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We report the complete genome sequence of an avian orthoavulavirus 13 strain, isolated from a white-fronted goose in the Odesa region of Ukraine in 2013. The detection of avian orthoavulavirus 13 in Ukraine confirms that the geographic distribution of this virus extends beyond Asia.

Live bird markets (LBMs) in Asian countries are considered hubs for the spread of several poultry viruses. In Pakistan, there is a lack of uniformity in practices used in LBMs, which leads to the spread of poultry diseases. A cross-sectional survey was conducted in June-October 2017 to determine the circulation of Newcastle disease virus (NDV) in chickens being sold in live bird retail stalls (LBRSs) and to identify potential risk factors associated with estimated prevalence. A total of 189 stalls (Vigilancia y evaluación de factores de riesgo para el virus de la enfermedad de Newcastle en puestos de venta al menudeo de aves vivas en el distrito de Lahore en Pakistán. Los mercados de aves vivas (LBM, por sus siglas en inglés) en los países asiáticos se consideran centros de propagación de varios virus aviares. En Pakistán, existe una falta de uniformidad en las prácticas utilizadas en los mercados de aves vivas, lo que conduce a la propagación de enfermedades avícolas. Se realizó una encuesta transversal de junio a octubre del 2017 para determinar la circulación del virus de la enfermedad de Newcastle (NDV) en pollos que se venden en puestos minoristas de aves vivas y para identificar posibles factores de riesgo asociados con la prevalencia estimada. Se visitó un total de 189 puestos (

In ovo vaccination has been employed by the poultry industry for over 20 years to control numerous avian diseases. Unfortunately, in ovo live vaccines against Newcastle disease have significant limitations, including high embryo mortality and the inability to induce full protection during the first two weeks of life. In this study, a recombinant live attenuated Newcastle disease virus vaccine containing the antisense sequence of chicken interleukin 4 (IL-4), rZJ1*L-IL4R, was used. The rZJ1*L-IL4R vaccine was administered in ovo to naïve specific pathogen free embryonated chicken eggs (ECEs) and evaluated against a homologous challenge. Controls included a live attenuated recombinant genotype VII vaccine based on the virus ZJ1 (rZJ1*L) backbone, the LaSota vaccine and diluent alone. In the first of two experiments, ECEs were vaccinated at 18 days of embryonation (DOE) with either 104.5 or 103.5 50% embryo infectious dose (EID50/egg) and chickens were challenged at 21 days post-hatch (DPH). In the second experiment, 103.5 EID50/egg of each vaccine was administered at 19 DOE, and chickens were challenged at 14 DPH. Chickens vaccinated with 103.5 EID50/egg of rZJ1*L-IL4R had hatch rates comparable to the group that received diluent alone, whereas other groups had significantly lower hatch rates. All vaccinated chickens survived challenge without displaying clinical disease, had protective hemagglutination inhibition titers, and shed comparable levels of challenge virus. The recombinant rZJ1*L-IL4R vaccine yielded lower post-vaccination mortality rates compared with the other in ovo NDV live vaccine candidates as well as provided strong protection post-challenge.

Newcastle disease virus (NDV) has a wide avian host range and a high degree of genetic variability, and virulent strains cause Newcastle disease (ND), a worldwide concern for poultry health. Although NDV has been studied in Nigeria, genetic information about the viruses involved in the endemicity of the disease and the transmission that likely occurs at the poultry-wildlife interface is still largely incomplete. Next-generation and Sanger sequencing was performed to provide complete (n = 73) and partial genomic sequence data (n = 38) for NDV isolates collected from domestic and wild birds in Nigeria during 2002-2015, including the first complete genome sequences of genotype IV and subgenotype VIh from the African continent. Phylogenetic analysis revealed that viruses of seven different genotypes circulated in that period, demonstrating high genetic diversity of NDV for a single country. In addition, a high degree of similarity between NDV isolates from domestic and wild birds was observed, suggesting that spillovers had occurred, including to three species that had not previously been shown to be susceptible to NDV infection. Furthermore, the first spillover of a mesogenic Komarov vaccine virus is documented, suggesting a previous spillover and evolution of this virus. The similarities between viruses from poultry and multiple bird species and the lack of evidence for host adaptation in codon usage suggest that transmission of NDV between poultry and non-poultry birds occurred recently. This is especially significant when considering that some viruses were isolated from species of conservation concern. The high diversity of NDV observed in both domestic and wild birds in Nigeria emphasizes the need for active surveillance and epidemiology of NDV in all bird species.

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.

