New Avian Paramyxoviruses Type I Strains Identified in Africa Provide New Outcomes for Phylogeny Reconstruction and Genotype Classification

Renata Servan De Almeida,Gilles Balança,Dominique Martinez,Véronique Jestin,Julien Cappelle,Véronique Chevalier,Olivier Fridolin Maminiaina,Saliha Hammoumi,Sophie Molia,Colette Grillet,Ould El Mamy Bezeid,Marthin Dakouo,Flavie Goutard,Emmanuel Albina,Abbas Diarra,Nicolas Gaidet,Patricia Gil,Hassen Chaka,Abdallah Traoré,Samia Guendouz,Peter N Thompson ,K Samaké ,François-Xavier Briand

doi:10.1371/journal.pone.0076413

Abstract

Newcastle disease (ND) is one of the most lethal diseases of poultry worldwide. It is caused by an avian paramyxovirus 1 that has high genomic diversity. In the framework of an international surveillance program launched in 2007, several thousand samples from domestic and wild birds in Africa were collected and analyzed. ND viruses (NDV) were detected and isolated in apparently healthy fowls and wild birds. However, two thirds of the isolates collected in this study were classified as virulent strains of NDV based on the molecular analysis of the fusion protein and experimental in vivo challenges with two representative isolates. Phylogenetic analysis based on the F and HN genes showed that isolates recovered from poultry in Mali and Ethiopia form new groups, herein proposed as genotypes XIV and sub-genotype VIf with reference to the new nomenclature described by Diel’s group. In Madagascar, the circulation of NDV strains of genotype XI, originally reported elsewhere, is also confirmed. Full genome sequencing of five African isolates was generated and an extensive phylogeny reconstruction was carried out based on the nucleotide sequences. The evolutionary distances between groups and the specific amino acid signatures of each cluster allowed us to refine the genotype nomenclature.

Highlights

Newcastle disease (ND) is one of the most severe infectious diseases of birds, poultry, and has been the cause of major economic losses worldwide [1]
Detection and Initial Characterization of Newcastle disease virus (NDV) Isolates in African Samples Using real-time RT-PCR detection, we found 421 samples positive for NDV among 9,609 domestic samples (4.38%, 95% CI: 4–4.8%) and 211 positive samples among 10,343 collected from wild birds (2.04%, 95% CI: 1.8–2.3)
The 2007/Mali/ML029 and 2007/Mali/ML031 isolates have five basic amino acids on their cleavage site and a V118 associated with the cleavage site (112RRRKR116QFV), a motif described only rarely, and just recently in the neighboring country, Burkina Faso [22]

Summary

Introduction

Newcastle disease (ND) is one of the most severe infectious diseases of birds, poultry, and has been the cause of major economic losses worldwide [1]. V, HN, NP, P and L proteins play a role in virulence [6,7,8,9], the most important molecular determinant of virulence appears linked to the amino acid motif present at the protease cleavage site of the F0 precursor of the fusion protein [10]. In virulent isolates, this motif is constituted of basic amino acids, and rapid typing of this region by RT-PCR and sequencing is a good indicator of the NDV pathotype. Other viral factors affect the virulence of isolates, so pathogenicity should be confirmed by in vivo tests, including the intracerebral pathogenicity index (ICPI) in 1-day-old chickens, the mean death time (MDT) of specific-pathogen-free hen’s embryos after inoculation, and the intravenous pathogenicity index (IVPI) in 6-week-old chickens [2]

Methods

Results

Conclusion