Genome characterization of feline morbillivirus from Italy

Evaluation of next generation sequencing approaches for SARS-CoV-2

Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.

Feline Morbillivirus: Clinical Relevance of a Widespread Endemic Viral Infection of Cats

Feline morbillivirus (FeMV) was first isolated in 2012 from stray cats in Hong Kong. It has been found in association with tubulointerstitial nephritis (TIN), the most common cause of feline chronic kidney disease (CKD). However, viral host spectrum and virus tropism go beyond the domestic cat and kidney tissues. The viral genetic diversity of FeMV is extensive, but it is not known if this is clinically relevant. Urine and kidney tissues have been widely tested in attempts to confirm associations between FeMV infection and renal disease, but samples from both healthy and sick cats can test positive and some cross-sectional studies have not found associations between FeMV infection and CKD. There is also evidence for acute kidney injury following infection with FeMV. The results of prevalence studies differ greatly depending on the population tested and methodologies used for detection, but worldwide distribution of FeMV has been shown. Experimental studies have confirmed previous field observations that higher viral loads are present in the urine compared to other tissues, and renal TIN lesions associated with FeMV antigen have been demonstrated, alongside virus lymphotropism and viraemia-associated lymphopenia. Longitudinal field studies have revealed persistent viral shedding in urine, although infection can be cleared spontaneously.

Characterization of Epizootic Hemorrhagic Disease Virus Serotype 8 in Naturally Infected Barbary Deer (Cervus elaphus barbarus) and Culicoides (Diptera: Ceratopogonidae) in Tunisia

Epizootic hemorrhagic disease (EHD) is a Culicoides-borne disease of domestic and wild ruminants caused by EHD virus (EHDV). This virus circulates in multiple serotypes. In late September 2021, a novel strain belonging to EHDV-8 was reported in cattle farms in Central-Western Tunisia, and in the fall of 2022, the same virus was also detected in Italy and Spain. In the present study, we described EHDV-8 occurrence in deer and, a preliminary identification of the potential Culicoides species responsible for virus transmission in selected areas of Tunisia. EHDV-8 was identified in deer carcasses found in 2021 and 2022 in the national reserve of El Feidja, Jendouba, Northwestern Tunisia, and isolated on cell culture. Instead, insect vectors were collected in October 2021 only in the areas surrounding the city of Tozeur (Southern Tunisia) where EHDV-8 cases in cattle were confirmed. Morphological identification showed that 95% of them belonged to the Culicoides kingi and Culicoides oxystoma species and both species tested positive for EHDV-8 RNA. C. imicola was not detected in this collection and EHDV-8 RNA was not evidenced in vector pools collected in 2020, prior to official EHDV-8 emergence. EHDV whole genome sequences were also obtained directly from infected biological samples of deer and positive vectors. EHDV-8 sequences obtained from deer and vectors share a nucleotide identity ranging from 99.42 to 100% and amino acid identity from 99.18 to 100% across all genome segments with the EHDV-8/17 TUN2021 reference sequence.

Genetic Diversity and Evolution of Viruses Infecting Felis catus: A Global Perspective

Cats harbor many important viral pathogens, and the knowledge of their diversity has been greatly expanded thanks to increasingly popular molecular sequencing techniques. While the diversity is mostly described in numerous regionally defined studies, there lacks a global overview of the diversity for the majority of cat viruses, and therefore our understanding of the evolution and epidemiology of these viruses was generally inadequate. In this study, we analyzed 12,377 genetic sequences from 25 cat virus species and conducted comprehensive phylodynamic analyses. It revealed, for the first time, the global diversity for all cat viruses known to date, taking into account highly virulent strains and vaccine strains. From there, we further characterized and compared the geographic expansion patterns, temporal dynamics and recombination frequencies of these viruses. While respiratory pathogens such as feline calicivirus showed some degree of geographical panmixes, the other viral species are more geographically defined. Furthermore, recombination rates were much higher in feline parvovirus, feline coronavirus, feline calicivirus and feline foamy virus than the other feline virus species. Collectively, our findings deepen the understanding of the evolutionary and epidemiological features of cat viruses, which in turn provide important insight into the prevention and control of cat pathogens.

Epizootic Hemorrhagic Disease Virus Serotype 8, Italy, 2022

We describe the detection of epizootic hemorrhagic disease virus (EHDV) serotype 8 in cattle farms in Sardinia and Sicily in October-November 2022. The virus has a direct origin in North Africa; its genome is identical (>99.9% nucleotide sequence identity) to EHDV serotype 8 strains detected in Tunisia in 2021.

Epizootic Haemorrhagic Disease Virus Serotype 8 in Tunisia, 2021

Epizootic haemorrhagic disease (EHD) is a Culicoides-borne viral disease caused by the epizootic haemorrhagic disease virus (EHDV) associated with clinical manifestations in domestic and wild ruminants, primarily white-tailed deer (Odocoileus virginianus) and cattle (Bos taurus). In late September 2021, EHDV was reported in cattle farms in central/western Tunisia. It rapidly spread throughout the country with more than 200 confirmed outbreaks. We applied a combination of classical and molecular techniques to characterize the causative virus as a member of the serotype EHDV-8. This is the first evidence of EHDV- 8 circulation since 1982 when the prototype EHDV-8 strain was isolated in Australia. This work highlights the urgent need for vaccines for a range of EHDV serotypes.

