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Intestinal samples collected from 43 commercial broiler and 33 commercial turkey flocks from all regions of the United States during 2005 and 2006 were examined for the presence of astrovirus, rotavirus, reovirus, and coronavirus by reverse transcription-polymerase chain reaction (PCR), and for the presence of groups 1 and 2 adenovirus by PCR. Phylogenetic analysis was performed to further characterize the viruses and to evaluate species association and geographic patterns. Astroviruses were identified in samples from 86% of the chicken flocks and from 100% of the turkey flocks. Both chicken astrovirus and avian nephritis virus (ANV) were identified in chicken samples, and often both viruses were detected in the same flock. Turkey astrovirus type-2 and turkey astrovirus type-1 were found in 100% and 15.4% of the turkey flocks, respectively. In addition, 12.5% of turkey flocks were positive for ANV. Rotaviruses were present in 46.5% of the chicken flocks tested and in 69.7% of the turkey flocks tested. Based upon the rotavirus NSP4 gene sequence, the chicken and turkey origin rotaviruses assorted in a species-specific manner. The turkey origin rotaviruses also assorted based upon geographical location. Reoviruses were identified in 62.8% and 45.5% of chicken and turkey flocks, respectively. Based on the reovirus S4 gene segment, the chicken and turkey origin viruses assorted separately, and they were distinct from all previously reported avian reoviruses. Coronaviruses were detected in the intestinal contents of chickens, but not turkeys. Adenoviruses were not detected in any chicken or turkeys flocks. Of the 76 total chicken and turkey flocks tested, only three chicken flocks were negative for all viruses targeted by this study. Most flocks were positive for two or more of the viruses, and overall no clear pattern of virus geographic distribution was evident. This study provides updated enteric virus prevalence data for the United States using molecular methods, and it reinforces that enteric viruses are widespread in poultry throughout the United States, although the clinical importance of most of these viruses remains unclear.

Avian metapneumovirus (aMPV), classified within the Pneumoviridae family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, of which subtypes A and B are widely distributed across the world. In January 2024, an outbreak of severe respiratory disease occurred on turkey and chicken farms across different states in the US. Metagenomics sequencing of selected tissue and swab samples confirmed the presence of aMPV subtype B. Subsequently, all samples were screened using an aMPV subtype A and B multiplex real-time RT-PCR kit. Of the 221 farms, 124 (56%) were found to be positive for aMPV-B. All samples were negative for subtype A. Six whole genomes were assembled, five from turkeys and one from chickens; all six assembled genomes showed 99.29 to 99.98% nucleotide identity, indicating a clonal expansion event for aMPV-B within the country. In addition, all six sequences showed 97.74 to 98.58% nucleotide identity with previously reported subtype B sequences, e.g., VCO3/60616, Hungary/657/4, and BR/1890/E1/19. In comparison to these two reference strains, the study sequences showed unique 49–62 amino acid changes across the genome, with maximum changes in glycoprotein (G). One unique AA change from T (Threonine) to I (Isoleucine) at position 153 in G protein was reported only in the chicken aMPV sequence, which differentiated it from turkey sequences. The twelve unique AA changes along with change in polarity of the G protein may indicate that these unique changes played a role in the adaptation of this virus in the US poultry. This is the first documented report of aMPV subtype B in US poultry, highlighting the need for further investigations into its genotypic characterization, pathogenesis, and evolutionary dynamics.

Marek’s disease virus (MDV) is a highly contagious tumor virus that causes detrimental outbreaks in poultry. Since its initial description, the virus’s virulence and acuteness have progressively increased. During this study, we investigated suspected tumorigenic cases of MDV-1 infection among different avian species (chicken, ducks, and turkey) in various Egyptian governorates, including Al-Sharqia, Gharbia, Dakahlia, Port Said, Damietta, and Fayoum, between 2020 and 2023. A molecular study targeting the virulent oncogenic Meq gene revealed that the tumorigenic masses in chicken and duck tissues were identified as virulent MDV-1, but turkeys with cauliflower-like ovarian tumors showed negative results. The isolated MDV-1 strain of chicken origin was given the designation YLE2021 and the sequence was submitted to GenBank with accession number PQ59985. Sequence analysis revealed a partial Meq open reading frame encoding 296 amino acids and contains seven proline motifs, three of them are interrupted (187 PLQPP 191, 195 PAPP198, 224 PPQPP 228). Experimental infection of one-day-old specific-pathogen-free (SPF) chickens with a strain recovered from a chicken tumor resulted in 40% of infected birds showing the classical neural form of MDV infection. No parenchymal tumors were observed, and the virus could be molecularly detected in the peripheral blood mononuclear cells (PMNCs) of infected and neighboring uninfected SPF birds. In conclusion, this is the first report to identify the presence of MDV-1 in Egyptian ducks. Further investigations are recommended to detect the main cause of the turkeys’ tumor. Continuous molecular monitoring of circulating field viruses is crucial to investigate the mechanisms behind the increase in virus evolution, which could lead to increased virus virulence and allow the virus to evade vaccine protection.

