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There are several viral diseases in captive birds. Aves polyomavirus 1 (APyV) and beak and feather disease virus (BFDV) are among the most important in Psittaciformes. The occurrence of these agents has been widely described in various parts of the world; however, little is known about these viruses in South America. APyV and BFDV can cause high morbidity with feather alterations and even mortality. Other variable symptoms could appear depending on the host’s age and taxonomic group. The aim of this study was to detect APyV and BFDV in samples of captive exotic and native Psittaciformes in Brazil. Samples from 120 birds with clinical signs compatible with APyV and/or BFDV were examined. In total, 57 (47.5%) positive birds were found, of which 21 (17.5%) had APyV and 41 (34.17%) had BFDV. Five animals (4.17%) presented concurrent infection. Phylogenetic analysis showed a divergent APyV strain and a diversity of Brazilian BFDV strains. Our study shows that these viruses are present at a significant frequency in captive exotic and native Psittaciformes in Brazil. This study also highlights the need for constant epidemiologic surveillance to preserve bird biodiversity with a focus on endangered Psittaciformes species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-022-00785-3.

Salmonella Gallinarum (SG) is the causative agent of fowl typhoid (FT), a disease that is harmful to the poultry industry. Despite sanitation and prophylactic measures, this pathogen is associated with frequent disease outbreaks in developing countries, causing high morbidity and mortality. We characterized the complete genome sequence of Colombian SG strains and then performed a comparative genome analysis with other SG strains found in different regions worldwide. Eight field strains of SG plus a 9R-derived vaccine were subjected to whole-genome sequencing (WGS) and bioinformatics analysis, and the results were used for subsequent molecular typing; virulome, resistome, and mobilome characterization; and a comparative genome study. We identified 26 chromosome-located resistance genes that mostly encode efflux pumps, and point mutations were found in gyrase genes (gyrA and gyrB), with the gyrB mutation S464T frequently found in the Colombian strains. Moreover, we detected 135 virulence genes, mainly in 15 different Salmonella pathogenicity islands (SPIs). We generated an SPI profile for SG, including C63PI, CS54, ssaD, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-6, SPI-9, SPI-10, SPI-11, SPI-12, SPI-13, and SPI-14. Regarding mobile genetic elements, we found the plasmids Col(pHAD28) and IncFII(S) in most of the strains and 13 different prophage sequences, indicating a frequently obtained profile that included the complete phage Gifsy_2 and incomplete phage sequences resembling Escher_500465_2, Shigel_SfIV, Entero_mEp237, and Salmon_SJ46. This study presents, for the first time, the genomic content of Colombian SG strains and a profile of the genetic elements frequently found in SG, which can be further studied to clarify the pathogenicity and evolutionary characteristics of this serotype.

Avian infectious laryngotracheitis (ILT) is a respiratory disease that causes severe economic losses in the poultry industry, mainly due to high morbidity and mortality and reduced egg production. Molecular characterization was performed on samples collected from flocks in the Brazilian States of São Paulo, Pernambuco, and Minas Gerais during 2015 and 2016 that presented clinical signs of respiratory disease. End-point PCR was used for viral detection, and DNA sequencing was used for differentiation of vaccine and field strains. Molecular analysis based on the infected cell protein (ICP4) gene separated four of the nine samples together with previous Brazilian isolates (São Paulo and Minas Gerais), one sample was grouped on the same branch as Minas Gerais strains (along with another related sample), one sample was separately branched but still related to the tissue culture origin (TCO) vaccine strain, and two samples were grouped on the same branch as the TCO vaccine strain. Molecular analysis of the thymidine kinase (TK) gene showed the existence of strains of both high and low virulence. The characterization of two fragments of the ICP4 gene and a fragment of the TK gene in this study suggested that the virus circulating in Guatapará, as well as those in Barretos and Itanhandu, that is causing respiratory problems in birds is a highly virulent field strain. The clinical signs point to a TCO vaccine strain that most likely underwent some reversal event and is a latent reactivated infection.

