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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Anim. Sci.</journal-id>
<journal-title>Frontiers in Animal Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Anim. Sci.</abbrev-journal-title>
<issn pub-type="epub">2673-6225</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fanim.2025.1603264</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Animal Science</subject>
<subj-group>
<subject>Brief Research Report</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Development of a TaqMan-based quantitative real-time PCR for the detection of Porcine circovirus type 3</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Hu</surname>
<given-names>Zhiqiang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/3020254/overview"/>
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</contrib>
<contrib contrib-type="author" equal-contrib="yes">
<name>
<surname>Lai</surname>
<given-names>Ranran</given-names>
</name>
<xref ref-type="aff" rid="aff3">
<sup>3</sup>
</xref>
<xref ref-type="author-notes" rid="fn003">
<sup>&#x2020;</sup>
</xref>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Xu</surname>
<given-names>Wei</given-names>
</name>
<xref ref-type="aff" rid="aff4">
<sup>4</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/1316515/overview"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Guan</surname>
<given-names>Ran</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Li</surname>
<given-names>Mingxiang</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/2231767/overview"/>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Zhimin</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
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</contrib>
<contrib contrib-type="author">
<name>
<surname>Hao</surname>
<given-names>Guiying</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<uri xlink:href="https://loop.frontiersin.org/people/3043753/overview"/>
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</contrib>
<contrib contrib-type="author" corresp="yes">
<name>
<surname>Yan</surname>
<given-names>Guangwen</given-names>
</name>
<xref ref-type="aff" rid="aff1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff2">
<sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="fn001">
<sup>*</sup>
</xref>
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</contrib-group>
<aff id="aff1">
<sup>1</sup>
<institution>Key Laboratory of Animal Epidemic Disease Detection and Prevention in Panxi District, Xichang University</institution>, <addr-line>Xichang</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff2">
<sup>2</sup>
<institution>College of Animal Science, Xichang University</institution>, <addr-line>Xichang</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff3">
<sup>3</sup>
<institution>Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd.</institution>, <addr-line>Dezhou</addr-line>,&#xa0;<country>China</country>
</aff>
<aff id="aff4">
<sup>4</sup>
<institution>MOA Key Laboratory of Animal Virology, Center for Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University</institution>, <addr-line>Hangzhou</addr-line>,&#xa0;<country>China</country>
</aff>
<author-notes>
<fn fn-type="edited-by">
<p>Edited by: Carlos Tejeda, Austral University of Chile, Chile</p>
</fn>
<fn fn-type="edited-by">
<p>Reviewed by: Nguyen Dinh-Hung, University of Arizona, United States</p>
<p>Xiaoyan Wu, Shandong Xiehe University, China</p>
</fn>
<fn fn-type="corresp" id="fn001">
<p>*Correspondence: Guangwen Yan, <email xlink:href="mailto:ygwdky@126.com">ygwdky@126.com</email>
</p>
</fn>
<fn fn-type="equal" id="fn003">
<p>&#x2020;These authors have contributed equally to this work</p>
</fn>
</author-notes>
<pub-date pub-type="epub">
<day>14</day>
<month>07</month>
<year>2025</year>
</pub-date>
<pub-date pub-type="collection">
<year>2025</year>
</pub-date>
<volume>6</volume>
<elocation-id>1603264</elocation-id>
<history>
<date date-type="received">
<day>31</day>
<month>03</month>
<year>2025</year>
</date>
<date date-type="accepted">
<day>23</day>
<month>06</month>
<year>2025</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#xa9; 2025 Hu, Lai, Xu, Guan, Li, Zhang, Hao and Yan</copyright-statement>
<copyright-year>2025</copyright-year>
<copyright-holder>Hu, Lai, Xu, Guan, Li, Zhang, Hao and Yan</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/">
<p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</p>
</license>
</permissions>
<abstract>
