Identification of Two Porcine Reproductive and Respiratory Syndrome Virus Variants Sharing High Genomic Homology but with Distinct Virulence

A chimeric porcine reproductive and respiratory syndrome virus 1 strain containing synthetic ORF2-6 genes can trigger T follicular helper cell and heterologous neutralizing antibody responses and confer enhanced cross-protection

The prevalence of porcine reproductive and respiratory syndrome virus 1 (PRRSV1) isolates has continued to increase in Chinese swine herds in recent years. However, no effective control strategy is available for PRRSV1 infection in China. In this study, we generated the first infectious cDNA clone (rHLJB1) of a Chinese PRRSV1 isolate and subsequently used it as a backbone to construct an ORF2-6 chimeric virus (ORF2-6-CON). This virus contained a synthesized consensus sequence of the PRRSV1 ORF2-6 gene encoding all the envelope proteins. The ORF2-6 consensus sequence shared > 90% nucleotide similarity with four representative strains (Amervac, BJEU06-1, HKEU16 and NMEU09-1) of PRRSV1 in China. ORF2-6-CON had replication efficacy similar to that of the backbone rHLJB1 virus in primary alveolar macrophages (PAMs) and exhibited cell tropism in Marc-145 cells. Piglet inoculation and challenge studies indicated that ORF2-6-CON is not pathogenic to piglets and can induce enhanced cross-protection against a heterologous SD1291 isolate. Notably, ORF2-6-CON inoculation induced higher levels of heterologous neutralizing antibodies (nAbs) against SD1291 than rHLJB1 inoculation, which was concurrent with a higher percentage of T follicular helper (Tfh) cells in tracheobronchial lymph nodes (TBLNs), providing the first clue that porcine Tfh cells are correlated with heterologous PRRSV nAb responses. The number of SD1291-strain-specific IFNγ-secreting cells was similar in ORF2-6-CON-inoculated and rHLJB1-inoculated pigs. Overall, our findings support that the Marc-145-adapted ORF2-6-CON can trigger Tfh cell and heterologous nAb responses to confer improved cross-protection and may serve as a candidate strain for the development of a cross-protective PRRSV1 vaccine.

Isolation, identification, recombination analysis and pathogenicity experiment of a PRRSV recombinant strain in Sichuan Province, China

Since 2013, the porcine reproductive and respiratory syndrome virus type 2 (PRRSV-2), lineage 1.8 (NADC30-like PRRSV) has emerged and become widely prevalent in China. The NADC30-like PRRSV poses significant challenges for disease control, primarily because of its propensity for frequent mutations and recombinations. We successfully isolated and identified a NADC30-like strain, designated SCCD22, in Chengdu, Sichuan Province, China. We meticulously examined the genetic recombination properties and evaluated its pathogenicity in 28-day-old piglets. SCCD22 showed 93.02% nucleotide homology with the NADC30 PRRSV strain, and its non-structural protein 2 coding region showed the same 131 amino acid deletion pattern as that seen in NADC30. Furthermore, we identified two recombination events in SCCD22: one in the NSP2 region (1,028-3,290 nt), where it was highly similar to the JXA1-like strain GZ106; and another in the NSP10 ~ 12 region (9,985-12,279 nt), closely resembling the NADC30-like strain CY2-1604. Piglets infected with SCCD22 exhibited clinical symptoms such as elevated body temperature, prolonged fever, reduced appetite, and roughened fur. Postmortem examinations underscored the typical lung pathology associated with PRRSV, indicating that the lungs were the primary affected organs. Furthermore, extended viral shedding accompanied by progressive viremia was observed in the serum and nasal excretions of infected piglets. In summary, this study reports a domestic PRRSV recombination strain in the Sichuan Province that can provide critical insights into preventing and controlling PRRSV in this region.

