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Genomic characterization of classical swine fever virus LOM variants with 3′-UTR INDELs from pigs on Jeju Island, South Korea

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Guehwan Jang at Kyungpook National University
Guehwan Jang
Joo-Ah Kim
Joo-Ah Kim
Joo-Ah Kim
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Hyekyung Yoo
Hyekyung Yoo
Hyekyung Yoo
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Kyungsu Yang
Kyungsu Yang
Kyungsu Yang
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Abstract

Classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, due to the accidental introduction of the LOM vaccine strain in 2014. Since this reemergence, the previously CSFV-free region has experienced numerous outbreaks, causing the virus to become endemic in provincial herds. In this study, we determined the complete genome sequences and investigated the molecular characteristics of LOM-derived field CSFV strains with unique insertion-deletion (INDEL) mutations in the 3′-untranslated region (UTR) that were responsible for ongoing sporadic outbreaks on Jeju Island in 2019. The Jeju LOM-derived variants that emerged in 2019 had their own INDEL signatures in the 3′-UTR, resulting in changes to the predicted secondary stem-loop structures. The genomes of these strains were 12,297–12,302 nucleotides in length, one nucleotide (nt) shorter or one, two, or four nt longer than the reference LOM strain. The 3′-UTR INDEL variants shared 98.8–99.0% and 98.3–98.6% identity with the LOM strain at the polyprotein and full-genome level, respectively. The total number of genetic variations between the LOM vaccine strain and the 3′-UTR INDEL isolates ranged from 161 to 202 and 37 to 45 at the nucleotide and amino acid level, respectively. These mutations were broadly dispersed throughout the genome and particularly clustered in NS2 and the 3′-UTR, possibly triggering a reversion to low virulence and allowing the virus to adapt to improve its persistence in the field. This study provides important information about the genetic evolution of LOM-derived CSFV circulating in the free region, and suggests that it arose from continuous non-lethal mutations to ensure viral fitness in host animals.
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Vol.:(0123456789)
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Archives of Virology (2020) 165:1691–1696
https://doi.org/10.1007/s00705-020-04651-1
ANNOTATED SEQUENCE RECORD
Genomic characterization ofclassical swine fever virus LOM variants
with3′‑UTR INDELs frompigs onJeju Island, South Korea
GuehwanJang1· Joo‑AhKim2· HyekyungYoo3· KyungsuYang3· Hyoung‑SeokYang4· ChangnamPark4·
KyongjuJeong4· Choi‑KyuPark5· YoungS.Lyoo6· ChangheeLee1
Received: 9 September 2019 / Accepted: 10 April 2020 / Published online: 11 May 2020
© Springer-Verlag GmbH Austria, part of Springer Nature 2020
Abstract
Classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, due to the accidental introduc-
tion of the LOM vaccine strain in 2014. Since this reemergence, the previously CSFV-free region has experienced numer-
ous outbreaks, causing the virus to become endemic in provincial herds. In this study, we determined the complete genome
sequences and investigated the molecular characteristics of LOM-derived field CSFV strains with unique insertion-deletion
(INDEL) mutations in the 3′-untranslated region (UTR) that were responsible for ongoing sporadic outbreaks on Jeju Island
in 2019. The Jeju LOM-derived variants that emerged in 2019 had their own INDEL signatures in the 3′-UTR, resulting in
changes to the predicted secondary stem-loop structures. The genomes of these strains were 12,297–12,302 nucleotides in
length, one nucleotide (nt) shorter or one, two, or four nt longer than the reference LOM strain. The 3′-UTR INDEL variants
shared 98.8–99.0% and 98.3–98.6% identity with the LOM strain at the polyprotein and full-genome level, respectively. The
total number of genetic variations between the LOM vaccine strain and the 3′-UTR INDEL isolates ranged from 161 to 202
and 37 to 45 at the nucleotide and amino acid level, respectively. These mutations were broadly dispersed throughout the
genome and particularly clustered in NS2 and the 3′-UTR, possibly triggering a reversion to low virulence and allowing the
virus to adapt to improve its persistence in the field. This study provides important information about the genetic evolution
of LOM-derived CSFV circulating in the free region, and suggests that it arose from continuous non-lethal mutations to
ensure viral fitness in host animals.
