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Putative classification of viral genome sequences detected in pooled stool samples of healthy chickens. Percentages express relative amounts of viral genomes assigned to each particular family (or unclassified) within the total number of contigs obtained. (a) Overview of the de novo-assembled Illumina reads. (b) Percentages of eukaryotic viral contigs distributed in different viral families.
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This study is focused on the identification of the fecal virome of healthy chickens raised in high-density, export-driven poultry farms in Brazil. Following high-throughput sequencing, a total of 7,743 de novo-assembled contigs were constructed and compared with known nucleotide/amino acid sequences from the GenBank database. Analyses with BLASTx r...
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... a non-redundant database using BLASTX and BLASTN programmes. Among 7743 assem- bled contigs, 44.5 % had no similarity to any sequences in GenBank, in agreement with previous findings in human stool samples [10,17]. Approximately 4 % (279) of the sequences showed similarity to known eukaryotic viral sequences with an E-value cut-off of 10 À3 . Fig. 1(a) presents the taxonomic classification and the relative amount of the putative viral genomes assembled from the samples ...
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... RNA viruses, the identified viral genomes could be assigned to families Caliciviridae, Picobirnaviridae, Picor- naviridae and Reoviridae (Fig. 1b). Table S1 (available in the online Supplementary Material) presents a summary of the eukaryotic viral sequences detected in the present ...
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... region coding for part of the hexon-associated protein VIII gene, often used for phylogenetic analyses [21]. As such, this was the only geno- mic segment that could be compared with previously reported counterparts. The deduced, partial aa hexon sequence obtained here, named FAdV RS/BR/2015/52, clus- ters with FAdV-D type 9 (GenBank NC_000899) (Fig. ...
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... The results for the common carp suggest variability within the dynamic ecosystem of Laguna de Chignahuapan, unlike a closed ecosystem animal farm, such as commercial poultry or pigs for human consumption, where these ecosystems have biosecurity measures that focus on reducing the entry of microorganisms that could cause disease in animals. Consequently, the virome in these farm animals comprises fewer viral families than did the virome of carp in this study (Shan et al., 2011;Lima et al., 2017). In pigs, a constant presence of some viral families (Picornaviridae, and Caudovirales before known as Myoviridae and Podoviridae) can be observed in all individuals (Yang et al., 2022). ...
Introduction: The common carp (Cyprinus carpio) is a species that has been
used worldwide as a source of protein for humans because of its adaptive
capacity to the environment; however, it is also an invasive species. In Mexico,
it was introduced to provide an easily accessible source of protein to people in
rural areas until its extensive nationwide distribution. The community of viruses in
these fish is not completely known.
Methods: Massive sequencing, i.e.,whole metagenome shotgun (WMS) sequencing,
and bioinformatic analysis were used to describe the viral community of common
carp (Cyprinus carpio) living in a natural preserved wetland.
Results: Through sequencer Illumina NextSeq 500/550 we got 484,953,684
sequences from ten samples of fecal content of carp (5 samples to DNA and 5
samples to RNA). The virome comprised 30 viral families (13 DNA families and 17
RNA families), among which viruses related to vertebrates stood out, for example
Orthoherpesviridae, Parvoviridae, Astroviridae, Poxviridae, Hantaviridae
and Picornaviridae.
Discussion: The most abundant viral taxa corresponded to bacteriophages, most
of which are of polyphyletic origin. The results of this work contribute to the
knowledge of the different viral taxa found in the common carp in the wild and
indicate that these viral taxa may play a role in health and productivity of
fish farms.
... Pigs are omnivorous mammals that are frequently kept as livestock and are a significant component of animal protein for consumption by humans all over the world [1]. China is one of the biggest pig farming countries in the world. ...
Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.
... Multiple studies have been undertaken to analyse viral communities, including the eukaryotic faecal virome of healthy broilers (Lima et al., 2017), viromes of broilers with active respiratory tract infections (Sajnani et al., 2018), and the previously mentioned intestinal microbiota and RNA viromes of 'sentinel' birds placed on commercial broiler farms (Day et al., 2015). From the literature, it is apparent that there is a knowledge gap in the role of phages in the poultry virome. ...
