Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa

BACKGROUND

Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.

METHODS

The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.

RESULTS

The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).

CONCLUSION

The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.

Viral pathogen detection in U.S. game-farm mallard (Anas platyrhynchos) flags spillover risk to wild birds

The threat posed by emerging infectious diseases is a major concern for global public health, animal health and food security, and the role of birds in transmission is increasingly under scrutiny. Each year, millions of mass-reared game-farm birds are released into the wild, presenting a unique and a poorly understood risk to wild and susceptible bird populations, and to human health. In particular, the shedding of enteric pathogens through excrement into bodies of water at shared migratory stop-over sites, and breeding and wintering grounds, could facilitate multi-species long-distance pathogen dispersal and infection of high numbers of naive endemic birds annually. The Mallard (Anas platyrhynchos) is the most abundant of all duck species, migratory across much of its range, and an important game species for pen-rearing and release. Major recent population declines along the US Atlantic coast has been attributed to game-farm and wild mallard interbreeding and the introduction maladaptive traits into wild populations. However, pathogen transmission and zoonosis among game-farms Mallard may also impact these populations, as well as wildlife and human health. Here, we screened 16 game-farm Mallard from Wisconsin, United States, for enteric viral pathogens using metatranscriptomic data. Four families of viral pathogens were identified - Picobirnaviridae (Genogroup I), Caliciviridae (Duck Nacovirus), Picornaviridae (Duck Aalivirus) and Sedoreoviridae (Duck Rotavirus G). To our knowledge, this is the first report of Aalivirus in the Americas, and the first report of Calicivirus outside domestic chicken and turkey flocks in the United States. Our findings highlight the risk of viral pathogen spillover from peri-domestically reared game birds to naive wild bird populations.

Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants

A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.

Virome of Australia's most endangered parrot in captivity evidenced of harboring hitherto unknown viruses

IMPORTANCE

The impact of circulating viruses on the critically endangered, orange-bellied parrot (OBP) population can be devastating. The OBP already faces numerous threats to its survival in the wild, including habitat loss, predation, and small population impacts. Conservation of the wild OBP population is heavily reliant on supplementation using OBPs from a managed captive breeding program. These birds may act as a source for introduction of a novel disease agent to the wild population that may affect survival and reproduction. It is, therefore, essential to monitor and assess the health of OBPs and take appropriate measures to prevent and control the spread of viral infections. This requires knowledge of the existing virome to identify novel and emerging viruses and support development of appropriate measures to manage associated risk. By monitoring and protecting these animals from emerging viral diseases, we can help ensure their ongoing survival and preserve the biodiversity of our planet.

Development and Evaluation of a Monoclonal Antibody-Based Blocking Enzyme-Linked Immunosorbent Assay for the Detection of Antibodies against Novel Duck Reovirus in Waterfowl Species

The novel duck reovirus (NDRV) is an emerging pathogen that causes disease in various waterfowl species. Since the outbreak, it has caused huge economic losses to the duck industry in China. A rapid, reliable, and high-throughput method is required for epidemiological investigation and evaluation of vaccine immunogenicity. A good first step would be establishing an enzyme-linked immunosorbent assay (ELISA) that could detect NDRV antibodies in different breeds of ducks and geese from the serum and egg yolk. This study used a recombinant NDRV σB protein and a corresponding horseradish peroxidase (HRP)-labeled monoclonal antibody to develop a blocking ELISA (B-ELISA). The cutoff value of the B-ELISA was 37.01%. A total of 212 serum samples were tested by the B-ELISA, and the virus neutralization test (VNT) was the gold standard test. The sensitivity and specificity of the B-ELISA were 92.17% (106/115) and 97.94% (95/97), respectively. The agreement rates between the B-ELISA and VNT were 94.81% (kappa value, 0.896). The B-ELISA could specifically recognize anti-NDRV sera without cross-reacting with other positive serums for other major diseases in ducks and geese. The inter- and intra-assay coefficients of variation (CVs) of the B-ELISA and VNT assays were acceptable. In conclusion, the novel B-ELISA could be a rapid, simple, safe, and economically attractive alternative to the VNT in assessing duck flocks' immunity status and in epidemiological surveillance in multiple waterfowl species. IMPORTANCE NDRV disease is a new epidemic disease in waterfowl that first appeared in China. Compared with the classical DRV (CDRV), NDRV is associated with more severe symptoms, a higher mortality rate, and a broader host range. NDRV has become the prevalent genotype in China. At present, there are no commercially available diagnostic products for the NDRV disease. VNT, as the gold standard serologic test, is not only time-consuming and laborious, but also has high requirements for facilities and equipment, which is not suitable for clinical application. Conventional ELISA requires specific antispecies conjugates that are not currently available. B-ELISA not only has the advantage of higher analysis specificity, but also can be used to test specific antibodies against different waterfowl species, because no species-specific conjugates are required in such detection. Therefore, it is necessary to establish a B-ELISA for the detection of antibodies against NDRV in waterfowl species.