<p>Porcine circovirus type 3 (PCV3) is a recently identified member of the porcine circovirus family, primarily associated with conditions such as dermatitis and nephropathy syndrome, reproductive failure, and multisystem inflammatory lesions in swine. There has been a significant increase in the prevalence of PCV3 in China, attracting considerable attention. Consequently, there is an urgent need for a highly sensitive, cost-effective, and efficient method for the detection of clinical samples. This study developed a TaqMan-based quantitative real-time PCR (TaqMan-qPCR) assay utilizing specific probes and primers designed based on the PCV3-REP gene. Following the optimization of reaction conditions, sensitivity analysis determined that the detection limit of this method was 7.3&#x2009;&#xd7;&#x2009;10<sup>0</sup> copies/&#xb5;L. Specificity analysis demonstrated no cross-reactivity with other common porcine pathogens, underscoring its specificity. Furthermore, the inter- and intra-assay coefficients of variation were both less than 1%, indicating high reproducibility. A total of 2,454 clinical samples were collected and analyzed using the developed method. The findings revealed that the prevalence of PCV3 was highest in testicular fluid samples, with a rate of 71.28% and the lowest detected Cq values among all sample types, indicating a significant likelihood of vertical transmission of PCV3. Additionally, oral fluid samples exhibited the second highest positive rate at 59.83%, highlighting the importance of monitoring infection rates in fattening pig herds from a veterinary perspective. In conclusion, this study successfully developed a highly sensitive and specific TaqMan-qPCR method, which is effective for detecting PCV3 across a variety of clinical samples.</p>
</abstract>
<kwd-group>
<kwd>porcine circovirus type 3</kwd>
<kwd>REP gene</kwd>
<kwd>TaqMan-qPCR</kwd>
<kwd>clinical sample</kwd>
<kwd>detection rate</kwd>
</kwd-group>
<counts>
<fig-count count="3"/>
<table-count count="2"/>
<equation-count count="1"/>
<ref-count count="39"/>
<page-count count="8"/>
<word-count count="3545"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-in-acceptance</meta-name>
<meta-value>Animal Physiology and Management</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec id="s1" sec-type="intro">
<title>Introduction</title>
<p>Porcine circovirus (PCV), a member of the family <italic>Circoviridae</italic> and the genus <italic>Circovirus</italic>, is characterized as a non-enveloped, covalently closed, single-stranded icosahedral DNA virus. Notably, PCV is the smallest known animal DNA virus capable of autonomous replication, comprising four primary types: PCV1, PCV2, PCV3, and PCV4 (<xref ref-type="bibr" rid="B19">Opriessnig et&#xa0;al., 2020</xref>). Porcine circovirus type 3 (PCV3), a recently identified virus, was first detected in the United States in 2016 and has since been reported in pig farms globally (<xref ref-type="bibr" rid="B20">Ouyang et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B27">Tan et&#xa0;al., 2021</xref>). Research indicates that PCV3 infection is linked to dermatitis and nephropathy syndrome, reproductive failure, and multisystem inflammatory lesions in swine (<xref ref-type="bibr" rid="B12">Jiang et&#xa0;al., 2020</xref>). Additionally, PCV3 is considered a potential etiological agent of porcine respiratory disease complex (PRDC) and reproductive disorders in certain instances (<xref ref-type="bibr" rid="B13">Kim et&#xa0;al., 2018</xref>). The PCV3 genome comprises single-stranded DNA approximately 2.0 kb in length, exhibiting high conservation and specificity, with significant sequence divergence from other known porcine circoviruses, such as PCV2 and PCV4 (<xref ref-type="bibr" rid="B3">Cui et&#xa0;al., 2022</xref>). Research conducted by Ye et&#xa0;al. indicated that PCV3 shares approximately 44% nucleotide sequence homology with PCV2 (<xref ref-type="bibr" rid="B35">Ye et&#xa0;al., 2018</xref>). In a separate study, Zhang et&#xa0;al. found that the genetic homology between PCV3 and PCV4 is 43.2% (<xref ref-type="bibr" rid="B37">Zhang et&#xa0;al., 2020</xref>). The genome of PCV3 includes several critical genes, notably the viral capsid gene (CAP) and the replication-associated gene (REP), which are integral to the virus&#x2019;s replication and infection mechanisms (<xref ref-type="bibr" rid="B30">Wang et&#xa0;al., 2024</xref>). In recent years, there has been a notable increase in the prevalence of PCV3 in China, garnering considerable attention. Reports have documented a 12.2% positivity rate for PCV3 in pig samples across 21 provinces in China (<xref ref-type="bibr" rid="B22">Qi et&#xa0;al., 2019</xref>). Furthermore, a separate study identified a positivity rate of 31.18% in central China, underscoring the virus&#x2019;s widespread dissemination across various regions and pig populations (<xref ref-type="bibr" rid="B34">Xu et&#xa0;al., 2018</xref>). In the context of intensified pig farming in China, particularly following the outbreak of African swine fever virus (ASFV), many large-scale farms have established their own testing laboratories to conduct routine surveillance for ASFV and other pathogens, including PCV3. Consequently, the development and implementation of effective laboratory testing methods are crucial for the epidemiological investigation of PCV3.</p>
