Event Title First Global Alliance for Research on Avian Diseases (GARAD) Conference
Session Title Unknown
Event Date & Time On Tue, 30 Jun 2015 at 12:05:00 - 12:25:00
Venue Edmond J. Safra Lecture Theatre
Abstract Title Strain Identification of Avian Pathogens: Benefits, Techniques and Challenges
Authors Amir NoorMohammadi
Affiliations Faculty of Veterinary Sciences, The University of Melbourne, Australia
Abstract Content

Strain identification of avian pathogens has a wide range of implications for the local and global poultry industries. These include insights on epidemiology of infectious diseases, and capacity for characterisation of live vaccines before introduced into a given country. Ideally, strain identification techniques must be accurate, simple, affordable and rapid, and have the capacity to predict the virulence of the organism. A large number of techniques have been reported for strain identification of avian pathogens. Serotyping (e.g. VN using hyper-immune polyclonal sera) have been applied for strain classification of avian pathogens such as IBV and FAdV. This however is a time consuming process and requires purified and cloned organism. Also results may not necessarily correlate with protectotype of the organism. Moreover this technique is not applicable for organisms such as ILTV where strains are serologically indistinguishable from each other. Genotyping of the avian pathogens are increasingly used for strain identification purposes. Earlier methods involved analysis of the genome often using RFLP of the whole genomic DNA but this involves considerable time and cost for isolation and propagation of the organism, and preparation of the genomic DNA. More recently, sequence analysis of specific genes, often amplified by PCR, has become the method of choice in many diagnostic laboratories. However this method too is not readily available in all laboratories, as it may be time consuming and often requires interpretation of the results by an expert. Various techniques have been reported to facilitate a non-objective analysis of the PCR products. These include but not restricted to RFLP, SSCP, DGGE, arbitrarily primed PCR, probe-based real-time PCRs, and HRM curve analysis. Despite these advancements, a number of impediments prohibit extensive use of the current strain identification techniques as a routine procedure in diagnostic laboratories. Most importantly, for many pathogens, there is no universally accepted target gene(s) for typing and or inconsistency in the primers used for amplification of the target gene. Also current strain typing techniques do not necessarily correlate with virulence or tissue tropism of the organism under investigation. Finally the usefulness of the test may vary depending on the organisms found in a given geographical location. With a significant decrease in cost and time associated in whole-genome sequencing, it is suspected that this method will become the method of choice for strain identification of avian pathogens in near future. However a major advancement towards automisation of assembly, annotation and comparative analysis of sequences is necessary before this technique can be adopted a routine tool for strain identification of avian pathogens in diagnostic laboratories.