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California sea lion, mesenteric adipose. Adipocytes vary in size and are surrounded, separated, and partially to completely replaced by epithelioid and foamy macrophages with low numbers of lymphocytes, plasma cells, and neutrophils. Rare adipocyte remnants are within multinucleated giant cells (arrow). Hematoxylin and eosin, 40× magnification.
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An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Hist...
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... The virus can spread horizontally to other people when it is discharged from the respiratory or digestive system of an infected host. So far, bocaparvoviruses have been identified from a variety of animal hosts; cats [8,11], pigs [12], California sea lions [13], gorillas [14], dogs [15] bats [16] and rats [17] which suggested that they have a very broad host range. BOVs are known to undergo a high incidence of genetic recombination [18,19], and can be disseminated across species to new hosts [20]. ...
The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.
... An analysis pipeline was used to analyze sequence data [24]. Briefly, we used taxonomy information to identify the human genome and bacterial and fungal sequences from the NCBI nt database for subtraction. ...
Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.
... Porcine bufavirus (PBuV, Ungulate protoparvovirus 2) DNA was detected in feces from domestic pigs with and without posterior paraplegia living at five affected, and one unaffected, farms in Hungary in 2016 [294]. The virus has been detected in diarrheic pigs in China and healthy pigs in the USA, although disease association is unknown [295][296][297][298]. California sea lion parvovirus DNA was detected in the mesenteric lymph node of a stranded, free-ranging California sea lion with disseminated granulomatous inflammation and necrotizing steatitis and vasculitis [299]. The clinical significance of this virus, however, remains undetermined as five additional mammalian viruses were also detected in the lymph node and in situ hybridization of multiple tissues was negative. ...
In line with the Latin expression “sed parva forti” meaning “small but mighty,” the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
... Among protoparvoviruses, Carnivore protoparvovirus 1 (containing both canine parvovirus 2 (CPV-2) and feline panleukopenia virus (FPV)) [7], Carnivore protoparvovirus 3 (canine Bufavirus (CBuV)) [8], and the Carnivore protoparvovirus 4 (fox parvovirus) [9] have all been found in foxes. Still to be investigated is the host distribution of the remaining recently identified protoparvoviruses of marine carnivores, such as the sea otter parvovirus (species Carnivore protoparvovirus 2) [10,11], the fur seal parvovirus [12] and the California sea lion parvovirus [13]. ...
... Foxes (n = 50), lynx, mink, ermines, and coyotes were sampled in Newfoundland, while fox (n = 137), marten, and dog samples originated from Labrador. Seals were Viruses 2021, 13,1969 4 of 13 collected in Newfoundland but are known to frequent both Newfoundland and Labrador waters. Sampling locations included four different regions of Newfoundland, and areas surrounding several communities in Labrador ( Figure 1). ...
... A promoter could be identified in the 3′ terminal part of the NS1 region of all viruses, suggesting that the structural and non-structural genes are transcribed from two different promoters. Comparing the Newlavirus genomes with their closest known relative, the California sea lion parvovirus (CSLP) [13] (see below), revealed a conserved pattern with two big ORFs coding for the NS1 (617 amino acids) and VP2 (586-590 amino acids) proteins. Additionally, a short ORF was present in all viruses starting 7 nucleotides downstream of the start of VP2 (Figure 2). ...
The genus Protoparvovirus (family Parvoviridae) includes several viruses of carnivores. We describe a novel fox protoparvovirus, which we named Newlavirus as it was discovered in samples from Newfoundland and Labrador, Canada. Analysis of the full non-structural protein (NS1) sequence indicates that this virus is a previously uncharacterized species. Newlavirus showed high prevalence in foxes from both the mainland (Labrador, 54/137, 39.4%) and the island of Newfoundland (22/50, 44%) but was not detected in samples from other carnivores, including coyotes (n = 92), lynx (n = 58), martens (n = 146), mink (n = 47), ermines (n = 17), dogs (n = 48), and ringed (n = 4), harp (n = 6), bearded (n = 6), and harbor (n = 2) seals. Newlavirus was found at similar rates in stool and spleen (24/80, 30% vs. 59/152, 38.8%, p = 0.2) but at lower rates in lymph nodes (2/37, 5.4%, p < 0.01). Sequencing a fragment of approximately 750 nt of the capsid protein gene from 53 samples showed a high frequency of co-infection by more than one strain (33.9%), high genetic diversity with 13 genotypes with low sequence identities (70.5–87.8%), and no geographic segregation of strains. Given the high prevalence, high diversity, and the lack of identification in other species, foxes are likely the natural reservoir of Newlavirus, and further studies should investigate its distribution.
