Molecular epidemiology of porcine reproductive and respiratory syndrome viruses isolated from 1991 to 2013 in Taiwan

Co-circulation of lineage 1 and lineage 3 porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2) in Taiwan during 2018-2024

Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major concern in swine production. This study investigates the molecular epidemiology of lineage 1 and lineage 3 PRRSV-2 in Taiwan between 2018 and 2024. A total of 43,977 samples were collected across 15 counties in Taiwan, and 13,611 tested positive for PRRSV by real-time PCR. Among of them, 501 complete ORF5 sequences were determined and analyzed. The identified PRRSV-2 sequences belonged to either lineage 1 (specifically sublineage L1A which could be divided into at least Clade A, Clade B, and Clade C; 117/501, 23.4 %) or lineage 3 (384/501, 76.6 %). Surprisingly, among the 117 lineage 1 PRRSV-2 sequences, 103 (88.0 %) were from sow-related specimens whereas only 14 (12.0 %) from nursery pigs. Phylogeographic data revealed multiple bidirectional transmissions between central and southern Taiwan, followed by spread to the northern and eastern regions. This imply that the lineage 1 PRRSV-2 caused high mortality and abortion rates in sows and has spread to the entire Taiwan island. The present study provides the first description of the current epidemic state and spread of foreign lineage 1 PRRSV-2 strains in Taiwan during 2018-2024.

Pathogenicity and antigenic characterization of a novel highly virulent lineage 3 porcine reproductive and respiratory syndrome virus 2

BACKGROUND/PURPOSE

Porcine reproductive and respiratory syndrome virus (PRRSV) is a pathogen with a negative economic impact on the global swine industry. In 2019, a suspected highly pathogenic strain, NPUST-108-929/2019 (108-929), was isolated from a pig farm in Pingtung with an outbreak of high mortality and analyzed. The characteristics of PRRSV 108-929 have barely been studied.

METHODS

This study was to evaluate pathogenicity through animal challenge experiments using PRRSV 108-929 and antigenic characterization of this novel PRRSV.

RESULTS

This PRRSV strain is PRRSV 2, belonging to lineage 3 based on open reading frame 5 sequence analysis. Four putative N-linked glycosylation sites (N32, N35, N44 and N51) are located on glycoprotein 5. Experimental results revealed that high fever occurred at 3 days postinoculation (dpi) in the high-titer inoculation (HIN) group (2 × 104 TCID50/mL), 8 dpi in the high-titer contact (HC) group, 4 dpi in the low-titer inoculation (LIN) group (2 × 103 TCID50/mL) and 9 dpi in the low-titer contact (LC) group. All pigs in each PRRSV 108-929 challenge and contact group showed severe clinical signs, such as high fever (>40.5 °C) and significant weight loss. Deaths occurred only in the HIN group; the survival rate was 60 %. All the piglets except the control group piglets showed high viremia titers (6.04-8.28 log10 copies/μL).

CONCLUSION

The pathogenic characteristics of PRRSV 108-929 suggest that it is a highly virulent PRRSV strain at both the farm and laboratory levels.

Analysis of the genetic evolution and recombination of the PRRSV-2 GP2 protein in China from 1996 to 2023

Porcine reproductive and respiratory syndrome (PRRS) is among the most serious infectious diseases of pigs worldwide. It is caused by PRRSV and frequently mutates and recombines. To date, however, there have been relatively few studies that have analyzed the GP2 membrane protein of this virus. In this study, we compared 570 nucleotide sequences of the PRRSV-2 GP2 protein obtained from the NCBI GenBank database, which were subjected to phylogenetic analysis. We selected 64 representative strains to investigate the genetic evolution and recombination of the GP2 protein in China. Lineages 1 and 8 were the most prevalent, while lineages 5 and 8 showed closer genetic relationships. The nucleotide similarities of the 570 GP2 sequences ranged from 83.0% to 100%, with amino acid similarities from 80.2% to 100%. Recombinant analysis indicated lineage 1 strains had the highest recombination probability. Comparison of amino acid sequences showed substitutions without deletions or insertions, with lineage 1 exhibiting the most substitutions and lineage 8 the fewest. These findings enhance understanding of PRRSV-2 genetic variation and provide a foundation for further studies on GP2 and vaccine development.

