TNF-Mediated Inhibition of Classical Swine Fever Virus Replication Is IRF1-, NF-κB- and JAK/STAT Signaling-Dependent.

The sera from pigs infected with virulent classical swine fever virus (CSFV) contain substantial amounts of tumor necrosis factor (TNF), a prototype proinflammatory cytokine with pleiotropic activities. TNF limits the replication of CSFV in cell culture. In order to investigate the signaling involved in the antiviral activity of TNF, we employed small-molecule inhibitors to interfere specifically with JAK/STAT and NF-κB signaling pathways in near-to-primary endothelial PEDSV.15 cells. In addition, we knocked out selected factors of the interferon (IFN) induction and signaling pathways using CRISPR/Cas9. We found that the anti-CSFV effect of TNF was sensitive to JAK/STAT inhibitors, suggesting that TNF induces IFN signaling. Accordingly, we observed that the antiviral effect of TNF was dependent on intact type I IFN signaling as PEDSV.15 cells with the disrupted type I IFN receptor lost their capacity to limit the replication of CSFV after TNF treatment. Consequently, we examined whether TNF activates the type I IFN induction pathway. With genetically modified PEDSV.15 cells deficient in functional interferon regulatory factor 1 or 3 (IRF1 or IRF3), we observed that the anti-CSFV activity exhibited by TNF was dependent on IRF1, whereas IRF3 was dispensable. This was distinct from the lipopolysaccharide (LPS)-driven antiviral effect that relied on both IRF1 and IRF3. In agreement with the requirement of IRF1 to induce TNF- and LPS-mediated antiviral effects, intact IRF1 was also essential for TNF- and LPS-mediated induction of IFN-ß mRNA, while the activation of NF-κB was not dependent on IRF1. Nevertheless, NF-κB activation was essential for the TNF-mediated antiviral effect. Finally, we observed that CSFV failed to counteract the TNF-mediated induction of the IFN-ß mRNA in PEDSV.15 cells, suggesting that CSFV does not interfere with IRF1-dependent signaling. In summary, we report that the proinflammatory cytokine TNF limits the replication of CSFV in PEDSV.15 cells by specific induction of an IRF1-dependent antiviral type I IFN response.

Detection and Genome Sequencing of SARS-CoV-2 in a Domestic Cat with Respiratory Signs in Switzerland.

Since the emergence of coronavirus disease (COVID-19) in late 2019, domestic cats have been demonstrated to be susceptible to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) under natural and experimental conditions. As pet cats often live in very close contact with their owners, it is essential to investigate SARS-CoV-2 infections in cats in a One-Health context. This study reports the first SARS-CoV-2 infection in a cat in a COVID-19-affected household in Switzerland. The cat (Cat 1) demonstrated signs of an upper respiratory tract infection, including sneezing, inappetence, and apathy, while the cohabiting cat (Cat 2) remained asymptomatic. Nasal, oral, fecal, fur, and environmental swab samples were collected twice from both cats and analyzed by RT-qPCR for the presence of SARS-CoV-2 viral RNA. Both nasal swabs from Cat 1 tested positive. In addition, the first oral swab from Cat 2 and fur and bedding swabs from both cats were RT-qPCR positive. The fecal swabs tested negative. The infection of Cat 1 was confirmed by positive SARS-CoV-2 S1 receptor binding domain (RBD) antibody testing and neutralizing activity in a surrogate assay. The viral genome sequence from Cat 1, obtained by next generation sequencing, showed the closest relation to a human sequence from the B.1.1.39 lineage, with one single nucleotide polymorphism (SNP) difference. This study demonstrates not only SARS-CoV-2 infection of a cat from a COVID-19-affected household but also contamination of the cats' fur and bed with viral RNA. Our results are important to create awareness that SARS-CoV-2 infected people should observe hygienic measures to avoid infection and contamination of animal cohabitants.

Potential mechanical transmission of Lumpy skin disease virus (LSDV) by the stable fly (Stomoxys calcitrans) through regurgitation and defecation.

