Genetic typing of classical swine fever virus

Pathogenicity and Genetic Characterization of Vietnamese Classical Swine Fever Virus: 2014-2018

Here, we examined the pathogenicity and genetic differences between classical swine fever viruses (CSFV) isolated on pig farms in North Vietnam from 2014–2018. Twenty CSFV strains from 16 pig farms were classified as genotype 2 (sub-genotypes 2.1b, 2.1c, and 2.2). The main sub-genotype, 2.1c, was classified phylogenetically as belonging to the same cluster as viruses isolated from the Guangdong region in South China. Strain HY58 (sub-genotype 2.1c), isolated from pigs in Vietnam, caused higher mortality (60%) than the Vietnamese ND20 strain (sub-genotype 2.2). The Vietnamese strain of sub-genotype 2.1b was estimated to have moderate virulence; indeed, genetic analysis revealed that it belongs to the same cluster as Korean CSFV sub-genotype 2.1b. Most CSFVs circulating in North Vietnam belong to sub-genotype 2.1c. Geographical proximity means that this genotype might continue to circulate in both North Vietnam and Southern China (Guangdong, Guangxi, and Hunan).

Identification of E2 with improved secretion and immunogenicity against CSFV in piglets

BACKGROUND

Outbreaks of Classical swine fever virus (CSFV) cause significant economic losses in the swine industry. Vaccination is the major method to prevent and control the disease. As live attenuated vaccines fail to elicit differentiable immunity between infected and vaccinated animals, subunit vaccine was considered as an alternative candidate to prevent and eradicate CSFV. Subunit vaccines present advantages in DIVA immunogenicity and safety. The technology was limited due to the low yield and the high cost with multiple and large doses. The native E2 signal peptide has not been well defined before. Here, the aim of this study is to develop a cost-effective and efficacious E2 vaccine candidate against CSFV with signal peptide and E2 sequence selection.

RESULTS

A novel CSFV E2 sequence (E2ZJ) was identified from an epidemic strain of Zhejiang for outstanding secretion in baculovirus and enhanced immunogenicity. E2 secretion induced with the selected signal peptide, SPZJ (SP23), increase at least 50% as compared to any other signal peptides tested. Besides, unique antigenic features were identified in E2ZJ. As indicated with immunized sera in IFA against CSFV infection, E2ZJ elicited CSFV antibodies at the earlier stage than other E2 types tested in mice. Moreover, higher level of neutralizing and CSFV antibodies against CSFV with E2ZJ was detected than other E2s with the same dosage at 28 dpi. Further, E2ZJ successfully elicited neutralizing immunity in piglets. A single dose of 5 μg of E2ZJ was sufficient to induce protective antibodies against CSFV in piglets and provided 100% protection against lethal virus challenge.

CONCLUSIONS

Our studies provide evidence that E2ZJ guided by a novel E2 signal peptide (SPZJ) was efficiently secreted and presented significantly improved immunogenicity than conventional E2 vaccines. Moreover, a single dose of 5 μg E2ZJ is efficacious against CSFV in piglets.

The potential efficacy of the E2-subunit vaccine to protect pigs against different genotypes of classical swine fever virus circulating in Vietnam

Purpose

To date, many kinds of classical swine fever (CSF) vaccines have been developed to protect against this disease. However, the efficacy of these vaccines to protect the pig against field CSF strains needs to be considered, based on circulating strains of classical swine fever virus (CSFV).

Materials and Methods

Recombinant E2-CSFV protein produced by baculovirus/insect cell system was analyzed by western blots and immunoperoxidase monolayer assay. The effect of CSFV-E2 subunit vaccines was evaluated in experimental pigs with three genotypes of CSFV challenge. Anti-E2 specific and neutralizing antibodies in experimental pigs were analyzed by blocking enzyme-linked immunosorbent assay and neutralization peroxidize-linked assay.

Results

The data showed that CSFV VN91-E2 subunit vaccine provided clinical protection in pigs against three different genotypes of CSFV without noticeable clinical signs, symptoms, and mortality. In addition, no CSFV was isolated from the spleen of the vaccinated pigs. However, the unvaccinated pigs exhibited high clinical scores and the successful virus isolation from spleen. These results showed that the E2-specific and neutralizing antibodies induced by VN91-E2 antigen appeared at day 24 after first boost and a significant increase was observed at day 28 (p<0.01). This response reached a peak at day 35 and continued until day 63 when compared to controls. Importantly, VN91-E2 induced E2-specific and neutralizing antibodies protected experimental pigs against high virulence of CSFVs circulating in Vietnam, including genotype 1.1, 2.1, and 2.2.

Conclusion

These findings also suggested that CSFV VN91-E2 subunit vaccine could be a promising vaccine candidate for the control and prevention of CSFV in Vietnam.

Selection and Characterization of CSFV-Specific Single-Domain Antibodies and Their Application along with Immunomagnetic Nanobeads and Quantum Dots

Outbreak of classical swine fever (CSF) results in high mortality and thus causes severe economic losses in the swine industry. Single-domain antibody (sdAb) is the smallest antigen-binding molecule derived from camelid heavy-chain antibodies and has the potential to be used as a molecular probe for detection of CSF virus (CSFV). In this study, two sdAb fragments against the E2 antigen of CSFV were obtained, expressed in vitro. The functional characteristics analysis indicated that the recombinant sdAbE2-1 and sdAbE2-2 have excellent binding activity, specificity, and high affinity with equilibrium constant value of 3.34 × 10⁻⁷ and 1.35 × 10⁻⁸ M to E2 protein. Then, sdAbE2s were conjugated with quantum dots (QD)/AF488 to synthesize two molecular probes for imaging CSFV distribution in cells. The sdAbE2-1 was also labeled with carboxyl-magnetic beads to construct immunomagnetic nanobeads (IMNBs) able to capture CSFV virions and recombinant E2 protein. QD/AF455-sdAbE2s probes colocalised with CSFV virions in swine testis cells, and IMNBs were used as a detection template and proved to bind specifically with CSFV virions and E2 protein. The selected sdAb fragments and sdAb-based molecular probes may be used for the rapid identification of CSFV during field outbreaks and for research on CSFV and host interactions.

Impact of a Live Attenuated Classical Swine Fever Virus Introduced to Jeju Island, a CSF-Free Area

Here, we examine the effects of LOM(Low virulence of Miyagi) strains isolated from pigs (Jeju LOM strains) of Jeju Island, where vaccination with a live attenuated classical swine fever (CSF) LOM vaccine strain was stopped. The circulation of the Jeju LOM strains was mainly caused by a commercial swine erysipelas (Erysipelothrix rhusiopathiae) vaccine mixed with a LOM vaccine strain, which was inoculated into pregnant sows of 20 pig farms in 2014. The Jeju LOM strain was transmitted to 91 pig farms from 2015 to 2018. A histopathogenic investigation was performed for 25 farms among 111 farms affected by the Jeju LOM strain and revealed pigs infected with the Jeju LOM strain in combination with other pathogens, which resulted in the abortion of fetuses and mortality in suckling piglets. Histopathologic examination and immunohistochemical staining identified CSF-like lesions. Our results also confirm that the main transmission factor for the Jeju LOM strain circulation is the vehicles entering/exiting farms and slaughterhouses. Probability estimates of transmission between cohabiting pigs and pigs harboring the Jeju LOM strain JJ16LOM-YJK08 revealed that immunocompromised pigs showed horizontal transmission (r = 1.22). In a full genome analysis, we did not find genetic mutation on the site that is known to relate to pathogenicity between Jeju LOM strains (2014–2018) and the commercial LOM vaccine strain. However, we were not able to determine whether the Jeju LOM strain (2014–2018) is genetically the same virus as those of the commercial LOM vaccine due to several genetic variations in structure and non-structure proteins. Therefore, further studies are needed to evaluate the pathogenicity of the Jeju LOM strain in pregnant sow and SPF pigs and to clarify the characteristics of Jeju LOM and commercial LOM vaccine strains.