<p>Currently, the laboratory diagnostic techniques for PCV3 predominantly include <italic>in situ</italic> hybridization (ISH), immunohistochemistry (IHC), polymerase chain reaction (PCR), and enzyme-linked immunosorbent assay (ELISA) (<xref ref-type="bibr" rid="B27">Tan et&#xa0;al., 2021</xref>). While ISH and IHC are effective for detecting viral presence in tissue cells, they are not suitable for field-based clinical monitoring. The ELISA technique, which primarily focuses on the detection of antibodies against PCV3, is relatively expensive and thus not ideal for large-scale studies. Conversely, the quantitative real-time PCR (qPCR) method is currently regarded as the most effective approach for pathogen detection in intensive pig farming environments. It has been successfully employed for the detection of various porcine pathogens, including ASFV (<xref ref-type="bibr" rid="B11">Hu et&#xa0;al., 2024</xref>), porcine diarrhea viruses (<xref ref-type="bibr" rid="B24">Ren et&#xa0;al., 2024b</xref>), and certain bacterial pathogens (<xref ref-type="bibr" rid="B23">Ren et&#xa0;al., 2024a</xref>). In this study, we designed a pair of specific primers and a dual-quenched probe targeting the conserved region of the PCV3-REP gene to develop a fluorescent quantitative PCR method specifically for PCV3 detection. The establishment of this method provides a robust foundation for the rapid diagnosis of PCV3 in clinical settings and for conducting large-scale epidemiological investigations.</p>
</sec>
<sec id="s2" sec-type="materials|methods">
<title>Materials and methods</title>
<sec id="s2_1">
<title>Primers and probes</title>
<p>Using DNAStar software, we analyzed the sequence of the PCV3-REP gene (Accession number: MK656956.1) obtained from GenBank to design a specific pair of primers and a TaqMan probe with Primer Express 3.0. The designed primers are as follows: 5&#x2019;-GGTGGGATGGTTATAATG-3&#x2019; (forward) and 5&#x2019;-TAGCCACAAAATTAACAAAC-3&#x2019; (reverse), while the TaqMan probe is 5&#x2019;-FAM-CACCCTTAACAGGAACCCTCAGA-BHQ1-3&#x2019;. These primers and probe target a conserved region within the sequence, resulting in an amplified gene fragment measuring 141 base pairs. The synthesis of both primers and the probe was conducted by Sangon Biotech (Shanghai) Co., Ltd.</p>
</sec>
<sec id="s2_2">
<title>Standard plasmid</title>
<p>The pUC57-PCV3 standard plasmid was constructed by synthesizing and cloning gene sequences amplified from the REP gene of the PCV3 genome into the pUC57 vector. The quantification of this standard plasmid was performed using a UV-visible spectrophotometer, with copy numbers determined using a specific formula (<xref ref-type="bibr" rid="B38">Zhao et&#xa0;al., 2023</xref>). Subsequently, the plasmids underwent serial 10-fold dilutions, yielding concentrations ranging from 7.3&#xd7;10<sup>9</sup> to 7.3&#xd7;10<sup>0</sup> copies/&#x3bc;L, and were stored at -20&#xb0;C for future applications.</p>
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</sec>
<sec id="s2_3">
<title>Optimization of reaction conditions</title>
<p>The concentrations of primers and probes were systematically optimized using standard plasmid templates within a 20 &#x3bc;L reaction volume, utilizing the AceQ Universal U+Probe Master Mix V2 (Vazyme #Q513). Primer concentrations (10 &#x3bc;M) were varied from 0.2 to 0.8 &#x3bc;L each, while probe concentrations (10 &#x3bc;M) ranged from 0.1 to 0.4 &#x3bc;L each. These variations were tested alongside annealing temperatures (AT) ranging from 55&#xb0;C to 61&#xb0;C. The primary aim was to minimize the quantification cycle (Cq) value while maximizing the increase in fluorescence intensity (&#x394;Rn), thereby enhancing both the amplification efficiency and sensitivity of the reaction.</p>
</sec>
<sec id="s2_4">
<title>Evaluation of sensitivity and construction of standard curves</title>
<p>Amplification was performed using a standard plasmid template subjected to 10-fold serial dilutions, with concentrations spanning from 7.3&#xd7;10<sup>9</sup> to 7.3&#xd7;10<sup>0</sup> copies/&#x3bc;L under optimized conditions. The resulting amplification kinetic curves were analyzed, and a standard curve for the established TaqMan-qPCR method was constructed by plotting the logarithm of the copy number of the positive standard plasmid on the x-axis against the Cq values on the y-axis. This analysis enabled the derivation of the standard linear regression equation for the method.</p>
</sec>
<sec id="s2_5">
<title>Evaluation of specificity</title>
<p>To assess the specificity of the TaqMan-qPCR method, the assay was conducted to detect the cDNA of several viruses, including Classical Swine Fever Virus (CSFV), Porcine Epidemic Diarrhea Virus (PEDV), Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), Pseudorabies Virus (PRV), Foot-and-Mouth Disease Virus (FMDV), Swine Influenza Virus (SIV), and Porcine Circovirus Type 2 (PCV2). The pUC57-PCV3 standard plasmid was employed as the positive control, whereas double-distilled water (ddH<sub>2</sub>O) served as the negative control.</p>
</sec>
<sec id="s2_6">
<title>Evaluation of reproducibility</title>