A Deletion Encompassing the Furin Cleavage Site in the Spike Encoding Gene Does Not Alter SARS-CoV-2 Replication in Lung Tissues of Mink and Neutralization by Convalescent Human Serum Samples

SARS-CoV-2 has been shown to lose the furin polybasic cleavage site (FCS) following adaptation on cell culture. Deletion occurring in this region, which may include also the FCS flanking regions, seem not to affect virus replication in vitro; however, a chimeric SARS-CoV-2 virus without the sole FCS motif has been associated with lower virulence in mice and lower neutralization values. Moreover, SARS-CoV-2 virus lacking the FCS was shed to lower titers from experimentally infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. In this study, we investigated the replication kinetics and cellular tropism of a SARS-CoV-2 isolate carrying a 10-amino acid deletion in the spike protein spanning the FCS in lung ex vivo organ cultures of mink. Furthermore, we tested the neutralization capabilities of human convalescent SARS-CoV-2 positive serum samples against this virus. We showed that this deletion did not significantly hamper neither ex vivo replication nor neutralization activity by convalescent serum samples. This study highlights the importance of the preliminary phenotypic characterization of emerging viruses in ex vivo models and demonstrates that mink lung tissues are permissive to the replication of a mutant form of SARS-CoV-2 showing a deletion spanning the FCS. Notably, we also highlight the need for sequencing viral stocks before any infection study as large deletions may occur leading to the misinterpretation of results.

First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa

Influenza D virus (IDV) was first isolated in 2011 in the USA and has since been shown to circulate in cattle, pigs, sheep, wild boar, and camels. In Africa, there is limited data on the epidemiology of IDV and, so, we investigated the presence of IDV among domestic ruminants and wild animals in Namibia by screening nasal swabs using an IDV-specific molecular assay. IDV RNA was detected in bovines (n=2), giraffes (n=2) and wildebeest (n=1). The hemagglutinin-esterase-fusion (HEF) gene from one of the bovine and the wildebeest samples was successfully sequenced as well as the full genome for the second bovine sample. Phylogenetic analysis of the HEF gene positioned the African virus variants within the D/OK lineage but with a long branch. The African variant had an amino acid diversity of 2.41% and most likely represents a distinct genotype within the lineage. Notably, the polymerase acidic protein gene (PA) was more closely related to a different lineage (D/660), indicative of potential reassortment. This is the first genetic characterization of IDV in Africa and it adds important data to our understanding of the global IDV distribution.

West Nile Virus Lineage 2 Overwintering in Italy

In January 2022, West Nile virus (WNV) lineage 2 (L2) was detected in an adult female goshawk rescued near Perugia in the region of Umbria (Italy). The animal showed neurological symptoms and died 15 days after its recovery in a wildlife rescue center. This was the second case of WNV infection recorded in birds in the Umbria region during the cold season, when mosquitoes, the main WNV vectors, are usually not active. According to the National Surveillance Plan, the Umbria region is included amongst the WNV low-risk areas. The necropsy evidenced generalized pallor of the mucous membranes, mild splenomegaly, and cerebral edema. WNV L2 was detected in the brain, heart, kidney, and spleen homogenate using specific RT-PCR. Subsequently, the extracted viral RNA was sequenced. A Bayesian phylogenetic analysis performed through a maximum-likelihood tree showed that the genome sequence clustered with the Italian strains within the European WNV strains among the central-southern European WNV L2 clade. These results, on the one hand, confirmed that the WNV L2 strains circulating in Italy are genetically stable and, on the other hand, evidenced a continuous WNV circulation in Italy throughout the year. In this report case, a bird-to-bird WNV transmission was suggested to support the virus overwintering. The potential transmission through the oral route in a predatory bird may explain the relatively rapid spread of WNV, as well as other flaviviruses characterized by similar transmission patterns. However, rodent-to-bird transmission or mosquito-to-bird transmission cannot be excluded, and further research is needed to better understand WNV transmission routes during the winter season in Italy.

Reemergence of an atypical bluetongue virus strain in goats, Sardinia, Italy

Bluetongue virus (BTV) is the etiologic agent of bluetongue, a WOAH (founded as Office International des Épizooties, OIE)-notifiable economically important disease of ruminants. BTV is transmitted by Culicoides biting midges and 24 different "classical" serotypes have been reported to date. In recent years, several putative novel BTV serotypes, often referred to as "atypical" BTVs, have been documented. These are characterized by unusual biological characteristics, most notably avirulence and vector-independent transmission. Here, we describe the recurrence of such an atypical virus strain BTV-X ITL2021 detected in goats six years after its first discovery in Sardinia, Italy. Combined serological and genome analysis results clearly suggest that the two strains belong to the same BTV serotype. However, unlike the 2015 strain, BTV-X ITL2021 was successfully isolated in BSR cell-culture allowing further serological characterization. Lastly, seropositivity for BTV-X ITL2021 was detected by virus-neutralization in approximately 74% of animals tested, suggesting that this atypical BTV serotype has been circulating undetected in asymptomatic animals for years.

Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia

Human orthopneumovirus (HRSV) is a virus belonging to the Pneumovirus genus that causes lower respiratory tract infections (LRTI) in infants worldwide. In Tunisia, thousands of infants hospitalized for LRTI are found to be positive for HRSV but no whole genome sequences of HRSV strains circulating in this country are available thus far. In this study, five nasal swab samples collected at different time points from a three-month-old female baby with severe immunodeficiency that was hospitalized for acute bronchiolitis were investigated by next generation sequencing. The Tunisian sequences from this study originated from samples collected in 2021, belong to the ON1 genotype of HRSV-A, and are clustered with European sequences from 2019 and not from 2020 or 2021. This is most likely related to local region-specific transmission of different HRSV-A variants due to the COVID-19 related travel restrictions. Overall, this is the first report describing the whole genome sequence of HRSV from Tunisia. However, more sequence data is needed to better understand the genetic diversity and transmission dynamic of HRSV.

