A recent study by Butt and others demonstrates that random next generation sequencing can be successfully used for diagnostic identification and genotyping of Newcastle disease viruses present in paraffin embedded fixed (FFPE) chicken tissues.
Dr. Afonso’s team used this approach to characterize the Newcastle disease virus genomes from field collected samples obtained during disease outbreaks in commercial poultry in Pakistan. The feasibility of FFPE tissues to provide quality sequence for Newcastle disease virus complete genomes and the ability to conduct epidemiological studies using field tissue samples was demonstrated. FFPE is one of the most common type of sample used by pathologists and the information provided by the genotyping is important to trace outbreaks and to develop vaccines.
The USDA team demonstrated the precise identification of the agent in spleens, lungs, brains, and small intestines of chickens. The complete coding sequences of the viruses from the FFPE samples provided better resolution than single or partial gene sequencing and identified the variants of Newcastle disease virus that were circulating at the moment. It demonstrated the superiority of random deep sequencing over other conventional methods such as PCR, real time PCR or Sanger sequencing. This type of fine epidemiologic resolution is important to trace the origin of viruses.
Using FFPE tissues is advantageous because the samples can easily and safely be transported to sequencing labs as all pathogens are inactive. The approach is also practical because FFPE tissues are a primary type of sample used in routine pathologic testing. As the technique did not require any virus enrichment procedure, it is likely applicable to detect other types of viral agents.
The use of a non-targeted random sequencing approach made it unnecessary to develop a previous hypothesis or to use virus specific reagents for this type of diagnostics, thus suggest that “agnostic diagnostic” may become a reality soon.
You can read the complete article here:
Butt SL, Dimitrov KM, Zhang J, Wajid A, Bibi T, Basharat A, Brown CC, Rehmani SF, Stanton JB, Afonso CL. Enhanced phylogenetic resolution of Newcastle disease outbreaks using complete viral genome sequences from formalin-fixed paraffin-embedded tissue samples. Virus Genes. 2019 Aug;55(4):502-512. doi: 10.1007/s11262-019-01669-9. Epub 2019 May 14. PubMed PMID: 31089865.