Classical swine fever (CSF) is one of the most serious trans-
boundary viral diseases affecting domestic pigs and wild
boar [1]. Because of its tremendous economic impact on the
global pig industry, CSF is notifiable to the World Organi-
zation for Animal Health (OIE) [12]. The disease is caused
by CSF virus (CSFV), a small, enveloped single-stranded,
(+) sense RNA virus of the genus Pestivirus, family Flavi-
viridae. Recently, the species to which this virus belongs
was renamed "Pestivirus C" [14]. Although CSF has been
successfully eradicated in several countries, it remains spo-
radic or endemic in most parts of the world where there
is industrialized pig production, including Asia, Eastern
Europe, and South and Central America [1]. For effective
CSF control, live attenuated vaccines are used to reduce the
disease burden in most countries where CSFV is endemic
[8]. Similarly, over the past four decades, South Korea has
implemented a nationwide vaccination policy using an
attenuated LOM strain derived from a low-virulence strain
of a Japanese Miyagi isolate to combat CSF [9]. Despite
this national vaccination campaign, only Jeju Province, the
largest island of South Korea, located 80km away from the
mainland at its closest point, successfully became a CSF-
free region in 1999 and maintained its CSF-free status for
over 10years [15]. However, the CSFV reemerged on Jeju
Island in 2014 following the unintentional infection of the
immunologically naïve pig population with the LOM strain
[6, 7]. The LOM vaccine strain has since spread through the
provincial stock farms and has now become endemic in the
Handling Editor: Tim Skern.
Guehwan Jang and Joo-Ah Kim contributed equally to this work
and share co-first authorship.
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s0070 5-020-04651 -1) contains
supplementary material, which is available to authorized users.
* Changhee Lee
changhee@knu.ac.kr
Extended author information available on the last page of the article
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
... Subsequent animal studies have revealed clinical adverse effects of the used LAV-LOM in pigs [17,20]. Since its reemergence, there have been frequent reports of pig farms affected by LAV-LOM-derived CSFV on Jeju Island (Fig. 1), indicating the establishment of endemic CSF that aggravates socioeconomic losses to the provincial pig industry [20,21]. ...
... For the control and eradication of CSF on Jeju Island, the provincial government considered switching to a vaccination policy using desirable vaccines that fulfill the requirements, includingsafetyandtheDIVAconcept,suchasCSFVE2subunit vaccines. Like the LOM vaccine, the LOM-derived field strains circulating in Jeju swine populations are grouped within the genotype 1.1 clade [17,18,21]. Considering these issues, Jeju Island necessitates an effective alternative vaccine [22].Inaddition,theCSF-E2vaccinewasdemonstrated to confer effective protection against multiple genotypes 1.1, 1.2, and 2.1 of CSFV [22][23][24][25]. ...
... The cells were maintained at 37°C in a humidified atmosphere containing 5% CO2. The commercial CSFV LAV-LOM strain (GenBank accession number: MK121886) was obtained from ChoongAng Vaccine Laboratories (CAVAC, Daejeon, Korea) [18] and was propagated in LLC-PK1 cells as described previously [21]. ...
Monitoring and evaluation of provincial classical swine fever immunization implementation with an E2 subunit vaccine in Jeju Island, South Korea
Article
Full-text available
  • Jan 2024
Purpose Accidental vaccination with a live attenuated low-virulence strain of Miyagi (LOM) vaccine led to the reemergence of classical swine fever virus (CSFV) in Jeju province, South Korea in 2014. To control the continual outbreaks of LOM-derived CSFV, the provincial government launched a provincial mass vaccination project using a CSF-E2 subunit vaccine. We conducted this study to assess the herd immunity level and outcomes of E2 vaccine-based immunization in breeding and growing herds on Jeju Island during 2020–2021. Materials and Methods A large-scale vaccination trial using the Bayovac CSF-E2 vaccine investigated its efficacy in breeding and growing herds under farm application conditions (10 CSFV-affected and three CSFV-naïve swine farms). Results The level of herd immunity in each farm was classified into three (S1–S3) and six (G1–G6) profiles in breeding and growing herds, respectively. Immunity monitoring revealed a remarkable improvement in the herd immunity status in all farms. The majority (10/13) of farms, including CSFV-free farms, showed the S1G1 immunity profile in 2021, indicating the appropriate implementation of the advised vaccination regime. Moreover, there were significant decreases in Erns seropositivity from 100% to 50% and 25.9% to 4.3% at farm and pig levels, respectively. In particular, all farms were confirmed as CSFV free in the growing-finishing herds. Conclusion Our large-scale trial demonstrated the effectiveness of the E2 subunit vaccine in establishing herd immunity stabilization and eliminating CSFV circulation in the affected farms and highlighted the need for a provincial vaccination policy to regain the CSF-free status on Jeju Island.