West Nile Virus Lineage 1 in Italy: Newly Introduced or a Re-Occurrence of a Previously Circulating Strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008-2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory active.

The envelope protein of Usutu virus attenuates West Nile virus virulence in immunocompetent mice

West Nile virus (WNV) and Usutu virus (USUV) are the two most widespread mosquito-borne flaviviruses in Europe causing severe neuroinvasive disease in humans. Here, following standardization of the murine model with wild type (wt) viruses, we engineered WNV and USUV genome by reverse genetics. A recombinant virus carrying the 5' UTR of WNV within the USUV genome backbone (r-USUV_{5'-UTR WNV}) was rescued; when administered to mice this virus did not cause signs or disease as wt USUV suggesting that 5' UTR of a marked neurotropic parental WNV was not per se a virulence factor. Interestingly, a chimeric virus carrying the envelope (E) protein of USUV in the WNV genome backbone (r-WNV_E-USUV) showed an attenuated profile in mice compared to wt WNV but significantly more virulent than wt USUV. Moreover, except when tested against serum samples originating from a live WNV infection, r-WNV_E-USUV showed an identical antigenic profile to wt USUV confirming that E is also the major immunodominant protein of USUV.

Feline Morbillivirus in Southern Italy: Epidemiology, Clinico-Pathological Features and Phylogenetic Analysis in Cats

Feline morbillivirus (FeMV) was isolated for the first time in 2012 with an association with chronic kidney disease (CKD) suggested. This study aimed at investigating in cats from southern Italy FeMV prevalence and risk factors for exposure to FeMV, including the relationship with CKD; sequencing amplicons and analyzing phylogeny of PCR positive samples. Blood serum, K₃EDTA blood and urine samples from 223 cats were investigated. Ten carcasses were also evaluated. FeMV RNA was detected in 2.4% (5/211) blood and 16.1% (36/223) urine samples. One carcass tested positive by qPCR_FeMV from kidney, urinary bladder, and submandibular lymph nodes. Antibodies against FeMV were detected in 14.5% (28/193) cats. We followed up 27 cats (13 FeMV positive cats) and documented in some cases urine shedding after up to 360 days. Older and foundling cats and cats living in rescue catteries, were more frequently infected with FeMV. A significant correlation between FeMV and higher serum creatinine values or low urine specific gravity was found. FeMV positivity was significantly associated with retroviral infection, and the presence of some clinical signs apart from CKD clinicopathological markers. Our study highlights the possibility of a link between FeMV exposure and CKD and a general impairment of feline health.

Feline morbillivirus in northwestern Italy: first detection of genotype 1-B

OBJECTIVES

A novel morbillivirus was recently described in stray and domestic cats in Asia, the USA and Europe. Most cats infected with feline morbillivirus (FeMV) showed lower urinary tract or kidney disease. Although the association of FeMV infection and kidney diseases has been suggested, the virus pathogenicity remains unclear. The present study aimed to investigate the distribution of FeMV infection, as well as the relationship between FeMV infection and kidney diseases in cats from northwestern Italy.

METHODS

A total of 153 urine samples (150 individuals and three pools) and 50 kidney samples were collected and included in the study; total RNA was extracted and a reverse transcription quantitative PCR (RT-qPCR) was performed in order to identify FeMV. Kidneys were also submitted to anatomopathological examination. Phylogenetic analysis and isolation attempts were carried out on positive samples. In FeMV-positive cats, urinalysis and blood analysis were performed.

RESULTS

FeMV RNA was detected in 7.3% of urine samples and in 8% of kidney samples, both in healthy cats and in cats with clinical signs/post-mortem lesions compatible with kidney disease. At histopathological examination, tubulointerstitial nephritis (TIN) was shown in 3/4 positive kidney samples, but a clear relationship between FeMV and TIN was not observed. Isolation attempts were unsuccessful, although the urine sample of one castrated male cat hosted in a cattery showed a positive signal in RT-qPCR until the fourth cell passage. Phylogenetic analysis revealed that this FeMV strain belonged to genotype 1-B. In the same cattery, a second genotype 1-B variant was detected from a urine pool. Urinalysis showed proteinuria in three cats, while at blood analysis three cats presented altered creatinine levels.

CONCLUSIONS AND RELEVANCE

Data reported suggest the presence of a FeMV sub-cluster distinct from the strain previously isolated in Italy, whose role in renal disorders remains uncertain.

First detection of Feline morbillivirus infection in white-eared opossums (Didelphis albiventris, Lund, 1840), a non-feline host

Feline Morbillivirus (FeMV) was first detected in 2012 in domestic cats from Hong Kong and was found to be associated with tubulointerstitial nephritis and chronic kidney disease. In subsequent studies in other countries, FeMV was detected in asymptomatic cats. However, it is not clear whether FeMV plays a role as a pathogen in the kidney diseases of cats, and other epidemiological data are still unknown. To date, studies have reported the presence of FeMV exclusively in domestic cats. This study is the first molecular detection of the FeMV RNA associated with pathological and immunohistochemical findings in a synanthropic marsupial, the white-eared opossum (Didelphis albiventris), inhabiting peri-urban areas of north-central Parana, Southern Brazil. Molecular techniques identified the viral RNA in the lungs and kidneys. Histopathologic evaluation of these tissues revealed interstitial pneumonia in the lungs with lymphocytic nephritis and tubular necrosis in the kidneys. Immunohistochemistry assays detected positive intralesional immunoreactivity to N protein of FeMV within the lungs and kidneys. A FeMV opossum strain was isolated in Crandell Rees feline kidney lineage cells, resulting in syncytia formation and cell death. Therefore, these results support the ability of FeMV to infect other mammal species and reinforce the possibility of the opossum to be a disseminator of this virus among domestic and wild animals.