Antibiotics are frequently used in poultry production, but broad-spectrum antibiotics are problematic in driving antimicrobial resistance (AMR) within the food chain. Consequently, alternative antimicrobials are needed to treat bacterial infections and bacteriophages (phages) could provide an effective approach. Phages are natural parasites of bacteria and have been used therapeutically to treat both human and animal infections, including within poultry for over a hundred years. This chapter will provide an overview on the potential applications of phages within the poultry industry to reduce pathogen levels throughout the production process. It will include discussion on what phages are, where they are found, experimental poultry phage efficacy studies, phage products currently being sold commercially, the impact of phages on the poultry microbiome and advantages and limitations of using phages therapeutically. The research discussed in this chapter demonstrates the safety and efficacy of phages to reduce pathogen abundance within poultry production and supports their use.
... However, in our study, parvoviral reads represented 5.5% of the total viral reads. The abundance of parvovirus-associated reads in NGS studies of fecal avian viral genome is highly variable, ranging from 1.7% of the eukaryotic viruses [45] to nearly 30% of the total virus reads [34,46]. Nevertheless, several parvovirus taxa may be more represented than others, reaching a prevalence of up to 27% in field surveys [15]. ...
The introduction of invasive birds into new ecosystems frequently has negative consequences for the resident populations. Accordingly, the increasing population of monk parakeets (Myiopsitta monachus) in Europe may pose a threat because we have little knowledge of the viruses they can transmit to native naïve species. In this study, we describe a new dependoparvovirus detected by metagenomic analysis of cloacal samples from 28 apparently healthy individuals captured in urban areas of Madrid, Spain. The genomic characterization revealed that the genome encoded the NS and VP proteins typical of parvoviruses and was flanked by inverted terminal repeats. No recombination signal was detected. The phylogenetic analysis showed that it was closely related to a parvovirus isolated in a wild psittacid in China. Both viruses share 80% Rep protein sequence identity and only 64% with other dependoparvoviruses identified in Passeriformes, Anseriformes, and Piciformes and are included in a highly supported clade, which could be considered a new species. The prevalence was very low, and none of the additional 73 individuals tested positive by PCR. These results highlight the importance of exploring the viral genome in invasive species to prevent the emergence of novel viral pathogenic species.
... The two genera including avian viruses, Bavovirus and Nacovirus, were proposed in 2012 by Wolf et al. (2011Wolf et al. ( , 2012 after the identification of novel caliciviruses in chickens and turkeys in Northern Europe. Since then, bavoviruses and nacoviruses have been detected in chickens in America, Asia, and Europe (Kim et al., 2020;Lima et al., 2019Lima et al., , 2017Wolf et al., 2012). Additionally, several recent virus discovery and metagenomic investigations have identified genomes of novel caliciviruses in various avian hosts with some studies demonstrating high viral diversity and even the likely existence of several novel genera (Canuti et al., 2019;Phan et al., 2013;Shan et al., 2022;Wang et al., 2017;Wille et al., 2019Wille et al., , 2018. ...
Caliciviruses are ssRNA viruses that can infect a wide range of hosts, including birds. While several avian caliciviruses have been discovered, their taxonomy and host distribution are largely unknown. We molecularly characterized a novel calicivirus (trumpeter swan calicivirus: TruSCV) in trumpeter swans over-wintering in south-west British Columbia, Canada. The positivity rate was 20.3% (14/69) and there were no significant differences in infection rates between males (5/34, 14.7%) and females (9/35, 25.7%) or among considered age groups (juveniles: 4/14, 28.6%; sub-adults: 1/9, 11.1%; adults: 9/46, 19.6%). Twelve infected swans died of lead poisoning, one because of starvation, and one from physical injuries. TruSCV complete genome possessed the typical organization and protein motifs of caliciviruses and a type 2 IRES and its closest relative was a virus circulating in Australian ducks. Phylogenetic analyses showed the existence of 34 different but monophyletic avian caliciviruses. These viruses, while having conserved genomic organization and protein motifs, possess different IRES types and group in several divergent clades, with only two of them corresponding to currently defined genera, highlighting the need for epidemiological investigations and systematic analyses to better define their taxonomy. Follow-up studies are needed to elucidate the diversity, distribution, and pathogenic potential of TruSCV.
... Viral metagenomic approaches (using random priming rather than target specific primers) allow the detection of viruses present in a sample without prior knowledge of its presence 17,18 as well as characterization of complex viral communities 19,20 . Indeed, reports of virus diversity in animals including bats [21][22][23] , pigs [24][25][26] , wild birds 27,28 , and chickens 29 have been published since the development of NGS methods. vidual farm dust samples and 56 pooled chicken feces were collected. ...
Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85–100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.