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... However, this provincial non-vaccination policy caused several CSF outbreaks on Jeju Island by the unintentional introduction or injection of the MLV-LOM into CSFV-naïve herds from the mainland of South Korea, drawing suspicion regarding the safety of this sole national commercial vaccine [8,[10][11][12]. Despite the benefits of its use for protection and prevention, the MLV-LOM carries authentic disbenefits of using the live attenuated vaccine, which includes the possibility of reversion to virulence and adverse effects in the field [13,14]. More importantly, like conventional live vaccines, the MLV-LOM has the inherent disadvantage that it cannot serologically differentiate infected from vaccinated animals (DIVA), thereby hampering CSF eradication, especially in endemic areas [2,4]. ...
... Jeju Island, an once CSF-free region, has faced an endemic circumstance since its last resurgence in 2014. The LOM-derived field strains continue to circulate in Jeju pig herds, causing sporadic outbreaks [13]. A vaccination strategy is demanded to impede the circulation of LOM field virus and to eliminate the disease, which needs vaccines, ideally with the safety, efficacy, and DIVA characteristics, such as CSFV E2 subunit marker vaccines. ...
... https://doi.org/10.7774/cevr.2022.11.3.264 scribed previously [13]. ...
Field evaluation of the safety and immunogenicity of a classical swine fever virus E2 subunit vaccine in breeding and nursery animals on Jeju Island, South Korea
Article
Full-text available
  • Sep 2022
Purpose: Classical swine fever (CSF) reemerged on CSF-free Jeju Island where vaccination is not practiced by the unintentional injection of a live attenuated vaccine (modified live attenuated vaccines-low-virulence Miyagi [MLV-LOM]) in 2014. Since the Jeju provincial authority is considering adopting a voluntary immunization policy using a CSF-E2 subunit vaccine to combat LOM-derived CSF endemic, this study aimed to evaluate in Jeju herds. Materials and methods: Two vaccination trials using the Bayovac CSF-E2 vaccine licensed for use in South Korea assessed the safety and humoral immunity of the CSF-E2 vaccine in breeding (trial 1) and nursery animals (trial 2) under farm application conditions. Results: Neither local nor systemic (including reproductive) adverse effects were objectively observed in pregnant sows and young piglets following a respective vaccination regime at pregnancy or weaning, respectively. Trial 1 showed that sows immunized with the CSF-E2 vaccine possessed high and consistent E2-specific and neutralizing antibody levels. The CSF-E2 vaccine-immunized pregnant sows subsequently conferred appropriate and steady passive immunity to their offspring. In trial 2, a double immunization scheme of the CSF-E2 vaccine in piglets at 40 and 60 days of age could elicit a consistent and long-lasting adequate antibody response. Additionally, the two trials detected no Erns-specific antibody responses, indicating that CSF-E2 vaccine can differentiate infected from vaccinated animals (DIVA). Conclusion: Our trial data collectively provide invaluable information on applying the CSF-E2 subunit vaccine to circumvent the possible drawbacks associated with the MLV-LOM concerning the safety, efficacy, and DIVA, in the LOM-endemic field farms and contribute to advanced CSF eradication on Jeju Island.
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... At present, the LOM-derived CSFV strain is endemic in the western region of Jeju Island and undergoing substantial genetic drift (Jang et al., 2019). Furthermore, our previous study reported LOM-derived field CSFV variants with unique insertion-deletion (INDEL) mutations in the 3′-UTR responsible for current sporadic outbreaks on Jeju Island (Jang et al., 2020). Due to suspicion regarding the safety and reversion-to-virulence of the commercial LOM vaccine strain, this study aimed to investigate pathogenic traits of an LOM Jeju variant with 3′-UTR INDEL in vivo. ...
... Due to suspicion regarding the safety and reversion-to-virulence of the commercial LOM vaccine strain, this study aimed to investigate pathogenic traits of an LOM Jeju variant with 3′-UTR INDEL in vivo. (Jang et al., 2020). The viruses were independently propagated in LLC-PK1 cells, as described previously (Jang et al., 2020). ...