Epidemiology and Genetic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in the Hunan and Hebei Provinces of China

Porcine reproductive and respiratory syndrome virus (PRRSV) is a significant threat to the pig industry in China. However, the epidemiological characteristics of PRRSV after the outbreak of African swine fever in China were not thoroughly investigated. In the present study, the serological and epidemiological investigations of PRRSV in pigs from the Hunan and Hebei provinces of China were assessed. The results showed that 73.12% (95% CI 71.74-74.49) of pigs were positive for PRRSV-special antibody by enzyme-linked immunosorbent assay. Out of 5799 samples, 482 (8.31%, 95% CI 7.60-9.02) samples were positive for PRRSV nucleic acids. The positive rates of PRRSV in healthy pigs from farms and slaughterhouses were 2.27% (47/2072) and 7.70% (217/2818), which were lower than that in diseased pigs (23.98%, 218/909). Furthermore, the full-length OFR5 gene sequences of 43 PRRSV strains were sequenced and analysed. Phylogenetic analysis revealed that 43 isolates were classified into three lineages, namely lineage 1 (n = 24), lineage 8 (n = 15), and lineage 3 (n = 4). Lineage 1 could be further divided into sublineage 1.5 (n = 2) and sublineage 1.8 (n = 22), and lineage 8 was classified into sublineage 8.1 (n = 3) and sublineage 8.7 (n = 12). Collectively, our findings revealed the severe prevalence of PRRSV in the Hunan and Hebei provinces, where sublineage 1.8 and sublineage 8.7 predominated. The present study provides the update information of the epidemiological and genetic characteristics of PRRSV in the investigated regions, which will be beneficial for PRRS control.

Molecular Characterization of the Nsp2 and ORF5s of PRRSV Strains in Sichuan China during 2012-2020

Porcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen that poses a serious threat to the global pig industry. Sichuan Province is one of the largest pig breeding provinces in China. There is a lack of reports on the continuous surveillance and systematic analysis of prevalent strains of PRRSV in Sichuan Province in recent years. To fill this gap, a total of 539 samples were collected from 13 breeding regions in Sichuan during 2012-2020. The detection result showed that the positive rate of PRRSV was 52.32% (282/539). The ORF5s and Nsp2 were obtained and further analyzed, with Chinese reference strains downloaded from the GenBank. Phylogenetic analysis showed that the PRRSV strains sequenced in this study belonged to PRRSV-1 and PRRSV-2 (lineage 1, 3, 5 and 8). In total, 168 PRRSV-2 strains were selected for ORF5 analyses, and these strains were classified into sub-lineage 8.7 (HP-PRRSV), sub-lineage 5.1 (classical PRRSV), sub-lineage 1.8 (NADC30-like), sub-lineage 1.5 (NADC34-like) and sub-lineage 3.5 (QYYZ-like), accounting for 60.71% (102/168), 11.31% (19/168), 18.45% (31/168), 2.97% (5/168) and 6.55% (11/168) of the total analyzed strains, respectively. The Nsp2 of identified PRRSV strains exhibited a nucleotide identity of 44.5-100%, and an amino acid identity of 46.82-100%. The ORF5 of the identified PRRSV strains exhibited a nucleotide identity of 81.3-100%, and an amino acid identity of 78.5-100%. A sequence analysis of ORF5 revealed that the mutation sites of GP5 were mainly concentrated in HVR1 and HVR2 and the virulence sites. In summary, the HP-PRRSV, NADC30-like PRRSV, Classic-PRRSV, QYYZ-like PRRSV, NADC34-like PRRSV and PRRSV-1 strains exist simultaneously in pigs in Sichuan. NADC30-like PRRSV was gradually becoming the most prevalent genotype currently in Sichuan province. This study suggested that PRRSV strains in Sichuan were undergoing genomic divergence.

CD163-Expressing Porcine Macrophages Support NADC30-like and NADC34-like PRRSV Infections

Porcine reproductive and respiratory syndrome virus (PRRSV) has a strict cell tropism. In addition to the primary alveolar macrophages, PRRSV is strictly cytotropic to African green monkey kidney cells, such as MARC-145 cells; however, MARC-145 cells are not infected by most NADC30-like and NADC34-like PRRSV strains. The essential scavenger receptor CD163 has been proved to mediate productive infection of PRRSV in various non-permissive cell lines. In this study, we systematically tested the porcine CD163 stably expressing 3D4/21 cells for infections with various PRRSV strains. The results showed that the porcine CD163-expressing macrophages support the infections of PRRSV2 of lineages 1, 5, and 8, as evidenced by Western blotting, immunofluorescence assay, quantitative PCR, and virus titration assay. Considering the current prevalence of NADC30-like and NADC34-like PRRSV2 of lineage 1 in China, the CD163-expressing macrophages are very useful for PRRSV research and disease management.

