Genetic characterization of parvoviruses identified in stray cats in Nigeria.

Parvoviruses are a major cause of haemorrhagic gastroenteritis, leukopenia and high mortality in cats and dogs. In this study, the presence and genetic characteristics of parvoviruses circulating among cats in Nigeria are reported. Faecal samples of stray cats from live animal markets in southwestern (Oyo and Osun States) and north-central (Kwara State) Nigeria were screened for the presence of parvoviral DNA using a qPCR. Positive samples were further characterized using a qPCR based on minor groove binder probes. Overall, 85/102 (83.3 %) stray cats tested positive for feline panleukopenia virus (FPV) DNA and one cat was co-infected with canine parvovirus-2 type a. Sequence analysis of the complete capsid region of 15 Nigerian FPV strains revealed that they were up to 99.9 % similar to the American reference strain FPV-b at the nucleotide level, and three of them presented amino acid mutations in key capsid residues. This is the first report of identification and molecular characterization of FPV strains in cats in Nigeria. The high prevalence of the virus emphasizes the need for constant surveillance of the circulation of parvoviruses in Nigeria and underscores the need to deploy an effective vaccination strategy.

Hepadnavirus Infection in a Cat with Chronic Liver Disease: A Multi-Disciplinary Diagnostic Approach.

A 3-year-old female stray, shorthair cat, with clinical signs and serum chemistry markers indicative of hepatic disease, was diagnosed with domestic cat hepadnavirus (DCH) infection. Coupling molecular and serological data, the infection was seemingly contextualized into a chronic phase, since IgM anti-core antibodies, a marker of early-stage Hepatitis B Virus (HBV) infection, were not detected. However, the cat possessed IgG anti-core, a common indicator of chronic HBV infection in human patients and did not show seroconversion to the anti-DCH surface antigen, considered protective during HBV infection and associated with long-term protective immunity. On genome sequencing, the DCH strain showed 98.3% nucleotide identity to strains previously identified in Italy.

An Outbreak of Limping Syndrome Associated with Feline Calicivirus.

Feline calicivirus (FCV) is a common viral pathogen found in domestic cats. FCV is highly contagious and demonstrates a high genetic variability. Upper respiratory tract disease, oral ulcerations, salivation, and gingivitis-stomatitis have been regarded as typical clinical signs of FCV infection. Ulcerative dermatitis, abortion, severe pneumonia, enteritis, chronic stomatitis, and virulent systemic disease have been reported more sporadically. Limping syndrome has been also described either in naturally or experimentally FCV-infected cats. In this study, we monitored a small outbreak of FCV infection in two household cats, in which limping disease was monitored with a 12-day lag time. The complete genome sequence was determined for the viruses isolated from the oropharyngeal and rectal swabs of the two animals, mapping up to 39 synonymous nucleotide mutations. The four isolates were sensitive to low pH conditions and trypsin treatment, a pattern usually associated with viruses isolated from the upper respiratory tract. Overall, the asynchronous pattern of infections and the results of genome sequencing suggest that a virus of respiratory origin was transmitted between the animals and that the FCV strain was able to retain the limping disease pathotype during the transmission chain, as previously observed in experimental studies with FCV strains associated with lameness.

Novel parvovirus in an outbreak of fatal enteritis in European hedgehogs (Erinaceus europaeus), Italy, 2022.

Starting from June 2022, increased mortality associated with enteric signs was reported in European hedgehogs (Erinaceus europaeus) recovered at a regional wildlife rescue center, in Apulia, Italy. Cases of enteric disease were observed until the end of the breeding season, despite increased biosafety measures. A novel parvovirus was identified using metaviromic, and parvovirus-like particles were observed in the stools on electron microscopy observation. The virus was detected in the fecal samples of all the animals tested (n = 9) and in the internal organs (liver, spleen, and kidney) of three out of nine animals using a specific quantitative assay. In the full-length genome, the parvovirus was closely related (90.4% nt) to a chaphamaparvovirus identified in an Amur hedgehog (Erinaceus amurensis) in Asia and to chaphamaparvoviruses (≤ 70% nt) detected in bats and rodents. Since chaphamaparvoviruses are considered as pathogen in rodents, it will be important to investigate the pathogenic role, if any, of these parvoviruses in hedgehogs. IMPORTANCE European hedgehogs (Erinaceus europaeus) are common in Europe. This species has been shown to harbor occasionally zoonotic pathogens, including bacteria, fungi, and viruses. Exploring the virome of wildlife animals is important for animal conservation and also to assess zoonotic risks. Our metaviromic investigation identified a novel parvovirus from an outbreak of enteritis in European hedgehogs housed in a wildlife rescue center, extending the spectrum of potential viral pathogens in this species.

