Xiaofeng Zhai, Wen Zhao, Kemang Li, Cheng Zhang, Congcong Wang, Shuo Su, Jiyong Zhou, Jing Lei, Gang Xing, Haifeng Sun, Zhiyu Shi and Jinyan Gu. Genome Characteristics and Evolution of Pseudorabies Virus Strains in Eastern China from 2017 to 2019[J]. Virologica Sinica, 2019, 34(6): 601-609. doi: 10.1007/s12250-019-00140-1
Citation: Xiaofeng Zhai, Wen Zhao, Kemang Li, Cheng Zhang, Congcong Wang, Shuo Su, Jiyong Zhou, Jing Lei, Gang Xing, Haifeng Sun, Zhiyu Shi, Jinyan Gu. Genome Characteristics and Evolution of Pseudorabies Virus Strains in Eastern China from 2017 to 2019 .VIROLOGICA SINICA, 2019, 34(6) : 601-609.  http://dx.doi.org/10.1007/s12250-019-00140-1

2017-2019年华东地区伪狂犬病病毒的基因组及进化特征

  • 通讯作者: 粟硕, shuosu@njau.edu.cn, ORCID: http://orcid.org/0000-0003-0187-1185
  • 收稿日期: 2019-03-06
    录用日期: 2019-04-24
    出版日期: 2019-07-05
  • 自2011年底以来,中国南方爆发了伪狂犬病病毒(PRV),给养猪业带来了重大经济损失。我们之前报道了中国的变异型PRV和重组,这可能是持续流行病的根源。在这里,我们分析了2017年至2019年间华东集约化养猪场的样本,并对主要糖蛋白gB,gC,gD和gE进行了测序,以研究PRV的进化特征。基于gC基因,我们发现PRV变体属于进化枝2并且通过PRV流行过程鉴定了创始效应。此外,我们检测了进化枝间和进化枝内重组,特别是菌株FJ-ZXF和FJ-W2的gB基因之间的进化枝间重组,它们是进化枝1株的重组体。还观察到特定的氨基酸变化和可能与功能变化相关的正选择位点。中国PRV出现的特征需要持续监测和开发能够提供针对特定PRV变体的免疫力的疫苗。

Genome Characteristics and Evolution of Pseudorabies Virus Strains in Eastern China from 2017 to 2019

  • Corresponding author: Shuo Su, shuosu@njau.edu.cn
  • ORCID: http://orcid.org/0000-0003-0187-1185; 
  • Received Date: 06 March 2019
    Accepted Date: 24 April 2019
    Published Date: 05 July 2019
  • Since late 2011, outbreaks of pseudorabies virus (PRV) have occurred in southern China causing major economic losses to the pig industry. We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics. Here, we analyzed samples from intensive pig farms in eastern China between 2017 and 2019, and sequenced the main glycoproteins (gB, gC, gD, and gE) to study the evolution characteristics of PRV. Based on the gC gene, we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic. In addition, we detected inter- and intra-clade recombination; in particular, inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2, which were recombinant with clade 1 strains. We also found specific amino-acid changes and positively selected sites, possibly associated with functional changes. This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.

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    Genome Characteristics and Evolution of Pseudorabies Virus Strains in Eastern China from 2017 to 2019

      Corresponding author: Shuo Su, shuosu@njau.edu.cn
    • 1. MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China
    • 2. Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China

    Abstract: Since late 2011, outbreaks of pseudorabies virus (PRV) have occurred in southern China causing major economic losses to the pig industry. We previously reported that variant PRV forms and recombination in China could be the source of continued epidemics. Here, we analyzed samples from intensive pig farms in eastern China between 2017 and 2019, and sequenced the main glycoproteins (gB, gC, gD, and gE) to study the evolution characteristics of PRV. Based on the gC gene, we found that PRV variants belong to clade 2 and detected a founder effect during by the PRV epidemic. In addition, we detected inter- and intra-clade recombination; in particular, inter-clade recombination in the gB genes of strains FJ-ZXF and FJ-W2, which were recombinant with clade 1 strains. We also found specific amino-acid changes and positively selected sites, possibly associated with functional changes. This analysis of the emergence of PRV in China illustrates the need for continuous monitoring and the development of vaccines against specific variants of PRV.