<p>The TaqMan-qPCR method was implemented using pUC57-PCV3 standard plasmids at concentrations ranging from 7.3&#xd7;10<sup>5</sup> to 7.3&#xd7;10<sup>1</sup> copies/&#x3bc;L as templates, with each concentration evaluated in triplicate under optimized reaction conditions. Each experimental batch included three replicates per dilution level, and the resulting Cq values underwent statistical analysis to determine both intra- and inter-group coefficients of variation. This analysis enabled the evaluation of the method&#x2019;s reproducibility and stability.</p>
</sec>
<sec id="s2_7">
<title>Clinical sample testing</title>
<p>Nine clinical samples stored in our lab were tested simultaneously using both the developed TaqMan-qPCR method and a commercial qPCR kit. The results from the developed method were compared with those from the commercial method. Furthermore, a total of 2,454 clinical samples were collected from pig farms in Sichuan Province by farmers and subsequently sent to our laboratory for analysis. These samples comprised semen (n=1,101), oropharyngeal swabs (n=645), piglet testicular processing fluid (n=94), oral fluid (n=239), and pig serum (n=375). Semen and testicular processing fluid samples were chosen randomly for routine pathogen detection. The other samples were from pigs with respiratory symptoms. Each sample, with a volume of 300 &#x3bc;L, was processed using the NPA-96E automated nucleic acid extractor, developed by Hangzhou Boer Technology Co., Ltd. Post-extraction, qPCR analysis was conducted on 2 &#x3bc;L of the isolated DNA using the TaqMan-qPCR technique. The pUC57-PCV3 standard plasmid was utilized as a positive control, while ddH<sub>2</sub>O served as a negative control. A Cq value of less than 40 was established to indicate positive results.</p>
</sec>
<sec id="s2_8">
<title>Statistical analysis</title>
<p>The positivity rates of PCV3 across the different sample types were expressed as absolute and relative frequencies (%) with a 95% confidence interval (CI), calculated using the Clopper-Pearson method. Cq values of PCV3-positive samples were presented as mean &#xb1; standard deviation. Data visualization was conducted using GraphPad Prism 10.0 software, and statistical significance was assessed via the one-way ANOVA, with P&lt;0.05 indicating significant difference.</p>
</sec>
</sec>
<sec id="s3" sec-type="results">
<title>Results</title>
<sec id="s3_1">
<title>Optimization of reaction conditions</title>
<p>Initially, the volumes of primers and probes were first optimized at an AT of 60&#xb0;C. As detailed <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S1</bold>
</xref>, the Cq values were minimized with primer volumes of 0.4 &#x3bc;L and probe volumes of 0.2 &#x3bc;L across various template concentrations. Additionally, the AT condition was further optimized. According to <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S2</bold>
</xref>, the lowest Cq values were observed at 60&#xb0;C for template concentrations of 7.30&#xd7;10<sup>5</sup>, 7.30&#xd7;10<sup>3</sup>, 7.30&#xd7;10<sup>1</sup>, and 7.30&#xd7;10<sup>0</sup> copies/&#x3bc;L. Consequently, the optimized reaction conditions were as follows: an initial incubation at 37&#xb0;C for 2 minutes, followed by denaturation at 95&#xb0;C for 5 minutes. This was succeeded by 40 cycles comprising denaturation at 95&#xb0;C for 10 seconds and annealing at 60&#xb0;C for 30 seconds. The optimal reaction volume was determined to be 20 &#x3bc;L, consisting of 10 &#x3bc;L of 2&#xd7; AceQ Universal U+Probe Master Mix V2, 0.4 &#x3bc;L each of forward and reverse primers (10 &#x3bc;mol/L), 0.2 &#x3bc;L of probe (10 &#x3bc;mol/L), and 2 &#x3bc;L of template, with deionized water added to reach a final volume of 20 &#x3bc;L.</p>
</sec>
<sec id="s3_2">
<title>Establishment of the standard curve</title>
<p>The TaqMan-qPCR assay demonstrated proficiency in detecting standard plasmids at concentrations ranging from 7.3&#xd7;10<sup>9</sup> to 7.3&#xd7;10<sup>0</sup> copies/&#x3bc;L, exhibiting a strong linear correlation. The assay&#x2019;s minimum detectable concentration was determined to be 7.3&#xd7;10<sup>0</sup> copies/&#x3bc;L (<xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1A</bold>
</xref>). As shown in <xref ref-type="fig" rid="f1">
<bold>Figure&#xa0;1B</bold>
</xref>, the standard curve equation was y = -3.377x + 39.207, with a coefficient of determination (R&#xb2;) of 0.998 and an efficiency (Eff%) of 99.756%.</p>
<fig id="f1" position="float">
<label>Figure&#xa0;1</label>
<caption>
<p>Amplification curve <bold>(A)</bold> and standard curve <bold>(B)</bold> of the TaqMan-qPCR method for detection of PCV3. 1-10: 7.3&#xd7;10<sup>9</sup> to 7.3&#xd7;10<sup>0</sup> copies/&#x3bc;L.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fanim-06-1603264-g001.tif">
<alt-text content-type="machine-generated">Panel A shows an amplification plot with curves representing fluorescence over cycles, numbered one to ten. Panel B displays a standard curve graph plotting cycle threshold (Ct) against the starting quantity, with a linear regression line marked by red squares.</alt-text>