Investigating the genetic diversity of CRESS DNA viruses in cats identifies a novel feline circovirus and unveils exposure of cats to canine circovirus.

Circular replication-associated protein (Rep)-encoding single stranded (CRESS) DNA viruses include Circoviruses which have been found in several animal species and in human specimens. Circoviruses are associated with severe disease in pigs and birds and with respiratory and gastrointestinal disorders and systemic disease in dogs. In cats there are only a few anecdotical studies reporting CRESS DNA viruses. In this study, a total of 530 samples (361 sera, 131 stools, and 38 respiratory swabs) from cats, were screened for the presence of CRESS DNA viruses. Overall, 48 (9.0%) of 530 samples tested positive using a pan-Rep PCR. A total of 30 Rep sequences were obtained. Ten sequences of fecal origin were tightly related to each other (82.4-100% nt identity) and more distantly related to mongoose circoviruses (68.3 to 77.2% nt identity). At genome level these circoviruses displayed the highest nt identity (74.3-78.7%) to mongoose circoviruses thus representing a novel circovirus species. Circoviruses from different animal hosts (n = 12) and from humans (n = 8) were also identified. However, six Rep sequences were obtained from serum samples, including canine circoviruses, a human cyclovirus and human and fish-associated CRESS DNA viruses. The presence of these viruses in the sera would imply, to various extent, virus replication in the animal host, able to sustain viremia. Overall, these findings indicate a wide genetic diversity of CRESS DNA viruses in cats and warrant further investigations.

Identification of new astroviruses in synanthropic squamates.

Astroviruses have been identified in a wide variety of animal species and are associated with gastro-intestinal disease in humans. Pathologies due to extra-intestinal localization are known in different hosts. We report the detection of astroviruses in synanthropic squamate reptile species (Podercis siculus and Tarentola mauritanica). Fecal samples were collected from 100 squamates from urban and peri-urban areas of three regions in South Italy and tested for the presence of astroviruses using a broadly reactive (pan-astrovirus) RT-PCR protocol targeting the RNA-dependent RNA polymerase. Astrovirus RNA was detected in 11% of the samples and for six strains a 3 kb-long fragment at the 3' end of the genome was sequenced, obtaining information on the complete capsid-encoding ORF2 sequence. Viral RNA was also detected in the brain of one of the positive animals. The sequences generated from the astrovirus strains shared low nucleotide identities in the ORF2 (< 43.7%) with other known reptilian astrovirus sequences, hinting to the massive genetic diversity of members of this viral family. Based on the partial RdRp gene of the sequenced strains, however, we observed species-specific patterns, regardless of the geographic origin of the animals, and we also identified a possible inter-species transmission event between geckoes and lizards.

A Cold Case of Equine Influenza Disentangled with Nanopore Sequencing.

Massive sequencing techniques have allowed us to develop straightforward approaches for the whole genome sequencing of viruses, including influenza viruses, generating information that is useful for improving the levels and dimensions of data analysis, even for archival samples. Using the Nanopore platform, we determined the whole genome sequence of an H3N8 equine influenza virus, identified from a 2005 outbreak in Apulia, Italy, whose origin had remained epidemiologically unexplained. The virus was tightly related (>99% at the nucleotide level) in all the genome segments to viruses identified in Poland in 2005-2008 and it was seemingly introduced locally with horse trading for the meat industry. In the phylogenetic analysis based on the eight genome segments, strain ITA/2005/horse/Bari was found to cluster with sub-lineage Florida 2 in the HA and M genes, whilst in the other genes it clustered with strains of the Eurasian lineage, revealing a multi-reassortant nature.