    • Pseudorabies virus (PRV) is a herpes virus belonging to the genus Varicellovirus (Murphy et al. 2000). Pigs are the primary hosts and reservoirs of PRV. PRV causes reproductive disturbances in pregnant sows and lethal disease in newborn piglets. This condition is referred to as Aujeszky's disease, which causes serious economic losses worldwide (He et al. 2019a). PRV is a double-stranded DNA virus that encodes more than 70 proteins, including the viral capsids, coats, and envelopes (Pomeranz et al. 2005). Among these proteins, glycoprotein B (gB), gD, and gC induce cellular and humoral immune responses (Ober et al. 1998, 2000; Ye et al. 2015), while gE is the major virulence determinant of pig PRV (Kimman et al. 1992; Wang et al. 2014). These four genes are commonly used to monitor the evolution of PRV (Sozzi et al. 2014; He et al. 2019a).

      Many countries are currently declared free of PRV infection. In China, effective pseudorabies control was achieved by vaccination with the Bartha-K61 strain with 80% of pig farms adhering to vaccination between the 1990s and late 2011 (Tong and Chen 1999). However, in late 2011, PRV outbreaks occurred in several pig herds immunized with the Bartha-K61 strain. The outbreaks rapidly compromised most pig farms in northern China and resulted in huge economic losses to the swine industry (An et al. 2013). The causative agent was confirmed to be novel PRV strains that were genetically different from the classical PRV strains (He et al. 2019a). Due to enhanced pathogenicity and genetic differentiation, these strains were considered as newly emerged variants (Hu et al. 2015; Sun et al. 2016). Further investigation demonstrated that the Bartha-K61 vaccine does not provide full protection against the PRV variants (Hu et al. 2015). However, the Chinese vaccine reference strain Ea is genetically closely related to the newly emerged variant. It is suggested that the epidemic variant PRVs of China may have undergone mutations caused by host immune pressure over a long period of time and evolved into a new variant of PRV (Wang et al. 2017).

      A major impediment to understanding the origin, evolution, and diversity of PRV in China is the lack of PRV sequences. Frequent recombination events have been detected in RNA and some DNA viruses, which explain the maintenance of a high evolutionary rate (Su et al. 2016, 2017; Li et al. 2018). Thus studying the evolution and recombination occurring in PRV could provide a new perspective on the potential direction of outbreak. To this end, the phylogenetic relationships between the new Chinese strains and the globally emerging and historic PRV strains were analyzed based on the main glycoproteins (gB, gD, gE, and gC) of 27 strains from eastern China obtained from 2017 to 2019.

    • A total of 587 samples were collected from the lungs, lymph nodes, kidney, spleen, and brain of pigs suspected to be infected with PRV from intensive pig farms in eastern China including the Anhui, Fujian, Shandong, and Jiangsu provinces (Fig. 1) between 2017 and 2019 (Table 1). Sample homogenates were prepared by freeze–thaw cycles followed by centrifugation at 5000 ×g for 5 min. The supernatants were then harvested for DNA extraction. Positive samples confirmed by polymerase chain reaction (PCR) were used for virus isolation. For virus isolation, tissues were grinded, filtered using a 0.22-μm membrane, and inoculated into Vero cells. The cells were then incubated until obvious cytopathic effect (CPE) developed. Virus was further plaque purified.

      Figure 1.  Map indicating PRV-Central China positive farms in China. Different colors indicate the different provinces in China. The PRV reference sequences used in this study were from these colored provinces. The provinces marked with yellow stars are the provinces with positive samples in this study. Provinces with shadow coverage indicate significant association between virus and geographic location.