In recent years, reports of chicken astrovirus (CAstV) infections in commercial birds have increased, affecting the poultry industries in Brazil and worldwide. The objective of this study was to use molecular methods to characterize the CAstV found in one breeding and three different incubation companies that reported increased embryonic mortality and the appearance of birds with white chick syndrome. RT-qPCR with SYBR green chemistry was used to determine the presence of the virus in the faeces of breeders, organs of neonatal chickens, and unhatched embryos. By sequencing the ORF2 gene that codes for the viral capsid, the strains responsible for these clinical signs were characterized using strains previously reported in Brazil, North America, Europe, and Asia. The percentage of identity of the amino acid sequences compared with those from group A was less than 41% (37.01% to 40.52%) and the identity with those from subgroups Bi, Bii, and Biii was less than 90% (81.81% to 89.85%). Therefore, the sequences were characterized within subgroup Biv with identity greater than 95% (95.26% to 99.59%), together with CAstV strains previously found in Brazil, Canada, and the United States. Using antigenicity prediction tools, 14 highly conserved peptides located on the surface of the capsid protein were considered potentially responsible for inducing the immune response in the host. Our data provide important information related to the increase in embryo mortality in vertically-infected birds, reinforcing the potential association of white chick syndrome with CAstV Biv subgroup. CAstV infections were found in farms and incubators with increased embryo mortality.Brazilian CAstV Biv strains were associated with white chick syndrome.Antigenic peptides were predicted on the surface of the capsid protein. CAstV infections were found in farms and incubators with increased embryo mortality. Brazilian CAstV Biv strains were associated with white chick syndrome. Antigenic peptides were predicted on the surface of the capsid protein.

Chicken parvovirus (ChPV) is an agent frequently associated with runting stunting syndrome (RSS). This syndrome has been reported in association with ChPV in many countries, including Brazil, however, studies characterizing the virus on a molecular level are scarce, and ChPV pathogenicity in day-old chicks remains unclear. The aim of the present work was to establish the molecular characteristics of ChPV, determine the pathogenicity of ChPV in SPF chicks and detect and quantify ChPV by qPCR in several tissues and chicks of different ages. The experimental challenge was performed at one day of age, and daily and weekly observations were performed and five birds from each experimental group (mock and infected birds) were euthanized to perform the different analysis. ChPV genome copies were detected and quantified by qPCR in gut, spleen, thymus, kidney, pancreas, proventriculus and bursa. Clinically, the infected group presented with diarrhea 24 h post-infection, which persisted until 42 days of age. The small intestine was distended, and its contents were aqueous and foamy. Enteritis and dilated crypts with cyst shapes were observed in intestinal segments. Acute pancreatitis associated with lymphocytic nodules, infiltrating lymphocytes and plasma cells between the pancreatic acinus was observed. Koch&rsquo, s postulate was demonstrated and the genetic characterization of the VP1 gene showed that the Brazilian ChPV isolate belongs to the ChPV II group.

Fowlpox (FP) is a common epitheliotropic disease in chickens that is usually controlled by live attenuated vaccines. However, there have been some reports of outbreaks of FP in recent years, even in vaccinated flocks, presenting as atypical lesions and feathering abnormalities in chickens. These findings can be associated with fowlpox virus (FPV) with the reticuloendotheliosis virus (REV) integrated into its genome. In the present study, outbreaks of atypical FP were explored in vaccinated commercial laying hen flocks to determine the nature of the causative agent by histopathologic and molecular approaches. FPV and REV were detected and classified into subclade A1 of the genus Avipoxvirus and subtype 3 of REV (REV3), respectively. Additionally, heterogeneous populations of FPV with partial (containing only a remnant long terminal repeat-LTR) or total (all functional genes) integration of REV were identified by heterologous PCRs and detected considering reference integration sites. These results indicate the mechanism of chimeric genome FPV-REV associated with outbreaks and atypical clinicopathological manifestations in commercial laying hens for the first time in Brazil and in South America. In addition, this study demonstrates the emergence of REV integrated in the FPV genome in Brazilian chicken flocks.

White chick syndrome (WCS) is an emergent disease that affects hatchability and hatched chicks, resulting in high mortality and economic losses, and is related to chicken astrovirus (CAstV). This syndrome has been reported in several countries worldwide, and groups A iii and B vi of CAstV have been determined, however, in Brazil, the virus has not been genotyped. The innate immunity of chicks affected by WCS or any CAstV is poorly understood and studied, and it is important to determine whether relative cytokine expression occurs during the early stages of the life of chicks. The aim of the present investigation is to detect and molecularly characterize CAstV associated with WCS, examine the macroscopic and microscopic lesions in the jejunum and spleen, and determine cytokine expression in the jejunum, liver, spleen and thymus of chicks naturally infected with WCS. To do so, we applied a pathological and molecular approach for CAstV detection and characterization, as well as the quantification of the relative mRNA expression of several cytokine genes. The phylogenetic analyses of the sequences obtained herein classified CAstV as uniquely belonging to group B iv, showing a high similarity of nucleotides (NT) (75.7&ndash, 80.6%) and amino acids (AA) (84.2&ndash, 89.9%) with the members of group B and a low similarity of NT (46.7&ndash, 47.9%) and AA (37.8&ndash, 38.9%) with the virus belonging in group A. CAstV was also detected and quantified in the serum, spleen, thymus and jejunum, the latter being the organ where CAstV had the highest viral concentration. However, this organ did not present any microscopical alterations. In contrast, we observed necrotic hepatitis in the liver of the affected subjects. On the other hand, we observed the activation of several T helper 1 (Th1)- and T helper 2 (Th2)-cytokines (IFN-&gamma, IL-2, IL-8, IL-12p40, IL-15, TGF-&beta, 4, TNF-SF-15 and t-BET), without being able to control the viral replication due to the high concentration of viral particles in some organs, principally in the gut. One possible role of these cytokines is contributing to the control of inflammation and cell protection of intestinal cells, principally during the early activation of immune responses. However, the fact that these responses are not mature enough to control the viral infection means that more studies need to be carried out to elucidate this topic.

