Genetic characterization and phylogeny of pigeon paramyxovirus isolate (PPMV-1) from Pakistan

Abstract

BackgroundKnowing the genome characteristics of circulating Newcastle disease viruses [avian paramyxoviruses (APMV-1) and pigeon paramyxoviruses (PPMV-1)] is important to devise appropriate diagnostics and control strategies. APMVs originating from chicken and wildlife in Pakistan are well-elucidated; nevertheless, molecular characterization for the circulating PPMV-1 is largely unknown. FindingsHere, we have performed fusion (F) and hemagglutinin (HN) gene based characterization of PPMV-1 isolated from an outbreak in a pigeon flock. With F0 proteolytic cleavage site (112RRQKR↓F117), characteristic of velogenic/mesogenic serotype, the complete F and HN gene based sequence analysis of the isolate revealed evolutionary relationship to genotype VI. Further analysis of hyper-variable region of F-gene demonstrated clustering of the study isolate with genotype VIb. The deduced residue analysis for both F and HN protein showed a number of substitution mutations in the functional domains distinct from representative strains of each genotype including the vaccine strains; some of them were found exclusive to the study isolate. Conclusions Though limited and preliminary data, the findings enhance our knowledge towards circulating strains of PPMVs in Pakistan. Further studies are needed to ascertain its potential for transmission in the wild birds, commercial and backyard poultry and its subsequent shedding into the environment.

Genomic and biological characterization of Newcastle disease viruses isolated from migratory mallards (Anas platyrhynchos)

“…Both isolates showed a titer of log2 9 /50µl for HA in harvested allantoic fluid and showed an inhibition activity in HI assay. The F gene-based targeted amplification further confirmed both isolates as Newcastle disease viruses [2,36,37]. The mean death time (MDT) of both isolates was found to be 49.5-50 h with ± 4.4 standard deviation, that is considered typical for velogenic strains of…”

“…A 0.2 ml of filtrate was inoculated in 9 day-old embryonated chicken eggs and processed as per protocol described previously [37]. The harvested allantoic fluid was tested for NDV by standard hemagglutination (HA), hemagglutination inhibition (HI) assays using specific antisera [2,21] and F-gene based polymerase chain reaction (PCR) [36]. The mean infectious dose (EID50 ml -1 ) and pathogenicity (mean death time, MDT) were assessed separately.…”

A comparative genomic and evolutionary analysis of circulating strains of Avian avulavirus 1 in Pakistan

“…Across Pakistan, Avian avulavirus 1 strains of genotype VI (Akhtar et al 2016;Shabbir et al 2016), VII (Shabbir et al 2012a(Shabbir et al , b, 2013(Shabbir et al , 2016Munir et al, 2012a, b;Abbas et al 2014;Farooq et al 2014;Akhtar et al 2016;Habib et al 2018;Aziz-ul-Rahman et al 2018a and XIII (Miller et al 2015;Shabbir et al 2018) (Shabbir et al 2012;Munir et al 2012a, Qamar-un-Nisa et al 2017, Akhtar et al 2017, Israel and a public zoo in Mexico (Panshin et al 2002;Miller et al 2009). Therefore, the role of wild birds as natural reservoirs in dissemination of the virus cannot be overlooked.…”

“…Class-I contains nine distinct genotypes (I-IX) of avirulent strains that share a 15198 nt long genome, while class-II contains at least eighteen distinct genotypes (I-XVIII) of high virulent, low virulent and avirulent strains that have a 15186 and/or 15192 nt long genome (Aldous et al 2003;Kim et al 2007). Based on partial sequencing of F genes (375bp between 4597-4972 nts), avualviruses of genotypes I, II, VI, VII, XIII are further divided into different sub-genotypes of both virulent and avirulent strains isolated from a wide range of avian species (Shabbir et al 2012a(Shabbir et al , b, 2013(Shabbir et al , 2016Munir et al 2012a, b;Miller et al 2015;Akhtar et al 2016;Nath and Kumar 2015;Das andKumar 2017, Xue et al 2017;Barman et al 2017;Habib et al 2018;Aziz-ul-Rahman et al 2018a.…”

“…In this regard, a vast majority of studies in Pakistan have reported the epidemiology and surveillance of ND in commercial and domestic poultry and wild susceptible avian hosts. Historically, beginning in the 1990s, these studies were limited to serosurveillance (Numan et al 2005;Aziz-ul-Rahman et al 2017); whereas in recent years, partial genome-based studies have been conducted to investigate strain genotyping (Shabbir et al 2012a(Shabbir et al , 2013Munir et al 2012b;Farooq et al 2014;Akhtar et al 2016Akhtar et al , 2017Wajid et al 2018) while few studies involved in complete genome sequencing and biologic characterization of field circulating AAvV 1 strains (Munir et al 2012a;Shabbir et al 2012bShabbir et al , 2016Shabbir et al , 2018Habib et al 2018;Aziz-ul-Rahman et al 2018a.…”