Here, we report the complete genome sequence of an Avian coronavirus strain GA08-like isolate from a fecal sample from a broiler chicken collected in Georgia, USA, in 2004. The viral genome in this 15-year-old sample provides evidence for the circulation of the GA08-like strain at least 4 years before its first report in 2008., Here, we report the complete genome sequence of an Avian coronavirus strain GA08-like isolate from a fecal sample from a broiler chicken collected in Georgia in 2004. The viral genome in this 15-year-old sample provides evidence for the circulation of the GA08-like strain at least 4 years before its first report in 2008.

Here, we report the complete genome sequence of an Avian coronavirus strain GA08-like isolate from a fecal sample from a broiler chicken collected in Georgia, USA, in 2004. The viral genome in this 15-year-old sample provides evidence for the circulation of the GA08-like strain at least 4 years before its first report in 2008.

Here, we report the complete genome sequence of fowl adenovirus D (FAdV-D) isolated from a preserved 24-year-old pancreas sample of a broiler chicken embryo. The results of the sequence showed that the viral genome is 44,079 bp long., Here, we report the complete genome sequence of fowl aviadenovirus D (FAdV-D) isolated from a preserved 24-year-old pancreas sample of a broiler chicken embryo. The results of the sequence showed that the viral genome is 44,079 bp long.

Parvoviruses are commonly found in U.S. poultry and are associated with clinical disease. Here, we report the complete coding sequences of three chicken parvoviruses from broiler chickens from commercial farms in the state of Georgia.

Avian metapneumoviruses (aMPVs), which have been reported in many countries, cause acute upper respiratory tract disease in chickens and turkeys. Using next-generation sequencing, we report here the complete genome sequence of an aMPV subtype B strain that was isolated from a turkey in Hungary in 1989.

Avian metapneumoviruses (aMPVs), which have been reported in many countries, cause acute upper respiratory tract disease in chickens and turkeys. Using next-generation sequencing, we report here the complete genome sequence of an aMPV subtype B strain that was isolated from a turkey in Hungary in 1989.

Here, we report the complete genome sequence of Avian coronavirus strain ArkDPI of the GI-9 lineage, isolated from broiler chickens in North Georgia in 1994. This is the complete genome sequence of this vaccine strain, reisolated from broilers in the United States.

We report the complete genome sequences of 11 virulent Newcastle disease viruses. The isolates were obtained from vaccinated broiler and layer chickens in three different provinces of Indonesia in 2013 and 2014. Phylogenetic analysis revealed that all isolates belong to subgenotype VII.2 in the class II cluster.

Avian coronavirus, also known as infectious bronchitis virus, is a highly contagious respiratory pathogen of chickens that is responsible for major economic losses to the poultry industry around the globe. Here, we report the complete genome sequence of strain GA08 of the GI-27 lineage, isolated from a fecal sample from a broiler chicken collected in Georgia in 2015.

The Coronavirus Disease 2019 (COVID-19) is the first known pandemic caused by a coronavirus. Its causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appears to be capable of infecting different mammalian species. Recent detections of this virus in pet, zoo, wild, and farm animals have compelled inquiry regarding the zoonotic (animal-to-human) and reverse zoonotic (human-to-animal) transmissibility of SARS-CoV-2 with the potential of COVID-19 pandemic evolving into a panzootic. It is important to monitor the global spread of disease and to assess the significance of genomic changes to support prevention and control efforts during a pandemic. An understanding of the SARS-CoV-2 epidemiology provides opportunities to prevent the risk of repeated re-infection of humans and requires a robust One Health-based investigation. This review paper describes the known properties and the existing gaps in scientific knowledge about the zoonotic and reverse zoonotic transmissibility of the novel virus SARS-CoV-2 and the COVID-19 disease it causes.

The study was aimed to analyze the relation between individual genotypes and allelic variants of SNPs g.2141C>G of growth hormone gene, g.914T>A and g.257A>G of growth hormone receptor gene with growth and reproduction traits and to evaluate the populationgenetic structure in Aberdeen-Angus cattle (Bos taurus L., 1758) sample of Eastern Ukraine according SNPs studied. Allele C of SNP g.2141C>G has a positive correlation with birth weight, body stature, bigger rump, udder and total exterior evaluation score, shorter calving interval and better calve birth weight and negative correlation with calve average daily gain. Allele T of SNP g.914T>A has positive correlation with the muscle and udder size; live weight in each age, average daily gain, weight and average daily gain of calves born conform to the principle AA>TT≥TA. SNP g.257A>G showed a positive correlation for G allele with muscle size. The population is in equilibrium for SNPs g.2141C>G and g.257A>G, and in disequilibrium for SNP g.914T>A. The analysis showed no linkage disequilibrium between SNPs g.914T>A and g.257A>G. Inbreeding coefficient FST in Aberdeen-Angus group studied was 16.1%.