Enteric diseases affect poultry and cause important economic losses in many countries worldwide. Avian parvovirus has been linked to enteric conditions, such as malabsorption and runting-stunting syndrome (RSS), characterized by diarrhoea, and reduced weight gain and growth retardation. In 2013 and 2016, 79 samples were collected from different organs of chickens in Ecuador that exhibited signs of diarrhea and stunting syndrome, and analysed for the presence of chicken parvovirus (ChPV). The detection method of ChPV applied was Polymerase Chain Reaction (PCR), using primers designed from the conserved region of the viral genome that encodes the non-structural protein NS1. Out of the 79 samples, 50.6% (40/79) were positive for ChPV, and their nucleotide and amino acid sequences were analysed to determine their phylogenetic relationship with the sequences reported in the United States, Canada, China, South Korea, Croatia, Poland, Hungary, and Brazil. Strong similarity of nucleotide and amino acid sequences among all analyzed sequences and between the analysed and reference sequences was demonstrated, and the phylogenetic analysis clustered all the sequences within the same group, demonstrating a strong relation between the studied strains and the reference chicken parvovirus strains.

Aim: The objective of this study was to determine the presence of the variants of canine parvovirus (CPV)-2 in the city of Quito, Ecuador, due to the high domestic and street-type canine population, and to identify possible mutations at a genetic level that could be causing structural changes in the virus with a consequent influence on the immune response of the hosts. Materials and Methods: Thirty-five stool samples from different puppies with characteristic signs of the disease and positives for CPV through immunochromatography kits were collected from different veterinarian clinics of the city. Polymerase chain reaction and DNA sequencing were used to determine the mutations in residue 426 of the VP2 gene, which determines the variants of CPV-2; in addition, four samples were chosen for complete sequencing of the VP2 gene to identify all possible mutations in the circulating strains in this region of the country. Results: The results revealed the presence of the three variants of CPV-2 with a prevalence of 57.1% (20/35) for CPV-2a, 8.5% (3/35) for CPV-2b, and 34.3% (12/35) for CPV-2c. In addition, complete sequencing of the VP2 gene showed amino acid substitutions in residues 87, 101, 139, 219, 297, 300, 305, 322, 324, 375, 386, 426, 440, and 514 of the three Ecuadorian variants when compared with the original CPV-2 sequence. Conclusion: This study describes the detection of CPV variants in the city of Quito, Ecuador. Variants of CPV-2 (2a, 2b, and 2c) have been reported in South America, and there are cases in Ecuador where CVP-2 is affecting even vaccinated puppies.

Marek&rsquo, s disease virus (MDV) and the reticuloendotheliosis virus (REV) are two of the primary oncogenic viruses that significantly affect chickens. In Brazil, there have been no previous published reports on the presence of field REV alone or in coinfection. This retrospective study analyzes samples from a case of lymphoproliferative lesions from a backyard chicken flock. MDV and REV were detected by PCR and classified as MDV1 and REV3, respectively, through sequencing and phylogenetic analysis based on the glycoprotein B (gB) genes for MDV and the polymerase (pol) and envelope (env) genes for REV. Real-time PCR reactions were performed for MDV to rule out the presence of the Rispens vaccine strain. This is the first report of the presence of REV in coinfection with a MDV clinical case in Brazil and the first molecular characterization of REV in South America. This study highlights the importance of molecular diagnosis for REV and MDV in poultry. In addition, this study highlights the distribution of these two viruses worldwide and the latent risk of them solely or in coinfection to this part of the world.

