Abstract: Disclosed are methods to characterize at least one vims in at least one human patient by (a) extracting a viral polynucleotide from a biological sample from the at least one human patient, (b) sequencing the viral polynucleotide to generate viral polynucleotide sequence data; and, (c) characterizing the viral polynucleotide sequence data. Further aspects of the invention may include a system which enables user to quickly and accurately search and/or add to data bases that facilitate the identification and/or treatment of diseases caused by viruses.