Systemic Homologous Neutralizing Antibodies Are Inadequate for the Evaluation of Vaccine Protective Efficacy against Coinfection by High Virulent PEDV and PRRSV

G2 porcine epidemic diarrhea virus (G2 PEDV) and highly pathogenic porcine reproductive and respiratory syndrome virus 2 (HP-PRRSV2) are two of the most prevalent swine pathogens in China's swine herds, and their coinfection occurs commonly. Several PED and PRRS vaccines have been utilized in China for decades, and systemic homologous neutralizing antibodies (shnAbs) in serum are frequently used to evaluate the protective efficacy of PED and PRRS vaccines. To develop a vaccine candidate against G2 PEDV and HP-PRRSV2 coinfection, in this study, we generated a chimeric virus (rJSTZ1712-12-S) expressing S protein of G2 PEDV using an avirulent HP-PRRSV2 rJSTZ1712-12 infectious clone as the viral vector. The rJSTZ1712-12-S strain has similar replication efficacies as the parental rJSTZ1712-12 virus. In addition, animal inoculation indicated that rJSTZ1712-12-S is not pathogenic to piglets and can induce shnAbs against both G2 PEDV and HP-PRRSV2 isolates after prime-boost immunization. However, passive transfer study in neonatal piglets deprived of sow colostrum showed that rJSTZ1712-12-S-induced shnAbs may only decrease PEDV and PRRSV viremia but cannot confer sufficient protection against dual challenge of high virulent G2 PEDV XJ1904-34 strain and HP-PRRSV2 XJ17-5 isolate. Overall, this study provides the first evidence that shnAbs confer insufficient protection against PEDV and PRRSV coinfection and are inadequate for the evaluation of protective efficacy of PED and PRRS bivalent vaccine (especially for the PED vaccine). IMPORTANCE Porcine epidemic diarrhea virus (PEDV) and porcine reproductive and respiratory syndrome virus (PRRSV) coinfection occurs commonly and can synergistically reduce feed intake and pig growth. Vaccination is an effective strategy utilized for PED and PRRS control, and systemic homologous neutralizing antibodies (shnAbs) in serum are commonly used for protective efficacy evaluation of PED and PRRS vaccines. Currently, no commercial vaccine is available against PEDV and PRRSV coinfection. This study generated a chimeric vaccine candidate against the coinfection of prevalent PEDV and PRRSV in China. The chimeric strain can induce satisfied shnAbs against both PEDV and PRRSV after prime-boost inoculation in pigs. But the shnAbs cannot confer sufficient protection against PEDV and PRRSV coinfection in neonatal piglets. To the best of our knowledge, these findings provide the first evidence that shnAbs confer insufficient protection against PEDV and PRRSV coinfection and are inadequate for evaluating PED and PRRS bivalent vaccine protective efficacy.

Minor and major envelope proteins of PRRSV play synergistic roles in inducing heterologous neutralizing antibodies and conferring cross protection

High genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV) isolates is a major obstacle for the development of effective PRRS vaccines. A chimeric highly pathogenic PRRSV2 (HP-PRRSV2) strain containing the consensus sequence of ORF2-6 genes was constructed in our previous study, which could induce broadly neutralizing antibodies (bnAbs) and confer satisfied cross protection against virulent NADC30-like isolate. To further elucidate the roles of minor and major envelope proteins encoded by ORF2-4 and ORF5-6 genes in conferring cross protection, two chimeric HP-PRRSV2 strains (rJS-ORF2-4-CON and rJS-ORF5-6-CON) containing consensus sequences of ORF2-4 or ORF5-6 were constructed and rescued in this study. The rJS-ORF5-6-CON strain has similar replication efficiency as the backbone HP-PRRSV2 rJSTZ1712-12 virus, while rJS-ORF2-4-CON has significantly lower in vitro and in vivo replication efficiency comparing to rJS-ORF5-6-CON. Animal inoculation indicated that both rJS-ORF2-4-CON and rJS-ORF5-6-CON did not cause obvious clinical signs in piglets and could induce heterologous nAbs after immunization. Challenge with a virulent heterologous NADC30-like SD17-38 isolate showed that even though both immunized groups presented lower viremia, faster virus elimination, less fever and alleviated lung gross lesions when compared with the only challenged pigs, rJS-ORF2-4-CON and rJS-ORF5-6-CON could not confer enough cross protection. Considering the bnAbs and satisfied cross protection induced by the chimeric virus containing ORF2-6 consensus sequence, our results support that minor and major envelope proteins play synergistic roles in inducing broader nAbs and conferring better cross protection.