Novel Virus Identification through Metagenomics: A Systematic Review

Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.

Unravelling Bile Viromes of Free-Range Laying Chickens Clinically Diagnosed with Spotty Liver Disease: Emergence of Many Novel Chaphamaparvoviruses into Multiple Lineages

Spotty liver disease (SLD) causes substantial egg production losses and chicken mortality; therefore, it is a disease that concerns Australian egg farmers. Over the last few decades, much research has been conducted to determine the etiologic agents of SLD and to develop potential therapeutics; however, SLD still remains a major issue for the chicken industries globally and remained without the elucidation of potentially multiple pathogens involved. To help fill this gap, this study was aimed at understanding the viral diversity of bile samples from which the SLD-causing bacterium, Campylobacter hepaticus, has been isolated and characterised. The collected samples were processed and sequenced using high-throughput next-generation sequencing. Remarkably, this study found 15 galliform chaphamaparvoviruses (GaChPVs), of which 14 are novel under the genus Chaphamaparvovirus. Among them, nine were complete genomes that showed between 41.7% and 78.3% genome-wide pairwise similarities to one another. Subsequent phylogenetic analysis using the NS1 gene exhibited a multiple incursion of chaphamaparvovirus lineages, including a novel lineage of unknown ancestral history in free-range laying chickens in Australia. This is the first evidence of circulating many parvoviruses in chickens in Australia, which has increased our knowledge of the pathogen diversity that may have an association with SLD in chickens.

Serological investigation of Gyrovirus homsa1 infections in chickens in China

BACKGROUND

Gyrovirus homsa1 (GyH1) (also known as Gyrovirus 3, GyV3) is a non-enveloped, small, single-stranded DNA virus, which was first identified in children with acute diarrhea, and was subsequently detected in marketed chickens, broilers with transmissible viral proventriculitis (TVP), and mammals. GyH1 is a pathogenic virus in chickens, causing aplastic anemia, immunosuppression, and multisystem damage. However, the seroepidemiology of GyH1 infection in chickens remains unclear. Here, we investigated the seroprevalence of GyH1 in chickens by ELISA to reveal the endemic status of GyH1 in China.

RESULTS

An indirect ELISA with high sensitivity and specificity was developed for investigation of seroepidemiology of GyH1 in chickens in China. The seropositive rate of GyH1 ranged from 0.6% to 7.7% in thirteen provinces, and ranged from 4.1% to 8.1% in eight species chickens. The seropositive rate of GyH1 in broiler breeders was significantly higher than that of in layers. There was a negative correlation between seropositive rate and age of chickens. The highest and lowest seropositive rate were present in chickens at 30-60 days and over 180 days, respectively.

CONCLUSIONS

The seroepidemiological investigation results demonstrated that natural GyH1 infection is widespread in chickens in China. Different species showed different susceptibility for GyH1. Aged chickens showed obvious age-resistance to GyH1. GyH1 has shown a high risk to the poultry industry and should be highly concerned.

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

BACKGROUND

Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife.

RESULTS

Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident).

CONCLUSIONS

The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.

