I am interested in the evolution and epidemiology of infectious diseases especially viral infections, and how they interact with their hosts. Specifically, I am interested in using big data science technologies coupled with molecular and computational biology approaches to understand the evolutionary dynamics that shape viral diversity on a broad population scale to defining the evolutionary pathways of adaptation and transmission at the within-host level.

My research is currently focused on the molecular epidemiology, evolution and emergence of a wide range of human pathogenic viruses including Norovirus, HIV, HCV and SARS-CoV-2. Specific research projects are listed below:

Evolution and epidemiology of SARS-CoV-2

I am interested in examining the evolution and transmission of SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic and its onwards spread and evolution within affected communities.

Representative Publications

Evans A, Tully DC. Reconstructing the early spatiotemporal dynamics of SARS-CoV-2 Alpha variant across mainland Europe. In Preparation

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

This project focuses on addressing the public health emergency declared in the USA on the opioid epidemic particularly on the rising incidence of new HIV and HCV infections. In conjunction with the Ragon Institute of MGH, MIT and Harvard with funding from the National Institute on Drug Abuse (NIDA) and in partnership with several other federal agencies we are building an HCV next-generation sequencing center for capacity for implementation of the CDC's Global Hepatitis Outbreak and Surveillance Technology (“GHOST”). This technology will identify transmission links and support outbreak investigations and molecular surveillance among people who inject drugs.

As Identification of HIV/HCV transmission links and clusters will not only inform clinicians of the nature of the local HIV/HCV+ community, but also serve as an early warning sign of possible outbreaks. In particular, we are currently supporting the activities of 8 rural community and clinical research sites who are designed to conduct community assessments of HIV, HCV and comorbid conditions and intervention projects to increase public health services to prevent and detect HIV, HCV, HBV, STIs and linkage to care and drug treatment.

Collectively working with state and local community stakeholders we are interested in developing best practice responses that can be implemented by public health systems in rural regions in an bid to mitigate the opioid epidemic.

See the rural opioid initiative for more details.

Representative Publications:

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

Leveraging our recent work based on deep sequencing of plasma from acute HIV-1 infection our goal is to investigate the evolutionary processes that shape HCV transmission and pathogenesis. In collaboration with Professor Kim Page (University of New Mexico) and the UCSF UFO study we are studying HCV transmission using a sero-discordant injecting partnership study of young people who inject drugs. In an another setting we are examining HCV transmission and genetic diversity in the context of liver transplantation and from a single-source hemodialysis outbreak in Brazil.

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.

Norovirus

I have worked on NOROPATROL which is an initative to try and understand why noroviruses pandemics occur and how to control them. Recent work was presented as a talk at the 8th International Calcivirus Conference in May 2023 where I discussed the phylodynamic reconstruction of GII.4 outbreaks from across the UK. In addition, in collaboration with the CDC we have discovered a novel rare GII.4 variant with an amino acid insertion at the start of antigenic site A in the major capsid protein.

Representative Publications

Chhabra P†, Tully DC†, Mans J, Niendorf S, Barclay L, Cannon JL, Montmayeur AM, Hue S, Breuer J, Vinje J. Emergence of Novel Norovirus GII.4 Variant. Emerg Infect Dis. 2023 Dec 8;30(1). doi: 10.3201/eid3001.231003. Epub ahead of print. PMID: 38063078. († Contributed Equally)

Viral Metagenomics

I am interested in using metagenomc technology to discover novel viruses particularly in ticks which cause diseases in humans, livestock and wild animals. In the past I have been involved in various metagenomic projects.

Representative Publications

Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A; Viral Hemorrhagic Fever Consortium, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nature Biotechnology. 2019 Feb;37(2):160-168. doi: 10.1038/s41587-018-0006-x.

Piantadosi A, Freije CA, Gosmann C, Ye S, Park D, Schaffner SF, Tully DC, Allen TM, Dong KL, Sabeti PC, Kwon DS. Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection. J Virol. 2019 Jan 4;93(2):e00804-18. doi: 10.1128/JVI.00804-18.