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<front>
<journal-meta>
<journal-id journal-id-type="publisher-id">Front. Vet. Sci.</journal-id>
<journal-title>Frontiers in Veterinary Science</journal-title>
<abbrev-journal-title abbrev-type="pubmed">Front. Vet. Sci.</abbrev-journal-title>
<issn pub-type="epub">2297-1769</issn>
<publisher>
<publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="doi">10.3389/fvets.2023.1289570</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Veterinary Science</subject>
<subj-group>
<subject>Review</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group>
<article-title>Genetic background influences pig responses to porcine reproductive and respiratory syndrome virus</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author"><name><surname>Pei</surname> <given-names>Yangli</given-names></name>
<uri xlink:href="https://loop.frontiersin.org/people/1141084/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author"><name><surname>Lin</surname> <given-names>Chenghong</given-names></name>
<role content-type="https://credit.niso.org/contributor-roles/writing-original-draft/"/>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname> <given-names>Hua</given-names></name>
<uri xlink:href="https://loop.frontiersin.org/people/1245576/overview"/>
<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
<contrib contrib-type="author" corresp="yes"><name><surname>Feng</surname> <given-names>Zheng</given-names></name><xref rid="c001" ref-type="corresp"><sup>&#x002A;</sup></xref>
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<role content-type="https://credit.niso.org/contributor-roles/writing-review-editing/"/>
</contrib>
</contrib-group>
<aff><institution>Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes, School of Life Science and Engineering, Foshan University</institution>, <addr-line>Foshan</addr-line>, <country>China</country></aff>
<author-notes>
<fn fn-type="edited-by" id="fn0001">
<p>Edited by: Lingxue Yu, Chinese Academy of Agricultural Sciences, China</p>
</fn>
<fn fn-type="edited-by" id="fn0002">
<p>Reviewed by: Pu Sun, Chinese Academy of Agricultural Sciences, China; Qingkui Jiang, Rutgers University, Newark, United States</p>
</fn>
<corresp id="c001">&#x002A;Correspondence: Zheng Feng, <email>greatfz@126.com</email></corresp>
</author-notes>
<pub-date pub-type="epub">
<day>20</day>
<month>10</month>
<year>2023</year>
</pub-date>
<pub-date pub-type="collection">
<year>2023</year>
</pub-date>
<volume>10</volume>
<elocation-id>1289570</elocation-id>
<history>
<date date-type="received">
<day>06</day>
<month>09</month>
<year>2023</year>
</date>
<date date-type="accepted">
<day>09</day>
<month>10</month>
<year>2023</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright &#x00A9; 2023 Pei, Lin, Li and Feng.</copyright-statement>
<copyright-year>2023</copyright-year>
<copyright-holder>Pei, Lin, Li and Feng</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 reproductive and respiratory syndrome virus (PRRSV) is a highly infectious and economically significant virus that causes respiratory and reproductive diseases in pigs. It results in reduced productivity and increased mortality in pigs, causing substantial economic losses in the industry. Understanding the factors affecting pig responses to PRRSV is crucial to develop effective control strategies. Genetic background has emerged as a significant determinant of susceptibility and resistance to PRRSV in pigs. This review provides an overview of the basic infection process of PRRSV in pigs, associated symptoms, underlying immune mechanisms, and roles of noncoding RNA and alternative splicing in PRRSV infection. Moreover, it emphasized breed-specific variations in these aspects that may have implications for individual treatment options.</p>
</abstract>
<kwd-group>
<kwd>porcine reproductive and respiratory syndrome</kwd>
<kwd>pig breeds</kwd>
<kwd>genetic backgrounds</kwd>
<kwd>PRRSV</kwd>
<kwd>PRRSV receptors</kwd>
<kwd>innate immunity</kwd>
<kwd>acquired immunity</kwd>
</kwd-group>
<contract-num rid="cn1">2020B1515120016</contract-num>
<contract-num rid="cn2">2022B0202090001</contract-num>
<contract-sponsor id="cn1">Guangdong Basic and Applied Basic Research Foundation</contract-sponsor>
<contract-sponsor id="cn2">Key Technologies R&#x0026;D Program of Guangdong Province</contract-sponsor>
<counts>
<fig-count count="0"/>
<table-count count="2"/>
<equation-count count="0"/>
<ref-count count="127"/>
<page-count count="10"/>
<word-count count="10726"/>
</counts>
<custom-meta-wrap>
<custom-meta>
<meta-name>section-at-acceptance</meta-name>
<meta-value>Veterinary Infectious Diseases</meta-value>
</custom-meta>
</custom-meta-wrap>
</article-meta>
</front>
<body>
<sec sec-type="intro" id="sec1">
<label>1.</label>
<title>Introduction</title>