Epidemiological and Genetic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in South China Between 2017 and 2021

Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major threat to the swine industry in China and has caused enormous losses every year. To monitor the epidemiological and genetic characteristics of PRRSV in South China, 6,795 clinical samples from diseased pigs were collected between 2017 and 2021, and 1,279 (18.82%) of them were positive for PRRSV by RT-PCR detecting the ORF5 gene. Phylogenetic analysis based on 479 ORF5 sequences revealed that a large proportion of them were highly-pathogenic PRRSVs (409, 85.39%) and PRRSV NADC30-like strains (66, 13.78%). Furthermore, 93.15% of these highly-pathogenic strains were found to be MLV-derived. We next recovered 11 PRRSV isolates from the positive samples and generated the whole genome sequences of them. Bioinformatic analysis showed that seven isolates were MLV-derived. Besides, six isolates were found to be recombinant strains. These eleven isolates contained different types of amino acid mutations in their GP5 and Nsp2 proteins compared to those of the PRRSVs with genome sequences publicly available in GenBank. Taken together, our findings contribute to understanding the prevalent status of PRRSV in South China and provide useful information for PRRS control especially the use of PRRSV MLV vaccines.

The Construction and Immunogenicity Analyses of Recombinant Pseudorabies Virus With NADC30-Like Porcine Reproductive and Respiratory Syndrome Virus-Like Particles Co-expression

Porcine reproductive and respiratory syndrome (PRRS) and pseudorabies (PR) are highly infectious swine diseases and cause significant financial loss in China. The respiratory system and reproductive system are the main target systems. Previous studies showed that the existing PR virus (PRV) and PRRS virus (PRRSV) commercial vaccines could not provide complete protection against PRV variant strains and NADC30-like PRRSV strains in China. In this study, the PRV variant strain XJ and NADC30-like PRRSV strain CHSCDJY-2019 are used as the parent for constructing a recombinant pseudorabies virus (rPRV)-NC56 with gE/gI/TK gene deletion and co-expressing NADC30-like PRRSV GP5 and M protein. The rPRV-NC56 proliferated stably in BHK-21 cells, and it could stably express GP5 and M protein. Due to the introduction of the self-cleaving 2A peptide, GP5 and M protein were able to express independently and form virus-like particles (VLPs) of PRRSV in rPRV-NC56-infected BHK-21 cells. The rPRV-NC56 is safe for use in mice; it can colonize and express the target protein in mouse lungs for a long time. Vaccination with rPRV-NC56 induces PRV and NADC30-like PRRSV specific humoral and cellular immune responses in mice, and protects 100% of mice from virulent PRV XJ strain. Furthermore, the virus-neutralizing antibody (VNA) elicited by rPRV-NC56 showed significantly lower titer against SCNJ-2016 (HP-PRRSV) than that against CHSCDJY-2019 (NADC30-like PRRSV). Thus, rPRV-NC56 appears to be a promising candidate vaccine against NADC30-like PRRSV and PRV for the control and eradication of the variant PRV and NADC30-like PRRSV.

A Systematic Investigation Unveils High Coinfection Status of Porcine Parvovirus Types 1 through 7 in China from 2016 to 2020