... Smacoviruses were first detected in wild-living chimpanzee stool [49] and later described in the feces of healthy and diarrheic pigs [50], cattle [51], poultry [52], humans [53], and insects. Although these viruses are thought to infect eukaryotes, their actual host has not yet been confirmed. ...
In the Neotropical region, the white-winged vampire bat (Diaemus youngi) is the rarest of the three species of vampire bats. This bat species feeds preferentially on bird blood, and there is limited information on the viruses infecting D. youngi. Hence, this study aimed to expand the knowledge about the viral diversity associated with D. youngi by sampling and pooling the lungs, liver, kidneys, heart, and intestines of all animals using high-throughput sequencing (HTS) on the Illumina MiSeq platform. A total of three complete and 10 nearly complete circular virus genomes were closely related to gemykrogvirus (Genomoviridae family), smacovirus (Smacoviridae family), and torque teno viruses (TTVs) (Anelloviridae family). In addition, three sequences of bat paramyxovirus were detected and found to be closely related to viruses reported in Pomona roundleaf bats and rodents. The present study provides a snapshot of the viral diversity associated with white-winged vampire bats and provides a baseline for comparison to viruses detected in future outbreaks.
... Genomoviruses represent a large group of viruses that are widespread and were recently found in feces of many animal species, including birds such as mallard, robins, finches, chicken and black birds [12,63]. Genomoviruses have been detected in chicken samples from New Zealand [66] and Brazil [59,67]. ...
... Of note are two genomoviruses (accession numbers MN379616 and MN379617) that are highly similar, sharing 98% and 99% genome-wide pairwise identity to genomoviruses recovered from chicken dung flies (Fannia sp.; accession number MH545498) [68] and chicken feces (accession number MG846357) [59], respectively. Furthermore, MN379601 shares~96% genome-wide pairwise identity with a genomovirus (accession number KY056250) in chicken samples from Brazil [67]. These genomoviruses may represent a group that are associated with fungal species that are commonly found in poultry farms. ...
... Six of these (Porprismacovirus chicas2, Porprismacovirus chicas3, Porprismacovirus chicas4, Porprismacovirus chicas5, Porprismacovirus chicas6 and Porprismacovirus chicas7) are new species established to classify the ones discovered in this study [69]. The only other smacoviruses identified in chicken samples are from Brazil [59,67] and part of the Huchismacovirus (n = 6) and Porprismacovirus (n = 2) representing four species (Huchismacovirus chicas1, Huchismacovirus chicas2, Huchismacovirus humas1, Porprismacovirus chicas1) [69]. We found only one smacovirus (accession number MN379620) in two samples (C4 and C6), whereas all other are found in individual samples only ( Figure 2). ...
High-throughput sequencing approaches offer the possibility to better understand the complex microbial communities associated with animals. Viral metagenomics has facilitated the discovery and identification of many known and unknown viruses that inhabit mucosal surfaces of the body and has extended our knowledge related to virus diversity. We used metagenomics sequencing of chicken buccal swab samples and identified various small DNA viruses with circular genome organization. Out of 134 putative circular viral-like circular genome sequences, 70 are cressdnaviruses and 26 are microviruses, whilst the remaining 38 most probably represent sub-genomic molecules. The cressdnaviruses found in this study belong to the Circoviridae, Genomoviridae and Smacoviridae families as well as previously described CRESS1 and naryavirus groups. Among these, genomoviruses and smacoviruses were the most prevalent across the samples. Interestingly, we also identified 26 bacteriophages that belong to the Microviridae family, whose members are known to infect enterobacteria.
... The present metagenomics study further confirmed the circulation of two recently discovered uncultivable intestinal poultry viruses in Belgium. Sicinivirus was discovered as a new picornavirus with unknown clinical manifestation of poultry in 2012 in Ireland [66] and currently has a worldwide documented distribution [67][68][69][70], while a retrospective metagenomic analysis showed its presence in samples dating back to 2003 [71]. Our study identified a significant normalized Sicinivirus read count in a pool of respiratory and intestinal tissue samples, suggesting a relatively high viral load. ...
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.
... Interestingly, recent research efforts using electron microscopy, nextgeneration sequencing (NGS) and rapid diagnostic methods have described novel avian rotaviruses, astroviruses, parvoviruses, picornaviruses and calicivirus in chicken. These are small viruses linked to poultry diseases [50]. Members of the Siphoviridae, Herpesviridae, Retroviridae and Myoviridae viral families have also been recently reported in broiler chickens using NGS [51]. ...
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