<p>Porcine reproductive and respiratory syndrome (PRRS) is a highly destructive disease that was first identified in the United States in 1987, and later spread to Europe in 1990 (<xref ref-type="bibr" rid="ref1">1</xref>, <xref ref-type="bibr" rid="ref2">2</xref>). It poses a considerable economic risk to the swine industry (<xref ref-type="bibr" rid="ref3 ref4 ref5">3&#x2013;5</xref>). The estimated economic impact of PRRS on the entire herd of four Chinese farms experiencing outbreaks is &#x00A5;1424.37 per sow (<xref ref-type="bibr" rid="ref4">4</xref>). The PRRS virus (PRRSV) is the pathogen responsible for causing PRRS, characterized by its positive-stranded RNA nature and enveloped structure (<xref ref-type="bibr" rid="ref6">6</xref>). It belongs to the order Nidovirales and the family <italic>Arteriviridae</italic> (<xref ref-type="bibr" rid="ref6">6</xref>). PRRSVs are classified into PRRSV-1 and -2 genotypes that occur in Europe and North America, respectively (<xref ref-type="bibr" rid="ref7">7</xref>). PRRSV-1 and -2 share approximately 60% nucleotide identity (<xref ref-type="bibr" rid="ref1">1</xref>, <xref ref-type="bibr" rid="ref8">8</xref>); however, it is believed that they underwent separate evolutionary paths, originating from a distant common ancestor (<xref ref-type="bibr" rid="ref9">9</xref>). PRRSV-2 primarily targets cells of the monocyte/macrophage lineage, particularly porcine alveolar macrophages (PAMs) (<xref ref-type="bibr" rid="ref10">10</xref>).</p>
<p>The Prevention and control of PRRS poses a significant challenge. Current strategies include vaccination, herd management, biosecurity, and antiviral treatment (<xref ref-type="bibr" rid="ref11">11</xref>). However, the effectiveness of these measures varies depending on specific circumstances and implementation strategies. Vaccination shows promising results in reducing the incidence and severity of PRRS; however, it does not offer a complete solution (<xref ref-type="bibr" rid="ref12">12</xref>). Effective herd management (including monitoring and controlling pig movement) can help reduce the disease spread. Furthermore, biosecurity measures, such as disinfection and cleaning of facilities may help to prevent disease transmission (<xref ref-type="bibr" rid="ref11">11</xref>). Although antiviral treatment can reduce disease severity, although it is not a permanent cure and may not be cost-effective in all situations (<xref ref-type="bibr" rid="ref13">13</xref>). Therefore, further research is necessary to identify and develop more effective methods to prevent and control PRRS.</p>
<p>The genetic background of pigs is a significant factor determining their response to PRRSV. Various pig breeds and lines exhibit different levels of resistance to PRRSV infection (<xref ref-type="bibr" rid="ref14">14</xref>, <xref ref-type="bibr" rid="ref15">15</xref>). Meishan and Tongcheng (TC) breeds, known for their elevated resistance to PRRSV, are less susceptible to infection when compared to other breeds, such as the Large White (LW) (<xref ref-type="bibr" rid="ref16 ref17 ref18">16&#x2013;18</xref>). Moreover, specific pig tissues such as the lungs and lymph nodes may exhibit varying susceptibilities to PRRSV, which may be influenced by genetic factors (<xref ref-type="bibr" rid="ref19">19</xref>). Enhanced knowledge of the genetic factors contributing to the differences in PRRSV resistance among pig breeds potentially improves pig health and welfare, ultimately reducing the economic losses associated with PRRSV infection.</p>
<p>Overall, controlling PRRS remains a challenge, owing to the complex host-pathogen interactions despite extensive research efforts. Further research is required to develop effective countermeasures against the virus. This review focuses on the influence of genetic factors on pig responses to PRRSV, including differences among pig breeds and lines. Furthermore, we investigated PRRSV infection mechanisms and factors affecting the host response, such as the innate and adaptive immune systems. Additionally, alternative splicing events and noncoding RNAs involved in PRRSV infection and replication were explored. The potential implications of this research were to develop effective control strategies and breeding programs that utilize genetic information to improve pig health and productivity. This extensive knowledge will potentially enhance pig well-being, increase productivity, and promote worldwide sustainability of pig farming.</p>
</sec>
<sec id="sec2">
<label>2.</label>
<title>Varied receptor responses in different pig breeds upon PRRSV invasion</title>
<sec id="sec3">
<label>2.1.</label>
<title>Mechanisms of host cell entry</title>
