Journal of Clinical Virology 57 (2013) 378–380 Contents lists available at SciVerse ScienceDirect Journal of Clinical Virology jo u r n al hom epage: www.elsevier.com/locate/jcv Commentaries and Points of View Molecular epidemiology of viral diseases in the era of next generation sequencing Mayra Cruz-Rivera a , Joseph C. Forbi b,1 , Lilian H.T. Yamasaki c , Carlos A. Vazquez-Chacon b , Armando Martinez-Guarneros b , Juan C. Carpio-Pedroza b , Alejandro Escobar-Gutiérrez b , Karina Ruiz-Tovar b , Salvador Fonseca-Coronado d , Gilberto Vaughan b,*,1 a Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico b Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud, Mexico City, Mexico c Department of Biology, Institute of Bioscience, Language and Exact Science, São Paulo State University, São José do Rio Preto, SP, Brazil d Laboratorio de Inmunobiología de Enfermedades Infecciosas, Unidad de Investigación Multidisciplinaria, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico a r t i c l e i n f o Article history: Received 20 March 2013 Received in revised form 22 April 2013 Accepted 24 April 2013 In virology, molecular epidemiology is defined as the applica- tion of molecular methods to study the causation and dynamics of viral diseases in a population. In the study of viral diseases, this is determined by the transmission of the corresponding eti- ological agent on its host, and how this phenomenon affects the spread of the disease within the population. Molecular epidemi- ology uses information about genetic variation to investigate the evolution, transmission and pathogenesis of viral agents. Molecular epidemiological tools have provided important insights in the study of viral diseases, improving significantly our understanding about the history of infection, virus evolution, spread and disease trans- mission that have helped to implement public health policies. 1 The primary application of molecular epidemiology in virology has been to provide specific and sensitive identification of viral agents to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to deter- mine the distribution of a given disease and its association with epidemiologically important phenotypes among viral populations, genetic diversity and risk factors, allowing the implementation of tailored control programs. Thus, the understanding of transmission * Corresponding author at: Departamento de Investigaciones Inmunológicas, Instituto de Diagnóstico y Referencia Epidemiológicos, Carpio 470, México City 11340, Mexico. Tel.: +52 55 5342 7563; fax: +52 55 5341 3264. E-mail address: gilvaughan@yahoo.com (G. Vaughan). 1 Current address: Division of Viral Hepatitis, Centers for Disease Control and Prevention, United States. dynamics requires both population and evolutionary biology to determine the genetic structure and evolution of infectious agents. An important challenge in the study of the molecular epidemi- ology of viral diseases is the identification of genetic markers for complex traits of epidemiological significance. This is of particular interest in virology since the high genetic variation observed in many viruses results in the establishment of a swarm of genetically related but distinct viral variants within the host, named as quasispecies, further complicating the char- acterization of the viral population. 2 The development of new molecular tools has facilitated enormously the direct examina- tion of clinical and environmental samples. Until recently, the assessment of the complexity of the viral population has been per- formed by analyzing regions of the genome exhibiting different degrees of genetic variability and to a lesser extent the full-length viral genome. Different quantitative methods, such as popula- tion cloning, end-point limiting dilution and mass spectrometry, have been used to analyze the architecture of the intra-host viral population. 3–5 However, such methodologies have inherent limita- tions that further complicate the measuring of the viral population heterogeneity. 6 The complexity of mixtures and the difficulty in detecting low-frequency variants represent major challenges in the characterization of the structure of the viral population in clinical samples. 3 The arrival of a variety of next-generation sequencing (NGS) platforms has undoubtedly revolutionized the field of virology. 7 The hallmark feature of NGS technologies is the unprecedented high throughput, which results in the sequencing of hundreds of gigabases in a single experiment. These novel DNA sequencing 1386-6532/$ – see front matter. Published by Elsevier B.V. http://dx.doi.org/10.1016/j.jcv.2013.04.021