Analysis of oral microbiota in non-vital teeth and clinically intact external surface from patients with severe periodontitis using Nanopore sequencing: a case study.

Periodontal diseases include a wide range of pathological conditions, damaging the supporting structures of the teeth. Origin and propagation of periodontal disease is believed to be caused by dysbiosis of the commensal oral microbiota. The aim of this study was to evaluate the presence of bacteria in the pulp cavity of teeth with severe periodontal disease with clinically intact external surface. Periodontal (P) and endodontic (E) tissue samples of root canals from six intact teeth of three patients were sampled for analysis of microbial population using Nanopore technology. Streptococcus was the predominant genus in E samples. Porphyromonas (33.4%, p = 0.047), Tannerella (41.7%, p = 0.042), and Treponema (50.0%, p = 0.0064) were significantly more present in P than in E samples. Some samples (E6 and E1) exhibited a remarkable difference in terms of microbial composition, whilst Streptococcus was a common signature in samples E2 to E5, all which were obtained from the same patient. In conclusion, bacteria were identified on both the root surface and the root canal system, thus demonstrating the possibility of bacteria to spread directly from the periodontal pocket to the root canal system even in the absence of crown's loss of integrity.

Detection at high prevalence of newlavirus (protoparvovirus) in the carcasses of red foxes.

Wildlife conservation also relies on the study of animal virome. We identified the DNA of a novel fox protoparvovirus, newlavirus, with high (71%) prevalence in the carcasses of red foxes. On genome sequencing, high genetic diversity and possible recombination was observed, suggesting complex evolutionary dynamics in wildlife.

Endodontic Microbial Communities in Apical Periodontitis.

INTRODUCTION: Apical periodontitis (AP) represents an inflammatory condition of peri-radicular tissues due to invasion and colonization of bacteria in the root canals. Primary apical periodontitis (PAP) is associated with untreated necrotic root canal and can be efficiently treated with endodontic treatment to remove bacteria. Persistent/secondary apical periodontitis (SAP) is a perpetual periapical lesion due to unsuccessfully treated root canals after an initial apparent healing of the tooth. The aim of the study was evaluating the microbial communities associated with root canals using Nanopore sequencing. METHODS: Seventeen samples from the root canals of 15 patients with AP were Polymerase Chain Reaction-amplified for 16s ribosomal DNA gene and sequenced. Information regarding the presence or absence of AP symptoms, PAP and SAP, and periapical index of patients were recorded. RESULTS: Firmicutes, Bacteroidetes, and Actinobacteria were the most abundant phyla detected and Phocaeicola, Pseudomonas, Rothia, and Prevotella were the most prominent genera. In samples of patients with AP symptoms, the most frequent detected genera were Cutibacterium, Lactobacillus, Pseudomonas, Dialister, Prevotella, and Staphylococcus. In PAP samples, the most represented genera were Cutibacterium, Lactobacillus, Pseudomonas, and Prevotella, whilst in SAP cases were Cutibacterium, Prevotella, Atopobium, Capnocytophaga, Fusobacterium, Pseudomonas, Solobacterium, and Streptococcus. CONCLUSIONS: The results provide additional information on the microbiota of root-canals. These data evidence the complexity of the microbiota and the relationship with many clinical and endodontic conditions. Future studies must evaluate these conditions and identify their role in inducing bone damage and local and systemic disease, aiming to better elucidate the relationship between microbes and endodontic pathologies.

Feline Panleukopenia Virus in Dogs from Italy and Egypt.

Canine parvovirus and feline panleukopenia virus (FPV) are variants of Carnivore protoparvovirus 1. We identified and characterized FPV in dogs from Italy and Egypt using genomic sequencing and phylogenetic analyses. Cost-effective sequencing strategies should be used to monitor interspecies spread, evolution dynamics, and potential host jumping of FPV.

Diversity of CRESS DNA Viruses in Squamates Recapitulates Hosts Dietary and Environmental Sources of Exposure.

Replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses comprise viruses with covalently closed, circular, single-stranded DNA (ssDNA) genomes, and are considered the smallest known autonomously replicating, capsid-encoding animal pathogens. CRESS DNA viruses (phylum Cressdnaviricota) encompass several viral families including Circoviridae. Circoviruses are classified into two genera, Circovirus and Cyclovirus, and they are known to cause fatal diseases in birds and pigs. Circoviruses have also been identified in human stools, blood, and cerebrospinal fluid (CSF), as well as in various wild and domestic vertebrates, including reptiles. The synanthropic presence of Squamata reptiles has increased in the last century due to the anthropic pressure, which has shifted forested animal behavior to an urban and peri-urban adaptation. In this paper, we explored the diversity of CRESS DNA viruses in Squamata reptiles from different Italian areas representative of the Mediterranean basin. CRESS DNA viruses were detected in 31.7% (33/104) of sampled lizards and geckoes. Different CRESS DNA viruses likely reflected dietary composition or environmental contamination and included avian-like (n = 3), dog (n = 4), bat-like (n = 1), goat-like (n = 1), rodent-like (n = 4), and insect-like (n = 2) viruses. Rep sequences of at least two types of human-associated cycloviruses (CyV) were identified consistently, regardless of geographic location, namely, TN9-like (n = 11) and TN12-like (n = 6). A third human-associated CyV, TN25-like, was detected in a single sample. The complete genome of human-like CyVs, of a rodent-like, insect-like, and of a bat-like virus were generated. Collectively, the results recapitulate hosts dietary and environmental sources of exposure and may suggest unexpected ecological niches for some CRESS DNA viruses. IMPORTANCE CRESS DNA viruses are significant pathogens of birds and pigs and have been detected repeatedly in human samples (stools, serum, and cerebrospinal fluid), both from healthy individuals and from patients with neurological disease, eliciting in 2013 a risk assessment by the European Centre for Disease Prevention and Control (ECDC). Sequences of CRESS DNA viruses previously reported in humans (TN9, TN12, and TN25), and detected in different animal species (e.g., birds, dogs, and bats) were herein detected in fecal samples of synanthropic squamates (geckos and lizards). The complete genome sequence of six viruses was generated. This study extends the information on the genetic diversity and ecology of CRESS DNA viruses. Because geckos and lizards are synanthropic animals, a role in sustaining CRESS DNA virus circulation and increasing viral pressure in the environment is postulated.

A novel hepadnavirus in domestic dogs.

Hepadnaviruses have been identified in several animal species. The hepadnavirus prototype, human hepatitis B virus (HBV), is a major public health problem associated with chronic liver diseases and hepatocellular carcinoma. Recently, a novel hepadnavirus, similar to HBV, was identified in domestic cats. Since several pathogens can be shared between cats and dogs, we hypothesized that dogs could also harbor hepadnaviruses and we tested a collection of canine sera with multiple molecular strategies. Overall, hepadnavirus DNA was identified in 6.3% (40/635) of canine serum samples, although the viral load in positive sera was low (geometric mean of 2.70 × 102 genome copies per mL, range min 1.36 × 102-max 4.03 × 104 genome copies per mL). On genome sequencing, the canine hepadnaviruses revealed high nucleotide identity (about 98%) and similar organization to the domestic cat hepadnavirus. Altered hepatic markers were found in hepadnavirus-positive dogs, although the role of hepadnavirus in canine health remains to be elucidated.

Detection of antibodies against domestic cat hepadnavirus using baculovirus-expressed core protein.

A novel orthohepadnavirus (domestic cat hepadnavirus [DCH]) similar to human hepatitis B virus has been recently detected in serum and liver samples from domestic cats with chronic hepatitis and hepatocellular carcinoma. Molecular investigations by independent research groups around the world have revealed positivity rates ranging from 6.5% to 12.5% in blood samples and up to 14.0% in liver tissue. In this study, we screened an age-stratified collection of feline sera (n = 256) by using an antibody detection enzyme-linked immunosorbent assay based on the recombinant core antigen of DCH (DCHc). Specific antibodies (DCHc Abs) were detected with a prevalence of 25.0%. The DNA of DCH was detected in 35.9% (23/64) of seropositive cats and only in 1.0% (2/192) of seronegative animals. Based on the serological (IgG and IgM anti-DCHc) and virological status, the possible stages of DCH infection were predicted.