<p>The PRRSV genome is approximately 15 kbp in size and has a specific organization. The replicase genes are situated at the 5&#x2032;-end of the genome, whereas the genes encoding structural proteins are found at the 3&#x2032;-end (<xref ref-type="bibr" rid="ref20">20</xref>, <xref ref-type="bibr" rid="ref21">21</xref>). The viral genome consists of more than 10 open reading frames (ORFs). Over 66% of the viral genome is made up of ORF1a and ORF1b, which encode nonstructural proteins that serve crucial functions including protease and replicase activities. These proteins also modulate host genes that are vital for the replication of the virus. Conversely, ORFs 2&#x2013;7 encode the structural proteins required for virus formation (<xref ref-type="bibr" rid="ref21">21</xref>).</p>
<p>PRRSV processes of eight structural proteins, which include a small non-glycosylated protein and a group of glycosylated proteins: Glycoprotein (GP) 2ab, GP3, GP4, GP5, GP5a, matrix (M), and nucleocapsid (N) (<xref ref-type="bibr" rid="ref21">21</xref>, <xref ref-type="bibr" rid="ref22">22</xref>). The primary structural proteins encoded by ORFs 5, 6, and 7 are GP5, M, and N, respectively. While GP5 typically forms a heterodimer with M, there have been reports of GP5 homodimers (<xref ref-type="bibr" rid="ref23">23</xref>). Among the surface glycoproteins, GP2, GP3, and GP4, derived from ORFs 2, 3, and 4, respectively, act as minor components. Additionally, two very small non-glycosylated proteins, designated as 2b or E and 5a, are translated from ORF2b and ORF5a, respectively (<xref ref-type="bibr" rid="ref24">24</xref>, <xref ref-type="bibr" rid="ref25">25</xref>). The smooth exterior of the PRRSV virion is primarily attributed to the presence of short peptide sequences in the ectodomains of M and GP5. However, the larger ectodomains of GP2, GP3, and GP4 can also give rise to a few protrusions on the virus surface (<xref ref-type="bibr" rid="ref21">21</xref>).</p>
<p>Macrophages are the primary target cells for PRRSV infection (<xref ref-type="bibr" rid="ref10">10</xref>, <xref ref-type="bibr" rid="ref26 ref27 ref28">26&#x2013;28</xref>), playing a crucial role in immune modulation and contributing to the respiratory distress observed in pigs affected by the porcine respiratory disease complex. The following section provides an overview of the recognition of the virus by recipient cells (<xref rid="tab1" ref-type="table">Table 1</xref>) and the mechanisms involved.</p>
<table-wrap position="float" id="tab1">
<label>Table 1</label>
<caption>
<p>Major receptors and function during PRRSV infection.</p>
</caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Receptor</th>
<th align="left" valign="top">Function</th>
<th align="left" valign="top">References</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top">CD163</td>
<td align="left" valign="top">CD163 interacts with PRRSV glycoproteins GP4 and GP2a to form a multiprotein complex. The presence of CD163 SRCR5 is essential for PRRSV infection, with its absence in pigs conferring resistance against different PRRSV strains. Furthermore, CD163 plays a vital role in TIM-induced macropinocytosis during PRRSV infection</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref29 ref30 ref31 ref32 ref33 ref34 ref35 ref36">29&#x2013;36</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">Heparin sulfate (HS)</td>
<td align="left" valign="top">HS interacts with the M and GP5-M proteins of PRRSV, enabling efficient attachment of the virus to cells. However, it is not a prerequisite for PRRSV invasion of macrophages</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref37">37</xref>, <xref ref-type="bibr" rid="ref38">38</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">Sialoadhesin (Sn)</td>
<td align="left" valign="top">The N-terminal immunoglobulin domain of porcine Sn is critical factor that promotes PRRSV attachment to porcine alveolar macrophages (PAMs). Although it does not contribute to viral uncoating, Sn facilitates PRRSV internalization in expressing cells</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref39 ref40 ref41 ref42 ref43 ref44">39&#x2013;44</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">Vimentin</td>
<td align="left" valign="top">Vimentin directly interacts with PRRSV nucleocapsid protein, and the application of antivimentin antibodies effectively block PRRSV</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref45 ref46 ref47 ref48">45&#x2013;48</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">CD151</td>
<td align="left" valign="top">CD151 functions as an RNA-binding protein, and directly interacts with the 3&#x2032;-UTR RNA of PRRSV. CD151 overexpression enhances PRRSV infection in non-susceptible cells, whereas blocking CD151 with antibodies inhibits PRRSV infection in susceptible cells</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref49">49</xref>, <xref ref-type="bibr" rid="ref50">50</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">Non-muscle myosin heavy chain 9 (MYH9)</td>