Role of Wild Boar in the Spread of Classical Swine Fever in Japan

Since September 2018, nearly 900 notifications of classical swine fever (CSF) have been reported in Gifu Prefecture (Japan) affecting domestic pig and wild boar by the end of August 2019. To determine the epidemiological characteristics of its spread, a spatio-temporal analysis was performed using actual field data on the current epidemic. The spatial study, based on standard deviational ellipses of official CSF notifications, showed that the disease likely spread to the northeast part of the prefecture. A maximum significant spatial association estimated between CSF notifications was 23 km by the multi-distance spatial cluster analysis. A space-time permutation analysis identified two significant clusters with an approximate radius of 12 and 20 km and 124 and 98 days of duration, respectively. When the area of the identified clusters was overlaid on a map of habitat quality, approximately 82% and 75% of CSF notifications, respectively, were found in areas with potential contact between pigs and wild boar. The obtained results provide information on the current CSF epidemic, which is mainly driven by wild boar cases with sporadic outbreaks on domestic pig farms. These findings will help implement control measures in Gifu Prefecture.

U18666A inhibits classical swine fever virus replication through interference with intracellular cholesterol trafficking

The level of cholesterol in host cells has been demonstrated to affect viral infection. Our previous studies showed that cholesterol-rich membrane rafts mediated the entry of classical swine fever virus (CSFV) into PK-15 or 3D4/21 cells, but the role of cholesterol post entry was still not clear. In this study, we found that CSFV replication before fusion was affected when the cholesterol trafficking in infected cells was disrupted using a cholesterol transport inhibitor, U18666A. Our data showed that U18666A affected both the fusion and replication steps in the life cycle of the virus, but not its binding and entry steps. The subsequent experiments confirmed that niemann-pick C1 (NPC1), a lysosomal membrane protein that helps cholesterol to leave the lysosome, was affected by U18666A, which led to the accumulation of cholesterol in lysosomes and inhibition of CSFV replication. Imipramine, a cationic hydrophobic amine similar to U18666A, also inhibited CSFV replication via similar mechanism. Surprisingly, the antiviral effect of U18666A was restored by the histone deacetylase inhibitor (HDACi), Vorinostat, which suggested that HDACi reverted the dysfunction of NPC1, and intra-cellular cholesterol accumulation disappeared and CSFV replicability resumed. Together, these data indicated that CSFV transformed from early endosome and late endosome into lysosome after endocytosis for further replication and that U18666A was a potential drug candidate for anti-pestivirus treatment.

Prevalence of porcine circovirus type 3 in pigs in the southeastern Chinese province of Zhejiang

Background

Porcine circovirus type 3 (PCV3) was first reported in US in 2016. The virus was also identified later in China. Prevalence of PCV3 in Zhejiang province in southeastern China is not clear though it has been reported in many parts of China.

Results

PCV3 infection and its co-infection with other swine viral pathogens in pig herds of Zhejiang province were retrospectively investigated by quantitative PCR (qPCR) and its sero-prevalence by indirect ELISA. PCV3 was found positive in 67.1% of the 283 clinical samples taken from 2014 to 2017 as shown by qPCR. Single infection with PCV3 accounted for only one-third of the samples, and majority were of co-infections, predominantly with PEDV (41.6%) but generally low with other swine viruses. Indirect ELISA using the PCV3 capsid protein as the coating antigen revealed an average sero-positive rate of 52.6% (40.8 to 60.8%) in 2345 serum samples from 2011 to 2017, with earliest yet high positive findings in samples taken in 2012. Of 203 serum samples, the qPCR method showed more positive findings than ELISA (81.3% vs 56.2%). With 89 serum samples negative by ELISA, vast majority (n = 81) were found positive by qPCR. There was negative correlation in levels of PCV3 DNA and anti-capsid antibody response. ORF2-based phylogenetic analysis revealed three major groups (PCV3a, PCV3b and PCV3c) of the 200 strains, 38 from this study and 162 reference strains from GenBank. Most of the strains from this study were clustered into PCV3c. Of the putative signature residues of the capsid protein (aa 24, 27, 77 and 150) relative to the three groups, only the PCV3a group strains showed a distinct pattern of residues VKSI (95% of the strains), while the other two groups did not have such a ‘signature’ pattern.

Conclusions

Results from this study provided further evidence that the novel virus PCV3 was widely distributed in China and might have emerged in Zhejiang province before 2014, most probably back in 2012 when there was high PCV3 sero-prevalence. PCV3 might be viremic in pigs and could spread by fecal shedding.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1977-7) contains supplementary material, which is available to authorized users.

Experimental infection of pigs with a classical swine fever virus isolated in Japan for the first time in 26 years

Following an outbreak of classical swine fever (CSF) in Japan, 2018, CSFV JPN/1/2018 was isolated from an infected pig sample. In this study, we carried out a comparative experimental infection in pigs using this strain and the highly virulent ALD strain and compared outcomes, including clinical manifestation, virus shedding patterns and antibody responses. Although pigs inoculated orally or intramuscularly with JPN/1/2018 developed hyperthermia and had decreased leucocyte numbers, they survived for the whole experimental period and showed less severe clinical signs than those infected with the ALD strain. We confirmed the presence of characteristic multifocal infarction of the margin of the spleen that arises following infection with JPN/1/2018, albeit that this finding was not observed in all infected pigs. Both viruses efficiently spread to contact pigs in a similar manner, suggesting in transmissibility between the two strains. Viral RNAs were detected in all clinical samples, especially whole blood samples, before the pigs developed hyperthermia until at least approximately 2 weeks after inoculation. Our findings will be valuable for the investigations into epidemic events occurring in Japan and for establishing diagnostic strategies and control measures against CSF.

Classical Swine Fever in China-An Update Minireview

Classical swine fever (CSF) remains one of the most economically important viral diseases of domestic pigs and wild boar worldwide. The causative agent is CSF virus, it is highly contagious, with high morbidity and mortality rates; as such, it is an OIE-listed disease. Owing to a nationwide policy of vaccinations of pigs, CSF is well-controlled in China, with large-scale outbreaks rarely seen. Sporadic outbreaks are however still reported every year. In order to cope with future crises and to eradicate CSF, China should strengthen and support biosecurity measures such as the timely reporting of suspected disease, technologies for reliable diagnoses, culling infected herds, and tracing possible contacts, as well as continued vaccination and support of research into drug and genetic therapies. This mini-review summarizes the epidemiology of and control strategies for CSF in China.