This report describes the genome sequences of four Salmonella enterica subsp. enterica serovar Gallinarum ( Salmonella Gallinarum) strains isolated in Colombia in 2017 from layer breeders of different ages. The layer breeder flocks were presenting with an elevated mortality with lesions typical of fowl typhoid (FT).

Infectious bronchitis (IB) is one of the avian diseases with the greatest impact on poultry farming worldwide. In Brazil, strain BR-I (GI-11) is the most prevalent in poultry flocks. The present study aimed to develop a seminested RT-PCR assay specific for the diagnosis of BR-I IBV in Brazilian samples, targeting subunit 1 of the S gene. The detection limit of this assay was 10 copies of the IBV genome. In this study, 62.24% of 572 organ pools from the 5 regions of Brazil tested positive in a 3′UTR screening, and 84.83% were typed as BR-I IBV. BR-I was detected in the respiratory, digestive and urogenital tracts in pooled samples from all Brazilian geographical regions and in all the breeding systems analyzed. Specificity and sensitivity tests as well as phylogenetic analysis successfully confirmed the expected clustering of the sequences detected by this assay with the BR-I (GI-11) group. The nested PCR described in this study represents a suitable and valuable tool in the diagnosis, epidemiology, monitoring and vaccination decisions of IBV.

Chicken astrovirus (CAstV) is one of many viruses related to enteric diseases in poultry that are associated with Runting-Stunting Syndrome (RSS), which affects young chickens. CAstV was also recently associated with an unusual condition in chicks called “white chicks.” Some hatcheries in certain states of Brazil have reported several incubation problems, mortality, and the presence of chicks with white plumages over the past several months. These chicks were termed locally as “white chicks.” The present work investigated 30 chicks with this unusual condition using a multidisciplinary approach. Postmortem examination of each chick showed enlarged livers and intestines that were full of liquid and gas (30/30). The pancreas, kidneys, and spleen were pale (30/30). The other organs did not show any macroscopic alterations. CAstV, chicken parvovirus (ChPV), avian nephritis virus (ANV), avian rotavirus (ARtV), avian reovirus (AReoV), infectious bronchitis virus (IBV), and fowl adenovirus group I (FAdV-1) were tested in the intestines, pancreas, proventriculus, gizzard, liver, spleen, bursa, kidneys, thymus, lung, heart, brain, and yolk sac in each chick. All organs and yolk sacs were positive for CAstV in different titres and negative for the other tested viruses. The partial molecular characterization of the ORF 1b gene of CAstV using 28 sequences revealed a high similarity of the nucleotides and amino acids with sequences of CAstV from North America, Europe, and Asia, and our CAstV sequences clustered into a unique group that was separate from the other sequences. These results demonstrated that CAstV was associated with the white chick condition in Brazil. The virus was distributed in most organs, including the brain and yolk sac. These results suggest that the virus could be transmitted vertically. The molecular characterization also revealed that the CAstV associated with white chick condition was molecularly related to other CAstV sequences found worldwide.

Avian rotavirus A (ARtV-A) is a virus that affects young birds, causing acute diarrhea and economic losses in the poultry industry worldwide. The techniques used for the diagnosis of ARtV-A include electron microscopy, isolation in cell culture, and serology, as well as molecular techniques, such as the reverse transcription-polymerase chain reaction (RT-PCR). The objective of this work was to standardize a real-time RT-polymerase chain reaction (RT-qPCR) using SYBR Green chemistry for the rapid detection and quantification of ARtV-A from bird tissues and materials fixed on FTA cards on the basis of the nucleotide sequence of segment 6 (S6), which codes for the structural VP6 protein of ARtV-A. The results show the efficient amplification of the proposed target, with a limit of detection (LoD) of one copy gene (CG) per microliter of cDNA and a limit of quantification (LoQ) of 10 CGs per microliter. The efficiency of the primers was determined to be 95.66% using a standard curve, with an R2 value of 0.999 and a slope of &minus, 3.43. The specificity was determined using samples coinfected with ARtV-A, the chicken parvovirus, the chicken astrovirus, and the avian nephritis virus as positive controls and commercially available vaccines of the infectious bronchitis virus, infectious bursa disease virus, avian reovirus and healthy organs as negative controls. This technique, which lacks nonspecific PCR products and dimers, demonstrated greater sensitivity and specificity than conventional RT-PCR, and it reduced the analysis time by more than 50%.