Avian infectious bronchitis virus is the causative agent of a highly contagious disease that results in severe economic losses to the poultry industry worldwide. Here, we report the first coding-complete genome sequence of strain DMV/1639 of the GI-17 lineage, isolated from broiler chickens in Georgia in 2019.

A Newcastle disease virus was isolated from a chicken from a live bird market in the Mbeya region of Tanzania. Complete genome characterization of the isolate identified it as a member of subgenotype Vd. This is the first complete genome sequence of this subgenotype.

In May of 2018, virulent Newcastle disease virus was detected in sick, backyard, exhibition chickens in southern California. Since, the virus has affected 401 backyard and four commercial flocks, and one live bird market in California, and one backyard flock in Utah. The pathogenesis and transmission potential of this virus, along with two genetically related and widely studied viruses, chicken/California/2002 and chicken/Belize/2008, were evaluated in both 3-week- and 62-week-old chickens given a low, medium, or high challenge dose. All three viruses were highly virulent causing clinical signs, killing all the chickens in the medium and high dose groups, and efficiently transmitting to contacts. The three viruses also replicated in the reproductive tract of the adult hens. Virus shedding for all viruses was detected 24 hours after challenge, peaking with high titers at day 4 post challenge. Although not genetically identical, the studied isolates were shown to be phenotypically very similar, which allows the utilization of the available literature in the control of the current outbreak.

Our prior work has shown that live poultry vaccines have been intermittently isolated from wild birds sampled during field surveillance studies for Newcastle disease virus (NDV). Thus, we experimentally investigated the susceptibility of four native agriculturally associated wild bird species to the NDV LaSota vaccine and evaluated the shedding dynamics, potential transmission from chickens, and humoral antibody responses. To test susceptibility, we inoculated wild-caught, immunologically NDV-naïve house finches (Infección experimental y transmisión del virus de la vacuna contra la enfermedad de Newcastle en cuatro paseriformes silvestres. Nuestras investigaciones anteriores han demostrado que las vacunas vivas utilizadas en avicultura se han aislado de forma intermitente de aves silvestres muestreadas durante los estudios de vigilancia en el campo para el virus de la enfermedad de Newcastle (NDV). Por lo tanto, se investigó experimentalmente la susceptibilidad a la vacuna contra la enfermedad de Newcastle cepa LaSota en cuatro especies de aves silvestres y nativas asociadas con se han asociado con la agricultura y se evaluó la dinámica de transmisión, la transmisión potencial desde el pollo y las respuestas de anticuerpos humorales. Para evaluar la susceptibilidad, se inocularon pinzones mexicanos (Haemorhous mexicanus; n = 16), tordos cabecicafés (Molothrus ater; n = 9), cardenales (Cardinalis cardinalis; n = 6) y jilgueros norteamericanos (Spinus tristis; n = 12), todos de origen silvestre y sin exposición previa al virus de Newcastle. Estas aves se inocularon con 0.1 ml (106.7 dosis medias infecciosas para embrión de pollo [EID50]/ml) de la vacuna de Newcastle cepa LaSota a través de la vía oculonasal. Para determinar la transmisión entre pollos y aves silvestres, se inocularon de igual forma aves adulta tipo Leghorn libres de patógenos específicos y se alojaron en unidades de aislamiento en cohabitación con dos a cinco aves silvestres de las especies mencionadas anteriormente. Este diseño dio como resultado tres tratamientos: inoculación directa de aves silvestres (cinco grupos), exposición de aves silvestres a un pollo inoculado (dos grupos), o exposición a dos pollos inoculados (seis grupos), respectivamente. Se recolectaron muestras de sangre e hisopos de la orofaringe y de la cloaca antes y después de la infección con la vacuna viva. Todas las aves silvestres que se inocularon directamente con la vacuna LaSota eliminaron el virus, como se demostró mediante el aislamiento viral (VI). Los cardenales fueron la especie más susceptible con base en el aislamiento viral de uno a 11 días después de la inoculación con títulos de hasta 104.9 EID50/ml. Aunque todos los pollos inoculados eliminaron el virus LaSota y este virus estaba presente en el agua de bebida, la mayoría de las aves silvestres no inoculadas que cohabitaron con estos pollos permanecieron sin infectar durante 14 días, como lo demuestra el aislamiento viral. Sin embargo, un jilguero norteamericano resultó positivo mediante aislamiento viral a la transmisión de la vacuna a los siete días después de la inoculación y un pinzón mexicano resultó positivo para la transmisión de la vacuna mediante transcripción reversa y PCR en tiempo real a los 13 días después de la inoculación. Solo un tordo cabecicafé inoculado directamente (de un total de tres) y dos cardenales (de un total de dos) desarrollaron títulos de anticuerpos de inhibidores de la hemaglutinación específicos contra la enfermedad de Newcastle de 16, 16 y 128, respectivamente. No se detectaron signos clínicos en los pollos ni en las aves silvestres después de la inoculación.