Avian reovirus (ARV) has emerged as an important pathogen in turkeys, causing economic losses through tenosynovitis, necrotizing hepatitis, immunosuppression, and enteric disease. Despite its ubiquity, the evolutionary history of ARV cross-species transmission among chickens, turkeys, and wild birds remains poorly understood, hindering effective control and surveillance. This study investigates ARV temporal phylogenetics with an emphasis on interspecies transmission in turkeys. Whole genome sequences (WGSs) from seventy-seven turkey cases and one quail case at the Iowa State University Veterinary Diagnostic Laboratory, along with 74–136 segment sequences per gene from GenBank (1970–2023), were analyzed. Temporal phylogenetic analyses identified chickens as the ancestral host, with spillover into turkeys beginning in the mid-20th century, followed by stable transmission within turkey populations. Migration analyses revealed predominantly unidirectional transmission from chickens to turkeys. WGS analyses showed high variability in the M2 and σC-encoding region of the S1 segment, suggesting selective pressure on outer capsid proteins. M2, S1 σC, and L3 had the highest substitution rates, implicating their role in adaptation and antigenic diversity. These findings highlight the complexity of ARV evolution across hosts and underscore the need for robust genotyping schemes and surveillance strategies to mitigate outbreaks in poultry.

Following confirmation of the first case of the ongoing U.S. HPAI H5N1 epizootic in commercial poultry on February 8, 2022, the virus has continued to devastate the U.S. poultry sector and the pathogen has since managed to cross over to livestock and a few human cases have also been reported. Efficient outbreak management benefits greatly from timely detection and proper identification of the pathways of virus introduction and spread. In this study, we used changes in mortality rates as a proxy for HPAI incidence in a layer, broiler and turkey flock together with diagnostic test results to infer within-flock HPAI transmission dynamics. Mathematical modeling techniques, specifically the Approximate Bayesian Computation algorithm in conjunction with a stochastic within-flock HPAI transmission model were used in the analysis. The time window of HPAI virus introduction into the flock (TOI) and the adequate contact rate (ACR) were estimated. Then, using the estimated TOI together with the day when the first HPAI positive sample was collected from the flock, we calculated the most likely time to first positive sample (MTFPS) which reflects the time to HPAI detection. The estimated joint (i.e., all species combined) median of the MTFPS for different flocks was six days, the joint median most likely ACR was 6.8 newly infected birds per infectious bird per day, the joint median R 0 was 13 and the joint median number of test days per flock was two. These results were also grouped by species and by epidemic phase and discussed accordingly. We conclude that this findings from this and other related studies are beneficial for the different stakeholders in outbreak management. We recommend that combining TOI analysis with complementary approaches such as phylogenetic analyses is critically important for improved understanding of disease transmission pathways. The estimated parameters can also be used to parametrize mathematical models that can guide the design of surveillance protocols, risk analyses of HPAI spread, and emergency preparedness for HPAI outbreaks.

The aim of this study was to detect chicken parvovirus (ChPV) and turkey parvovirus (TuPV) on Turkish poultry farms and examine the molecular epidemiology of these viruses. In 2023, a total of 1,060 fecal samples were collected from 76 broiler farms and 30 turkey farms across various regions of Turkiye. The overall positivity rate was 72.3% (55/76) in broiler flocks and 70% (21/30) in turkey flocks. Among these, the positivity rate was 35% (7/20) in birds showing no signs of enteritis. The findings of this study suggest that, depending on the genetic variability of regional strains or the viral load, nested-PCR-based methods may prove more effective than single-step PCR for detecting ChPV and TuPV cases. Therefore, it is recommended to incorporate nested PCR in molecular epidemiological studies to minimize the risk of overlooking positive cases. Phylogenetic analysis of the VP1, VP2, and complete genome sequences of TUR/2023/ChPV and TR/2023/TuPV revealed that both strains clustered with American strains in distinct lineages. Analysis using the recombination detection programs RDP4.0 and SimPlot 3.5.1 strongly suggested that TUR/2023/ChPV may be a recombinant of strains from China and Brazil. Despite the observed genetic variability in the VP2 protein, an examination of B-cell epitopes showed a high degree of similarity between ChPV and TuPV strains. This study represents the first documentation of the emergence and prevalence of TuPVs in Turkiye, providing complete genome sequences for both ChPV and TuPV. Given the high prevalence and genetic diversity of these viruses and their presence in clinically asymptomatic birds, it is crucial for stakeholders in the poultry industry to implement regular flock screenings for these and similar viral pathogens. Proactive measures like these are essential for mitigating the economic impact of these important pathogens and developing effective preventive strategies.