This study determined the presence of Tremovirus A as the possible agent related to Avian Encephalomyelitis in broiler chicks from the states of São Paulo (SP) Paraná (PR), Goiás (GO), Santa Catarina (SC) and Rio Grande do Sul (RS), between the years 2006 and 2015. Samples of the nervous, digestive, respiratory, immune, and renal systems, plus muscular organs from broiler chicks with neurological problems such as ataxia and muscle tremors, and four (4) commercial vaccines as positive control, were tested by reverse-transcriptase (RT-PCR) amplification and DNA sequencing. A highly conserved region (P1) of the viral genome, was used to amplify a segment which encodes a structural protein VP4. Out of 112 samples, 46 were positive (42%) for Tremovirus A, that was identified in the nervous, digestive, respiratory, renal and immune systems. The phylogenetic analysis clustered together the nucleotide sequences of the 46 samples, the four commercial vaccine strains and the reference sequence of Calnek strain obtained from the GenBank. According to these results, we conclude that the presence of Tremovirus A in these Brazilian chicken flocks distributed in all states was due to flaws in the biosecurity measurements.

Avian bornaviruses (ABVs) are the causative agents of proventricular dilatation disease (PDD), a fatal neurologic disease considered to be a major threat to psittacine bird populations. We performed a reverse transcription PCR survey to detect the presence of canary avian bornavirus (CnBV) in birds of order Passeriformes related to different clinical manifestations, such as sudden death, neurologic signs, apathy, anorexia, excessive beak growth, and PDD. A total of 227 samples from captive and wild canaries were included, of which 80 samples were captive birds, comprising saffron finches (Detección de bornavirus aviar en aves paseriformes silvestres y en cautiverio en Brasil. Los bornavirus aviares (ABV, por sus siglas en inglés) son los agentes causantes de la enfermedad de la dilatación proventricular (PDD), una enfermedad neurológica mortal considerada como una de las principales amenazas para las poblaciones de aves psitácidas. Se realizó un muestreo por transcrpción reversa y PCR para detectar la presencia de bornavirus de los canarios (CnBV) en aves de orden Passeriformes relacionadas con diferentes manifestaciones clínicas, como muerte súbita, signos neurológicos, apatía, anorexia, crecimiento excesivo del pico y enfermedad de dilatación proventricular. Se incluyeron un total de 227 muestras de canarios en cautividad y silvestres, de las cuales 80 muestras fueron de aves en cautiverio, incluyendo jilgueros dorados (n =71) y canarios comunes (n = 9) y 147 muestras fueron aves silvestres distribuidas entre una variedad de especies. Dos muestras de aves cautivas (2/80) fueron positivas para bornavirus aviar; en aves silvestres, solo una muestra fue positiva para bornavirus aviar. Las muestras positivas se sometieron a secuenciación de ADN y solo se encontró el bornavirus de canarios serotipo 1, que es la primera vez que se detecta fuera de Alemania (Austria/Hungría), donde se detectó por primera vez en el año 2009. El análisis filogenético confirmó que el bornavirus de canarios serotipo 1 está presente en el orden Passeriformes en Brasil.

Enteric viruses play an important role in the Brazilian poultry industry due to the economic impact of resulting low yields of broilers, layers, and breeders. The most common enteric viruses affecting commercial flocks in Brazil include Fowl Adenovirus of group I (FAdV-I), Chicken Parvovirus (ChPV), Chicken Astrovirus (CAstV), Avian Nephritis Virus (ANV), Infectious Bronchitis Virus (IBV), Avian Reovirus (AReo), and Avian Rotavirus (ARtV). The aim of this study was to identify single and multiple infections using data obtained from 270 samples from eleven Brazilian states, corresponding to the period between 2010 and 2017. This was accompanied by an analysis of the relationship between the age of birds, clinical signs, and geographical distribution, using Polymerase Chain Reaction (PCR) and Reverse Transcription-PCR (RT-PCR) techniques. Twenty-five profiles of virus combinations were detected. Single infections were encountered in 86.3% of samples, and multiple infections were present in the remaining 13.7%. Both single and multiple infections affected all kinds of commercial chickens with digestive problems, stunting syndrome, decreases in egg and meat production, increased mortality, and respiratory signs. FAdV-I, ChPV, CAstV, ANV, and ARtV were mostly detected in young broilers, in contrast with IBV, which was detected in hens from one to greater than 51 weeks of age. These results exhibit the complexity of enteric diseases and the still poorly understood role of each pathogen as a unique etiological agent.

