Molecular Epidemiology and Forensics of RNA Viruses

The goal of forensic analysis of pathogens is not merely to detect the presence of the agent but also to identify the pathogen, its source, and its origin in a scientifi{ligature}cally based unequivocal way that can be used as evidence in court. Modern molecular techniques allow detailed analysis of the genetic code of organisms, permitting distinction of species, strains, and in some cases even individuals. To improve routine epidemiological analysis and meet the new demands of forensic microbiology, it is essential to identify all informative areas of the pathogen genome. The low mutation rate of Deoxyribonucleic Acid (DNA) systems allows the use of techniques including Single-Nucleotide Polymorphism (SNP) and Deletion Insertion Polymorphism (DIP) assays in forensic analysis. A modification of these assays based on melting temperature profiles of the DNA segments that composes of the total DNA sample, offers a less expensive genotyping method. Many important viral pathogens have an RNA genome. RNA viral pathogens are abundant in humans, animals, and plants. Due to the lack of proof reading of the RNA polymerases and high error rate of reverse transcriptases, RNA viruses exhibit high mutation rates that result in genetically heterogeneous populations in continuous competition; these are able to select the best-adapted variants for a particular environment in a quasi-deterministic fashion. Although evolution of RNA viruses seems to be largely unpredictable because of the nature of genetic drifts, the chance transmission bottlenecks, and the influence of host/environmental factors on the success of a determined quasi species, there must be a finite probability that a given nucleotide or amino acid can be substituted and still succeed as a new master sequence of a given viral population.