Subgrouping and analysis of relationships between classical swine fever virus identified during the 2018-2020 epidemic in Japan by a novel approach using shared genomic variants

Pathogenicity of genotype 2.1 classical swine fever virus isolated from Japan in 2019 in pigs

Classical swine fever (CSF) re-emerged in Japan in 2018 for the first time in 26 years. The disease has been known to be caused by a moderately pathogenic virus, rather than the highly pathogenic virus that had occurred in the past. However, the underlying pathophysiology remains unknown. This study conducted an experimental challenge on specific pathogen-free (SPF) pigs in a naïve state for 2, 4, and 6 weeks and confirmed the disease state during each period by clinical observation, virus detection, and pathological necropsy. We revealed the pathological changes and distribution of pathogens and virus-specific antibodies at each period after virus challenge. These results were comprehensively analyzed and approximately 70% of the pigs recovered, especially at 4- and 6-week post-virus challenge. This study provides useful information for future countermeasures against CSF by clarifying the pathogenicity outcomes in unvaccinated pigs with moderately pathogenic genotype 2.1 virus.

Assessing mammal fence crossing and local fence management in relation to classical swine fever spread in Japan

Infectious diseases at the wildlife-livestock-human interface have become a crucial issue, and evidence-based measures are growing increasingly important. One countermeasure against animal diseases in wildlife is using fencing to contain and reduce disease spread and transmission rates between wild populations; however, quantitative assessments on fencing are rare. Moreover, existing research on fencing has highlighted knowledge gaps on the social and ecological aspects relevant to the use and design of fences. To control the spread of classical swine fever, fences were installed from the east to west in Gifu Prefecture, Japan, by March 2019, with the aim of restricting wild boar movement. To clarify the process of installation and maintenance of the fences, we conducted semi-structured interviews with prefectural government officers in Gifu Prefecture. Additionally, we installed infrared-triggered cameras at fence locations with and without gaps to evaluate the fence permeability of mammals. We used a generalized linear mixed model to evaluate the relationship between the presence of gaps and the relative abundance and permeability of each mammal. Our findings showed that the occurrence of gaps was inevitable during the installation and management of wide-area perimeter fence in Japan, partly because of social factors. For example, fences could not be installed on roads that were frequently used by residents and were not adequately maintained owing to budgetary reasons in some cases. Analysis of footage from the infrared-triggered cameras revealed that several mammal species crossed the fence at gaps and even had the ability to cross the gapless parts of the fences. Wild boars crossed through the gaps regularly. It is possible that Sika deer, Japanese serows, raccoons, Japanese badgers, raccoon dogs, Japanese macaques, and feral cats crossed through fence gaps because their relative abundance was high at gap locations. In contrast, Japanese hares slipped through the fence mesh rather than crossing through the gaps. In conclusion, we suggest that coordination and collaboration among related parties, a sufficient supply of fence materials, and securing a budget for fence maintenance are important for fence installation and maintenance. Furthermore, as fence gaps are inevitable, technical development of countermeasures for these gaps could be effective.

Porcine circoviruses in wild boars in Nagano Prefecture, Japan

We investigated the prevalence of porcine circovirus 2 (PCV2) and 3 (PCV3) in wild boars captured or found dead in Nagano Prefecture in 2020. Based on PCR testing, 21 of 254 (8.3%) wild boars were PCV2-positive and 43 of 256 (16.8%) wild boars were PCV3-positive, 5 of 253 (2.0%) wild boars were both PCV2-positive and PCV3-positive. The frequency of detecting PCV3 in wild boars was significantly higher in adults than in juveniles (P=0.014). The PCV2-positive wild boars were found in all districts except for the North Alps and Hokushin, while PCV3-positive wild boars were found in all districts except for Suwa. This is the first report of PCV2 and PCV3 detected in wild boars in Japan.

Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK

The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak via full genome sequencing will be beneficial.

Pig farm vaccination against classical swine fever reduces the risk of transmission from wild boar

In 2018, classical swine fever (CSF) re-emerged in the Gifu Prefecture, central Japan, causing an on-going outbreak among wild boars and domestic pigs in the country. Consequently, oral vaccination for wild boar and compulsory vaccination for pig farms started in 2019. We have previously shown that, before vaccination in the Gifu Prefecture, the presence of CSF-infected wild boar near pig farms increased the risk of CSF transmission. This study aimed to re-evaluate the transmission risk from wild boars to pig farms under a vaccination program. The effectiveness of vaccination was evaluated by comparing the transmission risk estimated before and after the implementation of vaccinations. In this study, we focused on two affected areas, the Kanto (eastern Japan) and Kinki (west-central Japan) regions, in which eight of 11 infected farms were detected between the start of pig farm vaccinations and April 2021. Wild boar surveillance data from an area within a 50-km radius from the infected farms were used for analysis, consisting of 18,870 1-km grid cells (207 infected cells) in the Kanto region, and 15,677 cells (417 infected cells) in the Kinki region. The transmission rates in the post-vaccination period in the Kanto and Kinki regions were much lower than that in the pre-vaccination period in the Gifu Prefecture. The values of transmission kernels (h₀, transmission rate at 0 km) in the Kanto and Kinki regions decreased to 1% of the transmission kernel in the pre-vaccination period. In the pre-vaccination period, the risk of infection within 300 days was almost 95 % when one infected grid cell was detected within 1 km of a pig farm. Meanwhile, in the post-vaccination period, the risk of infection within 300 days was approximately 5% when several infected cells were detected within 1 km of a pig farm. Considering the limited effect of oral vaccination for wild boar due to distribution limitations in the Kanto and Kinki regions, vaccination on pig farms may seems to have mainly reduced the transmission risk from wild boar. However, despite the implementation of vaccination, the risk of infection on pig farms remains present due to the immunity gap of weaning pigs. Therefore, strict biosecurity measures on pig farms and an appropriate vaccination program are required to prevent and control CSF spread.

Genome variability of classical swine fever virus during the 2018-2020 epidemic in Japan

Although RNA viruses exhibit extensive sequence diversity, the mutation rate must be limited to ensure protein functions that maintain the viral life cycle. Here, we compared the whole genome sequences of 150 isolates of classical swine fever virus (CSFV), obtained from a single epidemic that occurred in Japan during 2018-2020. After the detection of the first case, the disease spread among both farm pigs and wild boars and caused severe impact on the pig industry. To evaluate the diversification of the CSFV genome that eliminated mutations negatively affecting viral transmission, the substitution sets inherited by at least two isolates were separately evaluated as shared single nucleotide variants (SNVs) or shared single amino acid variants (SAVs). Comparisons of 12 protein-coding regions indicated that the percentages of SNVs and SAVs in the multifunctional nonstructural protein NS3 were the lowest, and shared SAVs were not detected in another nonstructural protein, NS4A. This demonstrated purifying negative selection suppressing changes in the protein sequences of NS3 and NS4A during virus transmission in the field. In contrast, a high possibility of nonsynonymous substitution among shared SNVs was detected only in genes encoding the secreted protein E^rns and the nonstructural protein NS2, suggesting positive selection during the epidemic. Mapping of shared SAVs to the three-dimensional structure of E^rns revealed that shared SAVs were not present in the substrate-binding sites but were instead localized to the peripheral region of the protein. These data will support efforts toward the development of diagnostic methods, recombinant vaccines, and antiviral agents targeting conserved and indispensable viral genes.