High genetic diversity of Newcastle disease virus in poultry in West and Central Africa: cocirculation of genotype XIV and newly defined genotypes XVII and XVIII

Abstract

Despite rampant Newcastle disease virus (NDV) outbreaks in Africa for decades, the information about the genetic characteristics of the virulent strains circulating in West and Central Africa is still scarce. In this study, 96 complete NDV fusion gene sequences were obtained from poultry sampled in Cameroon, Central African Republic, Côte d'Ivoire, and Nigeria between 2006 and 2011. Based on rational criteria recently proposed for the classification of NDV strains into classes, genotypes, and subgenotypes, we revisited the classification of virulent strains, in particular those from West and Central Africa, leading to their grouping into genotype XIV and newly defined genotypes XVII and XVIII, each with two subgenotypes. Phylogenetic analyses revealed that several (sub)genotypes are found in almost every country. In Cameroon, most strains were related to vaccine strains, but a single genotype XVII strain was also found. Only three highly similar genotype XVII strains were detected in Central African Republic. Subgenotypes XVIIa, XVIIIa, and XVIIIb cocirculated in Côte d'Ivoire, while subgenotypes XIVa, XIVb, XVIIa, XVIIb, and XVIIIb were found in Nigeria. While these genotypes are so far geographically restricted, local and international trade of domestic and exotic birds may lead to their spread beyond West and Central Africa. A high genetic diversity, mutations in important neutralizing epitopes paired with suboptimal vaccination, various levels of clinical responses of poultry and wild birds to virulent strains, strains with new cleavage sites, and other genetic modifications found in these genotypes tend to undermine and complicate NDV management in Africa.

Fig 1

Collection sites in Côte d'Ivoire, Nigeria, Cameroon, and Central African Republic. Provinces or states visited are indicated by black points. In Côte d'Ivoire, numbers correspond to the following provinces: 1, Savanes; 2, Worodougou; 3, Zanzan; 4, Vallée du Bandama; 5, Moyen-Comoé; 6, Agnéby; 7, Bas-Sassandra; 8, Sud-Bandama; 9, Lagunes. (Base map © Map Resources.)

Fig 2

Detailed view of genotypes XIV and XVIII (A) and genotype XVII (B), as calculated in Fig. S1 in the supplemental material, that shows the phylogeny of 992 complete F gene sequences analyzed with the maximum likelihood method and the GTR+G+I nucleotide substitution model. Sequences obtained in this study are shown in bold. For Nigeria, the states are indicated as follows: Sokoto State, black circle; Yobe State, gray circle; Plateau State, white circle; Benue State, black square; Lagos State, gray square; Oyo State, white square. Accession numbers of previously published sequences available in GenBank are indicated. Only bootstrap values of ≥60% are shown. The scale corresponds to the number of base substitutions per site. GWH, Green Wood Hoopoe.

Fig 3

Summary of (sub)genotype XIV, XVII, and XVIII distribution in West and Central Africa (including previously published results from references , , , and 49). (Sub)genotypes are represented as follows: XIVa, black circle; XIVb, gray circle; XVII, black square; XVIIa, gray square; XVIIb, white square; XVIIIa, black triangle; XVIIIb, gray triangle; putative XIX, white circle. (Base map © Map Resources.)