Feline Morbillivirus Infection in Domestic Cats: What Have We Learned So Far?

Feline morbillivirus (FeMV) was identified for the first time in stray cats in 2012 in Hong Kong and, since its discovery, it was reported in domestic cats worldwide. Although a potential association between FeMV infection and tubulointerstitial nephritis (TIN) has been suggested, this has not been proven, and the subject remains controversial. TIN is the most frequent histopathological finding in the context of feline chronic kidney disease (CKD), which is one of the major clinical pathologies in feline medicine. FeMV research has mainly focused on defining the epidemiology, the role of FeMV in the development of CKD, and its in vitro tropism, but the pathogenicity of FeMV is still not clear, partly due to its distinctive biological characteristics, as well as to a lack of a cell culture system for its rapid isolation. In this review, we summarize the current knowledge of FeMV infection, including genetic diversity of FeMV strains, epidemiology, pathogenicity, and clinicopathological findings observed in naturally infected cats.

Molecular characterization of Feline paramyxovirus and Feline morbillivirus in cats from Brazil

This study is aimed at detecting Feline paramyxovirus (FPaV) and Feline morbillivirus (FeMV) in 35 urine samples from domestic cats, collected in 2019, with or without clinical signs of uropathies using a reverse transcription-polymerase chain reaction (RT-PCR) followed by semi-nested polymerase chain reaction (SN-PCR) assays to amplify a partial paramyxovirus L gene. Eight (22.9%) out of the 35 urine samples were positive for paramyxoviruses. Sequencing and phylogenetic analyses revealed that three samples were positive for FPaV, four samples were positive for FeMV, and it was not possible to determine which virus was present in one RT-SN-PCR positive urine sample. FPaV strains showed 100% nucleotide (nt) identity with each other and 97% nt identity with a Japanese 163 FPaV strain. The FeMV strains showed 85.9% nt identity with each other; three strains were similar to previously described Brazilian FeMV strains, and one strain clustered in a different branch of the phylogenetic tree together with the first described Chinese FeMV strain. This study provides the first description of FPaV strains in cats from Brazil and provides new information about the molecular characteristics of FPaV and FeMV strains circulating in domestic cats in Brazil.

A "One-Health" approach for diagnosis and molecular characterization of SARS-CoV-2 in Italy

The current pandemic is caused by a novel coronavirus (CoV) called SARS-CoV-2 (species Severe acute respiratory syndrome-related coronavirus, subgenus Sarbecovirus, genus Betacoronavirus, family Coronaviridae). In Italy, up to the 2nd of April 2020, overall 139,422 confirmed cases and 17,669 deaths have been notified, while 26,491 people have recovered. Besides the overloading of hospitals, another issue to face was the capacity to perform thousands of tests per day. In this perspective, to support the National Health Care System and to minimize the impact of this rapidly spreading virus, the Italian Ministry of Health involved the Istituti Zooprofilattici Sperimentali (IZSs), Veterinary Public Health Institutes, in the diagnosis of SARS-CoV-2 by testing human samples. The Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise is currently testing more than 600 samples per day and performing whole genome sequencing from positive samples. Sequence analysis of these samples suggested that different viral variants may be circulating in Italy, and so in Abruzzo region. CoVs, and related diseases, are well known to veterinarians since decades. The experience that veterinarians operating within the Public Health system gained in the control and characterization of previous health issues of livestock and poultry including avian flu, bluetongue, foot and mouth disease, responsible for huge economic losses, is certainly of great help to minimize the impact of this global crisis.

Specific capture and whole-genome phylogeography of Dolphin morbillivirus

Dolphin morbillivirus (DMV) is considered an emerging threat having caused several epidemics worldwide. Only few DMV genomes are publicly available. Here, we report the use of target enrichment directly from cetacean tissues to obtain novel DMV genome sequences, with sequence comparison and phylodynamic analysis. RNA from 15 tissue samples of cetaceans stranded along the Italian and French coasts (2008-2017) was purified and processed using custom probes (by bait hybridization) for target enrichment and sequenced on Illumina MiSeq. Data were mapped against the reference genome, and the novel sequences were aligned to the available genome sequences. The alignment was then used for phylogenetic and phylogeographic analysis using MrBayes and BEAST. We herein report that target enrichment by specific capture may be a successful strategy for whole-genome sequencing of DMV directly from field samples. By this strategy, 14 complete and one partially complete genomes were obtained, with reads mapping to the virus up to 98% and coverage up to 7800X. The phylogenetic tree well discriminated the Mediterranean and the NE-Atlantic strains, circulating in the Mediterranean Sea and causing two different epidemics (2008-2015 and 2014-2017, respectively), with a limited time overlap of the two strains, sharing a common ancestor approximately in 1998.

Molecular epidemiology and genome analysis of feline morbillivirus in household and shelter cats in Thailand

Background

Feline morbillivirus (FeMV) has been discovered in domestic cats associated with tubulointerstitial nephritis, but FeMV is also detected in healthy cats. This research aimed to identify and characterize the FeMV strains detected in a Thai cat population.

