Viral illness, applied molecular virology and antivirals

Abstract

The advent of molecular techniques for diagnosis has arguably affected the identification of viral pathogens in illness more than any other segment of pathology, addressing existing problems with timely direct diagnosis of viral pathogens, e.g., viral culture was often lengthy, highly specialised, and insensitive, and there was a relatively low clinical need as antiviral agents were often toxic, infrequently used, and their use was not informed by laboratory assessments. The world-wide human immunodeficiency virus (HIV) and hepatitis C virus (HCV) epidemics and increasing use of antiviral therapy, has driven laboratory surrogate markers of clinical response, particularly quantitation of viral RNA genotype determination, drug-resistance testing particularly for HIV. The techniques now routinely in use for HIV and HCV quantitation have flowed on to laboratory diagnosis of other viruses, particularly cytomegalovirus (CMV), human papillomavirus (HPV) and others. Molecular techniques are typically more sensitive, specific, semi-automatable, and sometimes more rapid. Viral quantitation is increasingly available for more viral pathogens, routinely for HIV, HCV, CMV, and Epstein-Barr virus (EBV). Multiplexing used to detect multiple agents of similar clinical relevance (respiratory viruses such as respiratory syncytial virus [RSV], influenza, adenovirus, and parainfluenza virus [PIV] 1,2,3) is now routinely in use in several laboratories, and commercial assays are available. Commercial assays available for quantitating HIV and HCV include RTPCR (Roche, in-house assays), bDNA (Siemens-Bayer), NASBA (Biomerieux), real-time RTPCR (Roche Taqman, Biomerieux EasyQ, Abbott Celerus) and many more are under development. Techniques improving throughput include automation of nucleic acid preparation and cycling, pooled targets (e.g., ARCBS HIV/HCV), use of new targets for diagnosis, and determination of resistance genotypes to direct therapy. Effective HIV and HCV treatment, with emergence of resistance to antivirals, has driven development of NAT targeting mutation sites associated with resistance, and software using sequence information to derive virtual phenotypes, processes now used for determining resistance of viruses, including influenza (H1N1 strains in the 2008 season), herpes simplex virus (HSV;immunocompromised patients on long term aciclovir), CMV (foscarnet and ganciclovir), hepatitis B virus (HBV) and less frequently varicella zoster virus (VZV). The era of assays that are highly specific (such as PCR), brought together in a multiplex format to answer specific questions is upon us, and design of such assays for individual patients (personalised medicine) is likely becoming a reality. Driving the use of such assays will be reductions in cost that are already occurring, and most importantly, clinical need.