<td align="left" valign="top">Interaction of MYH9 with PRRSV GP5 protein is indispensable to facilitate PRRSV internalization and intercellular spread</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref51 ref52 ref53">51&#x2013;53</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">Heat shock protein member 8 (HSPA8)</td>
<td align="left" valign="top">The PB domain of HSPA8 interacts with PRRSV GP4, and the ATPase activity of HSPA8 is crucial for PRRSV infection through clathrin-mediated endocytosis (CME). Furthermore, HSPA8 co-localizes with PRRSV on the cell surface, and plays a pivotal role in facilitating viral fusion and entry</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref54">54</xref>, <xref ref-type="bibr" rid="ref55">55</xref>)</td>
</tr>
</tbody>
</table>
</table-wrap>
<p>CD163 serves as a crucial receptor for PRRSV and plays a critical role in determining cell susceptibility to the virus (<xref ref-type="bibr" rid="ref29">29</xref>). It is a scavenger receptor glycoprotein predominantly found in mature macrophages and monocytes. The extracellular portion of CD163 comprises nine scavenger receptor cysteine-rich domains (SRCR) and two motifs rich in proline-serine&#x2013;threonine (PST), which are repeated multiple times (<xref ref-type="bibr" rid="ref56">56</xref>). The heterotrimeric GP2, GP3, and GP4 proteins of PRRSV bind to CD163, with GP2 and GP4 forming multiple interactions with different receptors (<xref ref-type="bibr" rid="ref30">30</xref>, <xref ref-type="bibr" rid="ref56">56</xref>). Pigs with a <italic>CD163</italic> gene knockout (KO) are non-permissive to PRRSV-2 infection (<xref ref-type="bibr" rid="ref31">31</xref>), and their macrophages show resistance to PRRSV-1 and -2 (<xref ref-type="bibr" rid="ref32">32</xref>). Recent studies show that CD163 SRCR5-deficient pigs are resistant to specific PRRSV-2 strains (<xref ref-type="bibr" rid="ref33">33</xref>, <xref ref-type="bibr" rid="ref34">34</xref>). Genetically engineered pigs with a modified CD163 SRCR5 domain display normal growth under standard conditions (<xref ref-type="bibr" rid="ref34">34</xref>, <xref ref-type="bibr" rid="ref35">35</xref>). This suggests that gene editing techniques targeting CD163 can potentially control and eradicate PRRS outbreaks.</p>
<p>CD163 participates in viral apoptotic mimicry, a strategy employed by certain viruses to infect host cells (<xref ref-type="bibr" rid="ref57">57</xref>). This mechanism involves viruses disguising themselves as apoptotic debris and engaging receptors on the surface of phagocytes that recognize phosphatidylserine (PtdSer), a marker of apoptosis (<xref ref-type="bibr" rid="ref58">58</xref>). These interactions activate signaling cascades and lead to actin rearrangements to facilitate endocytic engulfment, and subsequent degradation of viral particles (<xref ref-type="bibr" rid="ref59">59</xref>). Viruses adopt distinct mechanisms of apoptotic mimicry, giving rise to the concepts of classical and nonclassical apoptotic mimicry (<xref ref-type="bibr" rid="ref60">60</xref>). PRRSV capitalizes on viral apoptotic mimicry to induce macropinocytosis through the involvement of T cell immunoglobulin and mucin domain proteins TIM-1 and -4 (<xref ref-type="bibr" rid="ref57">57</xref>). During PRRSV infection, CD163 plays a vital role in facilitating TIM-induced macropinocytosis (<xref ref-type="bibr" rid="ref61">61</xref>). Consequently, PRRSV adopts an alternative route of infection via macrophage activity involving CD163.</p>
<p>Mammalian cells contain heparin sulfate (HS) as a glycosaminoglycan on their surface and in their extracellular matrix (<xref ref-type="bibr" rid="ref62">62</xref>). Heparin sulfate plays an important role in adhesion during PRRSV infection by interacting with M and GP5-M proteins during PRRSV infection (<xref ref-type="bibr" rid="ref37">37</xref>). Although not essential for PRRSV invasion of porcine alveolar macrophages (PAMs), HS enables PRRSV to adhere to non-susceptible cell lines without completing the subsequent infection steps (<xref ref-type="bibr" rid="ref38">38</xref>). PRRSV-1 and -2 exhibit different sensitivities to HS (<xref ref-type="bibr" rid="ref37">37</xref>). The treatment of PAMs with heparinase (which degrades HS) reduces PRRSV infection (<xref ref-type="bibr" rid="ref37">37</xref>). Moreover, PRRSV infection can activate NF-&#x03BA;B and cathepsin L, resulting in heparinase upregulation and processing, reduction in HS surface expression, and promotion of viral replication and release (<xref ref-type="bibr" rid="ref63">63</xref>).</p>