Results

Two-hundred and ninety-two samples (131 urine and 161 blood) derived from 261 cats (61 sheltered and 200 household cats) were included for investigating the FeMV prevalence using real-time reverse transcription PCR. The overall prevalence of FeMV detection was 11.9% (31/261) among both samples, which accounted for 14.5% (19/131) and 7.5% (12/161) of the urine and blood samples, respectively. Among the FeMV-PCR positive cats, the FeMV-detected prevalence was insignificantly associated with healthy cats (58.1%; 18/31) or urologic cats (41.9%; 13/31). Full-length genome analysis of these FeMV-Thai strains revealed that their genomes clustered together in the FeMV-1A clade with up to 98.5% nucleotide identity. Selective pressure analysis showed that overall FeMV-1 has undergone negative selection, while positive selection sites were more frequently observed in the phosphoprotein gene.

Conclusions

The detected FeMV infections in the Thai cat population were not correlated with urologic disorders, although the virus was more detectable in urine samples. The genetic patterns among the FeMV-1 Thai strains were more consistent. A large-scale study of FeMV in Thai cat samples is needed for further elucidation.

Detection of Astrovirus in a Cow with Neurological Signs by Nanopore Technology, Italy

In this study, starting from nucleic acids purified from the brain tissue, Nanopore technology was used to identify the etiological agent of severe neurological signs observed in a cow which was immediately slaughtered. Histological examination revealed acute non-suppurative encephalomyelitis affecting the brainstem, cerebrum, cerebellum, and medulla oblongata, while by using PCR-based assays, the nucleic acids of major agents for neurological signs were not detected. By using Nanopore technology, 151 sequence reads were assigned to Bovine Astrovirus (BoAstV). Real-time RT-PCR and in situ hybridization (ISH) confirmed the presence of viral RNA in the brain. Moreover, using the combination of fluorescent ISH and immunofluorescence (IF) techniques, it was possible to detect BoAstV RNA and antigens in the same cells, suggesting the active replication of the virus in infected neurons. The nearly whole genome of the occurring strain (BoAstV PE3373/2019/Italy), obtained by Illumina NextSeq 500, showed the highest nucleotide sequence identity (94.11%) with BoAstV CH13/NeuroS1 26,730 strain, an encephalitis-associated bovine astrovirus. Here, we provide further evidence of the role of AstV as a neurotropic agent. Considering that in a high proportion of non-suppurative encephalitis cases, which are mostly indicative of a viral infection, the etiologic agent remains unknown, our result underscores the value and versatility of Nanopore technology for a rapid diagnosis when the PCR-based algorithm gives negative results.

Early Renal Involvement in Cats with Natural Feline Morbillivirus Infection

Simple Summary

Feline morbillivirus is a newly discovered paramyxovirus infecting domestic cats. Its pathogenetic role in domestic cats is still debated, however some evidences suggest a potential involvement of this novel feline virus in the pathogenesis of feline chronic kidney disease. In this study, clinical data of cats infected by morbillivirus were retrospectively reviewed and compared with data obtained from healthy cats and cats affected by chronic kidney disease. The results of the present study suggest that this infection can be associated with the presence of a sub-clinical kidney damage and with different grades of renal dysfunction in cats younger than those typically affected by chronic kidney disease.

Abstract

Feline morbillivirus (FeMV) is a newly discovered paramyxovirus infecting domestic cats and its role in the pathogenesis of feline chronic kidney disease (CKD) has been suggested, however not confirmed. The primary aim of the study was to evaluate the renal damage associated with FeMV infection in cats. In this retrospective study, clinical and clinicopathological data were compared among 14 FeMV naturally infected, 21 CKD and 22 healthy cats. FeMV positive cats had serum chemistry analytes and main urine chemistry results similar to the healthy subjects. FeMV positive cats had significantly decreased urine specific gravity (median 1054, range 1022–1065) and urine creatinine (median 227.23 mg/dL, range 83.02–489.75) when compared with healthy cats (median 1067, range 1040–1080, p < 0.001; median 406.50 mg/dL, range 195.32–575.58; p < 0.001, respectively). Urine protein:creatinine ratio (UPC) results of FeMV and CKD were not different (median 0.20, range 0.08–1.03; median 0.23, range 0.10–0.80, respectively), however UPC results were significantly increased in both groups, if compared with healthy cats (median 0.1, range 0.04–0.250, p < 0.01). Based on clinical data, serum creatinine concentration, urine specific gravity and UPC results, CKD was suspected by clinicians in 3/14 FeMV cats. Urine protein sodium-dodecyl-sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in 10/13 (77%) FeMV cats indicated a tubular pattern, with a decrease of uromodulin and an increase in the number and intensity of low molecular weight proteins. FeMV infection can be associated with different grades of renal dysfunction ranging from mild tubular proteinuria with less concentrated urine to azotemia in cats younger than those typically affected by CKD.

Feline Morbillivirus, a New Paramyxovirus Possibly Associated with Feline Kidney Disease

Feline morbillivirus (FeMV) was first isolated in stray cats in Hong Kong in 2012. Since its discovery, the virus has been reported in domestic cats worldwide, including in Hong Kong, Japan, Italy, US, Brazil, Turkey, UK, Germany, and Malaysia. FeMV is classified in the Morbillivirus genus within the Paramyxoviridae family. FeMV research has focused primarily on determining the host range, symptoms, and characteristics of persistent infections in vitro. Importantly, there is a potential association between FeMV infection and feline kidney diseases, such as tubulointerstitial nephritis (TIN) and chronic kidney diseases (CKD), which are known to significantly affect feline health and survival. However, the tropism and viral entry mechanism(s) of FeMV remain unknown. In this review, we summarize the FeMV studies up to date, including the discoveries of various FeMV strains, basic virology, pathogenicity, and disease signs.