IMPORTANCE

Porcine reproductive and respiratory syndrome virus (PRRSV) has caused significant losses and posed threats to the swine breeding industry. To date, there have been comparatively few studies on the GP2 protein of PRRSV-2, and consequently, many unanswered questions remain regarding its pathogenicity-associated mechanisms and effects. We collected 570 nucleotide sequences of the GP2 protein of this virus and used these data to perform multifaceted analytical work in order to facilitate the understanding of the genetic evolution of this virus and recombinant mutations. These provide basic data for the follow-up study of GP2 and lay a foundation for further in-depth studies of this virus and vaccine development.

Circulating Lineage 3 Recombination with NADC30-Like and NADC34-Like Betaarterivirus suid 2 in Taiwan

Porcine respiratory and reproductive syndrome (PRRS) caused by Betaarterivirus suid leads to severe economic losses. The emergence of highly pathogenic Betaarterivirus suid 2 (PRRSV-II), such as NADC30 and NADC34, has been reported in the USA and several Asian countries. NADC30-like PRRSV-II was first reported in 2018 in Taiwan. To investigate the PRRSV variants currently circulating in Taiwan, sequences covering ORF2-5 of Taiwan PRRSV isolates collected between 2020 and 2023 were analyzed. Phylogenetic analysis of the ORF5 nucleotide sequence indicated that most of the Taiwan isolates were clustered in lineage 3 and three isolates were grouped in lineage 1 and were closely related to the NADC34 strain. Interestingly, these three NADC34-like Taiwan PRRSV isolates carried amino acid deletions similar to NADC30 and were more closely related to NADC30 strains than the NADC34 strains in the Nsp2 gene. Next-generation sequencing and recombination detection program showed potential recombination of lineage 3 with NADC30- and NADC34-like PRRSV-II. Our results suggest the presence of circulating mosaic recombinants and lineage 3 PRRSV-II in Taiwan during 2020 and 2023.

In Vivo and In Vitro Characterization of the Recently Emergent PRRSV 1-4-4 L1C Variant (L1C.5) in Comparison with Other PRRSV-2 Lineage 1 Isolates

The recently emerged PRRSV 1-4-4 L1C variant (L1C.5) was in vivo and in vitro characterized in this study in comparison with three other contemporary 1-4-4 isolates (L1C.1, L1A, and L1H) and one 1-7-4 L1A isolate. Seventy-two 3-week-old PRRSV-naive pigs were divided into six groups with twelve pigs/group. Forty-eight pigs (eight/group) were for inoculation, and 24 pigs (four/group) served as contact pigs. Pigs in pen A of each room were inoculated with the corresponding virus or negative media. At two days post inoculation (DPI), contact pigs were added to pen B adjacent to pen A in each room. Pigs were necropsied at 10 and 28 DPI. Compared to other virus-inoculated groups, the L1C.5-inoculated pigs exhibited more severe anorexia and lethargy, higher mortality, a higher fraction of pigs with fever (>40 °C), higher average temperature at several DPIs, and higher viremia levels at 2 DPI. A higher percentage of the contact pigs in the L1C.5 group became viremic at two days post contact, implying the higher transmissibility of this virus strain. It was also found that some PRRSV isolates caused brain infection in inoculation pigs and/or contact pigs. The complete genome sequences and growth characteristics in ZMAC cells of five PRRSV-2 isolates were further compared. Collectively, this study confirms that the PRRSV 1-4-4 L1C variant (L1C.5) is highly virulent with potential higher transmissibility, but the genetic determinants of virulence remain to be elucidated.

