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Dr Damien Tully

BSc PhD

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. For a full list of my own publications see this link. I have highlighted several recent publications at the bottom of this page.

Affiliations

Faculty of Epidemiology and Population Health
Department of Infectious Disease Epidemiology

Centres

Centre for the Mathematical Modelling of Infectious Diseases (CMMID)

Teaching

I teach on several modules within LSHTM, such as Molecular Virology and AIDS. More recently I am involved with development of the new MSc in Data Science and am a co-organiser of the Genomics Health Data module.

I supervise MSc student summer projects in 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

Building on my prior experiences I am interested in the evolution and epidemiology of viral infections, and interactions with their hosts. Specifically, I am integrating 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 from HIV, HCV and SARS-CoV-2.  Specific examples are listed below:

Evolution and epidemiology of SARS-CoV-2

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

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

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

 

Recent Publications (selected) 

  1. Villabona-Arenas CJ, Hanage WP, Tully DC. Phylogenetic interpretation during outbreaks requires caution. Nat Microbiol. 2020 Jul;5(7):876-877. doi: 10.1038/s41564-020-0738-5.
  2. 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 Infectious Disease. 2019 Apr;6(4):ofz125. doi: 10.1093/ofid/ofz125. eCollection 2019 Apr. 
  3. 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, 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. Epub 2019 Feb 4. 
  4. 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. Journal of Virology. 2019 Jan 15;93(2). doi: 10.1128/JVI.00804-18. 
  5. Wolski D, Foote PK, Chen DY, Lewis-Ximenez LL, Fauvelle C, Aneja J, Walker A, Tonnerre P, Torres-Cornejo A, Kvistad D, Imam S, Waring MT, Tully DC, Allen TM, Chung RT, Timm J, Haining WN, Kim AY, Baumert TF, Lauer GM. Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection.Immunity. 2017 Oct 17;47(4):648-663.e8. 
  6. Hedegaard DL, Tully DC, Rowe IA, Reynolds GM, Bean DJ, Hu K, Davis C, Wilhelm A, Ogilvie CB, Power KA, Tarr AW, Kelly D, Allen TM, Balfe P, McKeating JA. High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease. Journal of Hepatology. 2017 Jan;66(1):28-38. doi: 10.1016/j.jhep.2016.07.048. (co-first author)
  7. Tully DC, Hjerrild S, Leutscher PD, Renvillard SG, Ogilvie CB, Bean DJ, Videbech P, Allen TM, McKeating JA, Fletcher NF.Deep sequencing of hepatitis C virus reveals genetic compartmentalization in cerebrospinal fluid from cognitively impaired patients. Liver International. 2016 Oct;36(10):1418-24. Also see accompanying editorial entitled "Hepatitis C - the brain strain". 
  8. Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM. Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus. PLoS Pathogens. 2016 May;12(5):e1005619. 
  9. Mudd PA, Martins MA, Ericsen AJ, Tully DC, Power KA, Bean AT, Piaskowski SM, Duan L, Seese A, Gladden AD, Weisgrau KL, Furlott JR, Kim YI, Veloso de Santana MG, Rakasz E, Capuano S 3rd, Wilson NA, Bonaldo MC, Galler R, Allison DB, Piatak M Jr, Haase AT, Lifson JD, Allen TM, Watkins DI. Vaccine-induced CD8+ T cells control AIDS virus replication.Nature. 2012 Nov 1;491(7422):129-33. doi: 10.1038/nature11443. 
  10. Tully DC, Wood C. Chronology and evolution of the HIV-1 subtype C epidemic in Ethiopia. AIDS. 2010 Jun 19;24(10):1577-82.
  11. Tully DC, Fares MA. Shifts in the selection-drift balance drive the evolution and epidemiology of foot-and-mouth disease virus. J Virol. 2009 Jan;83(2):781-90. 
  12. Tully DC, Fares MA. The tale of a modern animal plague: tracing the evolutionary history and determining the time-scale for foot and mouth disease virus. Virology. 2008 Dec 20;382(2):250-6. 

For a full list of publications see this link.

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