A novel gyrovirus in a common pheasant (Phasianus colchicus) with poult enteritis and mortality syndrome

A novel gyrovirus was detected in an intestinal specimen of a common pheasant that died due to poult enteritis and mortality syndrome. The genome of the pheasant-associated gyrovirus (PAGyV) is 2353 nucleotides (nt) long and contains putative genes for the VP1, VP2, and VP3 proteins in an arrangement that is typical for gyroviruses. Gyrovirus-specific motifs were identified in both the coding region and the intergenic region of the PAGyV genome. The VP1 of PAGyV shares up to 67.6% pairwise nt sequence identity with reference sequences and forms a distinct branch in the phylogenetic tree. Thus, according to the recently described species demarcation criteria, PAGyV belongs to a novel species in the genus Gyrovirus, family Anelloviridae, for which we propose the name "Gyrovirus phaco 1".

Metagenome-Assembled Viral Genomes Analysis Reveals Diversity and Infectivity of the RNA Virome of Gerbillinae Species

Rodents are a known reservoir for extensive zoonotic viruses, and also possess a propensity to roost in human habitation. Therefore, it is necessary to identify and catalogue the potentially emerging zoonotic viruses that are carried by rodents. Here, viral metagenomic sequencing was used for zoonotic virus detection and virome characterization on 32 Great gerbils of Rhombomys opimus, Meriones meridianus, and Meiiones Unguiculataus species in Xinjiang, Northwest China. In total, 1848 viral genomes that are potentially pathogenic to rodents and humans, as well as to other wildlife, were identified namely Retro-, Flavi-, Pneumo-, Picobirna-, Nairo-, Arena-, Hepe-, Phenui-, Rhabdo-, Calici-, Reo-, Corona-, Orthomyxo-, Peribunya-, and Picornaviridae families. In addition, a new genotype of rodent Hepacivirus was identified in heart and lung homogenates of seven viscera pools and phylogenetic analysis revealed the closest relationship to rodent Hepacivirus isolate RtMm-HCV/IM2014 that was previously reported to infect rodents from Inner Mongolia, China. Moreover, nine new genotype viral sequences that corresponded to Picobirnaviruses (PBVs), which have a bi-segmented genome and belong to the family Picobirnaviridae, comprising of three segment I and six segment II sequences, were identified in intestines and liver of seven viscera pools. In the two phylogenetic trees that were constructed using ORF1 and ORF2 of segment I, the three segment I sequences were clustered into distinct clades. Additionally, phylogenetic analysis showed that PBV sequences were distributed in the whole tree that was constructed using the RNA-dependent RNA polymerase (RdRp) gene of segment II with high diversity, sharing 68.42-82.67% nucleotide identities with other genogroup I and genogroup II PBV strains based on the partial RdRp gene. By RNA sequencing, we found a high degree of biodiversity of Retro-, Flavi-, Pneumo-, and Picobirnaridae families and other zoonotic viruses in gerbils, indicating that zoonotic viruses are a common presence in gerbils from Xinjiang, China. Therefore, further research is needed to determine the zoonotic potential of these viruses that are carried by other rodent species from different ecosystems and wildlife in general.

Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna (Acridotheres tristis) in Australia

Invasive species exert a serious impact on native fauna and flora and have become the target of eradication and management efforts worldwide. Invasive avian species can also be important pathogen reservoirs, although their viromes and microbiomes have rarely been studied. As one of the top 100 invasive pest species globally, the expansion of Indian mynas (Acridotheres tristis) into peri-urban and rural environments, in conjunction with increasing free-ranging avian agricultural practices, may increase the risk of microbial pathogens jumping species boundaries. Herein, we used a meta-transcriptomic approach to explore the microbes present in brain, liver and large intestine of 16 invasive Indian myna birds in Sydney, Australia. From this, we discovered seven novel viruses from the families Adenoviridae, Caliciviridae, Flaviviridae, Parvoviridae and Picornaviridae. Interestingly, each of the novel viruses identified shared less than 80% genomic similarity with their closest relatives from other avian species, indicative of a lack of detectable virus transmission between invasive mynas to native or domestic species. Of note, we also identified two coccidian protozoa, Isospora superbusi and Isospora greineri, from the liver and gut tissues of mynas. Overall, these data demonstrate that invasive mynas can harbor a diversity of viruses and other microorganisms such that ongoing pathogen surveillance in this species is warranted.

