Research Article Comparative Genomics of Herpesviridae Family to Look for Potential Signatures of Human Infecting Strains Vikas Sharma, Fauzul Mobeen, and Tulika Prakash School of Basic Sciences, Indian Institute of Technology, Mandi 175005, India Correspondence should be addressed to Tulika Prakash; tulika@iitmandi.ac.in Received 14 January 2016; Accepted 24 April 2016 Academic Editor: Giuliana Napolitano Copyright © 2016 Vikas Sharma et al. Tis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Herpesviridae family is one of the signifcant viral families which comprises major pathogens of a wide range of hosts. Tis family includes at least eight species of viruses which are known to infect humans. Tis family has evolved 180–220 million years ago and the present study highlights that it is still evolving and more genes can be added to the repertoire of this family. In addition, its core-genome includes important viral proteins including glycoprotein B and helicase. Most of the infections caused by human herpesviruses have no defnitive cure; thus, search for new therapeutic strategies is necessary. Te present study fnds core-genome of human herpesviruses that difers from that of Herpesviridae family and nonhuman herpes strains of this family and might be a putative target for vaccine development. Te phylogenetic reconstruction based upon the protein sequences of core gene set of Herpesviridae family reveals the sharp splits of its diferent subfamilies and supports the hypothesis of coevolution of viruses with their hosts. In addition, data mining for cis-elements in the genomes of human herpesviruses results in the prediction of numerous regulatory elements which can be used for regulating the expression of viral based vectors implicated in gene therapies. 1. Introduction Human herpesviruses (HHVs) are one of the major human pathogens and are known to cause several diseases including herpes genitalis, infectious mononucleosis, and Kaposi’s sar- coma. Herpes simplex virus type 1 (HSV-1) and herpes sim- plex virus type 2 (HSV-2) are the most common pathogens among HHVs and cause several infections including genital or oral herpes, conjunctivitis, and encephalitis, commonly known as herpes simplex infection. Tis infection is incurable and around 90% of world's population is infected with one or both viruses [1]. If human simplex virus (HSV) induced encephalitis remains untreated, it has a very high (>70%) fatality rate [2]. Its management is also poor which results in death of a major proportion of patients while only a minor proportion returns to normal functions. In addition, Epstein-Barr virus (EBV) is another one of most common human pathogens and is implicated in a number of human malignancies. Previous study showed that EBV-attributable malignancies accounted for 1.8% of all cancer deaths in 2010 and this percentage is increased by 14.6% over a period of 20 years [3]. Tere are no defnitive therapies or drugs available for most of the HHV induced infections. Global burden of HHV induced infections is increasing rapidly which needs efective means of prognosis and therapeutics for its better management. On the other side, few members of HHVs including HSVs are also implicated as vectors for vaccine development and gene therapy of several diseases, namely, Parkinson’s disease and Alzheimer’s disease. Cis-elements play signifcant role in the regulation of these virus-vectors for desired gene expression. Tese aspects of HHVs make them signifcant for clinical and pharmaceutical research. HHVs belong to Herpesviridae family of Herpesvirales order under group I (dsDNA) in virus classifcation hierarchy. Members of Herpesviridae family are well characterized and are known to infect a wide range of hosts. In addition to humans, these hosts include mammals, birds, reptiles, amphibians, molluscs, and fsh. At least eight species of HHVs are found to infect humans. Based upon biological features and genomic attributes, members of Herpesviridae family have been classifed into three subfamilies including Alpha- herpesvirinae, Betaherpesvirinae, and Gammaherpesvirinae with their estimated origin being 180 to 220 million years ago [4]. Te Alphaherpesvirinae subfamily includes important Hindawi Publishing Corporation International Journal of Genomics Volume 2016, Article ID 9543274, 10 pages http://dx.doi.org/10.1155/2016/9543274