1. Infectious laryngotracheitis is a respiratory disease that affects the poultry industry worldwide. It is common in flocks with high-bird density, causing major economic losses. 2. In this study, a SYBR® FAST polymerase chain reaction (PCR) double-strand DNA intercalating agent assay was performed for the detection of infectious laryngotracheitis virus (ILTV) in clinical samples in comparison with a conventional nested-PCR, both based on the glycoprotein E encoding gene. This assay amplified 56 bp and was capable of detecting 19 to 1 copies of virus. 3. In total, 164 clinical samples were obtained from birds with respiratory problems from the period of 2009-2016. In the nested-PCR, there were 45.12% positive samples and 54.88% negative samples, while in the real-time PCR (qPCR), there were 81.1% positive samples and 18.9% negative samples. 4. In conclusion, qPCR from the DNA double-strand intercalating agent SYBR® GREEN FAST was useful for the diagnosis of ILTV because it detected samples that were negative in nested-PCR. This assay has advantages, such as a shortened processing-time, and no need for post-amplification processing (electrophoresis) with additional reagents, such as MgCl2 and agarose. Hence, qPCR proved to be useful, rapid and low cost for use with clinical samples.

Many viruses have been associated with runting and stunting syndrome (RSS). These viral infections mainly affect young chickens, causing apathy, depression, ruffled feathers, cloacal pasting, and diarrhea. Chicken Parvovirus (ChPV) is such an infection and has been detected in chickens showing signs of enteric diseases worldwide. Therefore, the present study aims to develop a sensitive real-time fast-qPCR assay based on SYBR&reg, Green for detection and quantification of ChPV. A 561-bp non-structural (NS) gene was amplified and cloned, and a pair of primers was designed based on conserved nucleotide sequences on the NS gene of ChPV, the intercalating DNA reagent SYBR&reg, Green was employed, and the Fast mode of a thermocycler was used. The assay detects 109 to 101 copies of the genome (CG). The limit of detection (LoD) was estimated to five CG, and the limit of quantification (LoQ) was estimated at ten CG. The standard curve efficiency was 101.94%, and the melting curve showed a unique clean peak and a melting temperature of 79.3 &deg, C. The assay was specific to amplify the ChPV NS gene, and no amplification was shown from other viral genomes or in the negative controls. A total of 141 samples were tested using the assay, of which 139 samples were found positive. The highest CG value of ChPV was 5.7 &times, 106 CG/uL of DNA without apparent clinical signs of enteric disturbance, and 4.6 &times, 106 CG/uL DNA were detected in chickens with RSS.

Avian adenovirus has been reported in many countries and is an infectious agent related with inclusion body hepatitis, hepatitis-hydropericardium syndrome (HHS), and respiratory and enteric conditions in chickens worldwide. The objective of this study was to detect and establish the molecular sequences of the hexon gene from the avian adenovirus strains of group I (FAdV-I) isolated from birds with hepatitis-hydropericardium syndrome (HHS), malabsorption syndrome and runting-stunting syndrome, to characterize the serotype of virus affecting commercial flocks in Brazil. Molecular characterization was performed by polymerase chain reaction (PCR), using specific primers to amplify the Loop 1 (L1) variable region of the hexon gene in the FAdV-I genome and subsequent sequencing of the PCR product for each positive sample. The results have revealed the presence of the FAdV-8a, FAdV-8b, and FAdV-11 serotypes circulating in Brazilian chicken flocks. Phylogenetic analysis grouped these sequences into three (3) distinct groups, 14 samples were aligned with the FAdV-11 group, three (3) samples in the FAdV-8b group and one (1) sample in the FAdV-8a group. The serotypes FAdV-8a, FAdV-8b, and FAdV-11 are circulating in Brazilian chicken flocks. Therefore, these results are very important for improvement biosecurity measurements and vaccine production. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s13337-018-0430-z) contains supplementary material, which is available to authorized users.

Infectious laryngotracheitis (ILT) is a respiratory disease of great importance that causes serious economic losses in the poultry industry. Its control is based on biosecurity procedures and vaccination programs that use live attenuated vaccines such as tissue culture origin (TCO), chicken embryo origin (CEO), and vectored vaccines. However, problems have been reported, such as the reversion of virulence, virus latency, and field virus outbreaks. Several molecular techniques have been developed to differentiate between the field and vaccine strains. This study was conducted to determine the presence of infectious laryngotracheitis virus (ILTV) in Brazil from 2012 to 2014. PCR-RFLP (restriction fragment length polymorphism) was used to detect and differentiate ILTV strains; DNA sequencing and predictive RFLP analysis were also used for this purpose. Molecular analysis detected the presence of ILTV in 15 samples that were characterized as strains of TCO vaccine origin. This study showed that the ILTV TCO vaccine strain has been circulating in commercial chicken flocks in Brazil since its introduction during the 2002 outbreak.