Metagenomics revealing new virus species in farm and pet animals and aquaculture

Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.

Epidemiology, pathological aspects and genome heterogeneity of feline morbillivirus in Italy

Feline morbillivirus (FeMV) is an emerging morbillivirus first described in cats less than a decade ago. FeMV has been associated with chronic kidney disease of cats characterized by tubulointerstitial nephritis (TIN), although this aspect is still controversial and not demonstrated with certainty. To investigate FeMV prevalence and genomic characteristics, an epidemiological survey was conducted in a total number of 127 household cats originating from two Italian regions, Abruzzi and Emilia-Romagna. A total number of 69 cats originating from three feline colonies were also enrolled for the study. Correlation with TIN was investigated by employing a total number of 35 carcasses. Prevalence of FeMV RNA was higher in urine samples collected from cats of colonies (P = 31.8%, CI 95% 22.1-43.6) compared to household cats (P = 8.66%, CI 95% 4.9-14.9) and in young and middle-aged cats while prevalence of FeMV Abs was higher in old cats. Sequences obtained straight from infected biological samples, either partial or complete, cluster into two clades within FeMV genotype 1, distantly related to FeMV genotype 2. Immunohistochemistry analysis of kidney sections of FeMV RNA positive cats revealed immunoreactivity within epithelial cells of renal tubuli and inflammatory cells. However, statistically significant association between FeMV and renal damages, including TIN, was not demonstrated (p= 0.0695, Fisher exact test). By virus histochemistry performed with FeMV-negative feline tissues and a FeMV isolate, tropism for different cellular types such as inflammatory cells residing in blood vessels of kidney and brain, airway epithelial cells, alveolar macrophages and to a lesser extent, the central nervous system, was demonstrated. Additional studies are warranted in order to establish viral tropism and immune response during the early phases of infection and to disentangle the role of FeMV in co-infection processes.

Feline morbillivirus in Northern Italy: prevalence in urine and kidneys with and without renal disease

Feline morbillivirus (FeMV) is an emerging virus that was first described in Hong Kong in 2012. Several reports suggested the epidemiological association of FeMV infection with chronic kidney disease (CKD) in cats. The aim of this study was to investigate the presence and the genetic diversity of FeMV as well as the relationship between FeMV infection and CKD in cats from Northern Italy. Urine (n = 81) and kidney samples (n = 27) from 92 cats admitted to the Veterinary Teaching Hospital of the University of Milan between 2014 and 2017 were investigated for FeMV infection. FeMV RNA was detected in one urine sample (1.23%; 95% CI: 0.03-6.68%) and in two kidneys (7.40%; 95% CI: 0.91-24.28%). FeMV RNA was revealed only in urine or kidneys of cats without evidence of CKD. Phylogenetic analysis showed that the three strains clustered with FeMV strains retrieved from public database, forming a distinct sub-cluster of FeMV. The presence of distinct genotypes of FeMV found in this study is in accordance with previous studies demonstrating that FeMV strains are genetically diverse. A clear relationship between the presence of FeMV infection and CKD in the cats from Northern Italy was not observed, confirming recent reports that do not support the hypothesis that FeMV infection is associated with the development of CKD.

Western Bluetongue virus serotype 3 in Sardinia, diagnosis and characterization

Over the last 20 years, Italy has experienced multiple incursions of different serotypes of Bluetongue virus (BTV), a Culicoides‐borne arbovirus, the causative agent of bluetongue (BT), a major disease of ruminants. The majority of these incursions originated from Northern Africa, likely because of wind‐blown dissemination of infected midges. Here, we report the first identification of BTV‐3 in Sardinia, Italy. BTV‐3 circulation was evidenced in sentinel animals located in the province of Sud Sardegna on September 19, 2018. Prototype strain BTV‐3 SAR2018 was isolated on cell culture. BTV‐3 SAR2018 sequence and partial sequences obtained by next‐generation sequencing from nucleic acids purified from the isolate and blood samples, respectively, were demonstrated to be almost identical (99–100% of nucleotide identity) to BTV‐3 TUN2016 identified in Tunisia in 2016 and 2017, a scenario already observed in past incursions of other BTV serotypes originating from Northern Africa.

Diagnosis and characterization of canine distemper virus through sequencing by MinION nanopore technology

Prompt identification of the causative pathogen of an infectious disease is essential for the choice of treatment or preventive measures. In this perspective, nucleic acids purified from the brain tissue of a dog succumbed after severe neurological signs were processed with the MinION (Oxford Nanopore Technologies, Oxford UK) sequencing technology. Canine distemper virus (CDV) sequence reads were detected. Subsequently, a specific molecular test and immunohistochemistry were used to confirm the presence of CDV RNA and antigen, respectively, in tissues. This study supports the use of the NGS in veterinary clinical practice with potential advantages in terms of rapidity and broad-range of molecular diagnosis.