      Strain name Origin Year Month No. GenBank
      gC gB gD gE
      ANHUI-1 China: Anhui 2018 Janurary MK922082 MK922098 MK610394 MK610413
      ANHUI-2 China: Anhui 2018 Janurary MK922083 MK922099 MK610395 MK610414
      ANHUI-3 China: Anhui 2018 March MK922084 MK922100 MK610396
      ANHUI-4 China: Anhui 2018 April MK922085 MK922101 MK610397
      ANHUI-5 China: Anhui 2018 April MK922086 MK922102
      Anhui-CZ33 China: Anhui 2017 Janurary MK934521 MK922119 MK934522
      Anhui-BB11 China: Anhui 2017 Janurary MK922079 MK922120
      Anhui-ZJ1 China: Anhui 2018 October MK922121
      FJ-1620 China: Fujian 2018 April MK922103 MK610398 MK610415
      FJ-2125 China: Fujian 2018 April MK922104 MK610399 MK610416
      FJ-5 China: Fujian 2018 May MK922087 MK922105 MK610400 MK610417
      FJ-Z1 China: Fujian 2018 May MK922088 MK922106 MK610401 MK610418
      FJ-Y21 China: Fujian 2018 May MK922107 MK610402 MK610419
      FJ-N1 China: Fujian 2018 May MK922089 MK922108 MK610403 MK610420
      FJ-N2 China: Fujian 2018 May MK922081 MK922109 MK610404 MK610421
      FJ-N3 China: Fujian 2018 May MK922090 MK922110 MK610405 MK610422
      FJ-N4 China: Fujian 2018 May MK922091 MK922111 MK610406 MK610423
      FJ-W2 China: Fujian 2018 May MK922112 MK610407 MK610424
      FJ-ZXF China: Fujian 2018 July MK922080 MK922113 MK610408 MK610425
      FJ-YXJSJ1 China: Fujian 2019 Janurary MK922092 MK922116 MK610409 MK610428
      FJ-YXJSJ2 China: Fujian 2019 Janurary MK922093 MK922117 MK610410 MK610429
      FJ-YY China: Fujian 2019 Janurary MK922094 MK922118 MK610411 MK610430
      FJ-QYQ3 China: Fujian 2019 Janurary MK922096 MK610412
      FJ-QYQ4 China: Fujian 2019 Janurary MK922097
      FJ-QYQ2 China: Fujian 2019 Janurary MK922095
      FJ-SHS1 China: Fujian 2019 Janurary MK922114 MK610426
      FJ-GSG5 China: Fujian 2019 Janurary MK922115 MK610427

      Table 1.  Sequence information of strains isolated in this study.

    • Virus DNA was extracted using the Virus Genomics DNA Isolation Kit (Tianlong Biotech, Suzhou, China) following the manufacturer's instructions. PRV was detected using a pair of specific PR-D-F/R primers (Supplementary Table S1) (Yue et al. 2009). PCR was performed in a 20-μL volume mixture comprising 10 μL of 2 × Taq Master mix (Vazyme Biotech, Shanghai, China), 7 μL of double distilled water (ddH2O), 1 μL of template DNA, 1 μL each of 10 pmol/μL forward and reverse primers. Thermocycler conditions used for PCR were 95 ℃ for 5 min, followed by 35 cycles of denaturation at 95 ℃ for 30 s, annealing at 59 ℃ for 30 s, and extension at 72 ℃ for 30 s, with a final extension at 72 ℃ for 10 min before storage at 4 ℃. The gB, gC, gD, and gE genes were also amplified (Supplementary Table S1) using the Phanta Max Super-Fidelity DNA polymerase (Vazyme Biotech, Shanghai, China) (Supplementary Table S1). Positive samples were sent to Tsingke (Nanjing, China) for DNA sequencing. Sequences were assembled using the BioEdit software (Hall 1999).

    • All PRV gB, gC, gD, and gE coding sequences from infected swine were collected from NCBI (https://www.ncbi.nlm.nih.gov/) (Supplementary Tables S2–S5), aligned using the MAFFT software (version 7.312) (Kazutaka et al. 2005) and manually adjusted using MEGA (version 7) (Kumar et al. 2016). The IQ tree software (version 1.6.5) was used to detect the best fit nucleotide substitution model according to the Bayesian information criterion (BIC) score (Lam-Tung et al. 2015). Maximum likelihood (ML) trees based on gB, gC, gD, and gE coding regions were reconstructed using RAxML (version 8.4.10) using the general time reversible (GTR) plus GAMMA distribution substitution model and 1000 bootstraps (Stamatakis 2014).