Complete Genome Sequences of Classical Swine Fever Virus Subgenotype 2.1 and 2.2 Strains Isolated from Vietnamese Pigs

Classical swine fever virus (CSFV) strains ND20 and HY78 were detected from infected pigs in the Xuan Truong-Nam Dinh and Hung Yen provinces in North Vietnam in 2014 and 2015, respectively. The most prevalent CSFV subgenotypes in Vietnam are 2.1 and 2.2, and these two complete genome sequences will help the CSFV prevention policy in Vietnam.

Classical swine fever virus (CSFV) strains ND20 and HY78 were detected from infected pigs in the Xuan Truong-Nam Dinh and Hung Yen provinces in North Vietnam in 2014 and 2015, respectively. The most prevalent CSFV subgenotypes in Vietnam are 2.1 and 2.2, and these two complete genome sequences will help the CSFV prevention policy in Vietnam. In particular, subgenotype 2.2 (ND20 strain) has been reported less worldwide, so it is worth sharing information about this subgenotype.

Genome Sequence of Classical Swine Fever Virus NIVEDI-165, Subtype 1.1, a Field Virus Strain Isolated from the Southern Part of India

The whole-genome sequence of an Indian field isolate of classical swine fever virus, NIVEDI-165, was found to be subtype 1.1, and it showed 89 to 99% amino acid identity and 84 to 99% nucleotide identity with four and five Indian classical swine fever virus (CSFV) isolates, respectively. To the best of our knowledge, this is the first report on a full-genome sequence of CSFV from South India.

Virulence evaluation of classical swine fever virus subgenotype 2.1 and 2.2 isolates circulating in China

Classical swine fever (CSF) remains an important pig disease in China, where it usually presents with mild or atypical clinical manifestations, with large scale outbreaks rarely seen. This has led to speculation about the possible circulation of viral strains of low virulence. To investigate this possibility, five field isolates within the predominant genotype 2 (2.1b, 2.1c, 2.1 h and 2.2) were evaluated and compared by experimental infection of naturally farrowed but colostrum-deprived piglets. All infected piglets displayed clinical signs, including persistent high fever, depression, anorexia, dyspnea, conjunctivitis, constipation, and hesitant gait. Typical pathological lesions, including pulmonary edema, hemorrhagic or cellulosic exudation, and swelling and hemorrhage of lymph nodes, were observed. Viremia and E^rns protein expression in the blood of all infected animals were detectable from 3 to 5 days post infection (DPI), their presence correlating with the onset of fever, clinical signs and leukopenia. E2 antibody did not develop in any of the field CSFV-infected piglets during the disease course, while E^rns antibody was detectable in 4-56% of infected animals at various time points. Mortalities ranged from 20 to 80% within 21 DPI, progressing to 100% by 43 DPI. Based on clinical scores and fatalities within 21 DPI, 2 of the 5 field isolates were classified as of moderate virulence and 3 of high virulence; i.e., no field isolates of low virulence were identified. The study has provided data supporting the use of these isolates as challenge viruses to evaluate the efficacy of current CSF vaccines.

Bungowannah virus in the affected pig population: a retrospective genetic analysis

Bungowannah virus, which belongs to the genus Pestivirus within the family Flaviviridae, has been associated with myocarditis and a high incidence of stillbirths in pigs. In 2003, the virus was initially detected in a large pig farming complex on two separate sites in New South Wales, Australia. Until now, it has not been detected at other locations. Despite a program of depopulation and disinfection, the virus could be only eradicated from one of the affected farm complexes, the Bungowannah unit, but became endemic on the second complex, the Corowa unit. In the present study, the genetic variability of virus isolates collected between 2003 and 2014 in the endemically infected population has been retrospectively investigated. Phylogenetic analysis carried out based on sequences of the E2 and NS5B coding regions and the full-length open-reading frame revealed that the isolates from the different farm sites are closely related, but that samples collected between 2010 and 2014 at the Corowa farm site clustered in a different branch of the phylogenetic tree. Since 2010, a high-genetic stability of this RNA virus within the Corowa farm complex, probably due to an effective adaptation of the virus to the affected pig population, could be observed.

Genome Sequence of a Classical Swine Fever Virus of Subgenotype 2.1, Isolated from a Pig in Japan in 2018

In 2018, classical swine fever virus (CSFV) was detected in Japan. Here, we report the whole-genome sequence of CSFV/JPN/1/2018.

In 2018, classical swine fever virus (CSFV) was detected in Japan. Here, we report the whole-genome sequence of CSFV/JPN/1/2018. This virus is closely related to isolates in East Asia and is classified under subgenotype 2.1. This is the first detection of a CSFV of this lineage in Japan.

Development of Recombinant Protein-Based Vaccine Against Classical Swine Fever Virus in Pigs Using Transgenic Nicotiana benthamiana

Classical swine fever virus (CSFV) is highly contagious, and fatal to infected pigs. Vaccines against CSFV have been developed from attenuated or modified live viruses. These vaccines are effective for immunization of animals, but they are associated with problems such as the accidental spreading of viruses to animals in the field, and with barriers to trade following vaccination. Here, we report the generation of transgenic Nicotiana benthamiana plants for large-scale, cost-effective production of E2 fusion protein for use as a recombinant vaccine against CSFV in pigs. Transgenic N. benthamiana plants harboring an intergenic, single-copy insertion of a chimeric gene encoding E2 fusion protein had high levels of transgene expression. For large-scale production of E2 fusion protein from leaf tissues, we developed a protein-purification protocol consisting of cellulose-binding domain (CBD)-cellulose-based affinity purification and size-exclusion gel-filtration chromatography. E2 fusion proteins showed high immunogenicity in piglets and provided protection against CSFV challenge. The CBD in the E2 fusion protein was also highly immunogenic. These results suggest that plant-produced recombinant E2 fusion proteins can be developed into cost-effective vaccines against CSFV, with the CBD as a marker antigen to differentiate between vaccination and natural infection.

Sub-subgenotype 2.1c isolates of classical swine fever virus are dominant in Guangdong province of China, 2018

Classical swine fever (CSF) continues to be a devastating infectious disease for the swine industry in China and commonly exists as wild or atypical types. From June 3rd to October 3rd, 2018, outbreaks of typical CSF cases with mortality rates of 42-86% occurred in 11 swine herds in five cities of Guangdong province, and were confirmed by RT-PCR. Phylogenetic analyses based on the nucleotide sequences of full-length E2 genes showed that the CSFV isolates collected in Guangdong, 2018 grouped into sub-subgenotype 2.1c and formed a separate clade from previously identified 2.1c isolates. Sequence comparison further confirmed the distance between the novel emergent and previously identified 2.1c isolates, with shared 94.5-98.2% and 97.8-99.7% identities at the nucleotide and amino acid levels respectively. Furthermore, 2.1c isolates collected in 2018 from Guangdong province contained a unique amino acid substitution (K174R) in the E2 protein in comparison with other 2.1c representative strains and CSFV 2.1, 2.2, 2.3 strains. Of note, the novel emergent 2.1c isolates are neutralized by sera from C-strain vaccinated sows, indicating that C-strain is still efficacious for protection against field isolates of CSFV.

Molecular detection and genomic characterization of porcine circovirus 3 in pigs from Northeast China

Background

First identified in the United States in 2016, porcine circovirus type 3 (PCV3) is a newly emerging porcine circovirus exhibiting a wide range of clinical syndromes, which may be associated with the pathogenicity observed in pigs.

Results

The aim of this study was to identify and characterize the full genome sequence of PCV3 strains circulating in Northeast China. Herein, 105 lung samples isolated from sick pigs in Northeast China during 2018 were analyzed for PCV3. Using PCR, the total PCV3-positive rate was 33.3% (35/105), with rates of 17.8% (8/45), 66.7% (10/15), and 37.8% (17/45) in Heilongjiang, Jilin, and Liaoning province, respectively. Additionally, our findings showed that PCV3-positive samples had a high rate of co-infection with PCV2, PPV6, and PPV7. To study the evolution of the PCV3 in Northeast China, we sequenced the entire genome of 13 strains of PCV3. The results of phylogenetic analyses revealed that PCV3 could be divided into two clades, PCV3a and PCV3b. Interestingly, a G deletion at position 1072 was found in the 1999 nt genome of PCV3-CN2018LN-4 (MH277118). The G deletion terminated replicase protein translation and induced a truncated replicase protein.

Conclusion

These results contribute to the understanding of PCV3 molecular epidemiology and evolution in Northeast China. A new strain of PCV3 with truncated replicase protein was identified.

Evolutionary dynamics of classical swine fever virus in South Korea: 1987-2017

The 5' UTR (n=102) and full-length E2 (n=37) genes of classical swine fever viruses (CSFVs) circulating in South Korea over the past 30 years (1987-2017) were examined to determine the evolutionary rate and estimated time of the most recent common ancestor (tMRCA). From 2000, the Korean classical swine fever (CSF) antigen changed from genotype 3 to 2, which comprises subgenotypes 2.1b (2002-2013) and 2.1d (2011-2017). There are genotypic variations in the full-length E2 gene of Korean CSFV genotypes 2.1b and 2.1d (seven separate amino acid substitutions); these are useful distinguishing markers. The mean substitution rate (×10³ substitutions/site/year) for Korean CSFV was estimated to be 2.2088 (95% highest posterior density (HPD): lower, 1.7045; upper, 2.7574) and the mean tMRCA was estimated to be 1901 (95% HPD: lower, 1865; upper, 1933). The effective population size of Korean CSFV genotype 2 increased rapidly from 2002 to 2003, after which it remained constant. The occurrence of CSF in Korea is expected to decline in the future; however, it will likely be more prevalent in wild boar than in domestic pigs. Thus, there is a risk of transmission from wild boar to breeding pigs.

Rab5, Rab7, and Rab11 Are Required for Caveola-Dependent Endocytosis of Classical Swine Fever Virus in Porcine Alveolar Macrophages

The members of Flaviviridae utilize several endocytic pathways to enter a variety of host cells. Our previous work showed that classical swine fever virus (CSFV) enters porcine kidney (PK-15) cells through a clathrin-dependent pathway that requires Rab5 and Rab7. The entry mechanism for CSFV into other cell lines remains unclear, for instance, porcine alveolar macrophages (3D4/21 cells). More importantly, the trafficking of CSFV within endosomes controlled by Rab GTPases is unknown in 3D4/21 cells. In this study, entry and postinternalization of CSFV were analyzed using chemical inhibitors, RNA interference, and dominant-negative (DN) mutants. Our data demonstrated that CSFV entry into 3D4/21 cells depends on caveolae, dynamin, and cholesterol but not clathrin or macropinocytosis. The effects of DN mutants and knockdown of four Rab proteins that regulate endosomal trafficking were examined on CSFV infection, respectively. The results showed that Rab5, Rab7, and Rab11, but not Rab9, regulate CSFV endocytosis. Confocal microscopy showed that virus particles colocalize with Rab5, Rab7, or Rab11 within 30 min after virus entry and further with lysosomes, suggesting that after internalization CSFV moves to early, late, and recycling endosomes and then into lysosomes before the release of the viral genome. Our findings provide insights into the life cycle of pestiviruses in macrophages.IMPORTANCE Classical swine fever, is caused by classical swine fever virus (CSFV). The disease is notifiable to World Organisation for Animal Health (OIE) in most countries and causes significant financial losses to the pig industry globally. Understanding the processes of CSFV endocytosis and postinternalization will advance our knowledge of the disease and provide potential novel drug targets against CSFV. With this objective, we used systematic approaches to dissect these processes in CSFV-infected 3D4/21 cells. The data presented here demonstrate for the first time to our knowledge that CSFV is able to enter cells via caveola-mediated endocytosis that requires Rab5, Rab7 and Rab11, in addition to the previously described classical clathrin-dependent pathway that requires Rab5 and Rab7. The characterization of CSFV entry will further promote our current understanding of Pestivirus cellular entry pathways and provide novel targets for antiviral drug development.

Complete genomic characteristics and pathogenic analysis of the newly emerged classical swine fever virus in China

BACKGROUND

Classical swine fever (CSF) is one of the most devastating and highly contagious viral diseases in the world. Since late 2014, outbreaks of a new sub-genotype 2.1d CSF virus (CSFV) had caused substantial economic losses in numbers of C-strain vaccinated swine farms in China. The objective of the present study was to explore the genomic characteristics and pathogenicity of the newly emerged CSFV isolates in China during 2014-2015.

RESULTS

All the new 8 CSFV isolates belonged to genetic sub-genotype 2.1d. Some genomic variations or deletions were found in the UTRs and E2 of these new isolates. In addition, the pathogenicity of HLJ1 was less than Shimen, suggesting the HLJ1 of sub-genotype 2.1d may be a moderated pathogenic isolate and the C-strain vaccine can supply complete protection.

CONCLUSIONS

The new CSFV isolates with unique genomic characteristics and moderate pathogenicity can be epidemic in many large-scale C-strain vaccinated swine farms. This study provides the information should be merited special attention on establishing prevention and control policies for CSF.

Immunogenicity of a live attenuated classical swine fever vaccine in pigs under field conditions

A study was conducted for assessing the immunogenicity of live classical swine fever (CSF) vaccine in pigs under field conditions. Pre immunization blood samples and post immunization (PI) blood samples at 30, 60, 90, and 120 days post immunization (DPI) were collected. Th1 response was assessed by the expression of IFN-γ, IL- 2 and IL-12, and serum antibody titres and IL-10 expression were studied for Th2 response. The mean±SE of IFN- γ gene response as fold change (2ΔΔCt values) at 30, 60, 90, and 120 days post immunization (DPI) were 9.61±0.65, 3.49±0.44, 2.22±0.407, and 3.12±1.35 respectively. IFN-γ response showed significantly increased fold change during PI period. Significant peak increase in the expression level was observed at 30 DPI. IL-2 gene response showed significantly increased fold change during PI (Mean expression at 30, 60, 90, and 120 DPI was 4.41, 2.61, 3.291 and 2.09 respectively) and peak increase was observed at 30 DPI. IL-12 response also showed significant increase during PI with a peak expression at 30 DPI (Mean fold changes at 30, 60, 90, and 120 days post immunization were 4.92, 2.97, 2.72, and 3.61 respectively). Maximum IL-10 expression was observed at 60 DPI (Mean fold change at 30, 60, 90, and 120 days post immunization were 3.364±0.723, 11.56±1.64, 4.73±1.01, and 2.599±1.05 respectively). Pre- and post-immunization antibody responses were monitored by enzyme linked immunosorbent assay. Antibody titres increased consistently from 30 days after primary immunization until 120 days. Montanide (gel 01) coupled PK-15 adapted live, CSV vaccine induced a good Th1 response followed by Th2 response.

Complete Genome Sequence of a Field Isolate of Classical Swine Fever Virus Belonging to Subgenotype 2.2 from India

The complete genome sequence of classical swine fever virus (CSFV) strain CSFV-UP-BR-KHG-06, from genotype 2.2, was determined. Comparative analysis based on the amino acid sequence of some important B-cell epitopes, T-cell epitopes, glycosylation sites, and conformational residues showed the striking differences between the group 2 virus KHG-06 and the vaccine strains HCLV/India and C-strain.

A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine

Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional microarrays that rely on passive hybridization. With further refinement, this novel, rapid, highly automated microarray technology has potential applications in multipathogen surveillance of livestock diseases.

Complete Genome Sequences of Three Sub-genotype 2.1b Isolates of Classical Swine Fever Virus in China

Introduction

Classical swine fever (CSF) has caused severe economic losses in pig production in many countries. Recent CSF outbreaks in China are mainly associated with sub-genotype 2.1 of CSF virus (CSFV). Although there is abundant information regarding 2.1 isolates, few data are available on whole-genome analysis.

Material and Methods

The biological and genome characteristics of three recently emerged Chinese CSFV isolates, i.e. SD2014-1, SD2014-2, and SD2014-3, were fully analysed.

Results

Sequence analysis showed that the isolates shared 83.4%–95.0% nucleotide identity with eight other CSFV isolates. In addition, the 5′ untranslated region (5′UTR) and the non-structural (NS) proteins NS3, NS4A, and NS4B were more conserved than other regions of the genome. Phylogenetic analysis based on the complete genome sequences or full-length structural protein E2 gene sequences revealed that the three isolates belonged to sub-genotype 2.1b. In addition, several unique molecular characteristics of the 5′UTR, 3′UTR, and E2 were identified.

Conclusion

The genomic variations of the three isolates will support further analysis of virulence determinants and the evolutionary trend of CSFV.

Retrospective study of porcine circovirus 3 infection in China

PCV3 is an emerging swine virus associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, respiratory diseases and systematic inflammation. Although first identified in 2015, the earliest case has been traced back to 2009 in the United States. In China, PCV3 infection was first detected in 2015, but little information has been available about its occurrence and prevalence there before 2015. In this study, 200 porcine clinical samples collected from 20 provinces, five autonomous regions and four municipalities between 1990 and 1999 were analysed for PCV3 infection by PCR. Results showed that 6.5% of the porcine samples collected from eight provinces and one autonomous region were PCV3 positive, with the earliest cases occurring in 1996. Nucleotide sequence analysis showed that PCV3 strains obtained in this study shared 96.6%-99.7% and 97.1%-99.4% sequence identity at the ORF2 gene and genome levels with all available reference strains from China and other countries, indicating the high genetic stability of PCV3 over the past 20 years.

Phylodynamics of classical swine fever virus with emphasis on Ecuadorian strains

Classic swine fever virus (CSFV) is a Pestivirus from the Flaviviridae family that affects pigs worldwide and is endemic in several Latin American countries. However, there are still some countries in the region, including Ecuador, for which CSFV molecular information is lacking. To better understand the epidemiology of CSFV in the Americas, sequences from CSFVs from Ecuador were generated and a phylodynamic analysis of the virus was performed. Sequences for the full-length glycoprotein E2 gene of twenty field isolates were obtained and, along with sequences from strains previously described in the Americas and from the most representative strains worldwide, were used to analyse the phylodynamics of the virus. Bayesian methods were used to test several molecular clock and demographic models. A calibrated ultrametric tree and a Bayesian skyline were constructed, and codons associated with positive selection involving immune scape were detected. The best model according to Bayes factors was the strict molecular clock and Bayesian skyline model, which shows that CSFV has an evolution rate of 3.2 × 10^-4 substitutions per site per year. The model estimates the origin of CSFV in the mid-1500s. There is a strong spatial structure for CSFV in the Americas, indicating that the virus is moving mainly through neighbouring countries. The genetic diversity of CSFV has increased constantly since its appearance, with a slight decrease in mid-twentieth century, which coincides, with eradication campaigns in North America. Even though there is no evidence of strong directional evolution of the E2 gene in CSFV, codons 713, 761, 762 and 975 appear to be selected positively and could be related to virulence or pathogenesis. These results reveal how CSFV has spread and evolved since it first appeared in the Americas and provide important information for attaining the goal of eradication of this virus in Latin America.

Deciphering the emergence, genetic diversity and evolution of classical swine fever virus

Classical swine fever (CSF) is one of the most important infectious diseases causing significant economic losses. Its causal agent, CSF virus (CSFV), is a member of the Pestivirus genus included into the Flaviviridae family. Previous molecular epidemiology studies have revealed the CSFV diversity is divided into three main genotypes and different subgenotypes. However, the classification system for CSFV has not yet been harmonized internationally. Similarly, the phylogeny and evolutionary dynamics of CSFV remain unclear. The current study provides novel and significant insights into the origin, diversification and evolutionary process of CSFV. In addition, the best phylogenetic marker for CSFV capable of reproducing the same phylogenetic and evolutionary information as the complete viral genome is characterized. Also, a reliable cut-off to accurately classify CSFV at genotype and subgenotype levels is established. Based on the time for the most recent common ancestor (tMRCA) reconstruction and cophylogenetic analysis, it was determined that CSFV emerged around 225 years ago when the Tunisian Sheep Virus jumped from its natural host to swine. CSFV emergence was followed by a genetic expansion in three main lineages, driven by the action of positive selection pressure and functional divergence, as main natural forces.

African and classical swine fever: similarities, differences and epidemiological consequences

For the global pig industry, classical (CSF) and African swine fever (ASF) outbreaks are a constantly feared threat. Except for Sardinia, ASF was eradicated in Europe in the late 1990s, which led to a research focus on CSF because this disease continued to be present. However, ASF remerged in eastern Europe in 2007 and the interest in the disease, its control and epidemiology increased tremendously. The similar names and the same susceptible species suggest a similarity of the two viral diseases, a related biological behaviour and, correspondingly, similar epidemiological features. However, there are several essential differences between both diseases, which need to be considered for the design of control or preventive measures. In the present review, we aimed to collate differences and similarities of the two diseases that impact epidemiology and thus the necessary control actions. Our objective was to discuss critically, if and to which extent the current knowledge can be transferred from one disease to the other and where new findings should lead to a critical review of measures relating to the prevention, control and surveillance of ASF and CSF. Another intention was to identify research gaps, which need to be closed to increase the chances of a successful eradication of ASF and therefore for a decrease of the economic threat for pig holdings and the international trade.

An outbreak of classical swine fever in pigs in Bangladesh, 2015

In a group of 22 healthy pigs aged between 4 and 6 months, 2 pigs became ill with high fever, complete anorexia, cough and abnormal swaying movements on 22 June 2015. One of them died on June 24 and the second died on July 3. Shortly after, the remaining pigs also fell ill and died from the same illness by 10 August 2015. We investigated the aetiology, epidemiological and clinical features of the outbreak. We recorded the clinical signs and symptoms for each pig with the date of onset of illness. Veterinarians conducted post-mortem examinations on the 12 dead pigs, they collected tissue samples from the dead pigs and placed them in a tube containing 1 mL of nucleic acid extraction buffer (lysis buffer). We tested all the tissue samples by real-time reverse transcription polymerase chain reaction (rRT-PCR) to detect classical swine fever virus (CSFV) because the animals' symptoms matched those of this disease. We also conducted a phylogentic analysis of the nucleotide sequence of the E2 gene segment of CSFV detected in a lung tissue sample. The attack rate (22/22) and the case fatality were 100%. The predominant symptoms of the disease included high fever, cough, diarrhoea and swaying movements of the hind legs prior to death. Of the 12 pigs tissue samples tested, all had evidence of the presence of CSFV RNA by rRT-PCR. The phylogenetic analysis indicated that the virus belongs to genotype 2.2, which is closely related to CSFV genotype 2.2 reported in India. Our investigation suggests that CSF is circulating in pigs, posing a risk for communities in Bangladesh that rely on pigs for economic income and dietary protein. Future research could focus on estimating the disease and economic burden of CSFV in pig rearing areas to determine if interventions might be warranted or cost-effective.

Epidemiology, diagnosis and control of classical swine fever: Recent developments and future challenges

Classical swine fever (CSF) represents a major health and trade problem for the pig industry. In endemic countries or those with a wild boar reservoir, CSF remains a priority for Veterinary Services. Surveillance as well as stamping out and/or vaccination are the principle tools of prevention and control, depending on the context. In the past decades, marker vaccines and accompanying diagnostic tests allowing the discrimination of infected from vaccinated animals have been developed. In the European Union, an E2 subunit and a chimeric live vaccine have been licensed and are available for the use in future disease outbreak scenarios. The implementation of commonly accepted and globally harmonized concepts could pave the way to replace the ethically questionable stamping out policy by a vaccination-to-live strategy and thereby avoid culling of a large number of healthy animals and save food resources. Although a number of vaccines and diagnostic tests are available worldwide, technological advancement in both domains is desirable. This work provides a summary of an analysis undertaken by the DISCONTOOLS group of experts on CSF. Details of the analysis can be downloaded from the web site at http://www.discontools.eu/.

Molecular characterization of classical swine fever virus isolates from India during 2012-14

Classical swine fever is a highly contagious and economically important viral disease of pigs. Outbreaks of classical swine fever virus (CSFV) were recorded in different places in the Kamrup district of Assam in India between the years 2012 and 2014. The nucleotide sequences of the 10 CSFV isolates were analyzed based on the partial nucleotide sequences of the E2, 5'NTR and NS5B genes. Phylogenetic analysis indicated the dominance of subgroup 2.2 along with 2.1 strains in the northeast part of India. Variation in the nucleotide sequences of E2, 5'NTR and 3'NS5B genes of CSFV allows tracking changes in the virus population over time. The study will provide epidemiological information useful for assessing CSFV circulating genogroups in India.

Phylogenetic analysis of Classical swine fever virus from archival formalin fixed clinical tissues reveals vietnamese origin of the isolates

Detection of Classical swine fever virus (CSFV) nucleic acid in archival formalin fixed tissue samples and their use for phylogenetic analysis was investigated. Ten samples were examined for the presence of CSFV nucleic acid by reverse transcriptase polymerase chain reaction (RT-PCR) amplification of 5'UTR and E2 gene. RT-PCR was found positive for 5'UTR fragment in eight samples while only one tissue samples showed amplification for E2 gene target fragment. For molecular epidemiology of the disease, 5'UTR PCR product of sample from Darbhanga (Bihar), was cloned and sequenced. The sequence was compared with the sequences available in database. The phylogenetic analysis reveals that the isolate belongs to subgroup 2.2 sharing 98.7% nucleotide identities with Vietnamese isolate (CaTh05-1, AB252170), indicating towards the possible origin of genogroup 2.2 CSFV isolates involved in the outbreak from Vietnam. From the study, it can be concluded that the tissue samples collected and stored in buffer formalin for years can be used to detect CSFV nucleic acid. Results are also suggestive of that the 5'UTR region of genome is more suitable target for RT-PCR based detection of CSFV in archival formalin fixed specimens. The study also indicates the potential of archival formalin fixed tissues for molecular epidemiology and genotyping of the CSF virus.

Classical Swine Fever-An Updated Review

Classical swine fever (CSF) remains one of the most important transboundary viral diseases of swine worldwide. The causative agent is CSF virus, a small, enveloped RNA virus of the genus Pestivirus. Based on partial sequences, three genotypes can be distinguished that do not, however, directly correlate with virulence. Depending on both virus and host factors, a wide range of clinical syndromes can be observed and thus, laboratory confirmation is mandatory. To this means, both direct and indirect methods are utilized with an increasing degree of commercialization. Both infections in domestic pigs and wild boar are of great relevance; and wild boars are a reservoir host transmitting the virus sporadically also to pig farms. Control strategies for epidemic outbreaks in free countries are mainly based on classical intervention measures; i.e., quarantine and strict culling of affected herds. In these countries, vaccination is only an emergency option. However, live vaccines are used for controlling the disease in endemically infected regions in Asia, Eastern Europe, the Americas, and some African countries. Here, we will provide a concise, updated review on virus properties, clinical signs and pathology, epidemiology, pathogenesis and immune responses, diagnosis and vaccination possibilities.

Comparative characterization analysis of synonymous codon usage bias in classical swine fever virus

Classical swine fever virus (CSFV) is responsible for the highly contagious viral disease of swine, and causes great economic loss in the swine-raising industry. Considering the significance of CSFV, a systemic analysis was performed to study its codon usage patterns. In this study, using the complete genome sequences of 76 CSFV representing three genotypes, we firstly analyzed the relative nucleotide composition, effective number of codon (ENC) and synonymous codon usage in CSFV genomes. The results showed that CSFV is GC-moderate genome and the third-ended codons are not preferentially used. Every ENC values in CSFV genomes are >50, indicating that the codon usage bias is comparatively slight. Subsequently, we performed the correspondence analysis (COA) to investigate synonymous codon usage variation among all of the CSFV genomes. We found that codon usage bias in these CSFV genomes is greatly influenced by G + C mutation, which suggests that mutational pressure may be the main factor determining the codon usage biases. Moreover, most of the codon usage bias among different CSFV ORFs is directly related to the nucleotide composition. Other factors, such as hydrophobicity and aromaticity, also influence the codon usage variation among CSFV genomes. Our study represents the most comprehensive analysis of codon usage patterns in CSFV genome and provides a basic understanding of the mechanisms for its codon usage bias.

Complete Genome Sequence of a Sub-Subgenotype 2.1i Isolate of Classical Swine Fever Virus from China

The complete genome sequence of a sub-subgenotype 2.1i isolate of classical swine fever virus (CSFV), GD317/2011, was determined. Notably, GD317/2011 is distant from the sub-subgenotype 2.1b isolate HEBZ at genes of E^rns, E1, E2, P7, NS2, NS5A and the 3′-nontranslated region (3′-NTR) but is closely related to that at genes of N^pro, Core, NS3, NS4A, NS4B, and NS5B.

Characterisation of Newly Emerged Isolates of Classical Swine Fever Virus in China, 2014-2015

Introduction

In 2014–2015, the epidemic of classical swine fever (CSF) occurred in many large-scale pig farms in different provinces of China, and a subgenotype 2.1d of CSF virus (CSFV) was newly identified.

Material and Methods

The phylogenetic relationship, genetic diversity, and epidemic status of the 2014–2015 CSFV isolates, 18 new CSFV isolates collected in 2015, and 43 other strains isolated in 2014–2015 were fully analysed, together with 163 CSFV reference isolates.

Results

Fifty-two 2014–2015 isolates belonged to subgenotype 2.1d and nine other isolates belonged to subgenotype 2.1b. The two subgenotype isolates showed unique molecular characteristics. Furthermore, the 2.1d isolates were found to possibly diverge from 2.1b isolates.

Conclusion

This study suggests that the Chinese CSFVs will remain pandemic.

Changing pattern of classical swine fever virus genogroup from classical 1.1 to emerging 2.2 in India

Classical swine fever (CSF) is one of the most important viral diseases of pigs with high economic impact. The causative agent, Classical swine fever virus (CSFV) is a member of genus Pestivirus in family Flaviviredae and is structurally and antigenically related to other members of the genus. The identification of virus strains and genotypes can conveniently be used to trace the origin and patterns of virus spread, which contribut substantially in control strategies. In the present study, we have partially sequenced and analysed the 5' untranslated region (UTR) and E2 regions of CSFV clinical samples (n = 24) from various parts of the country. Among the samples, the sequence alignment of 5'UTR and E2 regions revealed 96.7-100 and 94.7-100% identities at the nucleotide level, respectively. The samples under study showed the close resemblance to the other CSFV isolates reported in India. In phylogenetic analysis, all the field samples were clustered in subgroup 2.2. Thus the study presents a further phylogenetic evidence for the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in India. As the information regarding the molecular epidemiology the CSFV in india is very little, generation of such epidemiological data is warranted to help in comprehensing the nationwide disease control program to sustain the growth of pig industry in India.

Genetic and virulence characterization of classical swine fever viruses isolated in Mongolia from 2007 to 2015

Classical swine fever (CSF), a highly contagious viral disease affecting domestic and wild pigs in many developing countries, is now considered endemic in Mongolia, with 14 recent outbreaks in 2007, 2008, 2011, 2012, 2014, and 2015. For the first time, CSF viruses isolated from these 14 outbreaks were analyzed to assess their molecular epidemiology and pathogenicity in pigs. Based on the nucleotide sequences of their 5'-untranslated region, isolates were phylogenetically classified as either sub-genotypes 2.1b or 2.2, and the 2014 and 2015 isolates, which were classified as 2.1b, were closely related to isolates from China and Korea. In addition, at least three different viruses classified as 2.1b circulated in Mongolia. Experimental infection of the representative isolate in 2014 demonstrated moderate pathogenicity in 4-week-old pigs, with relatively mild clinical signs. Understanding the diversity of circulating CSF viruses gleans insight into disease dynamics and evolution, and may inform the design of effective CSF control strategies in Mongolia.

Circulation of multiple subtypes of bovine viral diarrhoea virus type 1 with no evidence for HoBi-like pestivirus in cattle herds of southern Italy

Pestiviruses of cattle include bovine viral diarrhoea 1 (BVDV-1) and 2 (BVDV-2) plus an emerging group, named HoBi-like pestivirus. In the present paper, the results of an epidemiological survey for pestiviruses circulating in cattle in southern Italy are presented. Molecular assays carried out on a total of 924 bovine samples detected 74 BVDV strains, including 73 BVDV-1 and 1 BVDV-2 viruses. Phylogenetic analysis carried out on partial 5'UTR and N^pro sequences revealed the presence of 6 different subtypes of BVDV-1 and a single BVDV-2c strain. BVDV-1 displayed a high level of genetic heterogeneity, which can have both prophylactic and diagnostic implications. In addition, the detection of BVDV-2c highlights the need for a continuous surveillance for the emergence of new pestivirus strains in cattle farms in southern Italy.

Quasispecies composition and diversity do not reveal any predictors for chronic classical swine fever virus infection

Classical swine fever (CSF) can run acute, chronic, and prenatal courses in both domestic pigs and wild boar. Although chronic infections are rare events, their epidemiological impact is very high due to the long-term shedding of virus. So far, little is known about the factors that influence disease course and outcome from either the host or virus's perspective. To elucidate the viral determinants, we analyzed the role of the viral populations for the development of chronic CSF virus (CSFV) infections. Three different animal trials that had led to both chronic and acute infections were chosen for a detailed analysis by deep sequencing. The three inocula represented sub-genogroups 2.1 and 2.3, and two viruses were wild-type CSFV, one derived from an infectious cDNA clone. These viruses and samples derived from acutely and chronically infected animals were subjected to next-generation sequencing. Subsequently, the derived full-length genomes were compared at both the consensus and the quasispecies level. At consensus level, no differences were observed between the parental viruses and the viruses obtained from chronically infected animals. Despite a considerable level of variability at the quasispecies level, no indications were found for any predictive pattern with regard to the chronicity of the CSFV infections. While there might be no direct marker for chronicity, moderate virulence of some CSFV strains in itself seems to be a crucial prerequisite for the establishment of long-term infections which does not need further genetic adaption. Thus, general host and virus factors need further investigation.

Competitive replication kinetics and pathogenicity in pigs co-infected with historical and newly invading classical swine fever viruses

Classical swine fever (CSF), an economically important and highly contagious disease of pigs, is caused by classical swine fever virus (CSFV). In Taiwan, CSFVs from field outbreaks belong to two distinct genotypes. The historical genotype 3.4 dominated from the 1920s to 1996, and since 1996, the newly invading genotype 2.1 has dominated. To explain the phenomenon of this virus shift in the field, representative viruses belonging to genotypes 2.1 and 3.4 were either inoculated alone (single infection) or co-inoculated (co-infection), both in vivo and in vitro, to compare the virus replication and pathogenesis. In pigs co-infected with the genotype 2.1 TD/96/TWN strain and the genotype 3.4 94.4/IL/94/TWN strain, the newly invading genotype 2.1 was detected earlier in the blood, oral fluid, and feces, and the viral loads were consistently and significantly higher than that of the historical genotype 3.4. In cell cultures, the ratio of secreted virus to cell-associated virus of the genotype 2.1 strain was higher than that of the genotype 3.4 strain. This study is the first to demonstrate a possible explanation of virus shift in the field, wherein the newly invading genotype 2.1 replicates more efficiently than did genotype 3.4 and outcompetes the replication and pathogenicity of genotype 3.4 in pigs in the field.

The European Classical Swine Fever Virus Database: Blueprint for a Pathogen-Specific Sequence Database with Integrated Sequence Analysis Tools

Molecular epidemiology has become an indispensable tool in the diagnosis of diseases and in tracing the infection routes of pathogens. Due to advances in conventional sequencing and the development of high throughput technologies, the field of sequence determination is in the process of being revolutionized. Platforms for sharing sequence information and providing standardized tools for phylogenetic analyses are becoming increasingly important. The database (DB) of the European Union (EU) and World Organisation for Animal Health (OIE) Reference Laboratory for classical swine fever offers one of the world’s largest semi-public virus-specific sequence collections combined with a module for phylogenetic analysis. The classical swine fever (CSF) DB (CSF-DB) became a valuable tool for supporting diagnosis and epidemiological investigations of this highly contagious disease in pigs with high socio-economic impacts worldwide. The DB has been re-designed and now allows for the storage and analysis of traditionally used, well established genomic regions and of larger genomic regions including complete viral genomes. We present an application example for the analysis of highly similar viral sequences obtained in an endemic disease situation and introduce the new geographic “CSF Maps” tool. The concept of this standardized and easy-to-use DB with an integrated genetic typing module is suited to serve as a blueprint for similar platforms for other human or animal viruses.

Entry of Classical Swine Fever Virus into PK-15 Cells via a pH-, Dynamin-, and Cholesterol-Dependent, Clathrin-Mediated Endocytic Pathway That Requires Rab5 and Rab7

Classical swine fever virus (CSFV), a member of the genus Pestivirus within the family Flaviviridae, is a small, enveloped, positive-strand RNA virus. Due to its economic importance to the pig industry, the biology and pathogenesis of CSFV have been investigated extensively. However, the mechanisms of CSFV entry into cells are not well characterized. In this study, we used systematic approaches to dissect CSFV cell entry. We first observed that CSFV infection was inhibited by chloroquine and NH4Cl, suggesting that viral entry required a low-pH environment. By using the specific inhibitor dynasore, or by expressing the dominant negative (DN) K44A mutant, we verified that dynamin is required for CSFV entry. CSFV particles were observed to colocalize with clathrin at 5 min postinternalization, and CSFV infection was significantly reduced by chlorpromazine treatment, overexpression of a dominant negative form of the EPS15 protein, or knockdown of the clathrin heavy chain by RNA interference. These results suggested that CSFV entry depends on clathrin. Additionally, we found that endocytosis of CSFV was dependent on membrane cholesterol, while neither the overexpression of a dominant negative caveolin mutant nor the knockdown of caveolin had an effect. These results further suggested that CSFV entry required cholesterol and not caveolae. Importantly, the effect of DN mutants of three Rab proteins that regulate endosomal traffic on CSFV infection was examined. Expression of DN Rab5 and Rab7 mutants, but not the DN Rab11 mutant, significantly inhibited CSFV replication. These results were confirmed by silencing of Rab5 and Rab7. Confocal microscopy showed that virus particles colocalized with Rab5 or Rab7 during the early phase of infection within 45 min after virus entry. These results indicated that after internalization, CSFV moved to early and late endosomes before releasing its RNA. Taken together, our findings demonstrate for the first time that CSFV enters cells through the endocytic pathway, providing new insights into the life cycle of pestiviruses.

IMPORTANCE

Bovine viral diarrhea virus (BVDV), a single-stranded, positive-sense pestivirus within the family Flaviviridae, is internalized by clathrin-dependent receptor-mediated endocytosis. However, the detailed mechanism of cell entry is unknown for other pestiviruses, such as classical swine fever (CSF) virus (CSFV). CSFV is the etiological agent of CSF, a highly contagious disease of swine that causes numerous deaths in pigs and enormous economic losses in China. Understanding the entry pathway of CSFV will not only advance our knowledge of CSFV infection and pathogenesis but also provide novel drug targets for antiviral intervention. Based on this objective, we used systematic approaches to dissect the pathway of entry of CSFV into PK-15 cells. This is the first report to show that the entry of CSFV into PK-15 cells requires a low-pH environment and involves dynamin- and cholesterol-dependent, clathrin-mediated endocytosis that requires Rab5 and Rab7.

Pigs immunized with a novel E2 subunit vaccine are protected from subgenotype heterologous classical swine fever virus challenge

Background

Classical swine fever (CSF) or hog cholera is a highly contagious swine viral disease. CSF endemic countries have to use routine vaccination with modified live virus (MLV) vaccines to prevent and control CSF. However, it is impossible to serologically differentiate MLV vaccinated pigs from those infected with CSF virus (CSFV). The aim of this study is to develop a one-dose E2-subunit vaccine that can provide protection against CSFV challenge. We hypothesize that a vaccine consisting of a suitable adjuvant and recombinant E2 with natural conformation may induce a similar level of protection as the MLV vaccine.

Results

Our experimental vaccine KNB-E2 was formulated with the recombinant E2 protein (Genotype 1.1) expressed by insect cells and an oil-in-water emulsion based adjuvant. 10 pigs (3 weeks old, 5 pigs/group) were immunized intramuscularly with one dose or two doses (3 weeks apart) KNB-E2, and 10 more control pigs were administered normal saline solution only. Two weeks after the second vaccination, all KNB-E2 vaccinated pigs and 5 control pigs were challenged with 5 × 10⁵ TCID₅₀ CSFV Honduras/1997 (Genotype 1.3, 1 ml intramuscular, 1 ml intranasal). It was found that while control pigs infected with CSFV stopped growing and developed high fever (>40 °C), high level CSFV load in blood and nasal fluid, and severe leukopenia 3–14 days post challenge, all KNB-E2 vaccinated pigs continued to grow as control pigs without CSFV exposure, did not show any fever, had low or undetectable level of CSFV in blood and nasal fluid. At the time of CSFV challenge, only pigs immunized with KNB-E2 developed high levels of E2-specific antibodies and anti-CSFV neutralizing antibodies.

Conclusions

Our studies provide direct evidence that pigs immunized with one dose KNB-E2 can be protected clinically from CSFV challenge. This protection is likely mediated by high levels of E2-specific and anti-CSFV neutralizing antibodies.