Porcine parvovirus genotype 1 (PPV1) causes reproductive disorder in swine and is prevalent in China. Recently, six new genotypes of PPVs (PPV2 through PPV7) have also been detected in Chinese swine herds. However, the coinfection status of all these seven genotypes of PPVs (PPV1-7) in China was not clarified yet. In this study, we developed a panel of PPV1–7 PCR assays with satisfied specificity, sensitivity and reproducibility and then applied to the detection of PPV1–7 in 435 clinical samples collected from eight provinces of China in 2016–2020. A total of 55.40% samples (241 out of 435) were PPV positive, while PPV2 and PPV3 (both 22.53%) belonging to the genus of Tetraparvovirus were the most prevalent genotypes. Noticeably, PPV1–7 strains were more prevalent in nursery and finishing pigs than in suckling pigs. In addition, coinfection could be detected in all eight provinces and 27.36% (119/435) samples were coinfected with two to five genotypes of PPVs. Meanwhile, the coinfection of PPVs with PCV2 was 22.30% (97/435). Twenty complete genomes of representative PPV1–7 were determined, and phylogenetic analysis confirmed the genotyping results by sequence comparisons and PCR assays. Remarkably, the PPV7 HBTZ20180519-152 strain from domestic pig was recombined from parental JX15-like and JX38-like isolates from wild boars. Selective pressure analysis based on VP2 sequences of PPV1–7 showed that they were predominantly under negative selection, while few positive selection sites could be detected in VP2 of PPV7. Overall, this systematic investigation unveils high prevalence and coinfection of PPV1–7 in China from 2016 to 2020.

IMPORTANCE Porcine parvoviruses (PPVs) are prevalent in China associating with reproductive failure in swine. The coinfection of seven genotypes of PPVs (PPV1-7) might have synergistic effects on PPV1 associated SMEDI syndrome. However, the coinfection status of PPV1–7 in China is not clear yet. This study showed that PPV1–7 strains are highly prevalent (55.40%) in China and mainly in nursery and finishing pigs in recent years. In addition, the coinfections of different genotypes of PPVs (27.36%) and PPVs with PCV2 (22.30%) are common. Geographic analysis indicated that different genotypes of PPVs are widely cocirculating in China. Intriguingly, a PPV7 strain from the domestic pig was detected as a recombinant from two wild boar isolates. Selective pressure analyses showed that PPV1–7 are mainly under purifying selection. Our findings provide the first systematic investigation on the prevalence, coinfection, and evolution of PPV1 through PPV7 in Chinese swineherds from 2016 to 2020.

Screening of Porcine Innate Immune Adaptor Signaling Revealed Several Anti-PRRSV Signaling Pathways

Porcine reproductive and respiratory syndrome virus (PRRSV) causes PRRS and is known to effectively suppress host innate immunity. The current strategies for controlling PRRSV are limited and complete understanding of anti-PRRSV innate immunity is needed. Here, we utilized nine porcine innate immune signaling adaptors which represent all currently known innate immune receptor signaling pathways for screening of anti-PRRSV activity. The analysis of PRRSV N gene transcription and protein expression both suggested that the multiple ectopic adaptors exhibited varying degrees of anti-PRRSV activities, with TRIF and MAVS most effective. To better quantify the PRRSV replication, the GFP signal of PRRSV from reverse genetics were measured by flow cytometry and similarly varying anti-PRRSV activities by different signaling adaptors were observed. Based on the screening data, and considering the importance of viral nucleic acid in innate immune response, endogenous TRIF, MAVS and STING were selected for further examination of anti-PRRSV activity. Agonist stimulation assay showed that MAVS and STING signaling possessed significant anti-PRRSV activities, whereas siRNA knockdown assay showed that TRIF, MAVS and STING are all involved in anti-PRRSV activity, with TLR3-TRIF displaying discrepancy in anti-PRRSV infection. Nevertheless, our work suggests that multiple pattern recognition receptor (PRR) signaling pathways are involved in anti-PRRSV innate immunity, which may have implications for the development of future antiviral strategies.

The Innate Immune DNA Sensing cGAS-STING Signaling Pathway Mediates Anti-PRRSV Function

Porcine reproductive and respiratory syndrome virus (PRRSV) modulates host innate immunity which plays a key role against PRRSV infection. As a RNA virus, PRRSV is mainly sensed by innate immune RNA receptors, whereas the role of innate immune DNA sensors in the PRRSV infection has not been elucidated. Here, we investigated the roles of DNA sensing cGAS-STING pathway in both PRRSV infected Marc-145 cells and porcine macrophages. The results show that in Marc-145 cells, the stable expression of STING with or without stimulations exhibited anti-PRRSV activity, and STING knockout heightened PRRSV infection. In CD163-3D4/21 porcine macrophages, either expression of STING or stimulation of cGAS-STING signaling obviously suppressed PRRSV infection, whereas in STING knockdown macrophages, the PRRSV infection was upregulated. Our results clearly demonstrate that the host cGAS-STING signal exerts an important antiviral role in PRRSV infection.