Lumpy skin disease (LSD) is a viral disorder of cattle caused by the lumpy skin disease virus (LSDV) which can induce severe infections leading to high economic losses. Being of African origin, the first LSD outbreaks in Europe occurred in Greece and later in the Balkan region. Little is known about the mode of transmission, especially in relation to the potential role of arthropods vectors. The purpose of our study was to investigate the role of Stomoxys calcitrans in the transmission of LSDV and their presence at different farms in Switzerland. Laboratory-reared flies were exposed to LSDV spiked-blood and incubated under a realistic fluctuating temperature regime. Body parts, regurgitated blood, and faecal samples were analysed by qPCR for the presence of viral DNA and infectious virus at different time points post-feeding (p.f.). LSDV DNA was detected in heads, bodies, and regurgitated blood up to three days p.f. and up to two days p.f. in the faeces. Infectious virus was isolated from bodies and faeces up to two days and in the regurgitated blood up to 12 h p.f. There was no increase in viral load, consolidating the role of S. calcitrans as mechanical vectors for LSDV. Stomoxys flies were present at all eight farms investigated, including a farm located at 2128 m asl. The persistence of LSDV in S. calcitrans in combination with the long flight ranges of this abundant and widespread fly might have implications on LSD epidemiology and on implementing control measures during disease outbreaks.

Long-Term Circulation of Atypical Porcine Pestivirus (APPV) within Switzerland.

In 2015, a new pestivirus was described in pig sera in the United States. This new "atypical porcine pestivirus" (APPV) was later associated with congenital tremor (CT) in newborn piglets. The virus appears to be distributed worldwide, but the limited knowledge of virus diversity and the use of various diagnostic tests prevent direct comparisons. Therefore, we developed an APPV-specific real-time RT-PCR assay in the 5'UTR of the viral genome to investigate both retro- and prospectively the strains present in Switzerland and their prevalence in domestic pigs. Overall, 1080 sera obtained between 1986 and 2018 were analyzed, revealing a virus prevalence of approximately 13% in pigs for slaughter, whereas it was less than 1% in breeding pigs. In the prospective study, APPV was also detected in piglets displaying CT. None of the samples could detect the Linda virus, which is another new pestivirus recently reported in Austria. Sequencing and phylogenetic analysis revealed a broad diversity of APP viruses in Switzerland that are considerably distinct from sequences reported from other isolates in Europe and overseas. This study indicates that APPV has already been widely circulating in Switzerland for many years, mainly in young animals, with 1986 being the earliest report of APPV worldwide.

Genetic stability of Schmallenberg virus in vivo during an epidemic, and in vitro, when passaged in the highly susceptible porcine SK-6 cell line.

Schmallenberg virus (SBV), an arthropod-borne orthobunyavirus was first detected in 2011 in cattle suffering from diarrhea and fever. The most severe impact of an SBV infection is the induction of malformations in newborns and abortions. Between 2011 and 2013 SBV spread throughout Europe in an unprecedented epidemic wave. SBV contains a tripartite genome consisting of the three negative-sense RNA segments L, M, and S. The virus is usually isolated from clinical samples by inoculation of KC (insect) or BHK-21 (mammalian) cells. Several virus passages are required to allow adaptation of SBV to cells in vitro. In the present study, the porcine SK-6 cell line was used for isolation and passaging of SBV. SK-6 cells proved to be more sensitive to SBV infection and allowed to produce higher titers more rapidly as in BHK-21 cells after just one passage. No adaptation was required. In order to determine the in vivo genetic stability of SBV during an epidemic spread of the virus the nucleotide sequence of the genome from seven SBV field isolates collected in summer 2012 in Switzerland was determined and compared to other SBV sequences available in GenBank. A total of 101 mutations, mostly transitions randomly dispersed along the L and M segment were found when the Swiss isolates were compared to the first SBV isolated late 2011 in Germany. However, when these mutations were studied in detail, a previously described hypervariable region in the M segment was identified. The S segment was completely conserved among all sequenced SBV isolates. To assess the in vitro genetic stability of SBV, three isolates were passage 10 times in SK-6 cells and sequenced before and after passaging. Between two and five nt exchanges per genome were found. This low in vitro mutation rate further demonstrates the suitability of SK-6 cells for SBV propagation.