<p>Sialoadhesin (Sn), also referred to as CD169 or SIGLIC-1, acts as a co-receptor for PRRSV invasion. The N-terminal immunoglobulin domain of porcine Sn is necessary and sufficient (<xref ref-type="bibr" rid="ref39">39</xref>, <xref ref-type="bibr" rid="ref40">40</xref>). Cells expressing Sn facilitate PRRSV internalization, but do not promote viral uncoating (<xref ref-type="bibr" rid="ref40">40</xref>). The collaboration between Sn and other receptors, such as CD163, sensitizes cells to PRRSV infection, promoting effective attachment, internalization, and disassembly of viral particles (<xref ref-type="bibr" rid="ref41">41</xref>, <xref ref-type="bibr" rid="ref42">42</xref>). The absence of Sn in genetically-edited pigs does not disrupt PRRSV attachment/internalization or have any effect on disease progression or histopathology (<xref ref-type="bibr" rid="ref64">64</xref>). This discrepancy between the <italic>in vitro</italic> and <italic>in vivo</italic> models of PRRSV receptors indicates conflicting outcomes. These findings suggest that Sn primarily plays a role in binding PRRSV to the macrophage surface rather than facilitating viral internalization.</p>
<p>Vimentin (VIM) is a crucial component of the PRRSV receptor complex and plays a key role in the intracellular replication and metastasis of PRRSV (<xref ref-type="bibr" rid="ref45">45</xref>, <xref ref-type="bibr" rid="ref46">46</xref>). It forms a polymer with other fine-cell bone frame microfilaments and interacts with the PRRSV nucleocapsid protein (<xref ref-type="bibr" rid="ref47">47</xref>). Vimentin can render normally non-susceptible cell lines susceptible to PRRSV infection. This highlights its involvement in the viral receptor complex (<xref ref-type="bibr" rid="ref45">45</xref>). Following PRRSV entry, vimentin undergoes reorganization facilitated by Serine 38 phosphorylation by calcium calmodulin-dependent protein kinase II gamma (<xref ref-type="bibr" rid="ref48">48</xref>). As a result of this reorganization, cage-like structures form around PRRSV replication complexes within the nucleus.</p>
<p>Tetraspanin superfamily member CD151 is an RNA-binding protein that interacts with the 3&#x2019;-UTR of the PRRSV genome and functions as an RNA-binding protein (<xref ref-type="bibr" rid="ref49">49</xref>). By silencing the CD151 gene in MARC-145 cells, PRRSV infection decreases significantly, and antibodies against CD151 prevent it entirely (<xref ref-type="bibr" rid="ref49">49</xref>). CD151 expression can be regulated by microRNAs (such as miR-506) that lead to a decrease in CD151 mRNA and protein levels, thereby resulting in the inhibition of PRRSV replication and viral release in MARC-145 cells (<xref ref-type="bibr" rid="ref50">50</xref>). CD151 possesses N-glycosylation and palmitoylation sites (<xref ref-type="bibr" rid="ref65">65</xref>); their involvement in regulating PRRSV infection requires further investigation.</p>
<p>Non-muscle myosin heavy chain 9 (MYH9) plays various roles in cell adhesion, polarization, morphogenesis, and migration (<xref ref-type="bibr" rid="ref66">66</xref>, <xref ref-type="bibr" rid="ref67">67</xref>). It interacts with PRRSV GP5, which is crucial for PRRSV internalization and intercellular spread. The C-terminal domain of MYH9 directly binds to the first ectodomain of viral GP5, and disruption of this interaction reduces PRRSV internalization (<xref ref-type="bibr" rid="ref51">51</xref>). Specific amino acid residues within the MYH9 C-terminal domain are believed to be key binding sites for GP5 (<xref ref-type="bibr" rid="ref52">52</xref>). Furthermore, MYH9 undergoes reorganization upon PRRSV infection, forming cage-like structures around the PRRSV replication complex (<xref ref-type="bibr" rid="ref53">53</xref>). MYH9 co-expression with CD163 enhances PRRSV infection (<xref ref-type="bibr" rid="ref51">51</xref>).</p>
<p>Heat shock protein member 8 (HSPA8) plays a role in various viral infections by regulating viral entry, replication, and assembly (<xref ref-type="bibr" rid="ref68">68</xref>). Inhibition of endogenous HSPA8 reduces PRRSV replication by decreasing viral attachment and internalization (<xref ref-type="bibr" rid="ref54">54</xref>). HSPA8 interacts with clathrin, and is involved in clathrin-mediated endocytosis (CME) (<xref ref-type="bibr" rid="ref69">69</xref>). The PB domain of HSPA8 interacts with PRRSV GP4, and HSPA8 ATPase activity is required for PRRSV infection via CME (<xref ref-type="bibr" rid="ref54">54</xref>). Moreover, HSPA8 co-localizes with PRRSV on the cell surface and facilitates viral fusion and entry (<xref ref-type="bibr" rid="ref54">54</xref>). HSPA8-based therapies show promise in clinical trials and vaccine development for other diseases. For instance, recombinant HSPA8 fused with GP3 and GP4 boosts immune responses and confers protective effects against the highly pathogenic PRRSV infection in pigs (<xref ref-type="bibr" rid="ref55">55</xref>). Therefore, HSPA8-based strategies have the potential for vaccine development.</p>
<p>The viral genome contains more than 10 ORFs. These ORFs encode nonstructural proteins crucial for viral replication. ORFs 2&#x2013;7 encode structural proteins that play vital roles in viral formation, and are necessary for viral particle assembly. PRRSV uses multiple receptors for entry into host cells, including CD163, Sn, HS, VIM, MYH9, CD151, CD209, and HSPA8. Understanding the interactions between PRRSV and these receptors offers potential targets to control and eradicate PRRSV outbreaks, and to develop vaccines and therapeutic strategies.</p>