1. Infectious bronchitis virus (IBV) variants in Brazil were isolated during 2010-2015 for epidemiological and molecular analysis to characterise the different variants and perform a bioinformatic analysis to compare with sequences of variants collected over the previous 40 years. 2. Of the 453 samples examined, 61.4% were positive for IBV and 75.9% of these were considered to have the BR-I genotype and were detected in birds of all ages distributed in all five Brazilian regions. 3. The ratio of non-synonymous substitutions per non-synonymous site (dN) to synonymous substitutions per synonymous site (dS), i.e. dN/dS, revealed a predominance of codons with non-synonymous substitutions in the first third of the S1 gene and a dN/dS ratio of 0.67. Additionally, prediction of N-glycosylation sites showed that most of the BR-I variants (from 2003 to early 2014) had an extra site at amino acid position 20, whereas the newest variants lacked this extra site. 4. These results suggest that Brazilian IBV variants probably underwent drastic mutations at various points between 1983 and 2003 and that the selection processes became silent after achieving a sufficiently effective antigenic structure for invasion and replication in their hosts. Brazilian IBV genotype BR-I is currently the predominant genotype circulating in Brazil and South America.

A comparative survey between non-systemic (paratyphoid Salmonellae) and systemic (S. Pullorum and S. Gallinarum) Salmonella strains was performed to produce a virulence gene profile for differentiation among the groups. The following virulence genes were evaluated: invA, spvC, sefC, pefA, fimY, sopB, sopE1, stn and avrA. There are substantial differences among paratyphoid Salmonellae, S. Pullorum, and S. Gallinarum regarding the genes sefC, spvC, sopE1 and avrA. A higher frequency of sefC, spvC, sopE1 and avrA genes were detected in S. Gallinarum and S. Pullorum when compared with strains from the paratyphoid group of Salmonella. These results may be useful for differentiating among different groups and serotypes.

Twenty-two flocks of turkeys affected by enteric problems, with ages between 10 and 104 days and located in the Southern region of Brazil, were surveyed for turkey by PCR for turkey astrovirus type 2 (TAstV-2), turkey coronavirus (TCoV), hemorrhagic enteritis virus (HEV), rotavirus, reovirus, Salmonella spp., and Lawsonia intracellularis (Li) infections. Eleven profiles of pathogen combination were observed. The most frequently encountered pathogen combinations were TCoV-Li, followed by TCoV-TAstV-2-Li, TCoV-TastV-2. Only TCoV was detected as the sole pathogen in three flocks. Eight and 19 flocks of the 22 were positive for TAstV-2 and TCoV, respectively. Six were positive for Salmonella spp. and L. intracellularis was detected in 12 turkey flocks. Reovirus and HEV were not detected in this survey. These results throw new light on the multiple etiology of enteritis in turkeys. The implications of these findings and their correlation with the clinical signs are comprehensively discussed, illustrating the complexity of the enteric diseases.

Poult enteritis complex has been associated with enteritis and reduction in growth rates in commercial turkeys worldwide. Intestinal samples from 76 turkey flocks from different Brazilian states affected or not with intestinal disorders were evaluated for the presence of adenovirus groups 1 and 2 (TAV), astrovirus types 1 and 2 (TAstV-1 and TAstV-2), turkey coronavirus (TCoV), reovirus, rotavirus, and avian nephritis virus (ANV) using PCR. The percentage of positive samples was categorized according to the geographic origin, age of the flocks, and presence of clinical signs of intestinal disease. The percentage of samples that were positive for at least one virus was 93.4%, whereas the percentage of samples that were positive for more than one virus was 69.7%. An average of 3.20 viruses per sample was detected in turkeys in the growing phase of the production cycle (1 to 4 wk of age). The TAstV-1 and TCoV were the most frequently observed viruses in growing phase turkeys and occurred simultaneously in 85% of these samples. In turkeys in the finishing phase of development (5 to 18 wk), a lower average number of viruses was observed (2.41), and the most frequent viruses isolated in these turkeys were TAstV-1 (57.1%) and rotavirus (51.8%). Overall, every virus was detected more frequently in growing phase turkeys than in finishing phase turkeys with the exception of TAV. Samples from flocks exhibiting clinical signs of intestinal disease showed a higher rate of positivity, and TAstV-1, TAstV-2, and TCoV were the most frequently occurring viruses in this cohort. Birds without clinical signs most frequently harbored TAstV-1 and rotavirus. Future studies should focus on the description and elucidation of the role of each virus, as well as the pathogenic and immunological implications of the different combinations of viruses in turkeys.

