Inferring the Source of Transmission with Phylogenetic Data

Volz, Erik M.; Frost, Simon D. W.
December 2013
PLoS Computational Biology;Dec2013, Vol. 9 Issue 12, p1
Academic Journal
Identifying the source of transmission using pathogen genetic data is complicated by numerous biological, immunological, and behavioral factors. A large source of error arises when there is incomplete or sparse sampling of cases. Unsampled cases may act as either a common source of infection or as an intermediary in a transmission chain for hosts infected with genetically similar pathogens. It is difficult to quantify the probability of common source or intermediate transmission events, which has made it difficult to develop statistical tests to either confirm or deny putative transmission pairs with genetic data. We present a method to incorporate additional information about an infectious disease epidemic, such as incidence and prevalence of infection over time, to inform estimates of the probability that one sampled host is the direct source of infection of another host in a pathogen gene genealogy. These methods enable forensic applications, such as source-case attribution, for infectious disease epidemics with incomplete sampling, which is usually the case for high-morbidity community-acquired pathogens like HIV, Influenza and Dengue virus. These methods also enable epidemiological applications such as the identification of factors that increase the risk of transmission. We demonstrate these methods in the context of the HIV epidemic in Detroit, Michigan, and we evaluate the suitability of current sequence databases for forensic and epidemiological investigations. We find that currently available sequences collected for drug resistance testing of HIV are unlikely to be useful in most forensic investigations, but are useful for identifying transmission risk factors.


Related Articles

  • Dangerous liaisons at the virological synapse. Piguet, Vincent; Sattentau, Quentin // Journal of Clinical Investigation;Sep2004, Vol. 114 Issue 5, p605 

    Cell-to-cell viral transmission facilitates the propagation of HIV-1 and human T cell leukemia virus type 1. Mechanisms of cell-to-cell transmission by retroviruses were not well understood until the recent description of virological synapses (VSs). VSs function as specialized sites of immune...

  • Treating cofactors can reverse the expansion of a primary disease epidemic. Gibson, Lee R.; Bingtuan Li; Remold, Susanna K. // BMC Infectious Diseases;2010, Vol. 10 Issue 1, p248 

    Background: Cofactors, "nuisance" conditions or pathogens that affect the spread of a primary disease, are likely to be the norm rather than the exception in disease dynamics. Here we present a "simplest possible" demographic model that incorporates two distinct effects of cofactors: that on the...

  • Fluctuations at a Low Mean Temperature Accelerate Dengue Virus Transmission by Aedes aegypti. Carrington, Lauren B.; Armijos, M. Veronica; Lambrechts, Louis; Scott, Thomas W. // PLoS Neglected Tropical Diseases;Apr2013, Vol. 7 Issue 4, p1 

    Background: Environmental factors such as temperature can alter mosquito vector competence for arboviruses. Results from recent studies indicate that daily fluctuations around an intermediate mean temperature (26°C) reduce vector competence of Aedes aeygpti for dengue viruses (DENV)....

  • Prevention and control of infections in the home. Embil, John M.; Dyck, Brenda; Plourde, Pierre // CMAJ: Canadian Medical Association Journal;5/26/2009, Vol. 180 Issue 11, pE82 

    The article discusses several recommendations for the prevention and control of infections at home. It highlights the necessity on the introduction and employment of a basic approach to limit the transmission of existing antimicrobial-resistant pathogens at home, which can be acquired and...

  • Immunopathogenesis of Dengue Virus Infection. Huan-Yao Lei; Trai-Ming Yeh, Julie Y. H.; Hsiao-Sheng Liu; Yee-Shin Lin; Shun-Hua Chen; Ching-Chuan Liu // Journal of Biomedical Science;2001, Vol. 8 Issue 5, p377 

    Dengue virus infection causes dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS), whose pathogeneses are not clearly understood. Current hypotheses of antibody-dependent enhancement, virus virulence, and IFN-γ/TNFα-mediated immunopathogenesis are...

  • Dynamics of Indirectly Transmitted Infectious Diseases with Immunological Threshold. Joh, Richard I.; Hao Wang; Weiss, Howard; Weitz, Joshua S. // Bulletin of Mathematical Biology;May2009, Vol. 71 Issue 4, p845 

    There are numerous examples of human pathogens which persist in environmental reservoirs while infectious outbreaks remain rare. In this manuscript, we consider the dynamics of infectious diseases for which the primary mode of transmission is indirect and mediated by contact with a contaminated...

  • 'Anything on a needle' is a bloodborne risk.  // Hospital Employee Health;Apr2008, Vol. 27 Issue 4, p47 

    This article focuses on the risk of transmission of disease from bloodborne pathogens to health care workers. This risk is not limited only to hepatitis and HIV. There have been incidents involving transmission of other pathogens from needlesticks, such as tuberculosis, Staphylococcus aureus and...

  • Appropriate Disinfection Techniques for Playing Surfaces to Prevent the Transmission of Bloodborne Pathogens. Grindle, Mikayla; Games, Kenneth E.; Eberman, Lindsey E.; Kahanov, Leamor; Caswell, Shane // International Journal of Athletic Therapy & Training;Sep2014, Vol. 19 Issue 5, p12 

    The article focuses on disinfection techniques for sports facilities for preventing the transmission of blood borne pathogens (BBP), microorganisms that transmit through blood or other potentially infectious material (OPIM) such as sputum, synovial fluid, semen. Topics discussed include...

  • Management of Exposure to Bloodborne Pathogens. . Gregson, Daniel // Journal of the Canadian Dental Association;Nov2000, Vol. 66 Issue 10, p544 

    The article tackles ways to manage exposure to bloodborne pathogens. The measures to manage exposure in health care facilities include general wound cleaning and testing a source patient for hepatitis B virus (HBV), hepatitis C virus (HCV) and human immunodeficiency virus (HIV). Antiviral...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics