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

Quantitative analysis of viremia and viral shedding in pigs infected experimentally with classical swine fever virus isolates obtained from recent outbreaks in Japan

Although classical swine fever occurred in September 2018 for the first time in 26 years, its virulence is thought to be moderate based on field observations by veterinary authorities and our previous experimental infections. We quantified viremia and viral shedding in pigs infected with recent Japanese classical swine fever virus isolates, as well as a highly virulent strain. The results show that pigs infected with the Japanese strains exhibited lower viremia and viral shedding than those infected with the highly virulent strain. However, horizontal transmission occurred in pigs infected with the Japanese strains, similar to those infected with the highly virulent strain. Additionally, viremia and neuralization antibodies coexisted in pigs infected with the Japanese strains, presenting challenges for control measures.

Rapid Identification of ASFV, CSFV and FMDV from Mongolian Outbreaks with MinION Short Amplicon Sequencing

African swine fever virus (ASFV), classical swine fever virus (CSFV), and foot-and-mouth disease virus (FMDV) cause important transboundary animal diseases (TADs) that have a significant economic impact. The rapid and unequivocal identification of these pathogens and distinction from other animal diseases based on clinical symptoms in the field is difficult. Nevertheless, early pathogen detection is critical in limiting their spread and impact as is the availability of a reliable, rapid, and cost-effective diagnostic test. The purpose of this study was to evaluate the feasibility to identify ASFV, CSFV, and FMDV in field samples using next generation sequencing of short PCR products as a point-of-care diagnostic. We isolated nucleic acids from tissue samples of animals in Mongolia that were infected with ASFV (2019), CSFV (2015), or FMDV (2018), and performed conventional (RT-) PCR using primers recommended by the Terrestrial Animal Health Code of the World Organization for Animal Health (WOAH). The (RT-) PCR products were then sequenced in Mongolia using the MinION nanopore portable sequencer. The resulting sequencing reads successfully identified the respective pathogens that exhibited 91–100% nucleic acid similarity to the reference strains. Phylogenetic analyses suggest that the Mongolian virus isolates are closely related to other isolates circulating in the same geographic region. Based on our results, sequencing short fragments derived by conventional (RT-) PCR is a reliable approach for rapid point-of-care diagnostics for ASFV, CSFV, and FMDV even in low-resource countries.

Pathology of the outbreak of subgenotype 2.5 classical swine fever virus in northern Vietnam

Classical swine fever (CSF) is an endemic disease in southeastern Asia and is one of the most important swine diseases in Vietnam. This study was conducted to characterize the pathology of natural cases of CSF in northern Vietnam in 2018 and their genetic prevalence. A total of 10 representative pigs were collected from four provinces (Hung Yen, Ha Noi, Quang Ninh and Thai Binh) during five outbreaks and examined pathologically. The gross and histopathological findings showed the disease was expressed as the acute or the subacute to chronic form of CSF, depending on the age of the animals. The most consistently observed lesions associated with infection by the classical swine fever virus (CSFV) included lymphoid depletions in tonsils, lymph node and spleen; histiocytic hyperplasia in spleen; cerebral haemorrhage; perivascular cuffing in the brain; renal erythrodiapedesis; urothelial vacuolation and degeneration and interstitial pneumonia. The immunohistochemical findings showed a ubiquitous CSFV antigen mainly in the monocytes/macrophages and in the epithelial and endothelial cells in various organs. CSFV neurotropism was also found in the small neurons of the cerebrum and the ganglia of the myenteric plexus. Analysis of the full-length envelope protein (E2) genome sequence showed that all strains were genetically clustered into subgenotype 2.5, sharing a nucleotide identity of 94.0%-100.00%. Based on the results of this study, the strain was categorized as a moderately virulent CSFV.

Dynamics of Classical Swine Fever Spread in Wild Boar in 2018-2019, Japan

The prolongation of the classic swine fever (CSF) outbreak in Japan in 2018 was highly associated with the persistence and widespread of the CSF virus (CSFV) in the wild boar population. To investigate the dynamics of the CSF outbreak in wild boar, spatiotemporal analyses were performed. The positive rate of CSFV in wild boar fluctuated dramatically from March to June 2019, but finally stabilized at approximately 10%. The Euclidean distance from the initial CSF notified farm to the farthest infected wild boar of the day constantly increased over time since the initial outbreak except in the cases reported from Gunma and Saitama prefectures. The two-month-period prevalence, estimated using integrated nested Laplace approximation, reached >80% in half of the infected areas in March–April 2019. The area affected continued to expand despite the period prevalence decreasing up to October 2019. A large difference in the shapes of standard deviational ellipses and in the location of their centroids when including or excluding cases in Gunma and Saitama prefectures indicates that infections there were unlikely to have been caused simply by wild boar activities, and anthropogenic factors were likely involved. The emergence of concurrent space–time clusters in these areas after July 2019 indicated that CSF outbreaks were scattered by this point in time. The results of this epidemiological analysis help explain the dynamics of the spread of CSF and will aid in the implementation of control measures, including bait vaccination.

Quantitative risk assessment of African swine fever virus introduction to Japan via pork products brought in air passengers' luggage

The spread of African swine fever (ASF) has reached pandemic levels over the last decade, and outbreaks of this disease in China, Mongolia, Vietnam and Cambodia in 2018 and 2019 could accelerate its transmission to neighbouring Asian territories. Thus, the risk that the ASF virus (ASFV) will be introduced to disease-free territories increases each year. Since Japan is an island nation, the most likely way in which ASFV would be introduced is via pork products brought in air passengers' luggage (PPAP). Therefore, in the present study, we assessed the risk of ASFV introduction to Japan via PPAP. For the purposes of this analysis, we considered 214 international commercial flights travelling from 47 origin territories to 31 destination airports as potential routes of ASFV introduction via PPAP. The risk was estimated quantitatively through a stochastic model that considered the volume of air passengers' luggage, the amount of confiscated pork products that were carried in air passengers' luggage and the disease status of the origin territory. The overall mean annual probability of ASFV introduction to Japan via PPAP was found to be 0.941 [95% confidence interval (CI), 0.661-1.000], which approximately corresponds to one introduction every 1.06 years. At the origin territory level, Mongolia was led as the highest risk territory, with a risk of 0.864 (95% CI, 0.434-1.000), followed by China (0.697; 0.223-0.999), Vietnam (0.662; 0.196-0.998) and the Russian Federation (0.136; 0.018-0.401). At the destination airport level, Narita International Airport had the highest risk (0.905; 0.537-1.000), followed by Kansai International Airport (0.496; 0.109-0.961), Tokyo International Airport (0.389; 0.072-0.879) and Chubu Centrair International Airport (0.338; 0.058-0.816). This information will help improve risk management activities and monitoring systems to prevent the introduction of ASFV to Japan.

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.

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.

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.

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.

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.