Genetic Characteristics of Three Single-Farm-Isolated Porcine Reproductive and Respiratory Syndrome Viruses with Novel Recombination among NADC30-Like, JXA1-Like, and QYYZ-Like Strains

Porcine reproductive and respiratory syndrome virus (PRRSV) is an economically devastating pathogenic microorganism that greatly affects the pork industry in the world. The genetic variation and frequent emergence of novel strains greatly hinder the control efforts of PRRSV. Therefore, monitoring the evolutionary dynamics is long and rewarding work for PRRSV researchers and practitioners to make the control strategy. Here, three novel PRRSV strains named CHbj2101, CHbj2102, and CHbj2103 were isolated from different nursery barns with various mortality rates from 6% to 17%, belonging to the same farm, but at different periods of the outbreak. The genomic sequencing and phylogenetic analyses indicated that these three isolates were all clustered with NADC30-like virus CHsx1401, sharing higher genomic similarity from 87.3% to 89.8%, and having the same molecular marker of 131 amino acid residues deletion at their nsp2 coding region, but varied mutagenesis among the antigenic sites in the region of GP2 to GP5. Among the available PRRSV sequences in the GenBank, the isolates CHbj2101 and CHbj2102 display the highest genomic identity (90.1% and 89.8%) with NADC30-like recombinant strain 15LN3, and the rest CHbj2103 shows the highest genomic identity (90.8%) with NADC30-like virus strain 15SC3. The recombination analysis indicated that all three isolates are generated by multiple recombination events among the NADC30-like virus (major parent, Lineage 1), HP-PRRSV vaccine-like virus (minor parent, Lineage 8), and QYYZ-like virus (minor parent, Lineage 3). The isolates CHbj2101 and CHbj2102 shared a similar recombination pattern, but CHbj2103 has a different pattern in nonstructural protein coding regions. To further investigate the recombination characteristics of QYYZ-like strains, we analyzed all available whole genomic sequences of QYYZ-like PRRSV, submitted during the year 1991 and 2021 (n = 83) in China. The result shows that almost all QYYZ-like strains were products of recombination and their immunogenicity or protective protein fragments (nsp2-nsp7 and GP2-GP4) were mainly from QYYZ. These results provide us with some better insight into the evolution process of PRRSV strains in the field and warn us to pay more attention to monitoring and reducing the PRRSV variant on farms to reduce the risk of novel emergence and outbreak.

Lineage 1 Porcine Reproductive and Respiratory Syndrome Virus Attenuated Live Vaccine Provides Broad Cross-Protection against Homologous and Heterologous NADC30-Like Virus Challenge in Piglets

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that endangers the swine industry worldwide. Recently, lineage 1 PRRSVs, especially NADC30-like PRRSVs, have become the major endemic strains in many pig-breeding countries. Since 2016, NADC30-like PRRSV has become the predominant strain in China. Unfortunately, current commercial vaccines cannot provide sufficient protection against this strain. Here, an attenuated lineage 1 PRRSV strain, named SD-R, was obtained by passaging an NADC30-like PRRSV strain SD in Marc-145 cells for 125 passages. Four-week-old PRRSV-free piglets were vaccinated intramuscularly with 105.0TCID50 SD-R and then challenged intramuscularly (2 mL) and intranasally (2 mL) with homologous NADC30-like PRRSV SD (1 × 105.0TCID50/mL) and heterologous NADC30-like PRRSV HLJWK108-1711 (1 × 105.0TCID50/mL). The results showed that antibodies against specific PRRSVs in 5 of 5 immunized piglets were positive after a 14-day post-vaccination and did not develop fever or clinical diseases after NADC30-like PRRSV challenges. Additionally, compared with challenge control piglets, vaccinated piglets gained significantly more weight and showed much milder pathological lesions. Furthermore, the viral replication levels of the immunized group were significantly lower than those of the challenge control group. These results demonstrate that lineage 1 PRRSV SD-R is a good candidate for an efficacious vaccine, providing complete clinical protection for piglets against NADC30-like PRRSVs.