Transcriptomic profiling reveals different innate immune responses in primary alveolar macrophages infected by two highly homologous porcine reproductive and respiratory syndrome viruses with distinct virulence

Porcine reproductive and respiratory syndrome virus (PRRSV) isolates show high genetic and pathogenic diversity. The mechanisms underlying different virulence of PRRSV isolates are still not fully clarified. Two highly homologous PRRSV isolates (XJ17-5 and JSTZ1712-12) with distinct virulence were identified in our previous study. To evaluate the association between host responses and different virulence, here we investigated the transcriptomic profiles of porcine alveolar macrophages (PAMs) infected with these two isolates. RNA-Seq results showed that there are 1932 differential expression genes (DEGs) between two PRRSV infected groups containing 1067 upregulation and 865 downregulation genes. Compared with the avirulent JSTZ1712-12 infected group, GO analysis identified significant enrichment gene sets not only associated with virus infection but also innate immune response in the virulent XJ17-5 infected group. In addition, KEGG analysis indicated significantly enriched genes associated with NOD-like and RIG-I-like receptor signaling pathways in XJ17-5 vs JSTZ1712-12 group. Furthermore, XJ17-5 isolate induced significantly higher levels of innate immune response associated genes (IL-1β, CXCL2, S100A8, OAS2, MX1, IFITM3, ISG15 and IFI6) than JSTZ1712-12 isolate, which were further confirmed by real-time PCR. Given that these two isolates share similar replication efficiency in vivo and in vitro, our results indicated that distinct virulence of PRRSV isolates is associated with different host innate immune responses.

Chimeric HP-PRRSV2 containing an ORF2-6 consensus sequence induces antibodies with broadly neutralizing activity and confers cross protection against virulent NADC30-like isolate

Due to the substantial genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV), commercial PRRS vaccines fail to provide sufficient cross protection. Previous studies have confirmed the existence of PRRSV broadly neutralizing antibodies (bnAbs). However, bnAbs are rarely induced by either natural infection or vaccination. In this study, we designed and synthesized a consensus sequence of PRRSV2 ORF2-6 genes (ORF2-6-CON) encoding all envelope proteins based on 30 representative Chinese PRRSV isolates. The ORF2-6-CON sequence shared > 90% nucleotide identities to all four lineages of PRRSV2 isolates in China. A chimeric virus (rJS-ORF2-6-CON) containing the ORF2-6-CON was generated using the avirulent HP-PRRSV2 JSTZ1712-12 infectious clone as a backbone. The rJS-ORF2-6-CON has similar replication efficiency as the backbone virus in vitro. Furthermore, pig inoculation and challenge studies showed that rJS-ORF2-6-CON is not pathogenic to piglets and confers better cross protection against the virulent NADC30-like isolate than a commercial HP-PRRS modified live virus (MLV) vaccine. Noticeably, the rJS-ORF2-6-CON strain could induce bnAbs while the MLV strain only induced homologous nAbs. In addition, the lineages of VDJ repertoires potentially associated with distinct nAbs were also characterized. Overall, our results demonstrate that rJS-ORF2-6-CON is a promising candidate for the development of a PRRS genetic engineered vaccine conferring cross protection.

Molecular Characterization of the Nsp2 and ORF5 (ORF5a) Genes of PRRSV Strains in Nine Provinces of China During 2016-2018