... (Jang et al., 2020). The viruses were independently propagated in LLC-PK1 cells, as described previously (Jang et al., 2020). ...
Pathogenicity of a novel classical swine fever LOM vaccine‐derived virus isolated on Jeju Island, South Korea
Article
Full-text available
  • Aug 2022
Background Reemergent local outbreaks of classical swine fever (CSF) occurred simultaneously in multiple pig farms on CSF‐free Jeju Island, South Korea, in 2014 because of inadvertent injection of a commercial CSF (LOM) vaccine into pregnant sows. The LOM virus has since spread across the island and has become endemic in Jeju herds, raising concern about possible reversion to the virulence of the LOM vaccine. We previously isolated LOM‐derived field CSF virus (CSFV) strains with unique insertion‐deletion (INDEL) mutations in the 3′‐untranslated region (UTR), designated LOM‐derived Jeju 3′‐UTR INDEL variants, from CSF‐recurrent swine farms on Jeju Island in 2019. Methods The present study conducted animal experiments to investigate whether a 2019 emergent LOM 3′‐UTR INDEL variant, KNU‐1905, has reverted to a pathogenic form in conventional pigs (n = 10). Results Experimental animal infection showed that pigs inoculated with the commercial LOM vaccine strain developed no adverse effects compared to the sham‐infected pigs. However, KNU‐1905 displayed pathogenic characteristics in pigs, including clinical symptoms (e.g., lethargy, conjunctivitis, nasal discharge, and diarrhoea), weight loss, and gross lesions. Moreover, viremia, virus shedding in faeces and nasal fluids, and viral loads in various tissues of all the KNU‐1905‐infected pigs were highly significant, in contrast to those of the LOM‐infected group in which CSFV RNA was detected only in the serum, nasal, and tonsil samples of one identical pig. Conclusions Overall, the LOM‐derived field isolate with molecular variations induced clinical adverse events in pigs, which commonly shed considerable amounts of CSFV. This study provides evidence that the genetic evolution of the LOM‐derived CSFV circulating on Jeju Island might have allowed the LOM vaccine to recover its primary prototype and that these variants might have induced chronic or persistent infection in pigs that can shed CSFV in field farms leading to a risk of transmission among pigs or farms in this former CSF‐free region.
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... Furthermore, these LOM strains were transmitted from pregnant sows to live offspring, resulting in wide spread of the virus. Another study showed that CSFV field isolates on Jeju Island were most closely related to the LOM strain, but appeared to have undergone substantial changes throughout the entire genome, particularly in the NS2 and 3 -untranslated regions [5]. Moreover, based on the case study carried out on Jeju Island, Korea, these authors noted that the possibility of genetic drift at other hotspots in the process of viral fitness selection cannot be excluded in the future [5]. ...
... Another study showed that CSFV field isolates on Jeju Island were most closely related to the LOM strain, but appeared to have undergone substantial changes throughout the entire genome, particularly in the NS2 and 3 -untranslated regions [5]. Moreover, based on the case study carried out on Jeju Island, Korea, these authors noted that the possibility of genetic drift at other hotspots in the process of viral fitness selection cannot be excluded in the future [5]. Likewise, these studies warn the dangers of using live viral strains for pig vaccination. ...
Field Application of a New CSF Vaccine Based on Plant-Produced Recombinant E2 Marker Proteins on Pigs in Areas with Two Different Control Strategies
Article
Full-text available
  • May 2021
A classical swine fever virus (CSFV)-modified live LOM (low-virulence strain of Miyagi) vaccine (MLV-LOM) to combat CSF has been used in places where the disease is prevalent around the world, including in Korea, except in Jeju Island. In general, modified live virus-based vaccines (MLV) are known to be highly effective in inducing immune responses. At the same time, MLVs also have potential dangers such as a circulation in the field. There is still a need for safer and more effective vaccines to control CSF in the field. In this study, we applied a new CSF vaccine based on plant-produced recombinant E2 marker proteins at two different locations, Jeju Island and a suburb of Pohang, using different CSF control strategies. The result suggested that vaccinated sows in Jeju Island highly developed immunogenicity and maintained stably until 102 days post-vaccination (dpv). Its piglets that received maternal antibodies were shown to carry high serological values and maintained them until 40 days of age, which was the end of the follow-up. Naïve piglets vaccinated at 40 days of age showed high serological values and these were maintained until 100 days of age (60 dpv), which was the end of the follow-up. The vaccine was also effective in inducing immune responses in newborn piglets that carried maternal antibodies received from MLV-LOM vaccine-immunized mother sows.