Astrovirus VA1 in patients with acute gastroenteritis.

Human astroviruses (AstVs) are usually associated with acute gastroenteritis. In recent years, atypical animal-like AstVs have been identified, but their pathogenic role in humans has not been determined. Starting from 2010, there has been a growing evidence that AstVs may also be associated with encephalitis in human and animal hosts. Some human atypical AstV strains (VA1, MLB1/MLB2) display neurotropic potential, as they have been repeatedly identified in patients with AstV-related encephalitis, chiefly in immunosuppressed individuals. In this study, a VA1-like AstV was identified from a single stool sample from an outbreak of foodborne acute gastroenteritis occurred in Italy in 2018. On genome sequencing, the virus was related to the VA1-like strain UK1 (99.3% at the nucleotide level). Similar viruses were also found to circulate in paediatric patients hospitalized with AGE in the same time span, 2018, but at low prevalence (0.75%, 3/401). Gathering epidemiological data on atypical AstVs will be useful to assess the risks posed by atypical AstV infections, chiefly in medically fragile patients.

An outbreak of neonatal enteritis in buffalo calves associated with astrovirus.

BACKGROUND: Enteritis of an infectious origin is a major cause of productivity and economic losses to cattle producers worldwide. Several pathogens are believed to cause or contribute to the development of calf diarrhea. Astroviruses (AstVs) are neglected enteric pathogens in ruminants, but they have recently gained attention because of their possible association with encephalitis in humans and various animal species, including cattle. OBJECTIVES: This paper describes a large outbreak of neonatal diarrhea in buffalo calves (Bubalus bubalis), characterized by high mortality, which was associated with an AstV infection. METHODS: Following an enteritis outbreak characterized by high morbidity (100%) and mortality (46.2%) in a herd of Mediterranean buffaloes (B. bubalis) in Italy, 16 samples from buffalo calves were tested with the molecular tools for common and uncommon enteric pathogens, including AstV, kobuvirus, and torovirus. RESULTS: The samples tested negative for common enteric viral agents, including Rotavirus A, coronavirus, calicivirus, pestivirus, kobuvirus, and torovirus, while they tested positive for AstV. Overall, 62.5% (10/16) of the samples were positive in a single round reverse transcription polymerase chain reaction (PCR) assay for AstV, and 100% (16/16) were positive when nested PCR was performed. The strains identified in the outbreak showed a clonal origin and shared the closest genetic relationship with bovine AstVs (up to 85% amino acid identity in the capsid). CONCLUSIONS: This report indicates that AstVs should be included in a differential diagnosis of infectious diarrhea in buffalo calves.

A longitudinal observational study in two cats naturally-infected with hepadnavirus.

Hepatitis B virus (HBV) is a major cause of liver disease in humans including chronic hepatitis and hepatocellular carcinoma. Domestic cat hepadnavirus (DCH), a novel HBV-like hepadnavirus, was identified in domestic cats in 2018. From 6.5 %-10.8 % of pet cats are viremic for DCH and altered serological markers suggestive of liver damage have been identified in 50 % of DCH-infected cats. DCH DNA has been detected in association with characteristic lesions of chronic hepatitis and with hepatocellular carcinoma in cats, suggesting a possible association. In this study longitudinal molecular screening of cats infected with DCH was performed to determine if DCH can cause chronic infections in cats. Upon re-testing of sera from five DCH-positive animals, 2-10 months after the initial diagnosis, three cats tested negative for DCH on two consecutive occasions using quantitative PCR. Two other cats remained DCH-positive, including an 8-month-old female cat re-tested four months after the initial positive result, and a 9-year-old male cat, which tested positive for DCH on six occasions over an 11-month period. The latter had a history of chronic hepatopathy with jaundice, lethargy and elevated serum alanine transaminase levels (ALT). During the period of observation, DCH titers ranged between 1.64 × 105 and 2.09 × 106 DNA copies/mL and ALT was persistently elevated, suggesting chronic infection. DCH DNA was not detected in oral, conjunctival, preputial and rectal swabs from the two animals collected at several time points. Long-term (chronic) infection would be consistent with the relatively high number of viremic cats identified in epidemiological investigations, with the possible association of DCH with chronic hepatic pathologies and with what described with HBV in human patients.