Background The remarkable diversity and mobility of Newcastle disease viruses (NDV) includes virulent viruses of genotype VI. These viruses are often referred to as pigeon paramyxoviruses 1 because they are normally isolated and cause clinical disease in birds from the Columbidae family. Genotype VI viruses occasionally infect, and may also cause clinical disease in poultry. Thus, the evolution, current spread and detection of these viruses are relevant to avian health. Results Here, we describe the isolation and genomic characterization of six Egyptian (2015), four Pakistani (2015), and two Ukrainian (2007, 2013) recent pigeon-derived NDV isolates of sub-genotype VIg. These viruses are closely related to isolates from Kazakhstan, Nigeria and Russia. In addition, eight genetically related NDV isolates from Pakistan (2014–2016) that define a new sub-genotype (VIm) are described. All of these viruses, and the ancestral Bulgarian (n = 2) and South Korean (n = 2) viruses described here, have predicted virulent cleavage sites of the fusion protein, and those selected for further characterization have intracerebral pathogenicity index assay values characteristic of NDV of genotype VI (1.31 to 1.48). A validated matrix gene real-time RT-PCR (rRT-PCR) NDV test detect all tested isolates. However, the validated rRT-PCR test that is normally used to identify the virulent fusion gene fails to detect the Egyptian and Ukrainian viruses due to mismatches in primers and probe. A new rapid rRT-PCR test to determine the presence of virulent cleavage sites for viruses from sub-genotypes VIg was developed and evaluated on these and other viruses. Conclusions We describe the almost simultaneous circulation and continuous evolution of genotype VI Newcastle disease viruses in distant locations, suggesting epidemiological connections among three continents. As pigeons are not migratory, this study suggests the need to understand the possible role of human activity in the dispersal of these viruses. Complete genomic characterization identified previously unrecognized genetic diversity that contributes to diagnostic failure and will facilitate future evolutionary studies. These results highlight the importance of conducting active surveillance on pigeons worldwide and the need to update existent rapid diagnostic protocols to detect emerging viral variants and help manage the disease in affected regions. Electronic supplementary material The online version of this article (10.1186/s12917-017-1211-4) contains supplementary material, which is available to authorized users.

The first complete genome sequences of four avian paramyxovirus serotype 10 (APMV-10) isolates are described here. The viruses were isolated from rockhopper penguins on the Falkland Islands, sampled in 2007. All four genomes are 15,456 nucleotides in length, and phylogenetic analyses show them to be closely related.

Background Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. Methods In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. Results Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25–30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2–3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. Conclusions This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0741-5) contains supplementary material, which is available to authorized users.

Aim. This study was focused on (i) detection of specifi c BVDV-antibodies within selected cattle farms, (ii) identifi cation of persistently infected (PI) animals and (iii) genetic typing of selected BVDV isolates. Methods. RNA extraction, real-time polymerase chain reaction, ELISA technique, sequencing. Results. Specifi c BVDV- antibodies were detected in 713 of 1,059 analyzed samples (67.3 per cent). This number is in agreement with fi ndings in many cattle herds around the world. However, the number of positive samples differed in the herds. While 57 samples out of 283 (20.1 per cent) were identifi ed in the fi rst herd, 400 out of 475 (84.2 per cent) and 256 out of 301 (85 per cent) animals were positive in the second and third herd. High number of animals with BVDV RNA was detected in all herds. The real-time PCR assay detected BVDV RNA in 5 of 1068 samples analyzed (0.5 per cent). 4 positive samples out of 490 (0.8 per cent) and 1 out of 301 (0.33 per cent) were found in the second and third herd. The genetic materials of BVDV were not found in the fi rst herd. Data on the number of PI animals were in accord with serological fi ndings in the cattle herds involved in our study. The genetic typing of viral isolates revealed that only BVDV, Type 1 viruses were present. The phylogenetic analysis confi rmed two BVDV-1 subtypes, namely b and f and revealed that all 4 viruses from the second farm were typed as BVDV-1b and all of them were absolutely identical in 5’-UTR, but virus from the third farm was typed as BVDV-1f. Conclusion. Our results indicated that the BVDV infection is widespread in cattle herds in the eastern Ukraine, that requires further research and development of new approaches to improve the current situation.

