genomic Surveillance. Journal of Viral Hepatitis. 2024 Feb 16. doi: 10.1111/jvh.13924

Tully DC. Leveraging genomic surveillance to enhance elimination strategies for hepatitis C virus. Lancet Microbe. 2022 Aug 16:S2666-5247(22)00204-X. doi: 10.1016/S2666-5247(22)00204-X. Epub ahead of print.

Hochstatter KR†, Tully DC†, Power KA, Koepke R, Akhtar WZ, Prieve AF, Whyte T, Bean DJ, Seal DW, Allen TM, Westergaard RP. Hepatitis C Virus Transmission Clusters in Public Health and Correctional Settings, Wisconsin, USA, 2016-20171. Emerging Infectious Diseases. 2021 Feb;27(2):480-489. doi: 10.3201/eid2702.202957. († Contributed Equally)


Understanding HCV genomic variation in the context of transmission, persistence and pathogenesis

Alongside population-level genomic surveillance, I am interested in the evolutionary processes operating during individual HCV infections and transmission events. Using deep viral sequencing, we investigate how HCV diversity is generated and transmitted between individuals, the size and composition of the viral transmission bottleneck, and how within-host evolution contributes to persistence and pathogenesis. In collaboration with Professor Kim Page and the UFO Study, we have studied HCV transmission within injecting partnerships among young people who inject drugs, combining detailed epidemiological information with viral genomic data to identify genetically supported transmission events. Related work has examined HCV diversity and transmission in other epidemiological settings, including liver transplantation and a single-source haemodialysis outbreak in Brazil. Together, these studies aim to connect within-host viral evolution with the transmission patterns observed at the population level.

Representative Publications:
Tully DC, Hahn JA, Bean DJ, Evans JL, Morris MD, Page K, Allen TM. Identification of Genetically Related HCV Infections Among Self-Described Injecting Partnerships. Clinical Infectious Diseases. 2021 Aug 27:ciab596. doi: 10.1093/cid/ciab596.

Hahn JA, Tully DC, Evans JL, Morris MD, Briceno A, Bean DJ, Allen TM, Page K. Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships. Open Forum Infect Dis. 2019 Apr 25;6(4):ofz125. doi: 10.1093/ofid/ofz125.