Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017

Authors: FERREIRA, HELENA - Orise Fellow; Taylor, Tonya; ABSALON, ANGEL - Vaxbiotek Sc; DIMITROV, KIRIL - Consultant; CORTES-ESPINOSA - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); BUTT, SALMAN - University Of Georgia; GORAICHUK, IRYNA - Consultant; VOLKENING, JEREMY - Base2bio; Suarez, David; Afonso, Claudio

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2019
Publication Date: 4/12/2019
Publication URL: http://handle.nal.usda.gov/10113/6540472
Citation: Ferreira, H.L., Taylor, T.L., Absalon, A.E., Dimitrov, K.M., Cortes-Espinosa, Butt, S.L., Goraichuk, I.V., Volkening, J.D., Suarez, D.L., Afonso, C.L. 2019. Presence of Newcastle disease viruses of sub-genotypes Vc and VIn in backyard chickens and in apparently healthy wild birds from Mexico in 2017. Virus Genes. 55(4):479-489. https://doi.org/10.1007/s11262-019-01663-1.
DOI: https://doi.org/10.1007/s11262-019-01663-1

Interpretive Summary: Newcastle disease is a world-wide problem of poultry caused by virulent isolates of Newcastle disease virus (NDV). This virus has been shown to infect at least 250 wild bird species across the world. Virulent NDV caused outbreaks in Mexico from 1988 to 2011 and again in 2016 and was isolated from both chickens and wild birds. Since 2016, no outbreaks have been reported; however a NDV free status is questionable. Due to the reoccurring circulation of NDV in Mexico, continuous surveillance is important to aid in understanding the role of wild birds in NDV epidemiology. Therefore, in 2017, swab samples were collected from chickens and wild birds from three different farms in Mexico, and MinION and Illumina sequencing technology were used to characterize new isolates and to show that NDV continues to circulate and evolve locally in Mexico despite the ongoing vaccination campaigns.

Technical Abstract: Virulent Newcastle disease viruses (NDV) have been present in Mexico since 1946, and recently, multiple outbreaks have been reported in the country. Here, we characterized eleven NDV isolated from apparently healthy wild birds and backyard chickens in three different locations of Jalisco, Mexico in 2017. Total RNA from NDV was reverse-transcribed, and 1285 nucleotides, which includes 3/4 of the fusion gene, was amplified and sequenced using a long-read MinION sequencing method. The sequences were 99.99–100% identical to the corresponding region obtained using the Illumina MiSeq. Phylogenetic analysis using MinION sequences demonstrated that nine virulent NDV from wild birds belonged to sub-genotypes Vc and VIn, and two backyard chicken isolates were of sub-genotype Vc. The sub-genotype Vc viruses had nucleotide sequence identity that ranged from 97.7 to 98% to a virus of the same sub-genotype isolated from a chicken in Mexico in 2010. Three viruses from pigeons had 96.3–98.7% nucleotide identity to sub-genotype VIn pigeon viruses, commonly referred to as pigeon paramyxovirus, isolated in the USA during 2000–2016. This study demonstrates that viruses of sub-genotype Vc are still present in Mexico, and the detection of this sub-genotype in both chickens and wild birds suggests that transmission among these species may represent a biosecurity risk. This is the first detection and complete genome sequencing of genotype VI NDV from Mexico. In addition, the utilization of an optimized long-read sequencing method for rapid virulence and genotype identification using the Oxford nanopore MinION system is demonstrated.