Next generation sequencing technologies: Tool to study avian virus diversity

Abstract

Summary. -Increased globalisation, climatic changes and wildlife-livestock interface led to emergence of novel viral pathogens or zoonoses that have become serious concern to avian, animal and human health. High biodiversity and bird migration facilitate spread of the pathogen and provide reservoirs for emerging infectious diseases. Current classical diagnostic methods designed to be virus-specific or aim to be limited to group of viral agents, hinder identifying of novel viruses or viral variants. Recently developed approaches of next-generation sequencing (NGS) provide culture-independent methods that are useful for understanding viral diversity and discovery of novel virus, thereby enabling a better diagnosis and disease control. This review discusses the different possible steps of a NGS study utilizing sequence-independent amplification, high-throughput sequencing and bioinformatics approaches to identify novel avian viruses and their diversity. NGS lead to the identification of a wide range of new viruses such as picobirnavirus, picornavirus, orthoreovirus and avian gamma coronavirus associated with fulminating disease in guinea fowl and is also used in describing viral diversity among avian species. The review also briefly discusses areas of viral-host interaction and disease associated causalities with newly identified avian viruses.

Genetic and pathogenic characterisation of 11 avian reovirus isolates from northern China suggests continued evolution of virulence

“…Thus, the full genomic characterisation of emerging ARV field strains will provide more detailed molecular data to better understand ARV mutations and/or recombination events that may influence the epidemiology and pathogenicity of the virus. We are currently sequencing the full genome of the MS01 strain using the MiSeq next-generation sequencing system (Illumina, San Diego, CA, USA) 32 33 34 . The full genome sequence will allow us to determine the locations of mutated sites in the complete sequences of all 10 genome segments by comparison with reference strain S1133.…”

Avian parvovirus: classification, phylogeny, pathogenesis and diagnosis

“…Sequence-independent techniques, such as next generation sequencing, have allowed the detection of avian viral genome diversity from healthy and affected birds Kapgate et al, 2015). The comparative metagenomics studies revealed ChPV genomic sequence diversity identified from RSSaffected and unaffected broilers (Devaney et al, 2016;Lima et al, 2017), and divergent turkey parvovirus sequences from turkey faeces (Reuter et al, 2014).…”

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome

“…Identification methods based on culture have disadvantages, such as long turnaround time, increased biohazard risks, and culture bias. The high-throughput feature of NGS enables the recovery of pathogen genomes from noncultured samples, and offers the potential for highly accurate pathogen identification and rapid clinical diagnoses [ 4 – 12 ]. Many researchers have reported the NGS-based identification of pathogens from various noncultured samples [ 13 – 21 ], such as Old World arenavirus (brain et al) [ 17 ], influenza virus (nasopharyngeal aspirate) [ 18 ], norovirus (feces) [ 18 ], dengue virus [ 19 ], yellow fever virus (serum) [ 20 ], Shiga-toxigenic Escherichia coli O104:H4 (feces) [ 21 ], and most recently, Ebola virus (serum et al) [ 13 – 16 ].…”