... Virus metagenomics library preparation and bioinformatics analyses were performed as described [29,30]. Viral-like particles (VLP) were enriched by homogenization of spleen and lung tissues and colon content from each horse followed by filtration and digestion with nuclease enzymes of supernatants to reduce the concentration of non-viral, capsidprotected, nucleic acids. ...
... Illumina sequence data analyses were conducted as described using BLASTx to detect reads and contigs showing translated protein sequences' similarity to all know eukaryotic viruses in RefSeq of GenBank. An in-house pipeline was used for removing bacterial and host genomes, trimming adaptor and primers, and de novo read assembly [29,30]. BLASTx was used for translated protein sequence similarity searches to all viral protein sequences in the GenBank database. ...
... Their NS1 and VP1 proteins showed 99.3% and 88% identities. The closest relatives of these proteins in GenBank's non-redundant database (in 1 March 2021) were from a lymph node of a California Sea Lion, protoparvovirus strain Hanchett_2 (MN982959) [29] with amino acid NS1 and VP1 identities of 49% and 40%. For the bocaparvovirus, the closest NS1 and VP1 proteins were from Dromedary camel bocaparvovirus 1 (KY640425) [34] from camels with amino acid identities of 54% and 50%. ...
Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and/or inoculation studies.
... Virus metagenomics library preparation and bioinformatics analyses were performed as described [27,28]. Viral-like particles (VLP) were first enriched by homogenization followed by filtration and digestion with nucleases enzymes of supernatants to reduce the concentration of noncapsid protected nucleic acids. ...
... Illumina sequence data analyses were conducted as described using BLASTx to detect reads and contigs showing translated protein sequences similarity to all know eukaryotic viruses in RefSeq of GenBank [28]. An in-house pipeline was used for removing bacterial and host genomes, trimming adaptor and primers, and assembling de novo assembly [27,28]. ...
... Illumina sequence data analyses were conducted as described using BLASTx to detect reads and contigs showing translated protein sequences similarity to all know eukaryotic viruses in RefSeq of GenBank [28]. An in-house pipeline was used for removing bacterial and host genomes, trimming adaptor and primers, and assembling de novo assembly [27,28]. BLASTx was used for translated protein sequence similarity to all viral protein sequences in the GenBank database. ...
Six foals from Southern California with interstitial pneumonia of undetermined etiology were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled and nucleic acids from virus-like particles were enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus as well as three previously uncharacterized viruses were identified. The complete ORFs genome of two closely related protoparvoviruses, of a bocaparvovirus, and the partial genome of a picornavirus were assembled. The parvoviruses were classified as member of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Feces, spleen, and lung samples from each animal were then PCR tested for these parvoviruses and picornavirus. Three foals were co-infected with the picornavirus and either protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with protoparvovirus only. No viral infection was detected in one animal. All parvoviruses were detected in both feces and spleen. Picornavirus, protoparvovirus, and eqcopivirus nucleic acids were detected in the lungs of one animal each. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus and the more partial genome of the third equine picornavirus and their detection in foals with interstitial pneumonia are therefore described here. Testing the possible involvement of these viruses in fatal interstitial pneumonia or other equine disease will require larger epidemiological and/or inoculation studies.
... These reads were submitted to GenBank under Biosample accession number SAMN18737161. Bioinformatics analyses were conducted as described using BLASTx to detect reads and contigs showing translated protein sequences similarity to all know eukaryotic viruses in RefSeq of GenBank [30]. ...
Circoviruses infect vertebrates where they can result in a wide range of disease signs or in asymptomatic infections. Using viral metagenomics we analyzed a pool of five sera from four healthy and one sick horse. Sequences from parvovirus-H, equus anellovirus, and distantly related to mammalian circoviruses were recognized. PCR identified the circovirus reads as originating from a pregnant mare with fever and hepatitis. That horse’s serum was also positive by real time PCR for equine parvovirus H and negative for the flavivirus equine hepacivirus. The complete circular genome of equine circovirus 1 strain Charaf (EqCV1-Charaf) was completed using PCR and Sanger sequencing. EqCV1 replicase showed 73–74% identity to those of their closest relatives, pig circoviruses 1/2, and elk circovirus. The closest capsid proteins were from the same ungulate circoviruses with 62–63% identity. The overall nucleotide identity of 72% to its closest relative indicates that EqCV1 is a new species in the Circovirus genus, the first reported in genus Equus. Whether EqCV1 alone or in co-infections can result in disease and its prevalence in different equine populations will require further studies now facilitated using EqCV1′s genome sequence.