Our study demonstrates the repeated isolation of vaccine-derived Newcastle disease viruses from different species of wild birds across four continents from 1997 through 2014. The data indicate that at least 17 species from ten avian orders occupying different habitats excrete vaccine-derived Newcastle disease viruses. The most frequently reported isolates were detected among individuals in the order Columbiformes (n = 23), followed in frequency by the order Anseriformes (n = 13). Samples were isolated from both free-ranging (n = 47) and wild birds kept in captivity (n = 7). The number of recovered vaccine-derived viruses corresponded with the most widely utilized vaccines, LaSota (n = 28) and Hitchner B1 (n = 19). Other detected vaccine-derived viruses resembled the PHY-LMV2 and V4 vaccines, with five and two cases, respectively. These results and the ubiquitous and synanthropic nature of wild pigeons highlight their potential role as indicator species for the presence of Newcastle disease virus of low virulence in the environment. The reverse spillover of live agents from domestic animals to wildlife as a result of the expansion of livestock industries employing massive amounts of live virus vaccines represent an underappreciated and poorly studied effect of human activity on wildlife.

Two complete genome sequences of Newcastle disease virus (NDV) are described here. Virulent isolates pigeon/Pakistan/Lahore/21A/2015 and pigeon/Pakistan/Lahore/25A/2015 were obtained from racing pigeons sampled in the Pakistani province of Punjab during 2015. Phylogenetic analysis of the fusion protein genes and complete genomes classified the isolates as members of NDV class II, genotype VI.

Here, we report the complete genome sequence of a virus of a putative new serotype of avian paramyxovirus (APMV). The virus was isolated from a white-fronted goose in Ukraine in 2011 and designated white-fronted goose/Ukraine/Askania-Nova/48-15-02/2011. The genomic characterization of the isolate suggests that it represents the novel avian paramyxovirus group APMV 13.

Here, we report the circulation of highly related virulent Newcastle disease viruses (NDV) in Bulgaria and Ukraine from 2002 until 2013. All of these NDV isolates have the same virulence-associated cleavage site (“113RQKR↓F117”), and selected ones have intracerebral pathogenicity index values ranging from 1.61 to 1.96. These isolates are most closely related to viruses circulating in Eastern Europe, followed by viruses isolated in Asia during the same period of time. Interestingly, the majority of the viruses were isolated from backyard poultry, suggesting the possibility of a “domestic” or “urban” cycle of maintenance. The molecular characterization of the nucleotide sequence of the complete fusion protein gene of the studied viruses suggests continued circulation of virulent NDV of sub-genotype VIId in Eastern Europe, with occasional introductions from Asia. Furthermore, the high level of genetic similarity among those isolates suggests that the NDV isolates of sub-genotype VIId from Bulgaria and Ukraine may have been part of a broader epizootic process in Eastern Europe rather than separate introductions from Asia or Africa. The continuous monitoring of backyard poultry flocks for the presence of circulating virulent NDV strains will allow early identification of Newcastle disease outbreaks.

Aim. The aim of the study was to analyze effects of SNPs CAPN316 in CAST282 in calpain and calpastatin genes on offspring productive traits produced by dairy and beef bulls. Methods. Data on offspring productivity included milk performance traits (for dairy bulls), birth weight and average daily gain (for beef bulls). Molecular genetic analysis was performed by PCR-RFLP. χ²-, t-tests and Pearson correlation coefficient were used for statistical analysis at significance levels of 0.05. Results. In progeny of dairy bulls number of alleles C in both SNPs demonstrated negative correlation with milk yield (r=-0.577), fat yield (r=-0.794) and protein yield (r =-0.798). G allele of CAPN316 (“wild type”) was associated with increased number of beef bulls progeny. Body weight and average daily gain was better in GG-bulls offspring. Conclusions. C alleles of SNPs CAPN316 in CAST282 being associated with meat quality traits were found to be ineffective in selection for milk production traits. Keywords: calpain and calpastatin genes, SNP, CAPN316, CAST282, bull’s genotype, evaluation on progeny, offspring productivity.

Background Avian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health. Methods In this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007–2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. Results Our results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes. Conclusions We identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent in wild bird populations. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0714-8) contains supplementary material, which is available to authorized users.