Evaluation of a type 2 modified live porcine reproductive and respiratory syndrome vaccine against heterologous challenge of a lineage 3 highly virulent isolate in pigs

Porcine reproductive and respiratory syndrome (PRRS) is one of the most common diseases in the global swine industry. PRRSV is characterized by rapid mutation rates and extensive genetic divergences. It is divided into two genotypes, which are composed of several distinct sub-lineages. The purpose of the present study was to evaluate the cross-protective efficacy of Fostera PRRS MLV, an attenuated lineage 8 strain, against the heterologous challenge of a lineage 3 isolate. Eighteen pigs were randomly divided into mock, MLV and unvaccinated (UnV) groups. The pigs in the MLV group were administered Fostera PRRS vaccine at 3 weeks of age and both the MLV and UnV groups were inoculated with a virulent PRRSV isolate at 7 weeks. Clinically, the MLV group showed a shorter duration and a lower magnitude of respiratory distress than the UnV group. The average days of fever in the MLV group was 3.0 ± 0.5, which was significantly lower than the 6.2 ± 0.5 days of the UnV group (P < 0.001). The average daily weight gains of the mock, MLV and UnV groups were 781 ± 31, 550 ± 44 and 405 ± 26 g/day, respectively, during the post-challenge phase. The pathological examinations revealed that the severity of interstitial pneumonia in the MLV group was milder compared to the UnV group. Furthermore, PRRSV viremia titers in the MLV pigs were consistently lower (10¹−10^1.5 genomic copies) than those of the UnV pigs from 4 to 14 DPC. In conclusion, vaccination with Fostera PRRS MLV confers partial cross-protection against heterologous challenge of a virulent lineage 3 PRRSV isolate.

Two novel recombinant porcine reproductive and respiratory syndrome viruses belong to sublineage 3.5 originating from sublineage 3.2

Porcine reproductive and respiratory syndrome virus (PRRSV) is an agent of porcine reproductive and respiratory syndrome (PRRS), which causes substantial economic losses to the swine industry. PRRSV displays rapid variation, and five lineages coexist in mainland China. Lineage 3 PRRSVs emerged in mainland China in 2005 and prevailed in southern China after 2010. In the present study, two lineage 3 PRRSV strains, which are named SD110-1608 and SDWH27-1710, were isolated from northern China in 2017. To explore the characteristics and origins of the two strains, we divided lineage 3 into five sublineages (3.1-3.5) based on 146 open reading frame (ORF) 5 sequences. Both strains and the strains isolated from mainland China were classified into sublineage 3.5. Lineage 3 PRRSVs isolated from Taiwan and Hong Kong were classified into sublineages 3.1-3.3 and sublineage 3.4, respectively. Recombination analysis revealed that SD110-1608 and SDWH27-1710 were derived from recombination of QYYZ (major parent strain) and JXA1 (minor parent strain). Sequence alignment showed that SD110-1608 and SDWH27-1710 shared a 36-aa insertion in Nsp2 with QYYZ isolated from Guangdong Province in 2010. Based on the evolutionary relationship among GP2a, GP3, GP4, GP5 and N proteins between sublineages 3.2 (FJ-1) and 3.5 (FJFS), we speculated that sublineage 3.5 (mainland China) originated from sublineage 3.2 (Taiwan, China). This study provides important information regarding the classification and transmission of lineage 3 PRRSVs.

A comparably high virulence strain of porcine reproductive and respiratory syndrome virus isolated in Taiwan

Porcine reproductive and respiratory syndrome virus (PRRSV) has been endemic in Taiwan since 1991. This study aimed to present a highly virulent PRRSV in Taiwan based on farm data collection and both in vitro and in vivo evaluations in virus challenge studies. This virulent PRRSV strain was first noticed on Farm TSYM due to continuously high nursery mortality rate and severe PRRSV-associated pneumonia. In phylogenetic surveillance, the PRRSV TSYM-strain remained in the predominant position for years, even with several other PRRSV strain invasions. In laboratory challenge trials, the TSYM-strain led to prolonged pyrexia, growth retardation, high mortality rates and high viremia titer that similar to the highly pathogenic PRRSV. The TSYM-strain isolate also triggered early interleukin-10 up-regulation and significantly higher infection rates under in vitro experiments. This study provides information of a comparably virulent strain in Taiwan and its appearance in both farm and laboratory levels.