Long-term infection of goats with bluetongue virus serotype 25.

Toggenburg Orbivirus (TOV) is the prototype of bluetongue virus serotype 25 (BTV-25). It was first detected in goats in Switzerland in 2008. The virus does not induce clinical signs in infected goats. In field samples viral RNA could be detected only in goats and never in other ruminants. BTV-25 RNA was repeatedly detected for more than one year in the blood of goats from a single flock in Principality of Liechtenstein. Since viral persistence over such a long period has never been reported for bluetongue, blood samples from 110 goats and 2 sheep of that flock were collected during a period of up to two years and analyzed for the presence of BTV-25 RNA and antibodies. Most of the animals which tested positive for BTV-25 RNA, remained positive during the whole investigation period. Moreover, five of these goats were BTV-25 RNA positive over a period of 19-25 months. A weak antibody response against BTV VP7 was commonly observed. As BTV-25 cannot be propagated in any culture system, the presence of virus could only be demonstrated in samples by viral RNA detection using RT-qPCR. To address the question of infectivity of the virus in blood from long-term positive animals, goats were experimentally infected with this blood. Viral replication was demonstrated by increasing RNA amounts. Thus, our findings provide evidence that BTV-25 can persist much longer in an infected host than known so far for other BTV serotypes. Hence, persistence of infectious BTV represents an additional important factor in BTV epidemiology.

Epidemiology of avian influenza virus in wild birds in Switzerland between 2006 and 2009.

After the spread of H5N1 highly pathogenic avian influenza virus (AIV) from Asia into Russia, the Middle East, Europe, and Africa in 2005-06, the Swiss national AIV surveillance program was extended. One of the new focal points was Lake Constance, where sentinel duck stations and swim-in traps were established within the project Constanze in collaboration with Germany and Austria. More than 2000 samples from 41 species were collected in Switzerland between September 2006 and December 2008. Approximately 4% were AIV-positive by quantitative reverse transcriptase-PCR. Subsequent typing revealed 13 different AIV subtypes, of which H5N2 and H9N2 were the most prevalent. All H7 isolates and all but one H5 isolate were characterized as low pathogenic; however, a highly pathogenic H5N1 AIV was detected in a healthy pochard. This study demonstrates that a wide selection of different AIV subtypes can cocirculate among the waterfowl population in wild bird habitats.

Detection of Toggenburg Orbivirus by a segment 2-specific quantitative RT-PCR.

Toggenburg Orbivirus (TOV) has been detected recently in healthy goats in Switzerland. The virus is related closely to bluetongue virus (BTV) and is considered tentatively as a 25th serotype of BTV. Upon detection of additional TOV-positive goats in Switzerland, Germany, and Italy, these TOV isolates were characterized genetically by partial sequencing of the viral genome segment 2 which encodes VP2, the major outer capsid protein of orbiviruses. A TOV-specific RT-qPCR was developed, targeting conserved areas within segment 2. Since TOV cannot be propagated up to now outside its natural host, a synthetic positive control for the RT-qPCR was constructed by cloning the entire coding region of segment 2 and subsequent in vitro transcription of RNA from both ends to obtain double-stranded RNA. The TOV-specific RT-qPCR was able to detect as few as 30 dsRNA copies and proved to be equally sensitive as a pan BTV assay that was shown previously to have a detection limit of 0.001 TCID(50).

Antigenic characterization of recombinant hemagglutinin proteins derived from different avian influenza virus subtypes.

Since the advent of highly pathogenic variants of avian influenza virus (HPAIV), the main focus of avian influenza research has been the characterization and detection of HPAIV hemagglutinin (HA) from H5 and H7 subtypes. However, due to the high mutation and reassortation rate of influenza viruses, in theory any influenza strain may acquire increased pathogenicity irrespective of its subtype. A comprehensive antigenic characterization of influenza viruses encompassing all 16 HA and 9 neuraminidase subtypes will provide information useful for the design of differential diagnostic tools, and possibly, vaccines. We have expressed recombinant HA proteins from 3 different influenza virus HA subtypes in the baculovirus system. These proteins were used to generate polyclonal rabbit antisera, which were subsequently employed in epitope scanning analysis using peptide libraries spanning the entire HA. Here, we report the identification and characterization of linear, HA subtype-specific as well as inter subtype-conserved epitopes along the HA proteins. Selected subtype-specific epitopes were shown to be suitable for the differentiation of anti-HA antibodies in an ELISA.