    • To analyze the correlation between each PRV sequence and geographical location after Markov Chain Monte Carlo (MCMC) analysis (Drummond and Rambaut 2007; He et al. 2019a), PRV sequences were first classified according to their country of isolation, while isolates from China were classified as eastern, northern, central, southern, and western China. The correlation was determined using the Bayesian Tip-Significance testing software (BaTS) (Parker et al. 2008). The parsimony score (PS) and association index (AI) statistics were calculated based on the gC gene MCMC analysis. When the P values of AI and PS were < 0.05, the correlation between PRV and geographical distribution was considered significant.

    • The gB, gC, gD, and gE ML trees were uploaded to Datamonkey (http://www.datamonkey.org/) to estimate sites and branched under selection (Delport et al. 2010; He et al. 2019b). The algorithms single-likelihood ancestor counting (SLAC), fast unconstrained Bayesian approximation (FUBAR), fixed effects likelihood (FEL), and mixed effects model of evolution (MEME) were used to identify selected sites. Positive selected branches were detected using an adaptive branch-site REL test for episodic diversification (aBSREL) algorithm (Kosakovsky Pond and Frost 2005; Murrell et al. 2012, 2013; Smith et al. 2015). A site was considered to be under positive selection if at least two algorithms were satisfied (P < 0.1 in SLAC, P < 0.05 in FEL and MEME, P > 0.9 in FUBAR).

    • Samples are collected from four provinces in eastern China (Anhui, Fujian, Shandong, and Jiangsu), but PRV positive sample only detected in Anhui and Fujian Province (Table 1). Of 587 samples, 48 were positive for PRV (positive rate of 8.18%). Sequencing analysis of the main PRV glycoproteins gB, gC, gD, and gE revealed maximum nucleotide sequence divergences of 1.8%, 0.3%, 0.3%, and 0.6% within the isolates, and 2.6%, 5.6%, 2.0%, and 3.7% compared with the reference isolates from GenBank, respectively. Maximum amino acid sequence divergences were 4.0%, 0.7%, 0.3%, and 1.1% within the isolates for gB, gC, gD, and gE, and 4%, 9.5%, 3.5%, and 6.6% from other GenBank isolates, respectively. In addition, we observed some special amino acid site changes in the gC and gE proteins. For gC, more than half of the strains had a S to G change at position 41, and R162H and S345L changes were observed in four of the twenty strains. Compared with the Bartha vaccine strain, in addition to some specific amino acid mutations, there were some specific insertions from residues 59–65 on gC. A T386M change was observed in 8 gE strains, and 4 strains displayed a L575P change (Fig. 2). However, in case of gB, two strains (FJ-W2 and FJ-ZXF) were similar to the clade 1 strain NIA3.

      Figure 2.  Sequence alignment and amino acid differences between strains sequenced here and GenBank isolates. The strains sequenced here are indicated in red. Variant PRVs are indicated in orange, early clade 2 strains in blue, and clade 1 strains in green. The yellow bar indicates different site among these sequences.

    • We reconstructed phylogenetic trees of PRV based on the gB, gD, gE, and gC genes using all PRV sequences available from infected pigs in GenBank and the sequences generated here (Figs. 3, 4). Strains sequenced in this study were mainly similar with strains distributed in Guangdong, Guangxi, Henan, Hainan, Shandong, Shanxi, Fujian and Hubei Province. Based on the ML trees, we concluded that four trees had similar structures and PRV could be divided into two main clades, clade 1 and clade 2. Most of the sequences generated here belonged to clade 2, similarly to variant PRV (He et al. 2019a). This indicates that variant PRV is epidemic in eastern China. However, we also found that the sequences of different genes clustered with different clades. For example, gB of strains FJ-W2 and FJZXF located in clade 1 (containing the Bartha vaccine strain) and was genetically closer to strains from other countries, while gD, gE (Fig. 3B, 3C) and gC (Fig. 4) clustered in clade 2. This is indicative of inter-clade recombination events occurring in the PRV epidemic. In addition, sequences of different strains within clade 2 were grouped in different sub-clades for different genes, suggesting intra-clade recombination during PRV epidemic in eastern China.