</sec>
<sec id="sec4">
<label>2.2.</label>
<title>Different pig breeds show varying expression of PRRSV receptor genes in lung tissues upon PRRSV infection</title>
<p>Chinese Dapulian pigs (DPL) exhibit increased resistance to PRRSV when compared to commercial Duroc&#x00D7;Landrace&#x00D7;Yorkshire (DLY) crossbred pigs, as evidenced by lower rectal temperatures and serum PRRSV copy numbers (<xref ref-type="bibr" rid="ref70">70</xref>). Analysis of lung tissue samples from PRRSV-uninfected DPL and DLY pigs show varied expression patterns of five PRRSV mediator genes (NMMHC-IIA, SIGLEC1, CD163, HSPG2, and VIM), with significantly higher mRNA expression levels of SIGLEC1, NMMHC-IIA, CD163, and VIM in DLY pigs than those in DPL pigs (<xref ref-type="bibr" rid="ref70">70</xref>). Another study revealed that the mRNA level of CD163 in PAMs of Dingyuan pigs is significantly lower than that of Jiangquhai pigs within 24&#x2009;h post-infection (hpi); this may account for the high resistance of Jiangquhai pigs to PRRSV (<xref ref-type="bibr" rid="ref71">71</xref>). Moreover, Sn expression in PAMs from Dingyuan pigs increase at a faster rate than that in PAMs from Jiangquhai pigs following viral infection (<xref ref-type="bibr" rid="ref71">71</xref>). This finding corresponds to the high PRRSV content in PAMs from Dingyuan pigs (<xref ref-type="bibr" rid="ref71">71</xref>). The increased mRNA expression levels of CD163 and Sn may contribute to more rapid viral invasion and wider penetration sites <italic>in vivo</italic> and <italic>in vitro</italic> (<xref ref-type="bibr" rid="ref72">72</xref>). Viral receptor expression varies among different pig breeds after PRRSV infection, and there are variations in the expression of PRRSV receptors (HS, Sn, CD163, CD151, and VIM) in the lung tissues of different pig breeds, even under normal physiological conditions (<xref ref-type="bibr" rid="ref47">47</xref>, <xref ref-type="bibr" rid="ref71">71</xref>, <xref ref-type="bibr" rid="ref73">73</xref>).</p>
<p>Variations in receptor expression and RNA abundance can lead to activation or inhibition of various pathways, resulting in distinct responses to PRRSV infection in different pig breeds. Further exploration of the mechanisms underlying these susceptibility differences could pave the way for the development of innovative approaches to control PRRSV infection in swine populations.</p>
</sec>
</sec>
<sec id="sec5">
<label>3.</label>
<title>Variation in manifestations in different pig breeds during PRRSV-infection</title>
<sec id="sec6">
<label>3.1.</label>
<title>Symptoms and lesions after PRRSV infection</title>
<p>The clinical manifestations of PRRS are influenced by multiple factors, including the virus strain, age and immune status of the host, production environment, productive state, and specific PRRSV strains. The typical symptoms during the acute phase of the disease include loss of appetite, weakness, fever, and respiratory difficulties. Respiratory dyspnea is commonly observed across all the age groups of pigs, although infected pregnant sows may exhibit more severe symptoms.</p>
<p>Pregnant sows are highly susceptible to PRRSV infection and may exhibit various clinical symptoms. This includes loss of appetite, abortions, transient discoloration of the ears (commonly known as blue ear disease, which affects approximately 2% of sows), early farrowing, prolonged anestrus, delayed return to heat after weaning, coughing, and respiratory signs (<xref ref-type="bibr" rid="ref74">74</xref>).</p>
<p>Symptoms in weaned and fattened piglets can be significant and may include hair loss, slight loss of appetite, mild respiratory problems (such as coughing), and localized skin redness. The mortality rate during this stage ranges from 10 to 20% and is influenced by hygiene and operational management. The presence of other microorganisms within a herd can increase mortality rates. Pigs aged 4&#x2013;12&#x2009;weeks born by infected sows exhibit clinical symptoms similar to those of suckling pigs, including loss of appetite, malabsorption, wasting, coughing, and pneumonia, and a 12% higher post-weaning mortality rate (<xref ref-type="bibr" rid="ref75">75</xref>, <xref ref-type="bibr" rid="ref76">76</xref>). Secondary bacterial infections can lead to lung and systemic abscesses, abscess-related lameness, or poor growth (<xref ref-type="bibr" rid="ref77">77</xref>, <xref ref-type="bibr" rid="ref78">78</xref>).</p>