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... Several reports described the possible emergence of new CSFV strains because of a positive selection pressure (positively selected strains). This evolutionary force resulted from a "bottleneck" effect due to the indiscriminate and mishandled use of conventional vaccines Hu et al., 2016;Jang et al., 2020;Ji et al., 2014;Luo et al., 2017;Pérez et al., 2012;Rios et al., 2017;Shen et al., 2011). Several authors have reported that prolonged suboptimal vaccination programs may have caused changes in the pathogenicity and antigenicity of the new emerging strains that could potentially escape vaccination (Coronado et al., 2019bHu et al., 2016;Jang et al., 2020;Ji et al., 2014;Shen et al., 2011). ...
... This evolutionary force resulted from a "bottleneck" effect due to the indiscriminate and mishandled use of conventional vaccines Hu et al., 2016;Jang et al., 2020;Ji et al., 2014;Luo et al., 2017;Pérez et al., 2012;Rios et al., 2017;Shen et al., 2011). Several authors have reported that prolonged suboptimal vaccination programs may have caused changes in the pathogenicity and antigenicity of the new emerging strains that could potentially escape vaccination (Coronado et al., 2019bHu et al., 2016;Jang et al., 2020;Ji et al., 2014;Shen et al., 2011). This may favour the high prevalence of chronic and persistent CSF, leading to unsuccessful control of the disease. ...
Classical swine fever virus: the past, present and future
Article
Full-text available
  • Sep 2020
Classical swine fever (CSF) is among the most relevant viral epizootic diseases of swine. Due to its severe economic impact, CSF is notifiable to the world organization for animal health. Strict control policies, including systematic stamping out of infected herds with and without vaccination, have permitted regional virus eradication. Nevertheless, CSF virus (CSFV) persists in certain areas of the world and has re-emerged regularly. This review summarizes the basic established knowledge in the field and provides a comprehensive and updated overview of the recent advances in fundamental CSFV research, diagnostics and vaccine development. It covers the latest discoveries on the genetic diversity of pestiviruses, with implications for taxonomy, the progress in understanding disease pathogenesis, immunity against acute and persistent infections, and the recent findings in virus-host interactions and virulence determinants. We also review the progress and pitfalls in the improvement of diagnostic tools and the challenges in the development of modern and efficacious marker vaccines compatible with serological tests for disease surveillance. Finally, we highlight the gaps that require research efforts in the future.
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... Despite decades of efforts, it is still difficult to eliminate CSF in endemically affected regions and re-emerging areas [30,31]. The emergence of moderate or attenuated CSFV strains results in persistent recessive infection and immunosuppression in pigs, making it more challenging to control CSF [32,33]. ...
Anti-Classical Swine Fever Virus Strategies
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  • Apr 2021
Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious swine disease with high morbidity and mortality, which has caused significant economic losses to the pig industry worldwide. Biosecurity measures and vaccination are the main methods for prevention and control of CSF since no specific drug is available for the effective treatment of CSF. Although a series of biosecurity and vaccination strategies have been developed to curb the outbreak events, it is still difficult to eliminate CSF in CSF-endemic and re-emerging areas. Thus, in addition to implementing enhanced biosecurity measures and exploring more effective CSF vaccines, other strategies are also needed for effectively controlling CSF. Currently, more and more research about anti-CSFV strategies was carried out by scientists, because of the great prospects and value of anti-CSFV strategies in the prevention and control of CSF. Additionally, studies on anti-CSFV strategies could be used as a reference for other viruses in the Flaviviridae family, such as hepatitis C virus, dengue virus, and Zika virus. In this review, we aim to summarize the research on anti-CSFV strategies. In detail, host proteins affecting CSFV replication, drug candidates with anti-CSFV effects, and RNA interference (RNAi) targeting CSFV viral genes were mentioned and the possible mechanisms related to anti-CSFV effects were also summarized.