Genetic characterization of toggenburg orbivirus, a new bluetongue virus, from goats, Switzerland.

A novel bluetongue virus (BTV) termed Toggenburg orbivirus (TOV) was detected in goats from Switzerland by using real-time reverse transcription-PCR. cDNA corresponding to the complete sequence of 7 of 10 double-stranded RNA segments of the viral genome was amplified by PCR and cloned into a plasmid vector. Five clones for each genome segment were sequenced to determine a consensus sequence. BLAST analysis and dendrogram construction showed that TOV is closely related to BTV, although some genome segments are distinct from the 24 known BTV serotypes. Maximal sequence identity to any BTV ranged from 63% (segment 2) to 79% (segments 7 and 10). Because the gene encoding outer capsid protein 2 (VP2), which determines the serotype of BTV, is placed within the BTV serogroup, we propose that TOV represents an unknown 25th serotype of BTV.

Phylogenetic characterization of H5N1 highly pathogenic avian influenza viruses isolated in Switzerland in 2006.

In the winter 2005/2006 H5N1 highly pathogenic avian influenza virus (HPAIV) reached Western Europe and caused numerous deaths primarily in migratory water birds. Between February and April 2006 34 cases of H5N1 HPAIV-infected dead water fowl were identified in Switzerland, almost exclusively occurring in the Lake Constance area, a large overwintering area for migratory birds in the eastern part of the country. In total, 13 of these virus isolates were genetically characterized in the present study by full-length nucleotide sequence analysis of the hemagglutinin and neuraminidase-coding region. All viruses could be confirmed as HPAIV based on the amino acid sequence of their hemagglutinin cleavage site. Phylogenetic analysis revealed that all the virus isolates were highly similar to each other and to other H5N1 strains found in neighboring countries. All analyzed Swiss virus isolates belonged to the influenza virus subclade 2.2.1.

Chimeric pestiviruses: candidates for live-attenuated classical swine fever marker vaccines.

The use of attenuated classical swine fever virus (CSFV) strains as live vaccines is no longer allowed for the control of classical swine fever in Europe, due to the inability to differentiate between infected and vaccinated animals (Differentiating Infected from Vaccinated Animals; DIVA), except as emergency vaccines or as bait vaccines for wild boars. Thus, the establishment of a DIVA vaccine(s) is of pivotal importance for the control of this infectious disease. In this study, recombinant versions of the live-attenuated vaccine strain CSFV Riems were generated by replacing parts of the E2 gene with the corresponding sequence of border disease virus strain Gifhorn. Three cDNA clones were constructed: pRiems-ABC-Gif, pRiems-A-Gif and pRiems-BC-Gif. Infectious particles were obtained from clones pRiems-ABC-Gif and pRiems-BC-Gif only, whereas transfected RNA from clone pRiems-A-Gif behaved like a replicon. Based on its ability to be differentiated in vitro from wild-type CSFV by mAbs, vRiems-ABC-Gif was assessed for immunogenicity and protection against challenge infection in pigs. Before challenge, no CSFV-specific anti-E2 antibodies could be detected with commercial E2-blocking ELISAs in vRiems-ABC-Gif-vaccinated animals, whereas vRiems-vaccinated pigs developed high titres of anti-E2 antibodies, confirming the marker properties of this vaccine candidate. After oral vaccination, only partial protection against challenge infection was observed in the vRiems-ABC-Gif vaccinees, whereas all intramuscularly vaccinated animals and all vRiems-vaccinated animals were fully protected. These experiments suggest that the strategy of exchanging specific antigenic epitopes among pestiviruses is a promising tool for the development of new CSFV marker vaccines.