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Dr Damien Tully

BSc PhD FHEA

Assistant Professor
IN EPIDEMIOLOGY, BIOSTATISTICS & BIOINFORMATICS

Room
104

LSHTM
Keppel Street
London
WC1E 7HT
United Kingdom

Tel.
+44 (0)207 612 7923

I joined the London School in November 2018 as an Assistant Professor in Epidemiology, Biostatistics and Bioinformatics. I earned a B.Sc (Hons) in Biology from the National University of Ireland, Maynooth and completed my Ph.D. at the Smurfit Institute of Genetics at Trinity College Dublin focusing on the evolutionary genetics of RNA viruses. After completing a postdoctoral fellowship at the Nebraska Center for Virology, University of Nebraska Lincoln where I led studies researching the evolution of HIV-1 infection in mother/infants pairs from Zambia. I joined the Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard as a research fellow in 2011 where my research centered on elucidating the viral-host interactions responsible for HIV-1 and HCV transmission and evolution. As a senior research scientist at Massachusetts General Hospital and the Ragon Institute my research focused on the application of innovative sequencing technology and algorithms to understand viral transmission and pathogen evolution.

I am an Associate Editor for BMC Infectious Diseases and have acted as a guest editor for PLoS Biology. 

Affiliations

Department of Infectious Disease Epidemiology
Faculty of Epidemiology and Population Health

Centres

Centre for the Mathematical Modelling of Infectious Diseases (CMMID)

Teaching

I teach on several modules across many MSc programmes at the School. I am a module organiser for the Genomics Health data module on the MSc in Data Science and the deputy module organiser of the HIV/AIDS distance learning module (IDM501). I am a Fellow of the Higher Education Academy (FHEA).

I supervise MSc student summer projects in infectious disease research, phylogenetics, viral evolution and molecular epidemiology. I welcome enquiries from people who would be interested in joining my group either as a postdoc or PhD student in the broad areas of molecular epidemiology, genomics, evolution and phylogenetics.

Research

I am interested in the evolution and epidemiology of infectious diseases especially viral infections, and how they interact with their hosts. Specifically, I am investigating both 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 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

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:

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

 

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.

 

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.

 

For a full list of publications see this link or refer to google scholar

Research Area
Diagnostics
Drug resistance
Surveillance
Viruses
Global Health
Mobile technologies
Outbreaks
Discipline
Genetic epidemiology
Genomics
Molecular epidemiology
Epidemiology
Microbiology
Molecular biology
Virology
Bioinformatics
Disease and Health Conditions
HIV/AIDS
Infectious disease
Emerging Infectious Disease
Hepatitis
Hospital acquired infection
Country
Brazil
China
United Kingdom
Uganda
United States of America
Region
East Asia & Pacific (all income levels)
European Union
North America
Sub-Saharan Africa (all income levels)

Selected Publications

Phylogenetic interpretation during outbreaks requires caution.
Villabona-Arenas CJ; Hanage WP; Tully DC
2020
NATURE MICROBIOLOGY
See more Publications