Porcine reproductive and respiratory syndrome virus (PRRSV) causes a highly contagious disease and brings huge economic losses to commercial pork production worldwide. PRRSV causes severe reproductive failure in sows and respiratory distress in piglets. To trace the evolution of PRRSV in pigs with respiratory diseases in some regions of China, 112 samples were collected from nine provinces in China during 2016–2018. All samples were detected by RT-PCR and analyzed by the Nsp2/ORF5 (ORF5a)-genes-phylogeny. Sequence analysis and recombination analysis were conducted on the Nsp2/ORF5 (ORF5a) genes of the identified strain in the study. The RT-PCR result shown that the positive rate of PRRSV was 50.89% (57/112). Phylogenetic analysis showed that the identified PRRSV strains were all NA genotype and belonged to lineage 1, 3, and 8. The Nsp2 gene of identified PRRSV strains exhibited nucleotide homologies of 53.0 ~ 99.8%, and amino acid homologies of 46.8 ~ 99.7%. The ORF5 gene of identified PRRSV strains exhibited nucleotide homologies of 82.4 ~ 100%, and amino acid homologies of 79.6 ~ 100%. Sequence analysis revealed that a discontinuous 30-amino-acid deletion (positions 481 and 533–561) and a 131-amino-acid discontinuity deletion (positions 323–433, 481, and 533–551) in Nsp2 of PPRSV isolates; all identified strains in this study may be wild strains, and most identified strains may be highly virulent strains. Sequence analysis of ORF5 and ORF5a revealed that the mutation sites of GP5 were mainly concentrated in the signal peptide and epitopes region, while the mutation sites of ORF5a were mainly concentrated in the transmembrane and the intramembrane region. The recombination analysis indicated that there may be multiple recombination regions in identified strains, and the recombination pattern was more complex. This study showed that the prevalent PRRSV strain in some regions of China was still HP-PRRSV, while NADC30 strain also occupied a certain proportion; different types of PRRSV strains showed different patterns and variation in China. This study suggested that the monitoring of PRRSV prevalence and genetic variation should be further strengthened.

Genomic characteristics and pathogenicity of a new recombinant strain of porcine reproductive and respiratory syndrome virus

Recombination is an important phenomenon that accelerates evolution and enriches the genetic diversity of porcine reproductive and respiratory syndrome virus (PRRSV). Recombinant PRRSV isolates sometimes have different genetic backgrounds. In this study, we report a recombinant PRRSV (SD-YL1712) isolated from a pig farm. The genome of SD-YL1712 is 15,014 nucleotides in length, and its nucleotide and amino acid sequence conservation is higher than that of PRRSV strain JXA1 except within the NSP2 region. The NSP2 region of SDYL1712 shares the highest nucleotide (85.9%) and amino acid (84.1%) sequence identity with PRRSV strain NADC30. SD-YL1712 was found to contain a characteristic 131-amino-acid deletion in the NSP2 region. Two recombination breakpoints were detected at nt 2134 and nt 3958 within the NSP2 region, which revealed that SD-YL1712 originated from a recombination event between NADC30-like and HP-PRRSV-derived MLV-like strains. Interestingly, SD-YL1712 had an additional deletion at position 586, similar to that found in strain TJnh1501. Moreover, the pathogenicity of strain SD-YL1712 was found to be similar to that of HP-PRRSV JXA1, which was higher than that of the CH1a strain. Further analysis indicated that SD-YL1712 might be a transitional intermediate in the evolution of TJbd1401 to TJnh1501.

Characterization of four types of MLV-derived porcine reproductive and respiratory syndrome viruses isolated in unvaccinated pigs from 2016 to 2020

Modified live vaccines (MLVs) have been utilized to combat porcine reproductive and respiratory syndrome (PRRS), which raises a serious concern about the MLV-derived PRRS virus (PRRSV) isolates. During the routine investigation of PRRSV in China, four lung samples collected from unvaccinated diseased pigs from 2016 to 2020 were detected as PRRSV positive. The PRRSVs shared high ORF5 identities to CH-1R, JXA1-R, TJM-F92 and RespPRRS MLV vaccines, respectively. The viruses were isolated in Marc-145 cells and denominated as SD1612-1, JS1703-21, JSTZ1907-714 and JSYC20-05-1. Genome comparison confirmed that these isolates share the highest genomic homologies to CH-1R (97.96%), JXA1-R (99.64%), TJM-F92 (99.00%) and RespPRRS MLV (99.57%) than any other known isolates. Genome-based phylogenetic analysis showed that SD1612-1 and CH-1R, JS1703-21 and JXA1-R, JSTZ1907-714 and TJM-F92, JSYC20-05-1 and RespPRRS MLV were grouped in the same branches. In addition, amino acids unique to corresponding vaccine attenuations were also identified in our isolates. Noticeably, amino-acids potentially associated with the virulence revision from MLV strains to parental virulent viruses were also identified in the MLV-derived isolates. Our results confirm that the four types of MLV-derived isolates are circulating and evolving in Chinese swine herds for years, which highlights the necessity for the fair use of PRRS MLVs.