Emergence of a virulent porcine reproductive and respiratory syndrome virus in Taiwan in 2018

In March 2018, an abortion storm caused by porcine reproductive and respiratory syndrome virus was confirmed in a farrow‐to‐finish pig herd in Taiwan. Open reading frame 5 and non‐structural protein 2 of the virus confirmed that the virus is closely related to the virulent strains circulating in the United States.

Genomic characteristics and pathogenicity of natural recombinant porcine reproductive and respiratory syndrome virus 2 harboring genes of a Korean field strain and VR-2332-like strain

Porcine reproductive and respiratory syndrome (PRRS), an economically-important disease caused by PRRS virus (PRRSV), has become endemic to most pig-producing countries. Point mutation and recombination are responsible for genetic heterogeneity, resulting in circulation of genetically-diverse strains. However, no natural recombinant PRRSV has yet been identified in Korea. Here, we successfully isolated natural recombinant PRRSV-2 (KU-N1202) using cell culture, investigated its genomic characteristics, and further evaluated its pathogenicity. KU-N1202 is a recombinant strain between Korean MN184-like and VR-2332-like strains. Specifically, ORF5 to partial ORF7 of the VR-2332-like strain was inserted into the backbone of a CP07-626-2-like strain. KU-N1202 induced mild-to-moderate clinical signs and mild histopathological changes with low viral loads in challenged pigs. Contact pigs showed minimal clinical signs and lower viral loads than those in the challenge group. This study demonstrates the genomic characteristics and pathogenicity of natural recombinant PRRSV-2, illustrating the potential importance of recombination in the field.

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A natural recombinant PRRSV-2 virus (KU-N1202) was isolated using cell culture.

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The virus harbored the genes from field strain and VR-2332-like strain.

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KU-N1202 induced mild-to-moderate clinical signs with low viral loads in challenged pig.

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Contact pigs showed minimal clinical signs with relatively low viral loads.

Emergence of novel recombination lineage 3 of porcine reproductive and respiratory syndrome viruses in Southern China

Lineage 3 of porcine reproductive and respiratory syndrome viruses, which belong to North America type 2, has a long epidemic history in China. The novel lineage 3 viruses constantly emerging in recent years are characterized by a high detection rate and significant pathogenicity. In this study, we investigated the prevalence of lineage 3 in southern China and selected two isolated strains for genome and virulence analyses. A cross-sectional epidemiology investigation indicated that the prevalence of lineage 3 antigens was 35.68% (95% CI: 27.6-44.3%) among 227 samples collected from over 100 infected farms from January 2016 to July 2017 in southern China. Two novel isolates of lineage 3 were selected. After 20 passages, Marc-145 cells were not susceptible to those viruses. Full-length genome analysis indicated that the two strains share 95.2% homology with each other and 95.7%-96.2% with highly pathogenic porcine reproductive and respiratory syndrome viruses (HP-PRRSVs; JXA1-like strain, lineage 8.7). Phylogenetic and molecular evolutionary results showed that for the two isolates, HP-PRRSV provides most of the ORF1 gene. Animal experiment revealed discrepancies in virulence between the strains. Although challenge resulted in 100% morbidity, the isolate carrying most of the HP-PRRSV ORF1 caused severe clinical symptoms and 40% mortality, whereas the other isolate containing part of the ORF1 gene caused no mortality. Overall, these findings suggest that lineage 3 viruses might be commonly circulating in most of southern China. Frequent recombination events within HP-PRRSVs of this lineage with changing virulence could represent potential threats to the pig industry.