      Figure 3.  Maximum likelihood trees reconstructed based on the gB, gD, and gE genes. Trees were reconstructed using RAxML (Version 8.4.10) with the general time reversible (GTR) plus GAMMA distribution substitution model, and 1000 bootstraps. The first layer of red dots indicates sequenced strains from this study. The second layer of colored circles indicates PRV host, and the third circle indicates country and regions of PRV. A gB gene. B gD gene. C gE gene. Red dots indicates PRV sequenced in this study.

      Figure 4.  Maximum likelihood trees reconstructed based on the gC gene. The tree was reconstructed using RAxML (Version 8.4.10) with the general time reversible (GTR) plus GAMMA distribution substitution model, and 1000 bootstraps. Colored lines indicate host and country of PRV. Red dots indicates PRV sequenced in this study.

    • Given that gC has the highest mutation rate and the largest number of reported sequences (Ye et al. 2015) among the glycoprotein-encoding genes, we studied the geographical correlation of PRV based on gC. We performed BaTS analysis and found that the P value of both AI and PS were < 0.01 (Table 2). Except for the P value of Malaysia, Belgium, Greece, United Kingdom, central China, and western China that equaled 1, the other 14 countries and regions showed a P value within 0.01. This is indicative of a strong correlation of PRV with geographical location, especially in some areas of China where the epidemic is more severe.

      Statistic Observed mean Lower 95% CI Upper 95% CI Nulsl mean Lower 95% CI Upper 95% CI Significance
      AI 13.08 11.37 14.72 28.24 27.39 28.93 0.00
      PS 102.28 98.00 107.00 201.63 198.27 204.85 0.00
      MC Eastern China 11.06 11.00 12.00 1.74 1.48 2.09 0.01
      MC USA 2.03 2.00 2.00 1.06 1.00 1.15 0.01
      MC Brazil 3.52 2.00 6.00 1.37 1.14 1.94 0.01
      MC Hungary 2.14 2.00 3.00 1.04 1.00 1.14 0.01
      MC China 6.65 3.00 10.00 2.44 2.21 3.02 0.01
      MC Malaysia 1 1.00 1.00 1.00 1.00 1.00 1.00
      MC Spain 4.26 2.00 7.00 1.06 1.00 1.17 0.01
      MC Germany 3.06 2.00 5.00 1.17 1.03 1.40 0.01
      MC Slovakia 2.07 2.00 3.00 1.02 1.00 1.06 0.02
      MC Italy 7.55 4.00 13.00 2.13 1.85 2.71 0.01
      MC Argentina 2.9 1.00 5.00 1.09 1.00 1.31 0.01
      MC Austria 1.8 1.00 2.00 1.01 1.00 1.03 0.01
      MC Croatia 5.47 3.00 7.00 1.05 1.00 1.13 0.01
      MC Belgium 1.47 1.00 3.00 1.09 1.00 1.29 1.00
      MC Central China 1.45 1.00 2.00 1.20 1.06 1.39 1.00
      MC North China 1.52 1.00 2.00 1.00 1.00 1.01 0.01
      MC Western China 1.01 1.00 1.00 1.00 1.00 1.01 1.00
      MC Greece 1.37 1.00 2.00 1.00 1.00 1.01 1.00
      MC South China 3.03 3.00 4.00 1.56 1.32 2.02 0.01
      MC United Kingdom 1 1.00 1.00 1.00 1.00 1.00 1.00
      Bold number remind the difference in geographic associations significantly.
      AI association index, PS parsimony score, MC monophyletic clade.

      Table 2.  Geographical correlation analysis of PRV based on gC.

    • Using the FUBAR and MEME methods, we detected positive selection at gB residues 43, 834 and 908, gE residue 348 according to all methods, and two gC residues (75 detected with FEL, SLAC and FUBAR; and 194 detected with SLAC and FUBAR). No positive selection was detected on gD (Supplementary Table S6). As expected, some selected residues have been associated with relevant functions. For example, gB site 43 is near the B-cell epitopes within residues 59 to 126 (Zaripov et al. 1999), site 75 on gC is associated with virus adsorption (Karger and Mettenleiter 1993), and site 194 is on the 1/3 N terminal of the gC protein, which is associated with the HS receptor-binding domain (Flynn and Ryan 1995, 1996). In addition, the amino acid sites in which we found changes in relation to the reference strains had also important functions. In particular, change S41G on gC results in a change in the glycosylation site from NSS to NGS.