</graphic>
</fig>
</sec>
<sec id="s3_3">
<title>Specificity testing</title>
<p>The optimized reaction protocol was applied to detect nucleic acids from a variety of porcine pathogens, including CSFV, PEDV, PRRSV, PRV, FMDV, SIV, and PCV2. The results indicated that the pUC57-PCV3 standard plasmids produced amplification curves specific to PCV3, while amplification curves were absent for other common porcine pathogens as well as for negative controls (<xref ref-type="fig" rid="f2">
<bold>Figure&#xa0;2</bold>
</xref>). These findings imply that the TaqMan-qPCR assay possesses a high degree of specificity, showing no cross-reactivity with prevalent porcine pathogens.</p>
<fig id="f2" position="float">
<label>Figure&#xa0;2</label>
<caption>
<p>The amplification curves of specificity testing.</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fanim-06-1603264-g002.tif">
<alt-text content-type="machine-generated">Line graph titled &#x201c;Amplification&#x201d; displaying &#x394;Rn values against cycles. A purple curve, labeled pUC57-PCV3, rises sharply after cycle 30, indicating significant amplification. Other lines, representing CSFV, PEDV, PRRSV, PRV, FMDV, SIV, and PCV2, remain flat near zero.</alt-text>
</graphic>
</fig>
</sec>
<sec id="s3_4">
<title>Repeatability testing</title>
<p>As illustrated in <xref ref-type="table" rid="T1">
<bold>Table&#xa0;1</bold>
</xref>, the intra-group coefficients of variation ranged from 0.29% to 0.97%, while the inter-group coefficients of variation ranged from 0.37% to 0.75%, indicating the method&#x2019;s excellent reproducibility.</p>
<table-wrap id="T1" position="float">
<label>Table&#xa0;1</label>
<caption>
<p>Intra-reproducibility and intra-repeatability test of the TaqMan-qPCR.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="3" align="left">Template concentration (copies/&#x3bc;L)</th>
<th valign="middle" colspan="3" align="left">Intra-assay variation</th>
<th valign="middle" colspan="3" align="left">Inter-assay variation</th>
</tr>
<tr>
<th valign="middle" rowspan="2" align="left">Average value</th>
<th valign="middle" rowspan="2" align="left">Standard deviation</th>
<th valign="middle" rowspan="2" align="left">CV</th>
<th valign="middle" rowspan="2" align="left">Average value</th>
<th valign="middle" rowspan="2" align="left">Standard deviation</th>
<th valign="middle" rowspan="2" align="left">CV</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="left">7.30&#xd7;10<sup>5</sup>
</td>
<td valign="middle" align="left">19.31</td>
<td valign="middle" align="left">0.12</td>
<td valign="middle" align="left">0.62%</td>
<td valign="middle" align="left">19.82</td>
<td valign="middle" align="left">0.07</td>
<td valign="middle" align="left">0.37%</td>
</tr>
<tr>
<td valign="middle" align="left">7.30&#xd7;10<sup>4</sup>
</td>
<td valign="middle" align="left">22.22</td>
<td valign="middle" align="left">0.14</td>
<td valign="middle" align="left">0.65%</td>
<td valign="middle" align="left">23.10</td>
<td valign="middle" align="left">0.17</td>
<td valign="middle" align="left">0.73%</td>
</tr>
<tr>
<td valign="middle" align="left">7.30&#xd7;10<sup>3</sup>
</td>
<td valign="middle" align="left">25.88</td>
<td valign="middle" align="left">0.08</td>
<td valign="middle" align="left">0.29%</td>
<td valign="middle" align="left">26.80</td>
<td valign="middle" align="left">0.13</td>
<td valign="middle" align="left">0.49%</td>
</tr>
<tr>
<td valign="middle" align="left">7.30&#xd7;10<sup>2</sup>
</td>
<td valign="middle" align="left">29.41</td>
<td valign="middle" align="left">0.29</td>
<td valign="middle" align="left">0.97%</td>
<td valign="middle" align="left">30.01</td>
<td valign="middle" align="left">0.23</td>
<td valign="middle" align="left">0.75%</td>
</tr>
<tr>
<td valign="middle" align="left">7.30&#xd7;10<sup>1</sup>
</td>
<td valign="middle" align="left">33.46</td>
<td valign="middle" align="left">0.32</td>
<td valign="middle" align="left">0.95%</td>
<td valign="middle" align="left">33.24</td>
<td valign="middle" align="left">0.21</td>
<td valign="middle" align="left">0.62%</td>
</tr>
</tbody>
</table>
</table-wrap>
</sec>
<sec id="s3_5">
<title>Clinical sample testing</title>
<p>A comparison was made between the TaqMan-qPCR method and the commercial qPCR kit using nine clinical samples. <xref ref-type="supplementary-material" rid="SM1">
<bold>Supplementary Table S3</bold>
</xref> showed that the results from the TaqMan-qPCR method were consistent with those from the commercial kit, indicating its effectiveness in detecting PCV3 in clinical samples. Then, we employed the established TaqMan-qPCR methodology to examine the detection rate of PCV3 across various sample types, with the findings detailed in <xref ref-type="table" rid="T2">
<bold>Table&#xa0;2</bold>