Development and application of a quadruplex real-time PCR assay for differential detection of porcine circoviruses (PCV1 to PCV4) in Jiangsu province of China from 2016 to 2020

To date, four species of porcine circoviruses (PCVs), including PCV1-4, have been reported to exist in the clinical cases. Fast and effective differential detection is critical to monitor the infection and co-infection status of PCVs for adopting reliable control strategies. However, currently available methods cannot simultaneously differentiate the four species of PCV strains. In this study, a quadruplex real-time PCR assay based on TaqMan probes was developed for differential detection of PCV1-4. The new quadruplex real-time PCR assay exhibited satisfied specificity, sensitivity, repeatability and reproducibility. In addition, the new assay was applied to the detection of 120 clinical samples collected from 2016 to 2020 in Jiangsu province of China and compared with previously reported PCV1-4 singleplex conventional PCR assays. Based on the clinical performance, the results from the quadruplex real-time PCR and conventional PCR assays showed 100% agreement. A total of 47 samples were detected as PCV positive by the quadruplex real-time PCR assay, including 1, 2, 1 samples were co-infected with PCV1 and PCV4, PCV2 and PCV3, PCV2 and PCV4, respectively. Full-length ORF2 sequencing and phylogenetic analysis supported the real-time PCR results that 5, 34, 8 and 4 of the 51 PCV sequences were PCV1, PCV2, PCV3 and PCV4, respectively. This study provides a promising alternative tool for rapid differential detection of PCVs and confirms the coexistence of all species of PCV1-4 strains in Jiangsu province in recent years.

The infectious cDNA clone of commercial HP-PRRS JXA1-R-attenuated vaccine can be a potential effective live vaccine vector

Multiple commercial porcine reproductive and respiratory syndrome (PRRS) modified live vaccines are currently utilized in Chinese swine herds due to the limited cross-protection of vaccines and coexistence of different PRRS viruses. In this study, an infectious cDNA clone of the highly pathogenic PRRS (HP-PRRS) vaccine JXA1-R strain was generated. We successfully rescued the virus from direct in vitro DNA transfection of rJXA1-R clone, which has similar growth kinetics to the parental JXA1-R virus in Marc-145 cells. To further evaluate the potential use of the cloned rJXA1-R virus as a live vector for foreign gene expression, the enhanced green fluorescent protein (EGFP) was inserted between non-structural and structural genes. Our results showed that the dynamic expression of EGFP can be visualized by live cell imaging system during the infection in Marc-145 cells. The availability of our cloned JXA1-R viruses provides a crucial platform to study the fundamental biology of HP-PRRS virus vaccine and also serves as a potential effective vector for developing live vector vaccines against swine pathogens.

High genetic diversity of Chinese porcine reproductive and respiratory syndrome viruses from 2016 to 2019

High genetic diversity and limited cross-protection are two major reasons for ineffective control of porcine reproductive and respiratory syndrome virus (PRRSV) infection. Therefore, it's important to dynamically monitor the prevalence of PRRSV for adopting appropriate control strategy. In this study, we analyzed PRRSV infection by detecting 712 clinical samples collected from 2016 to 2019 in China. Totally 100 samples were detected as PRRSV positive, including 2 and 98 samples were infected with PRRSV1 and PRRSV2, respectively. In addition, two out of the 98 PRRSV2 positive samples were co-infected with two distinct viruses. ORF5-based phylogenetic analysis showed that JXA1-like HP-PRRSV2 (lineage 8) and NADC30-like PRRSV2 (lineage 1) isolates are currently predominant, but QYYZ-like PRRSV2, CH-1a-like PRRSV2 and PRRSV1 isolates also co-exist in Chinese swine herds. In addition, two commercial MLV-derived viruses (TJM-F92-like and JXA1-R-like) were frequently detected. GP5 alignment also detected insertion and deletion in the extravirion domain. Our study presents the up-to-date PRRSV infection status and highlights the high genetic diversity of PRRSV currently circulating in China.

Special Issue "Emerging Viruses: Surveillance, Prevention, Evolution, and Control"

Emerging viruses represent a major concern for public health offices. Climate changes, the international migration of people and products, deforestation, and other anthropogenic activities (and their consequences) have been historically and continuously related to the emerging and re-emerging of new viruses, triggering an increasing number of notified outbreaks, epidemics, and pandemics. [...].