    • The Bartha-K61 vaccine was imported from Hungary to China and has been widely used since the late 1980s. Vaccination has been instrumental in controlling PRV for decades. Indeed, < 10% of serum samples were positive for PRV gE antibody between 2005 to 2010 (Tong and Chen 1999; Kong 2000). Since 2010, a PRV variant has emerged quickly in many pig farms that despite having vaccination programs in place, causing substantial losses to the pig industry in China (An et al. 2013; Wu et al. 2013; Luo et al. 2014). According to a recent report, 80.1% of investigated farms from 23 regions of China were PRV-positive (Yang 2015). Furthermore, gE-antibody positive rates increased to 58.2% in farms infected with variant PRV. We previously showed that from 2012 to 2017, the effective reproduction rate (Re) during each year for the variant PRV was more than 1, indicating a high risk of a variant PRV epidemic and the need for continuous monitoring in China (He et al. 2019a).

      From 2017 to 2019, some pig farms in the eastern China provinces of Fujian and Anhui suspected the presence of variant PRV, which we confirmed to be PRV by PCR. After virus isolation and sequencing of the main glycoprotein genes gB, gD, gE, and gC, we reconstructed the ML trees and classified these as variant PRVs (clade 2). Importantly, phylogenetic analysis of gD, gE, and gC revealed that all of the strains belong to clade 2. As for the gB gene, there were two strains (FJ-W2 and FJ-ZXF) similar to clade 1 strains, suggesting that some of these variant PRVs originated via recombination with clade 1. Although the recombination sites are different, similar recombination events have been reported in previous studies, suggesting recombination between wild strains and foreign epidemic strains (similar to the vaccine strains clade) in China (Ye et al. 2016; He et al. 2019a). Moreover, we also detected intra-clade recombination in clade 2. Recombination may result in changes of antigenicity, virulence, and thus immune failure (He et al. 2019a).

      We found a strong association between PRV and geographical location, indicating a founder effect along the PRV epidemic. Interestingly, the phylogeographic associations we observed were similar to those observed in previous reports, indicating that the PRV strains in China may have evolved independently, leading to the emergence of a variant strain (Wang et al. 2017). A founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived (Templeton 1980; Provine 2004). Therefore, the immune failure and observed specific amino acid mutations in critical epitopes suggest that different regions of China may need to develop different vaccines, formulate corresponding local policies, and indicate compensation strategies to control the prevalence of PRV.

      In addition, we also found some important amino acid differences and positively selected sites between the isolates sequenced here and reference sequences. Although some of the amino acid changes identified in this study were not positively selected, probably due to the limited number of sequences, some conclusions could be noted. In particular, S41G, R162H, and S345L changes on gC could alter receptor-binding and/or glycosylation that likely contributed to the emergence of variant PRV.

      In general, we conclude that the outbreak of PRV in eastern China may be due to immune failure, caused by the emergence of variant PRV via recombination and specific amino acid mutations and insertions in gC protein epitope compared with the Bartha vaccine strain. In addition, a founder effect also promoted the epidemic spread of PRV. Therefore, the development of new vaccines and novel monitoring strategies are necessary.

    • This work was financially supported by the National Key Research and Development Program of China (2017YFD0500101), the Natural Science Foundation of Jiangsu Province (BK20170721), the China Association for Science and Technology Youth Talent Lift Project (2017-2019).

    • XZ, WZ and SS designed the experiments. XZ, KL, CZ, CW and WZ carried out the experiments. CZ and XZ analyzed the data. JZ, JL, GX, HS, ZS and JG reviewed drafts of the paper, XZ, WZ and SS wrote the paper. SS checked and finalized the manuscript. All authors read and approved the final manuscript.

    • The authors declare that they have no conflict of interest.

    • This article does not contain any studies with human participants or animals performed by any of the authors.

    Figure (4)  Table (2) Reference (42) Relative (20)

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