Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.
In Tanzania, 62 roosters and 302 hens from the Kuchi, Morogoro Medium (MoroMed), and Ching’wekwe (Ching) ecotypes that also produced experimental chickens for the lentogenic infection study described by [17] were used to breed chickens for the natural velogenic NDV exposure trials. Similarly, in Ghana, 42 roosters and 128 hens from the Coastal Savannah (CS), Forest (FO), and Interior Savannah (IS) ecotypes that also produced experimental chickens for the lentogenic study described by [18] were used. All breeder birds in the two countries were raised in a controlled environment with ad libitum access to both feed and water. Experimental birds were produced in 3 hatches for the Tanzania ecotypes and in 6 hatches for the Ghana ecotypes, with each hatch comprising one replicate of the natural exposure trial. For all replicates, chicks were raised in a single pen under similar conditions, with ad libitum access to both water and feed. For each replicate of the natural challenge, birds that were suspected to be infected with velogenic NDV based on clinical signs were purchased from farmers or at a local market. Oropharyngeal and cloacal swabs samples were collected and RT-qPCR was performed to confirm the birds’ infection with mesogenic or velogenic NDV [29,30]. Sick birds were also screened for absence of infection with avian influenza virus, using a FluDETECT® Avian kit (Zoetis, Parsippany-Troy Hills, NJ, USA), in order to avoid introducing another major respiratory virus into the study. For each replicate, the screened sick birds were mixed with 40 healthy naïve birds in an isolated pen to amplify the infection and to standardize timing. Three days later, upon development of clinical signs, the resulting seeder birds were mixed with healthy experimental birds in a ratio of 25:1 in Ghana and 20:1 in Tanzania. Experimental birds were 28 days of age at the time of exposure for all replicates in Ghana, and 42, 35, and 28 days of age for replicates 1, 2, and 3, respectively, in Tanzania. All trials in both countries were terminated at 21 days post-exposure (dpe) and surviving birds were euthanized at that time. Birds that died before the end of the experiment died before 21 days. Across replicates, the natural exposure trials were conducted on a total of 1365 chickens in Ghana (CS (340), FO (708), and IS (317)), and on 1556 chickens in Tanzania (Kuchi (439), Ching (405), and MoroMed (712)). The natural exposure to velogenic NDV caused severe clinical symptoms and allowed observation of phenotypic responses of birds’ post-exposure. Survival time was recorded as the number of dpe when the bird died; birds that survived until 21 dpe were euthanized. Viral RNA was isolated from lachrymal fluid (tears) and cloacal swabs at 2, 4, 6, and 10 dpe using a MagMAX-96 viral RNA isolation kit (Life Technologies, Carlsbad, CA, USA) and quantified using qRT-PCR, following the procedures described in [31]. Average viral RNA was computed and transformed to log10. Blood samples were collected at 7 dpe to measure anti-NDV antibody levels by ELISA (IDEXX, Westbrook, ME, USA). Blood samples were also collected from all birds before NDV exposure using an enzyme-linked immunosorbent assay to measure the natural anti-KLH antibody in birds (MP Biomedicals Inc., Aurora, OH, USA). Lesions in the trachea, proventriculus, intestine (duodenum, jejunum, and ileum), and cecal tonsils were assessed and scored on the dead and euthanized birds on a scale of 0 to 5, where 0 indicated no visible lesions and 5 indicated severe lesions. Lesions scores were averaged across organs for each bird. Body weights were recorded at hatch and weekly thereafter prior to exposure, and at 0, 2, 4, 6, and 10 dpe. Pre-exposure growth rate (g/d) was calculated based on body weights at hatch and at exposure. Post-exposure growth rate (g/d) was calculated based on body weights at 0 and 4 dpe because few birds survived past 4 dpe. Whole blood was collected from breeders and chicks before exposure and placed on Whatman FTA cards (Sigma-Aldrich, St. Louis, MO, USA) for genomic DNA extraction. For breeders, genotyping was conducted on an Affymetrix Axiom 600K Array (Thermo Fisher Scientific Inc., Carlsbad, CA, USA) at GeneSeek (Lincoln, NE, USA). Genotypes for the Ghana and Tanzania