</xref>. The detection rate was highest in piglet testicular processing fluid, at 71.28% (95% CI: 60.98%-80.18%), followed by oral fluid samples at 59.83% (95% CI: 53.34%-66.07%). Notably, the positive detection rates in throat swabs and serum were substantially lower, at 13.33% (95% CI: 10.79%-16.27%) and 10.40% (95% CI: 7.56%-13.89%), respectively. PCV3 was also identified in semen samples, albeit at a minimal rate of 0.27% (95% CI: 0.09%-0.79%), suggesting a potential risk of PCV3 transmission within the boar population. Moreover, as illustrated in <xref ref-type="fig" rid="f3">
<bold>Figure&#xa0;3</bold>
</xref>, the comparative analysis of Cq values across different samples revealed that the Cq values in testicular fluid were significantly lower than those in other sample types (P&lt;0.05), while no significant differences were observed among the other sample types (P&gt;0.05).</p>
<table-wrap id="T2" position="float">
<label>Table&#xa0;2</label>
<caption>
<p>PCV3 positivity in different clinical samples.</p>
</caption>
<table frame="hsides">
<thead>
<tr>
<th valign="middle" rowspan="2" align="left">Sample type</th>
<th valign="middle" rowspan="2" align="left">No. of positive sample</th>
<th valign="middle" rowspan="2" align="left">No. of total samples</th>
<th valign="middle" rowspan="2" align="left">Positive rate</th>
<th valign="middle" rowspan="2" align="left">95% CI</th>
</tr>
</thead>
<tbody>
<tr>
<td valign="middle" align="left">Semen</td>
<td valign="middle" align="left">3</td>
<td valign="middle" align="left">1101</td>
<td valign="middle" align="left">0.27%</td>
<td valign="middle" align="left">0.09%- 0.79%</td>
</tr>
<tr>
<td valign="middle" align="left">Oropharyngeal swabs</td>
<td valign="middle" align="left">86</td>
<td valign="middle" align="left">645</td>
<td valign="middle" align="left">13.33%</td>
<td valign="middle" align="left">10.79%- 16.27%</td>
</tr>
<tr>
<td valign="middle" align="left">Testicular processing fluid</td>
<td valign="middle" align="left">67</td>
<td valign="middle" align="left">94</td>
<td valign="middle" align="left">71.28%</td>
<td valign="middle" align="left">60.98%- 80.18%</td>
</tr>
<tr>
<td valign="middle" align="left">Oral fluid</td>
<td valign="middle" align="left">143</td>
<td valign="middle" align="left">239</td>
<td valign="middle" align="left">59.83%</td>
<td valign="middle" align="left">53.34%- 66.07%</td>
</tr>
<tr>
<td valign="middle" align="left">Serum</td>
<td valign="middle" align="left">39</td>
<td valign="middle" align="left">375</td>
<td valign="middle" align="left">10.40%</td>
<td valign="middle" align="left">7.56%- 13.89%</td>
</tr>
</tbody>
</table>
</table-wrap>
<fig id="f3" position="float">
<label>Figure&#xa0;3</label>
<caption>
<p>Cq values in different PCV3-positive samples. Different letters indicate significant statistical differences (P&lt;0.05), and the same letter indicates no significant statistical differences (P&gt;0.05).</p>
</caption>
<graphic mimetype="image" mime-subtype="tiff" xlink:href="fanim-06-1603264-g003.tif">
<alt-text content-type="machine-generated">Dot plot showing Cq values for five sample types: semen, oropharyngeal swabs, testicular processing fluid, oral fluid, and serum. Each category has dots representing data points with varying mean and standard deviation, indicated by horizontal lines and brackets.</alt-text>
</graphic>
</fig>
</sec>
</sec>
<sec id="s4" sec-type="discussion">
<title>Discussion</title>
<p>The qPCR method represents a highly sensitive and specific detection technology that offers substantial advantages over traditional PCR methods (<xref ref-type="bibr" rid="B17">Maren et&#xa0;al., 2023</xref>). This technique has been effectively utilized in the detection of PCV3. It facilitates real-time monitoring of the PCR amplification process while enabling quantitative analysis of the RNA content of PCV3 in samples. Feng et&#xa0;al. have demonstrated that the sensitivity of qPCR is ten times greater than that of traditional PCR in detecting PCV3 (<xref ref-type="bibr" rid="B6">Feng et&#xa0;al., 2019</xref>). Presently, qPCR detection methods for PCV3 are primarily categorized into three types: SYBR Green-based qPCR, TaqMan-qPCR, and multiplex qPCR. The SYBR Green-based qPCR is a widely used fluorescent dye method that is both cost-effective and user-friendly. The established sensitivity of SYBR Green-based qPCR is 61.2 copies/&#x3bc;L (<xref ref-type="bibr" rid="B8">Han et&#xa0;al., 2019</xref>), 1.73 &#xd7; 10<sup>2</sup> copies/&#x3bc;L (<xref ref-type="bibr" rid="B1">Chen et&#xa0;al., 2018</xref>) targeting the REP gene, and 10<sup>2</sup> copies/&#x3bc;L targeting the CAP gene (<xref ref-type="bibr" rid="B39">Zou et&#xa0;al., 2018</xref>), all of which were lower than those of TaqMan-qPCR methods. The TaqMan-based qPCR specific for the PCV3 CAP gene was initially designed by Wang et&#xa0;al., achieving a limit of detection (LOD) of 10<sup>2</sup> copies/&#x3bc;L (<xref ref-type="bibr" rid="B29">Wang et&#xa0;al., 2017</xref>). Recent advancements in TaqMan protocols, with LOD ranging from 10 to 15 copies/&#x3bc;L targeting the REP and CAP genes, have been documented, further demonstrating that the positive detection rate of qPCR protocols significantly surpasses that of conventional PCR methods (<xref ref-type="bibr" rid="B6">Feng