Detection of multi-drug resistance and AmpC ß-lactamase/extended-spectrum ß-lactamase genes in bacterial isolates of loggerhead sea turtles (Caretta caretta) from the Mediterranean Sea.

Sea turtles are useful sentinels to monitor the dissemination of antimicrobial resistance (AMR) in the marine coastal ecosystems. Forty Gram negative bacteria were isolated from wounds of 52 injured Caretta caretta, living in the Mediterranean Sea. Bacteria were identified using 16S rRNA gene sequencing and tested for susceptibility to 15 antibiotics. In addition, NGS amplicon sequencing was performed to detect the presence of AmpC ß-lactamase genes (blaAmpC) and extended-spectrum ß-lactamase (ESBL) genes (blaCTX-M,blaSHV,blaTEM). Seventy-five percent of the isolates (30/40 isolates) exhibited multidrug resistance (MDR) phenotypes and 32.5% (13/40 isolates) were confirmed to be positive for at least one gene. The variants of ESBLs genes were blaCTX-M-3,blaTEM-236 and blaSHV-12. Variants of the blaAmpCß-lactamase gene i.e., blaACT-24, blaACT-2, blaACT-17, blaDHA-4 and blaCMY-37, were also detected. In addition, 4 isolates were found simultaneously harboring CTX and AmpC genes while 2 strains harbored 3 genes (blaACT-2+TEM-236+SHV-12, and blaCTX-M-3+ACT-24+TEM-236).

Identification of astroviruses in bovine and buffalo calves with enteritis.

Astroviruses (AstVs) have been identified in the stools of calves with enteritis and in the brain tissues of bovines with encephalitis but their pathogenic role has not been clarified. In this study, we report the detection and characterization of bovine and water buffalo AstV strains identified in young bovine and buffalo calves with enteritis in Italy between 2012 and 2015. By negative staining transmission electron microscopy (TEM) observation, AstV-like particles were identified in the stools of the animals and AstV RNA was confirmed molecularly. The sequence (~3.2-kb) at the 3' end of the genome was determined for two bovine and two buffalo AstVs. Sequence and phylogenetic analysis on the partial ORF1b and full-length ORF2 revealed a marked genetic diversity although the viruses were distantly related to other AstV identified from ruminants. Gathering sequence information on ruminant AstVs is important to understand the extent of inter-species circulation and for the development of reliable, specific diagnostic tools.

Genome sequence of an aichivirus detected in a common pipistrelle bat (Pipistrellus pipistrellus).

The family Picornaviridae includes important human and animal pathogens that are associated with a wide range of diseases and, in some cases, have zoonotic potential. During epidemiological surveillance of bats, we identified, by next-generation sequencing (NGS) techniques, the presence of picornavirus RNA in a common pipistrelle bat (Pipistrellus pipistrellus). By coupling NGS, primer-walking strategies, and sequence-independent protocols to obtain the sequences of the 5' and 3' termini, we reconstructed the genome sequence of picornavirus strain ITA/2017/189/18-155. The genome of the bat picornavirus is 8.2 kb in length and encodes a polyprotein of 2462 amino acids. A comparison of polyprotein sequences revealed that this virus is distantly related (65.1% and 70.9% sequence identity at the nucleotide and amino acid level, respectively) to a bat aichivirus identified in 2010. Phylogenetic analysis showed that this picornavirus clustered closely with members of the genus Kobuvirus, which also includes human and animal aichiviruses. The identification of aichiviruses in several animal hosts is providing hints that will lead to an understanding of their origin and evolutionary patterns.