View
A Critical Review about Different Vaccines against Classical Swine Fever Virus and Their Repercussions in Endemic Regions
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  • Feb 2021
Classical swine fever (CSF) is, without any doubt, one of the most devasting viral infectious diseases affecting the members of Suidae family, which causes a severe impact on the global economy. The reemergence of CSF virus (CSFV) in several countries in America, Asia, and sporadic outbreaks in Europe, sheds light about the serious concern that a potential global reemergence of this disease represents. The negative aspects related with the application of mass stamping out policies , including elevated costs and ethical issues, point out vaccination as the main control measure against future outbreaks. Hence, it is imperative for the scientific community to continue with the active investigations for more effective vaccines against CSFV. The current review pursues to gather all the available information about the vaccines in use or under developing stages against CSFV. From the perspective concerning the evolutionary viral process, this review also discusses the current problematic in CSF-endemic countries.
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Classical Swine Fever Outbreak after Modified Live LOM Strain Vaccination in Naive Pigs, South Korea
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  • Apr 2018
We report classical swine fever outbreaks occurring in naive pig herds on Jeju Island, South Korea, after the introduction of the LOM vaccine strain. Two isolates from sick pigs had >99% identity with the vaccine stain. LOM strain does not appear safe; its use in the vaccine should be reconsidered.
View
Proposed revision to the taxonomy of the genus Pestivirus, family Flaviviridae
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  • Aug 2017
We propose the creation of seven new species in the genus Pestivirus (family Flaviviridae) in addition to the four existing species, and naming species in a host-independent manner using the format Pestivirus X. Only the virus species names would change; virus isolates would still be referred to by their original names. The original species would be re-designated as Pestivirus A (original designation Bovine viral diarrhea virus 1), Pestivirus B (Bovine viral diarrhea virus 2), Pestivirus C (Classical swine fever virus) and Pestivirus D (Border disease virus). The seven new species (and example isolates) would be Pestivirus E (pronghorn pestivirus), Pestivirus F (Bungowannah virus), Pestivirus G (giraffe pestivirus), Pestivirus H (Hobi-like pestivirus), Pestivirus I (Aydin-like pestivirus), Pestivirus J (rat pestivirus) and Pestivirus K (atypical porcine pestivirus). A bat-derived virus and pestiviruses identified from sheep and goat (Tunisian sheep pestiviruses), which lack complete coding region sequences, may represent two additional species.
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Classical Swine Fever—An Updated Review
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Full-text available
  • Apr 2017
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. © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.
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Endemic outbreaks due to the re-emergence of classical swine fever after accidental introduction of modified live LOM vaccine on Jeju Island, South Korea
Article
  • Jan 2019
After the unintentional vaccination of the LOM vaccine strain in 2014, classical swine fever virus (CSFV) reemerged in naïve pig herds on Jeju Island, South Korea, which had been a CSF‐free region with a non‐vaccination policy for a decade. Since the re‐emergence, endemic outbreaks of CSFV have occurred in the island, causing enormous damage to provincial pig farms. The present study reports the complete genome sequences and molecular characterization of the LOM‐derived field CSFV strains responsible for the current outbreaks on Jeju Island. The emergent Jeju LOM‐derived isolates shared 98.9–99.7% and 98.7–99.0% nucleotide sequence identity at the E‐gene and whole‐genome levels compared to the LOM vaccine strain, respectively. Genetic and phylogenetic analyses indicated that the CSFV field isolates were closest to the LOM strains, but appeared to have undergone substantial evolution. The total number of nucleotide and amino acid differences between the LOM vaccine strain and LOM‐derived field isolates ranged from 111 and 28 to 148 and 42. These variations were found to be widely distributed throughout the genome and particularly accumulated in non‐structural proteins, which might be associated with the potential for LOM to revert to its original low pathogenic form and subsequent horizontal transmission in Jeju swine herds. These data improve our knowledge regarding safety of the LOM vaccine and inherent risk of reversion to natural virulence in host animals. This article is protected by copyright. All rights reserved.