et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B36">Yuan et&#xa0;al., 2020</xref>). In this study, we enhanced the TaqMan-PCR methodology targeting the REP gene of PCV3, achieving a detection sensitivity of 7.3 copies/&#x3bc;L, which surpasses previously reported methods. And the results obtained from clinical samples were consistent with those from a commercial kit, despite the comparison being limited to only nine samples. Furthermore, subsequent PCV3 sequencing results for some clinical samples aligned with the TaqMan-qPCR test outcomes (data not shown), thereby reinforcing the reliability of the established method. The REP gene of PCV3 is regarded as relatively conserved in multiple strains. An examination of the whole genome sequences of PCV3 strains collected in China, alongside a comparison with 34 PCV3 strains documented in the NCBI database, demonstrated that the conservation level of the REP gene exceeded 99% in both genetic and amino acid sequences, surpassing that of the CAP gene (<xref ref-type="bibr" rid="B16">Lv et&#xa0;al., 2023</xref>). Additionally, research by Feng et&#xa0;al. revealed that the LOD of the TaqMan-qPCR assay targeting the REP gene was ten times more sensitive than that of the conventional PCR assay targeting the Cap gene (<xref ref-type="bibr" rid="B6">Feng et&#xa0;al., 2019</xref>). Multiplex qPCR enables the simultaneous detection of multiple target genes within a single reaction, thereby enhancing detection efficiency and throughput, which is particularly advantageous for rapid screening of diverse pathogens (<xref ref-type="bibr" rid="B25">Rodriguez-Manzano et&#xa0;al., 2019</xref>). A duplex qPCR assay for PCV2 and PCV3, with LODs of 2.9 copies and 22.5 copies, respectively, reported a co-infection rate of 27.6% (94/340) (<xref ref-type="bibr" rid="B15">Li et&#xa0;al., 2018</xref>). Similarly, a PCV3/PCV4 duplex qPCR, with LODs of 51.7 copies and 67.7 copies for PCV3 and PCV4, respectively, identified a co-infection rate of 17.19% (11/64) (<xref ref-type="bibr" rid="B10">Hou et&#xa0;al., 2021</xref>). Nonetheless, the sensitivity of multiplex qPCR is generally lower compared to single-pathogen detection methods. Consequently, in practical applications, multiplex qPCR demonstrates distinct advantages in scenarios requiring the simultaneous detection of multiple pathogens, delivering comprehensive results rapidly (<xref ref-type="bibr" rid="B2">Chen et&#xa0;al., 2021</xref>). Nonetheless, for precise and specific detection, single TaqMan-qPCR is a more suitable option, particularly in diagnostic and clinical contexts.</p>
<p>Under clinical conditions, oral fluid samples are typically obtained from fattening pig herds, oropharyngeal swab samples from sows in confinement pens, testicular processing fluid samples from the testes of 3-day-old piglets, and serum samples from all pig herds (<xref ref-type="bibr" rid="B5">Fan et&#xa0;al., 2023</xref>). Notably, there are variations in the detection rates of PCV3 across different pig samples. According to literature reports, in 21 Polish pig farms, the detection rate of PCV3 was highest in oral fluids at 37.3%, whereas the detection rates in serum and fecal samples were 9.7% and 15.0%, respectively (<xref ref-type="bibr" rid="B33">Wo&#x17a;niak et&#xa0;al., 2020</xref>). Our findings demonstrate a significant detection rate of PCV3 in oral fluid samples, underscoring the veterinary importance of monitoring infection rates in fattening pig herds. In recent years, oral fluid samples have emerged as a more cost-effective and efficient alternative to serum samples for clinical detection purposes (<xref ref-type="bibr" rid="B9">Henao-Diaz et&#xa0;al., 2020</xref>). These samples have been utilized in the identification of various swine pathogens, including PRRSV (<xref ref-type="bibr" rid="B4">Decorte et&#xa0;al., 2015</xref>) and PCV2 (<xref ref-type="bibr" rid="B32">Wo&#x17a;niak et&#xa0;al., 2019</xref>; <xref ref-type="bibr" rid="B5">Fan et&#xa0;al., 2023</xref>). However, the unique characteristics of oral fluid samples during collection pose a risk of environmental contamination from sources such as feces and feed. Although existing literature suggests that organic matter does not compromise the sensitivity and specificity of diagnostic results, it may lead to sample turbidity, thereby affecting result accuracy (<xref ref-type="bibr" rid="B9">Henao-Diaz et&#xa0;al., 2020</xref>). Enhancing the precision of detection outcomes can be achieved by refining the collection and processing methods for oral fluid samples (<xref ref-type="bibr" rid="B9">Henao-Diaz et&#xa0;al., 2020</xref>). Literature suggests that sample contamination may be minimized by preventing the rope from touching the floor, specifically by setting the rope&#x2019;s bottom at the shoulder height of pigs (<xref ref-type="bibr" rid="B31">White et&#xa0;al., 2014</xref>; <xref ref-type="bibr" rid="B21">Pepin et&#xa0;al., 2015</xref>). Additionally, Gibert et&#xa0;al. have demonstrated that optimizing the sample centrifugation protocol can enhance the detection of PRRSV nucleic acids (<xref ref-type="bibr" rid="B7">Gibert et&#xa0;al., 2017</xref>). Furthermore, these samples are predominantly suitable for pathogen detection at the pen level (<xref ref-type="bibr" rid="B9">Henao-Diaz et&#xa0;al., 2020</xref>). Olsen et&#xa0;al. investigated the correlation between the detection rate of oral fluid and the infection rate in pigs within PRRSV-infected populations (<xref ref-type="bibr" rid="B18">Olsen et&#xa0;al., 2013</xref>). Nonetheless, further research is required to explore this relationship in the context of PCV3 infection.</p>