breeders were combined, and genotype data quality control was performed using AxiomTM Analysis Suite 3.1 (Applied Biosystems, Thermo Fisher Scientific Inc., Carlsbad, CA, USA), using similar thresholds as described in [18]. A total of 421,492 SNPs remained after quality control and were utilized for imputation analyses. The experimental birds were genotyped using targeted genotyping by sequencing (GBS) for the 5K SNP low-density panel described by [32], with 100 bp paired ends on 4 lanes of an Illumina NextSeq500 Hiseq at GeneSeek (Lincoln, NE, USA). Raw read sequence data were processed using an in-house shell script that utilized publicly available software tools (BWA (0.7.17), SAMtools (1.9), PICARDS (2.17.0), and BCFtools (1.9)), as described by [32]. Reads were aligned to the Gallus gallus version 5 reference genome and genotypes were called from the vcf using an in-house python script. The low density genotyped experimental birds were imputed to the high-density panel that the breeders were genotyped on using Fimpute [33], separately for each country. Experimental birds were assigned to half and full-sib families based on the distribution of genomic relationships among birds within each country. The three ecotypes within each country were previously found to have partial shared ancestries based on analysis of the high-density SNP genotypes of birds used in the lentogenic NDV challenge studies, as described by [17,18]. These studies used Admixture software [34] to determine the optimal number of subpopulations, which were 3 for the Ghana ecotypes [18] and 2 for the Tanzania ecotypes [17]. This same procedure was applied to the imputed genotypes of the experimental birds for the velogenic NDV exposure trials to quantify the proportional contributions of the 3 and 2 subpopulations for the Ghana and Tanzania experimental birds, respectively. Genetic parameters were estimated both by country and using the combined data. Asreml 4.2 software [35] was used to estimate variance components and heritability for each trait using the following univariate animal model: where Y is the phenotype, i.e., pre- and post-exposure growth rate, trachea, proventriculus, intestinal, cecal tonsil, and average lesion scores, natural antibody level, NDV antibody level at 10 dpe, tear and cloacal viral loads at 2, 4, 6, and 10 dpe, and survival time. Fixed effects included replicate, R (1 to 6 for Ghana and 1 to 3 for Tanzania), and population proportions (P), obtained as described above, fitted as one covariate for Tanzania and as two covariates for Ghana, as described by [17,18]. Random effects included animal genetic effects (A) with a genomic relationship matrix obtained based on the procedures described by [36], maternal environmental effects (M), and residuals (e). The maternal effect was removed from the model for traits for which it was estimated to be zero. For viral load traits and for natural and anti-NDV antibody levels, the effect of assay plate was added to the model as a fixed effect. For lesion scores, the effect of bird survival to the end of the trial (0/1) was added as a fixed effect. For the combined analyses, replicate by country and country-specific population proportion covariates were added. Phenotypic variance was estimated as the sum of the estimates of the animal genetic, maternal (if fitted), and residual variances. Heritability was estimated as the ratio of animal genetic and phenotypic variance estimates. Phenotypic and genetic correlations between traits recorded in the velogenic NDV trials were estimated separately for each country and combined using a bivariate version of the univariate models described above. Genetic correlations of the velogenic NDV phenotypes of the current study with phenotypes recorded in the lentogenic NDV trials [17,18] (pre- and post-infection growth rate, anti-NDV antibody levels at 10 days post-infection (dpi), viral load at 2 and 6 dpi, and viral clearance) were also estimated. Bivariate models were used, with the model as described above, for the velogenic NDV response traits and as described in [17,18] for the lentogenic NDV response traits. Because the lentogenic and velogenic NDV challenges were conducted using different birds but from the same ecotypes, environmental correlations were not estimable and were set equal to zero.