Detection of Inter-Lineage Natural Recombination in Avian Paramyxovirus Serotype 1 Using Simplified Deep Sequencing Platform

Abstract

Newcastle disease virus (NDV) is a prototype member of avian paramyxovirus serotype 1 (APMV-1), which causes severe and contagious disease in the commercial poultry and wild birds. Despite extensive vaccination programs and other control measures, the disease remains endemic around the globe especially in Asia, Africa, and the Middle East. Being a single serotype, genotype II based vaccines remained most acceptable means of immunization. However, the evidence is emerging on failures of vaccines mainly due to evolving nature of the virus and higher genetic gaps between vaccine and field strains of APMV-1. Most of the epidemiological and genetic characterizations of APMVs are based on conventional methods, which are prone to mask the diverse population of viruses in complex samples. In this study, we report the application of a simple, robust, and less resource-demanding methodology for the whole genome sequencing of NDV, using next-generation sequencing (NGS) on the Illumina MiSeq platform. Using this platform, we sequenced full genomes of five virulent Malaysian NDV strains collected during 2004–2013. All isolates clustered within highly prevalent lineage 5 (specifically in lineage 5a); however, a significantly greater genetic divergence was observed in isolates collected from 2004 to 2011. Interestingly, genetic characterization of one isolate collected in 2013 (IBS025/13) shown natural recombination between lineage 2 and lineage 5. In the event of recombination, the isolate (IBS025/13) carried nucleocapsid protein consist of 55–1801 nucleotides (nts) and near-complete phosphoprotein (1804–3254 nts) genes of lineage 2 whereas surface glycoproteins (fusion, hemagglutinin-neuraminidase) and large polymerase of lineage 5. Additionally, the recombinant virus has a genome size of 15,186 nts which is characteristics for the old genotypes I–IV isolated from 1930 to 1960. Taken together, we report the occurrence of a natural recombination in circulating strains of NDV in commercial poultry using NGS methodology. These findings will not only highlight the potential of RNA viruses to evolve but also to consider the application of NGS in revealing the genetic diversity of these viruses in clinical materials. Factors that drive these evolutionary events and subsequent impact of these divergences on clinical outcome of the disease warrant future investigations.

Comparative evolutionary and phylogenomic analysis of Avian avulaviruses 1–20

“…However, no putative breakpoints were observed in our analysis using SimPlot, GARD or RDP. Contrary to our predictions, a limited number of previous studies have reported an occurrence of natural recombination within avulaviruses (Satharasinghe et al, 2016) and, proposed that recombination may facilitate emergence of a novel/new mutant strain (Yin et al, 2011). Based on these observations, it is evident that recombination in avulavirues is a rare event probably due to non-segmented nature of the virus, apathogenic potential in wild birds, and stability of the genome.…”

Reciprocal complementation of bovine parainfluenza virus type 3 lacking either the membrane or fusion gene

“…Although several groups reported natural recombination between NDV strains (Chong et al, 2010;Han et al, 2008;Qin et al, 2008;Satharasinghe et al, 2016), there was no evidence of recombination between ∆M-EGFP and ∆F-mSB (Fig. 3A).…”

Effective inactivation of nipah virus in serum samples for safe processing in low-containment laboratories

“…Although we demonstrated that UV irradiation is an easy and effective method for the inactivation of NiV, we should consider that each viral genome of the mixture partially damaged by UV light could compensate for their damage to each other via RNA recombination. In paramyxovirus, events of RNA recombination have been reported in natural infection [29,30]. Thus, the combination of other methods with UV inactivation would ensure the e cacy of inactivation.…”