<p>The detection of viral presence in testicular fluid is considered a critical indicator of viral vertical transmission, as evidenced in studies on PEDV (<xref ref-type="bibr" rid="B26">Ryu et&#xa0;al., 2021</xref>) and Porcine group A rotavirus (<xref ref-type="bibr" rid="B14">Li et&#xa0;al., 2025</xref>). In this study, the prevalence of PCV3 in testicular fluid is the highest, with the lowest detected Cq values, suggesting potential vertical transmission of PCV3. Previous research has established that PCV3 can be transmitted from sows to their offspring, resulting in piglets being born with the virus (<xref ref-type="bibr" rid="B28">Vargas-Berm&#xfa;dez et&#xa0;al., 2021</xref>). Furthermore, a study conducted in Hunan Province, China, reported a significantly higher detection rate of PCV3 in sows experiencing reproductive issues compared to healthy sows, further highlighting the critical nature of vertical transmission (<xref ref-type="bibr" rid="B39">Zou et&#xa0;al., 2018</xref>). Interestingly, the positive rates of PCV3 in serum or throat swabs are relatively low, which could be attributed to the physiological stage or health status of the pigs tested.</p>
<p>In conclusion, this study developed a highly sensitive and specific TaqMan-qPCR method suitable for detecting PCV3 across various clinical samples, thereby providing an effective tool for monitoring the virus and investigating its epidemiological characteristics.</p>
</sec>
</body>
<back>
<sec id="s5" sec-type="data-availability">
<title>Data availability statement</title>
<p>Publicly available datasets were analyzed in this study. This data can be found here: Genbank accession number MK656956.1 (<ext-link ext-link-type="uri" xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MK656956.1">https://www.ncbi.nlm.nih.gov/nuccore/MK656956.1</ext-link>).</p>
</sec>
<sec id="s6" sec-type="ethics-statement">
<title>Ethics statement</title>
<p>The animal study was approved by The committee of experiment operational guidelines and animal welfare of Xichang University (approved permit number: xcc2024015). The study was conducted in accordance with the local legislation and institutional requirements.</p>
</sec>
<sec id="s7" sec-type="author-contributions">
<title>Author contributions</title>
<p>ZH: Writing &#x2013; original draft, Writing &#x2013; review &amp; editing, Funding acquisition, Project administration. RL: Writing &#x2013; original draft, Writing &#x2013; review &amp; editing, Methodology, Software. WX: Writing &#x2013; review &amp; editing, Methodology. RG: Resources, Writing &#x2013; review &amp; editing. ML: Resources, Writing &#x2013; review &amp; editing. ZZ: Methodology, Software, Writing &#x2013; review &amp; editing. GH: Writing &#x2013; review &amp; editing, Resources. GY: Funding acquisition, Project administration, Writing &#x2013; review &amp; editing.</p>
</sec>
<sec id="s8" sec-type="funding-information">
<title>Funding</title>
<p>The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by the Doctoral Research Initiation Project (YBZ2025004) and the Open project of State Key Laboratory of Animal Biotech Breeding (2025SKLAB6-05), and the Sichuan Science and Technology Program (2025YFHZ0058).</p>
</sec>
<sec id="s9" sec-type="COI-statement">
<title>Conflict of interest</title>
<p>Author RL was employed by the company Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd.</p>
<p>The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.</p>
</sec>
<sec id="s10" sec-type="ai-statement">
<title>Generative AI statement</title>
<p>The author(s) declare that no Generative AI was used in the creation of this manuscript.</p>
</sec>
<sec id="s11" sec-type="disclaimer">
<title>Publisher&#x2019;s note</title>
<p>All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.</p>
</sec>
<sec id="s12" sec-type="supplementary-material">
<title>Supplementary material</title>
<p>The Supplementary Material for this article can be found online at: <ext-link ext-link-type="uri" xlink:href="https://www.frontiersin.org/articles/10.3389/fanim.2025.1603264/full#supplementary-material">https://www.frontiersin.org/articles/10.3389/fanim.2025.1603264/full#supplementary-material</ext-link>
</p>
<supplementary-material xlink:href="Table1.docx" id="SM1" mimetype="application/vnd.openxmlformats-officedocument.wordprocessingml.document"/>
</sec>
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