Birds of the Cracidae family (curassows, guans, and chachalacas) are endemic of the Neotropics and 50 species are currently classified. Brazil has 22 species, seven of which are considered threatened. The Alagoas Curassow (Pauxi mitu) species is considered extinct in the wild; but about 120 birds are alive in captivity. Conservation of this species depends entirely on correct management. Health reports of both wildlife and captive curassows are rare. In this study the presence of Escherichia coli was evaluated in 23 healthy Alagoas Curassows from two private breeding centres. E. coli was isolated from cloacal swabs, and the presence of genes encoding cytotoxic necrotising factor 1 (cnf1), alpha-haemolysin (hly), aerobactin (iuc), serum resistance (iss) and the following adhesions: S fimbriae (sfa), pili associated with pyelonephritis (pap) and temperature-sensitive haemagglutinin (tsh) were investigated. E. coli was isolated from 78.3% (18/23) of the birds, and the percentage of curassows colonized by E. coli was similar between the two facilities. From the 22 E. coli isolates, 15 (68.2%) were positive for at least one virulence factor by PCR, and the most frequently found gene was iss (50%). No curassows had clinical signs of disease. Nevertheless, the presence of some E. coli strains may be a concern to the wildlife in captivity. Additional health surveillance studies are essential to guarantee successful conservation programmes for threatened cracids in Brazil. Aves da família Cracidae (mutuns, jacutingas e aracuãs) são endêmicas da região Neotropical com 50 espécies atualmente classificadas. O Brasil possui 22 espécies nesta família e sete delas são consideradas ameaçadas de extinção. O mutum-do-nordeste (Pauxi mitu) é considerado extinto na natureza, no entanto, aproximadamente 120 indivíduos são mantidos em cativeiro. A conservação desta espécie depende inteiramente de um manejo correto. Informações sobre o status sanitário de mutuns são raras, tanto em vida livre quanto em cativeiro. Neste estudo a presença de Escherichia coli foi avaliada em 23 mutuns-do-nordeste sadios de dois criatórios particulares. E. coli foi isolada a partir de suabes cloacais, em seguida, foi avaliada a presença de genes que codificam fator citotóxico necrotizante 1 (cnf1), alfa-hemolisina (hly), produção de aerobactina (iuc) e resistência sérica (iss) e genes que codificam os seguintes fatores de virulência: fímbria S (sfa), pili associado à pielonefrite (pap) e hemaglutinina termosensível (tsh). E. coli foi isolada de 78,3% (18/23) das aves e o percentual de mutuns positivos para E. coli foi semelhante entre as duas criações. De 22 isolados de E. coli, 15 (68,2%) foram positivos para pelo menos um fator de virulência pela PCR e o gene mais frequente foi o iss (50%). Nenhuma ave apresentava sinal clínico de doença, no entanto, a presença de determinadas cepas de E. coli pode representar uma preocupação em relação às aves silvestres mantidas em cativeiro. Estudos adicionais de monitoria do status sanitário do plantel são essenciais para garantir o sucesso de futuros programas de conservação de cracídeos ameaçados no Brasil.

Astroviruses have been associated with enteric disorders in many animal species, including chickens. Here, we describe the isolation, propagation, and pathological characteristics of chicken astrovirus (CAstV) in specific pathogen free (SPF) chicken embryonated eggs (CEE) from chickens with diarrhea and runting-stunting syndrome. The CEE were inoculated via the yolk sac route. Viral confirmation was carried out using PCR techniques and transmission electron microscopy negative staining with ammonium molybdate. The intestinal contents were screened for CAstV, and differential diagnostic testing was performed for avian nephritis virus, avian rotavirus, avian reovirus, chicken parvovirus, infectious bronchitis virus, and fowl adenovirus Group I to detect co-infection with other infectious agents. Seven- or 14-day-old CEEs presented with hemorrhages, edema, a gelatinous aspect, deformities, and dwarfism. The supporting membranes did not show any alterations. Here, we have described the isolation of CAstV and its pathological characteristics in SPF CEE.

This article reports a survey on turkey astrovirus (TAstV) and turkey coronavirus (TCoV) infections with RT-PCR in 17 turkey flocks affected by acute enteritis and two apparently normal turkey flocks located in the Southeastern region of Brazil by PCR (TAstV and TCoV). Seven out of the 17 affected flocks were positive for TAstV and 14 for TCoV, with seven co-infections. In one of the two apparently normal flocks, a TAstV-TCoV co-infection was found. Although a definitive association of these agents and the signs can not be made, the implications of these findings are discussed.