Metagenomic detection and characterisation of multiple viruses in apparently healthy Australian Neophema birds

Emerging viral pathogens are a significant concern, with potential consequences for human, animal and environmental health. Over the past several decades, many novel viruses have been found in animals, including birds, and often pose a significant threat to vulnerable species. However, despite enormous interest in virus research, little is known about virus communities (viromes) in Australian Neophema birds. Therefore, this study was designed to characterise the viromes of Neophema birds and track the evolutionary relationships of recently emerging psittacine siadenovirus F (PsSiAdV-F) circulating in the critically endangered, orange-bellied parrot (OBP, Neophema chrysogaster), using a viral metagenomic approach. This study identified 16 viruses belonging to the families Adenoviridae, Circoviridae, Endornaviridae, Picobirnaviridae and Picornaviridae. In addition, this study demonstrated a potential evolutionary relationship of a PsSiAdV-F sequenced previously from the critically endangered OBP. Strikingly, five adenoviral contigs identified in this study show the highest identities with human adenovirus 2 and human mastadenovirus C. This highlights an important and unexpected aspects of the avian virome and warrants further studies dedicated to this subject. Finally, the findings of this study emphasise the importance of testing birds used for trade or in experimental settings for potential pathogens to prevent the spread of infections.

RNA virome abundance and diversity is associated with host age in a bird species

Despite the ongoing interest in virus discovery, little is known about the factors that shape communities of viruses within individual hosts. Here, we address how virus communities might be impacted by the age of the hosts they infect, using total RNA sequencing to reveal the RNA viromes of different age groups of Ruddy Turnstones (Arenaria interpres). From oropharyngeal and cloacal swabs we identified 14 viruses likely infecting birds, 11 of which were novel, including members of the Reoviridae, Astroviridae, and Picornaviridae. Strikingly, 12 viruses identified were from juvenile birds sampled in the first year of their life, compared to only two viruses in adult birds. Both viral abundance and alpha diversity were marginally higher in juvenile than adult birds. As well as informing studies of virus ecology, that host age might be associated with viral composition is an important consideration for the future surveillance of novel and emerging viruses.

Torque teno virus from Korean domestic swine farms, 2017-2018

Background

Torque teno viruses (TTVs) have been detected worldwide, from a wide range of animals. Up to date, few studies focused on the prevalence of TTVs in general and swine torque teno viruses (TTSuVs) in particular in Korean swine farms.

Objective

This study aimed to investigate the appearance of TTSuVs and TTVs in sick pigs during the 2017–2018 period.

Materials and Methods

Molecular‐based method using TTSuV1‐, TTSuV2‐ and TTV3‐specific primers was used to screen for the viruses from either sera or pooled internal organs of sick pigs. For genetic characterization, genomic sequences of TTVs were sequenced by a primer walking method. Several bioinformatic tools have been utilized to investigate the genomic organization and genetic relationship of TTVs.

Results

Two years of prevalence survey reveal that the prevalence of TTSuV2 is about twice that of TTSuV1. Furthermore, we identified TTV of genogroup 3 in swine pooled organ samples. The genome of two strains, M265_Korea_2017 and N119_Korea_2018, are 3,817 bp in size; M265_2017 has three open reading frames (ORFs); and N119_2018 strain has four ORFs. The complete genome nucleotide sequencing of the two strains shows 98.4% homology, and the phylogenetic analysis of Open reading frame (ORF)1 indicates that the strains are located close to TUPB strain subgroup C of genogroup 3.

Conclusion

Our study provided the information of TTSuVs prevalence in swine farms in Korea and highlighted the presence of TTV genogroup 3 strains in pigs.