Antigenic relationship among zoonotic flaviviruses from Italy

Here we report studies of the antigenic relationship of West Nile virus (WNV) and Usutu virus (USUV), two zoonotic flaviviruses from Italy, together with a Japanese encephalitis virus (JEV) strain and compared them with their genetic relationship using the immunodominant viral E protein. Thirty-nine isolates and reference strains were inactivated and used to immunize rabbits to produce hyper immune sera. Serum samples were tested by neutralization against all isolates and results visualized by generating antigenic map. Strains of WNV, USUV, and JEV grouped in separate clusters on the antigenic map. JEV was closer antigenically to USUV (mean of 3.5 Antigenic Unit, AU, equivalent to a 2-fold change in antibody titer) than to WNV strains (mean of 6 AU). A linear regression model predicted, on average, one unit of antigenic change, equivalent to a 2-fold change in antibody titer, for every 22 amino acid substitutions in the E protein ectodomain. Overall, antigenic map was demonstrated to be robust and consistent with phylogeny of the E protein. Indeed, the map provided a reliable means of visualizing and quantifying the relationship between these flaviviruses. Further antigenic analyses employing representative strains of extant serocomplexes are currently underway. This will provide a more in deep knowledge of antigenic relationships between flaviviruses.

Reverse Genetics for Peste des Petits Ruminants Virus: Current Status and Lessons to Learn from Other Non-segmented Negative-Sense RNA Viruses

Peste des petits ruminants (PPR) is a highly contagious transboundary animal disease with a severe socio-economic impact on the livestock industry, particularly in poor countries where it is endemic. Full understanding of PPR virus (PPRV) pathobiology and molecular biology is critical for effective control and eradication of the disease. To achieve these goals, establishment of stable reverse genetics systems for PPRV would play a key role. Unfortunately, this powerful technology remains less accessible and poorly documented for PPRV. In this review, we discussed the current status of PPRV reverse genetics as well as the recent innovations and advances in the reverse genetics of other non-segmented negative-sense RNA viruses that could be applicable to PPRV. These strategies may contribute to the improvement of existing techniques and/or the development of new reverse genetics systems for PPRV.

Identification and genetic characterization of bovine enterovirus by combination of two next generation sequencing platforms

Prompt and accurate diagnosis is warranted for infectious diseases of domestic animals which may have a significant impact on animal production or clinical practice. In this study, the identification and genetic characterization of a bovine enterovirus (BEV) strain isolated from a calf with diarrhea, are described. Two different next generation sequencing platforms were employed. Shotgun metagenomic accomplished by MinION sequencing (Oxford Nanopore Technologies) allowed the identification of BEV RNA from a cell-culture isolate. BEV was then confirmed by a specific real time RT-PCR assay. To achieve the whole genome of this isolate, sequence reads obtained by MinION were coupled with those originating from NextSeq500 (Illumina). Genomic relatedness and phylogeny with extant BEV strains is also reported. Overall, this manuscript highlights the use of the portable MinION sequence technology as a tool for support diagnostics in veterinary practice.

A real-time RT-PCR assay for molecular identification and quantitation of feline morbillivirus RNA from biological specimens

The aim of this study was to develop a real-time RT-PCR to detect and quantitate feline morbillivirus (FeMV) RNA in biological samples. Primers and probe were targeted on a conserved region of FeMV P/V/C gene. To validate the assay with field samples, a total number of specimens of cats have been recruited including 264 urine and blood samples and compared with a generic RT-PCR targeting the L protein encoding gene of morbilliviruses. In addition, 385 tissue samples from 35 carcasses of cats have been also employed. RNA titres were low in all tested samples. Results also indicated the absence of cross-reaction with related morbilliviruses and existing pathogens of cats. In tissues with low levels of FeMV RNA, the presence of viral antigen was also evidenced by immunohistochemistry targeting the N viral protein. This newly described assay allows for a rapid, accurate and reliable quantitative detection of FeMV RNA that can be applied for diagnostics and research studies.

Outbreak of porcine epidemic diarrhoea virus (PEDV) in Abruzzi region, central-Italy

Here we report and characterize a porcine epidemic diarrhea (PED) outbreak which occurred in a swine fattening farm in the province of Teramo, Abruzzi region (central Italy), in January 2016. PED virus (PEDV) identification was determined by real-time RT-PCR performed on RNAs purified from fecal samples collected from two symptomatic pigs. Whole genome sequence (PEDV 1842/2016) was also obtained by next generation sequencing straight from RNA purified from one fecal sample. Genome comparison with extant global PEDV strains revealed a high nucleotide identity with recently reported European and American S-INDEL PEDVs. Efficient sequencing, share of genomic data combined with the implementation of epidemiological tools would be the ideal approach for study and analysis of transboundary infectious diseases as PED.

One after the other: A novel Bluetongue virus strain related to Toggenburg virus detected in the Piedmont region (North-western Italy), extends the panel of novel atypical BTV strains

In this rapid communication, a novel atypical bluetongue virus (BTV) strain detected in goats in the Piedmont region (north-western Italy) is described. This strain, BTV-Z ITA2017, is most related in Seg-2/VP-2 (83.8% nt/82.7% aa) to strain TOV of BTV-25. Reactive antisera of goats positive by cELISA for BTV antibodies failed to neutralize a chimeric virus expressing the outermost protein of TOV. Infected animals displayed low levels of RNAemia and absence of clinical signs consistent with bluetongue infection, a scenario described in animals infected with atypical BTV strains.