Poult enteritis (PE) is one of the most common diseases seen in young turkey flocks. Since 1993, more than 1800 cases of suspected PE have been submitted for examination by negative stain electron microscopy; this has involved more than 2400 individual results, because in many cases more than one virus was identified; at least 1500 individual results were positive for viruses. Viruses have been identified in poults as young as 3 days and up to 9 wk of age. The most commonly found viruses are rotavirus-like viruses and small round viruses ranging from 15 nm to 30 nm, either alone or in combination. Reovirus, birnavirus, and adenovirus have also been detected. There has been no evidence to suggest the presence of coronaviruses. This report summarizes our findings.

Adenoviruses are a diverse group of viruses that can cause a variety of diseases in poultry, including respiratory and gastrointestinal infections. In turkeys (Meleagris gallopavo), adenoviruses commonly cause hemorrhagic enteritis and, rarely, inclusion body hepatitis. In this study, we investigated fowl adenoviruses (FAdVs) circulating in turkeys in Egypt. Following clinical examination of 500 birds, a portion of the hexon gene was amplified from four out of 50 samples from diseased birds (8%), and one amplicon that produced a strong band was selected for sequencing. Molecular and phylogenetic analysis revealed that the virus in that sample belonged to serotype FAdV-8b. Histopathological and immunohistochemical examinations of prepared tissue sections were performed to confirm the pathological findings. Diseased birds exhibited ruffled feathers, low body weight, a crouching posture, and diarrhea. Gross examination revealed petechial hemorrhage on the spleen, swollen pale liver, and congested intestine. Microscopic examination revealed the presence of eosinophilic and basophilic intranuclear inclusion bodies, nuclear pyknosis, and apoptotic bodies in the liver, congestion, hemorrhage, and fibrosis in the lungs, and desquamation of enterocytes. The presence of viral antigens in the liver, lungs, and intestine was confirmed by immunohistochemistry. To our knowledge, this is the first report of the characterization of an outbreak of inclusion body hepatitis in turkeys (hybrid converter breeds) due to FAdV-8b in Egypt. This finding raises an epidemiological alarm, necessitating further studies, including full-genome sequencing, to trace the virus’s origin and genetic diversity.

Infection with the turkey hemorrhagic enteritis virus (THEV) can cause hemorrhagic enteritis, which affects young turkeys. This disease is characterized by bloody diarrhea and immunosuppression (IMS), which is attributed to apoptosis of infected B cells. Secondary infections due to IMS exacerbate economic losses. We performed the first transcriptomic analysis of a THEV infection to elucidate the mechanisms mediating THEV-induced IMS. After infecting and sequencing mRNAs of a turkey B-cell line, trimmed reads were mapped to the host turkey genome, and gene expression was quantified with StringTie. Differential gene expression analysis was followed by functional enrichment analyses using gprofiler2 and DAVID from NCBI. RT-qPCR of select genes was performed to validate the RNA-seq data. A total of 2343 and 3295 differentially expressed genes (DEGs) were identified at 12 hpi and 24 hpi, respectively. The DEGs correlated with multiple biological processes including apoptosis, ER unfolded protein response, and cell maintenance. Multiple pro-apoptotic genes, including APAF1, BMF, BAK1, and FAS were upregulated. Genes that play a role in ER stress-induced unfolded protein response including VCP, UFD1, EDEM1, and ATF4 were also upregulated and may contribute to apoptosis. Our data suggest that several biological processes and pathways including apoptosis and ER response to stress are important aspects of the host cell response to THEV infection. It is possible that interplay between multiple processes may mediate apoptosis of infected B-cells, leading to IMS.

Enteric diseases represent one of the main causes of morbidity and mortality in poultry production, especially in turkeys (Meleagris gallopavo), significantly affecting the profitability of the sector. Turkey enteric complex (PEC) is a multifactorial syndrome characterized by diarrhea, stunting, poor feed conversion, and increased mortality in young turkeys. Its aetiologia includes multiple avian enteric viruses, including astrovirus, rotavirus, reovirus, parvovirus, adenovirus, and coronavirus, which can act singly or in co-infection, increasing clinical severity. This study performs a systematic review of the literature on these viruses and a meta-analysis of their prevalence in different regions of the world. Phylogenetic analyses were used to assess the genetic diversity of the main viruses and their geographical distribution. The results show a wide regional and genetic variability, which underlines the need for continuous epidemiological surveillance. Health and production implications are discussed, proposing control strategies based on biosecurity, targeted vaccination, and optimized nutrition. These findings highlight the importance of integrated management to mitigate the impact of CSF in poultry.