<p>A range of clinical symptoms indicates potential issues in farrowing sows. These symptoms include anorexia, decreased water intake, reduced milk production, mastitis, premature delivery of piglets, discoloration of the skin (such as, verticillium wilt or blue vulva and ears), pressure sores, lethargy, respiratory symptoms (such as, coughing and pneumonia), mummified piglets, stillborn piglets, and weak piglets at birth (<xref ref-type="bibr" rid="ref77">77</xref>, <xref ref-type="bibr" rid="ref79">79</xref>).</p>
<p>Severe respiratory diseases and decreased survival rates are the most common issues in piglets. Other clinical symptoms included eyelid swelling, conjunctivitis, listlessness, significant weight loss, diarrhea, rough and unkempt fur, purple ear discoloration, and abnormal behavior (<xref ref-type="bibr" rid="ref76">76</xref>, <xref ref-type="bibr" rid="ref77">77</xref>).</p>
</sec>
<sec id="sec7">
<label>3.2.</label>
<title>Clinical features of PRRSV infected pigs</title>
<p>Artificial infection of TC pigs and LW pigs with HP-PRRSV results in similar symptoms of high fever. LW pigs have a temperature above 40.5&#x00B0;C from 0 to 3 days post-contact (dpc) and above 41.0&#x00B0;C from 4 to 7 dpc, while TC pigs have a temperature above 40.5&#x00B0;C from 1 to 3 dpc and above 41.0&#x00B0;C from 4 to 6 dpc (<xref ref-type="bibr" rid="ref18">18</xref>). However, the clinical signs are less severe in TC pigs than those in LW pigs, showing changes in lying behavior, less depression, deep breathing, skin flushing, and reduced food intake. Furthermore, TC pigs have significantly less inflammatory exudation (<italic>p</italic>&#x2009;&#x003C;&#x2009;0.01) and alveolar wall thickening (<italic>p</italic>&#x2009;&#x003C;&#x2009;0.05) when compared with LW pigs. Post-mortem analysis revealed varying degrees of swelling and bleeding in the brain, liver, and spleen, with jagged edges in the spleen (<xref ref-type="bibr" rid="ref18">18</xref>).</p>
<p>Similarly, a study involving 4-6-week-old piglets of Tibetan, ZangMei black (ZM), and LW piglets challenged with HP-PRRSV (JXA1) showed that LW piglets had a significant increase in rectal temperature from 2 dpi that remained elevated until 15 dpi (40.4&#x00B0;C&#x2009;&#x00B1;&#x2009;0.55). ZM piglets exhibit a significant increase in rectal temperature for 4 days (2&#x2013;5 dpi) with no readings above 40&#x00B0;C, and Tibetan piglets did not show any rectal temperature readings above 40&#x00B0;C. Anorexia, sneezing, coughing, and diarrhea appeared in the affected ZM and LW piglets within 2&#x2013;3 dpi; however, LW piglets experienced more severe symptoms, including increased shivering, hyperspasmia, and respiratory rates from 6 to 8 dpi. Some of the challenged LW piglets died at 9, 11, and 13 dpi, whereas Tibetan piglets did not exhibit typical signs or death throughout the 28-day period (<xref ref-type="bibr" rid="ref80">80</xref>). The observed clinical signs were aligned with corresponding changes in temperature and body weight gain. LW piglets showed decreased body weight during the second week following challenge, ZM piglets experienced weight loss during the first week, and Tibetan piglets showed consistent weight gain throughout the 4 weeks (<xref ref-type="bibr" rid="ref80">80</xref>).</p>
<p>Porcine reproductive and respiratory syndrome virus infection has a notable effect on the clinical presentation and growth performance of pigs, which can significantly vary among breeds. For example, LW pigs experience weight loss and mortality after PRRSV infection, whereas ZM pigs show no weight changes. In contrast, Tibetan pigs (known for their robust disease resistance) continue to exhibit weight gain throughout the infection (<xref ref-type="bibr" rid="ref80">80</xref>).</p>
</sec>
<sec id="sec8">
<label>3.3.</label>
<title>Viral load after PRRSV infection</title>
<p>TC pigs display significantly lower viral loads than LW pigs after artificial HP-PRRSV infection. Moreover, TC pigs display a reduced peak viral load and maintain a steady decline throughout the infection period. The maximum quantity of PRRSV particles in TC pigs is 0.4 times that found in LW pigs; this suggests a superior ability to control viral replication in TC pigs (<xref ref-type="bibr" rid="ref18">18</xref>).</p>
<p>A study of 100 pigs from NEI (a Large White-Landrace composite population) and 100 pigs from a cross between Hampshire and Duroc line (HD) inoculated with PRRSV (97&#x2013;7895 strain) indicated that the viremia titer was greater in HD pigs than that in NEI pigs on days 4, 7, and 14, whereas the viral titers in the lungs and bronchial lymph nodes were significantly higher in HD pigs (<xref ref-type="bibr" rid="ref14">14</xref>).</p>
<p>A study involving seven Miniature (MI) pigs and eight commercial Pietrain (PI) pigs challenged with an attenuated PRRSV strain shows that viremia peaks at 6 dpi, with 100% viremia observed in PI pigs and at 12 dpi, with 87% viremia noted in MI pigs (<xref ref-type="bibr" rid="ref81">81</xref>). MI pigs have a reduced duration of viremia. Different genetic susceptibilities to PRRSV may contribute to variations in antibody production (<xref ref-type="bibr" rid="ref81">81</xref>).</p>