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Novel poly-uridine insertion in the 3′UTR and E2 amino acid substitutions in a low virulent classical swine fever virus
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  • Jan 2017
In this study, we compared the virulence in weaner pigs of the Pinar del Rio isolate and the virulent Margarita strain. The latter caused the Cuban classical swine fever (CSF) outbreak of 1993. Our results showed that the Pinar del Rio virus isolated during an endemic phase is clearly of low virulence. We analysed the complete nucleotide sequence of the Pinar del Rio virus isolated after persistence in newborn piglets, as well as the genome sequence of the inoculum. The consensus genome sequence of the Pinar del Rio virus remained completely unchanged after 28 days of persistent infection in swine. More importantly, a unique poly-uridine tract was discovered in the 3′UTR of the Pinar del Rio virus, which was not found in the Margarita virus or any other known CSFV sequences. Based on RNA secondary structure prediction, the poly-uridine tract results in a long single-stranded intervening sequence (SS) between the stem-loops I and II of the 3′UTR, without major changes in the stem-loop structures when compared to the Margarita virus. The possible implications of this novel insertion on persistence and attenuation remain to be investigated. In addition, comparison of the amino acid sequence of the viral proteins Erns, E1, E2 and p7 of the Margarita and Pinar del Rio viruses showed that all non-conservative amino acid substitutions acquired by the Pinar del Rio isolate clustered in E2, with two of them being located within the B/C domain. Immunisation and cross-neutralisation experiments in pigs and rabbits suggest differences between these two viruses, which may be attributable to the amino acid differences observed in E2. Altogether, these data provide fresh insights into viral molecular features which might be associated with the attenuation and adaptation of CSFV for persistence in the field.
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Studying Classical Swine Fever Virus: Making the best of a bad virus.
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  • Dec 2014
  • VIRUS RES
Classical swine fever (CSF) is a highly contagious and often fatal disease that affects domestic pigs and wild boars. Outbreak of CSF can cause heavy economic losses to the pig industry. The strategies to prevent, control and eradicate CSF disease are based on containing the disease through a systematic prophylactic vaccination policy and a non-vaccination stamping-out policy. The quest for prevention, control and eradication of CSF has moved research forward in academia and industry, and has produced noticeable advances in understanding fundamental aspects of the virus replication mechanisms, virulence, and led to the development of new vaccines. In this review we summarize recent progress in CSFV epidemiology, molecular features of the genome and proteome, the molecular basis of virulence, and the development of anti-virus technologies. Copyright © 2014. Published by Elsevier B.V.
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Complete genome sequence of a novel porcine parainfluenza virus 5 isolate in Korea
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  • Jun 2013
  • ARCH VIROL
A novel cytopathogenic paramyxovirus was isolated from a lung sample from a piglet, using continuous porcine alveolar macrophage cells. Morphologic and genetic studies indicated that this porcine virus (pPIV5) belongs to the species Parainfluenza 5 in the family Paramyxoviridae. We attempted to determine the complete nucleotide sequence of the first Korean pPIV5 isolate, designated KNU-11. The full-length genome of KNU-11 was found to be 15,246 nucleotides in length and consist of seven nonoverlapping genes (3'-N-V/P-M-F-SH-HN-L-5') predicted to encode eight proteins. The overall degree of nucleotide sequence identity was 98.7 % between KNU-11 and PIV5 (formerly simian virus 5, SV5), a prototype paramyxovirus, and the putative proteins had 74.4 to 99.2 % amino acid identity to those of PIV5. Phylogenetic analysis further demonstrated that the novel pPIV5 isolate is a member of the genus Rubulavirus of the subfamily Paramyxovirinae. The present study describes the identification and genomic characterization of a pPIV5 isolate in South Korea.
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Prevalence of Classical Swine Fever Virus in Domestic Pigs in South Korea: 1999-2011
Article
The major policy for eradication of classical swine fever (CSF) in South Korea has focused on the implementation of compulsory vaccination of the susceptible pig population. A vaccine strain of CSF virus, the LOM strain, is used to maintain high herd seroconversion, a practice complementary to the 'stamping-out policy' and restriction of animal movement during disease outbreaks. To survey for the prevalence of CSF in domestic pigs in South Korea over the past 13 years (1999-2011), we tested 4 193 782 and 1 162 645 samples for antibodies and antigens, respectively. Whereas seropositivity for CSF antibodies has been maintained at over 95% in the mainland, in Jeju Island, where no-vaccination has been administered since 1999, seroprevalence has been below 1% during the last 3 years of study (2009-2011). The highest number of outbreaks in South Korea occurred in 2002 and 2003; since then, outbreaks have decreased each year, with the last CSF outbreak recorded in 2009. No outbreaks have occurred during the past 3 years, and a high level of herd immunity has been maintained in the mainland pig population for 8 years; therefore, South Korea could now switch to a no-vaccination policy throughout the country. However, the constant threat of the re-emergence of the disease in the susceptible pig population should be the main consideration in planning and carrying out the last phase of the CSF eradication process.
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