Novel putative Bluetongue virus in healthy goats from Sardinia, Italy

In recent years, novel Bluetongue virus (BTV) serotypes have been isolated and/or sequenced by researchers within the field. During Bluetongue surveillance activities, we identified a putative novel BTV serotype in healthy goats from Sardinia, Italy. RNAs purified from blood and serum samples were positive for BTV by a generic real time RT-PCR and c-ELISA, respectively, whereas genotyping and serotyping were unsuccessful. By NGS, the whole genome sequence was obtained from two blood samples (BTV-X ITL2015 strains 34200 and 33531). Overall, Seg 2 of BTV-X ITL2015 shows the highest identity (75.3-75.5% nt/77.4-78.1% aa) with recently isolated BTV-27s from Corsica and with the last discovered BTV XJ1407 from China (75.9% nt /78.2% aa), whereas it is less related with BTV-25 from Switzerland (73.0% nt/75.0% aa) and BTV-26 from Kuwait (62.0% nt/60.5% aa). A specific RT-qPCR targeting Seg 2 of BTV-X ITL2015 was assessed in this study. Considering the Seg 2/VP2 identity of BTV-X ITL2015 with BTV-25, 26, 27s and BTV XJ1407 and that serum of BTV-X ITL2015 infected goats failed to neutralize all tested extant serotypes, we propose the existence of a novel BTV serotype circulating in goats in Sardinia. Isolation was so far unsuccessful thus hampering proper antigenic characterization.

A novel Bluetongue virus serotype 3 strain in Tunisia, November 2016

Since 1998, southern Europe has experienced multiple incursions of different serotypes and topotypes of Bluetongue virus, a vector-borne transmitted virus, the causative agent of Bluetongue (BT), a major disease of ruminants. Some of these incursions originated from northern Africa, likely because of wind-blown dissemination of infected midges. In this report, we describe the detection and whole genome characterization of a novel BTV-3 strain identified in a symptomatic sheep in Tunisia. Sequences were immediately deposited with the GenBank Database under Accession Nos KY432369-KY432378. Alert and preparedness are requested to face the next vector seasons in northern Africa and the potential incursion of this novel strain in southern Europe.

Lethal distemper in badgers (Meles meles) following epidemic in dogs and wolves

Canine distemper virus (CDV) represents an important conservation threat to many wild carnivores. A large distemper epidemic sustained by an Arctic-lineage strain occurred in Italy in 2013, mainly in the Abruzzi region, causing overt disease in domestic and shepherd dogs, Apennine wolves (Canis lupus) and other wild carnivores. Two badgers were collected by the end of September 2015 in a rural area of the Abruzzi region and were demonstrated to be CDV-positive by real time RT-PCR and IHC in several tissues. The genome of CDV isolates from badgers showed Y549H substitution in the mature H protein. By employing all publicly available Arctic-lineage H protein encoding gene sequences, six amino acid changes in recent Italian strains with respect to Italian strains of dogs from 2000 to 2008, were observed. A CDV strain belonging to the European-wildlife lineage was also identified in a fox found dead in the same region in 2016, proving co-circulation of an additional CDV lineage.

Epidemiological and pathological study of feline morbillivirus infection in domestic cats in Japan

BACKGROUND

Feline morbillivirus (FmoPV) is a novel paramyxovirus found to infect domestic cats. FmoPV has been isolated in several countries in Asia and Europe and is considered to have genetic diversity. Also, it is suspected to be associated with feline renal diseases including tubulointerstitial nephritis (TIN), which affects domestic cats with a high incidence rate.

RESULTS

To clarify the state of FmoPV infection among domestic cats in Japan, an epidemiological survey was conducted. Twenty-one out of 100 cats were found to have serum antibodies (Ab) against FmoPV-N protein by indirect immunofluorescence assay (IF) using FmoPV-N protein-expressing HeLa cells. Twenty-two of the cats were positive for FmoPV RNA in the urine and/or renal tissues. In total, 29 cats were positive for Ab and/or viral RNA. These FmoPV-infected cats were classified into three different phases of infection: RNA+/Ab + (14 cats), RNA+/Ab- (8 cats) and RNA-/Ab + (7 cats). In immunohistochemistry (IHC), 19 out of 29 cats were positive for FmoPV-N protein in kidney tissues; however, the FmoPV-N protein was located in the inflammatory lesions with severe grade in only four out of the 19 cats. Since 15 out of 29 infected cats were positive for viral RNA and Ab, approximately half of the infected cats were persistently infected with FmoPV.

CONCLUSIONS

A statistically significant difference was observed between infection of FmoPV and the presence of inflammatory changes in renal lesions, indicating a relationship between FmoPV infection and feline renal diseases. However, we could not obtain histopathological evidence of a relationship between FmoPV infection and TIN.

Discovery and current research status of feline morbillivirus

Feline morbillivirus (FeMV) is an emerging virus that was first discovered in Hong Kong in 2012. FeMV is epidemiologically associated with kidney and other lower urinary tract diseases in cats. Phylogenetic analysis of its genome sequence indicates that FeMV is the most closely related to the members of genus morbillivirus, although FeMV is relatively distant in the phylogenetic analysis, and its target tissues and pathogenicity are different from the other members of the genus. The origin and routes of dissemination of FeMV are not clear since genetic types are not always correlated to the geographical distribution of the isolates. Since the discovery of the virus, several reports showed the epidemiological association of FeMV infection with kidney and lower urinary tract diseases in cats. However, the pathogenicity of FeMV is not clear yet due to paucity of the isolated virus strains and chronic nature of the subjected diseases. Diagnosis of FeMV infection has been performed using both nucleic acid and serological methods. However, there are no standard diagnostic methods to detect antibodies against FeMV, which will be useful to study epidemiology and pathogenicity of FeMV. Besides FeMV is an interesting subject as an additional member to the morbilliviruses possessing unusual characteristics comparing to the other morbilliviruses, further studies of FeMV is important in the veterinary field since it may lead to new therapies or prevention of chronic kidney diseases of cats.