... In the veterinary virology field, Delwart et al. introduced a rapid and simple protocol for the identification of known and new viruses, more than a decade ago, based on homogenization of animal tissues, filtration, centrifugation at 22,000× g for 2 h, and DNase treatment [34,35]. Since then, their extensive research has demonstrated the possibility of studying the virome in a diverse array of tissues and animal species, e.g., python liver [36], sea lion mesenteric lymph node [37], porcine heart and lung [38], and giant panda heart, liver, spleen, lung, and kidney [39], with minimal modification of the initial physical enrichment methodology. The library preparation (Nextera™ XT library preparation), sequencing technology (Illumina MiSeq), and especially the analysis of the obtained sequencing reads are crucial factors in the success of the aforementioned studies. ...
In recent years, refined molecular methods coupled with powerful high throughput sequencing technologies have increased the potential of virus discovery in clinical samples. However, host genetic material remains a complicating factor that interferes with discovery of novel viruses in solid tissue samples as the relative abundance of the virus material is low. Physical enrichment processing methods, although usually complicated, labor-intensive, and costly, have proven to be successful for improving sensitivity of virus detection in complex samples. In order to further increase detectability, we studied the application of fast and simple high-throughput virus enrichment methods on tissue homogenates. Probe sonication in high EDTA concentrations, organic extraction with Vertrel™ XF, or a combination of both, were applied prior to chromatography-like enrichment using Capto™ Core 700 resin, after which effects on virus detection sensitivity by the VIDISCA method were determined. Sonication in the presence of high concentrations of EDTA showed the best performance with an increased proportion of viral reads, up to 9.4 times, yet minimal effect on the host background signal. When this sonication procedure in high EDTA concentrations was followed by organic extraction with Vertrel™ XF and two rounds of core bead chromatography enrichment, an increase up to 10.5 times in the proportion of viral reads in the processed samples was achieved, with reduction of host background sequencing. We present a simple and semi-high-throughput method that can be used to enrich homogenized tissue samples for viral reads.
... assembly. Bioinformatic analysis was performed according to the protocol previously described by Deng et al.51,52 . Briefly, the non-viral sequences (i.e. ...
Classical insect-flaviviruses (cISFVs) and dual host-related insect-specific flavivirus (dISFV) are within the major group of insect-specific flavivirus. Remarkably dISFV are evolutionarily related to some of the pathogenic flavivirus, such as Zika and dengue viruses. The Evolutionary relatedness of dISFV to flavivirus allowed us to investigate the evolutionary principle of host adaptation. Additionally, dISFV can be used for the development of flavivirus vaccines and to explore underlying principles of mammalian pathogenicity. Here we describe the genetic characterization of a novel putative dISFV, termed Guapiaçu virus (GUAPV). Distinct strains of GUAPV were isolated from pools of Aedes terrens and Aedes scapularis mosquitoes. Additionally, we also detected viral GUAPV RNA in a plasma sample of an individual febrile from the Amazon region (North of Brazil). Although GUAPV did not replicate in tested mammalian cells, 3′UTR secondary structures duplication and codon usage index were similar to pathogenic flavivirus.
... Sequence data analysis was performed as previously described (40). Adaptor and primer sequences were trimmed using the default parameters of VecScreen, which is part of the BLAST package v2.2.31. ...
An outbreak of cat vomiting was observed in an animal shelter. Testing for known enteric feline pathogens did not identify a causative agent. Viral metagenomics on four mini pools of feces from cases and controls housed in the same area revealed the presence of feline astrovirus in all pools. Also found with fewer reads in one pool each were rotavirus I, carnivore bocaparvovirus 3, norovirus (NoV) GVI, and a novel dependovirus. The genome of the highly prevalent astrovirus was sequenced and classified into mamastrovirus species two, also known as feline astrovirus. Real-time RT-PCR on longitudinally acquired fecal samples from 11 sick cases showed 10 (91%) to be shedding astrovirus for as long as 19 days. Affected cats were sick for an average of 9.8 days, with a median of 2.5 days (range = 1–31 days). Unaffected control cats housed in the same areas during the outbreak showed five out of nine (56%) to also be shedding astrovirus. Feline fecal samples collected from the same animal shelter ~1 year before (n = 8) and after (n = 10) showed none to be shedding astrovirus, indicating that this virus was temporarily associated with the vomiting outbreak and is not part of the commensal virome for cats in this shelter. Together with the absence of highly prevalent known pathogens, our results support a role for feline astrovirus infection, as well as significant asymptomatic shedding, in an outbreak of contagious feline vomiting.