<p>Inoculation of eight purebred boars (two Landrace, three Yorkshire, and three Hampshire) with VR-2332 detected PRRSV RNA in the serum and PBMC between 4 and 11 dpi. The virus is not detected in the lymphoid tissues of Landrace pigs at 47 and 88 dpi, whereas Yorkshire and Hampshire pigs show varying viral loads in lymphoid tissues. Yorkshire and Hampshire boars exhibit higher resistance to PRRSV shedding in semen than Landrace boars (<xref ref-type="bibr" rid="ref82">82</xref>).</p>
<p>In 2015, Tibetan, Zang Mei, and Large White piglets were challenged with HP-PRRSV (JXA1). During the challenge, the serum viral load in LW piglets peaked at 7 dpi, which gradually decreased until 28 dpi. Zang Mei piglets had their viral peak virus at 4 dpi, which decreased rapidly, resulting in significantly lower viral loads when compared to LW piglets at 14 and 21 dpi (<xref ref-type="bibr" rid="ref80">80</xref>). Tibetan pigs consistently exhibited lower viral loads than the other two breeds throughout the challenge (<xref ref-type="bibr" rid="ref80">80</xref>).</p>
<p>The virus titer and mRNA abundance in PAM supernatants following inoculation with PRRSV NJGC <italic>in vitro</italic> show similar trends among Landrace, Erhualian, Suzhong, Jiangquhuai, Dingyuan, and Meishan breeds (<xref ref-type="bibr" rid="ref71">71</xref>).</p>
<p>Different breeds exhibit significant variations in clinical features, growth performance, and viral titers owing to genetic variations that ultimately affect their ability to combat PRRSV. Some breeds, such as Meishan and Tongcheng, demonstrate a genetic advantage in fighting the virus that results in a reduction in the duration of viremia.</p>
</sec>
</sec>
<sec id="sec9">
<label>4.</label>
<title>Varied immune responses in different pig breeds infected by PRRSV</title>
<p>The innate immune response serves as the initial defense against PRRSV that is known for its ability to evade the host immune system by downregulating pattern recognition receptors (PRRs) (<xref ref-type="bibr" rid="ref83">83</xref>). Despite viral evasion strategies, the innate immune response plays a vital role in controlling viral spread, minimizing tissue damage, and initiating the adaptive immune response (<xref ref-type="bibr" rid="ref84">84</xref>). Essential cytokines [including interleukin-1 (IL-1), interleukin-6 (IL-6), interleukin-10 (IL-10), and tumor necrosis factor-alpha (TNF-&#x03B1;)] have multifaceted roles in influencing the outcome of PRRSV infection (<xref rid="tab2" ref-type="table">Table 2</xref>) (<xref ref-type="bibr" rid="ref16">16</xref>, <xref ref-type="bibr" rid="ref85 ref86 ref87 ref88 ref89 ref90 ref91">85&#x2013;91</xref>). These cytokines modulate inflammation, exert antiviral effects, and activate immune cells (<xref ref-type="bibr" rid="ref92">92</xref>).</p>
<table-wrap position="float" id="tab2">
<label>Table 2</label>
<caption>
<p>Summary of different virus strains affecting different cell cytokines.</p>
</caption>
<table frame="hsides" rules="groups">
<thead>
<tr>
<th align="left" valign="top">Virus strain</th>
<th align="left" valign="top">Cell line</th>
<th align="center" valign="top">Cytokines</th>
<th align="center" valign="top">References</th>
</tr>
</thead>
<tbody>
<tr>
<td align="left" valign="top">JX, HV, VR2332</td>
<td align="left" valign="top">PAM</td>
<td align="center" valign="top">IL6&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref85">85</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">CH-1a, HV</td>
<td align="left" valign="top">PAM</td>
<td align="center" valign="top">IL8&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref86">86</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">CH-1a</td>
<td align="left" valign="top">PAM</td>
<td align="center" valign="top">IL15&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref87">87</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">JXwn06, CH-1a</td>
<td align="left" valign="top">PAM</td>
<td align="center" valign="top">IL12p40&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref88">88</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">WuH3</td>
<td align="left" valign="top">MARC-145</td>
<td align="center" valign="top">TNF-&#x03B1;&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref16">16</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">HV, CH-1a</td>
<td align="left" valign="top">PAM, MARC145</td>
<td align="center" valign="top">IL17&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref89">89</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">NVSL 97-7895</td>
<td align="left" valign="top">moDCs</td>
<td align="center" valign="top">IL10&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref90">90</xref>)</td>
</tr>
<tr>
<td align="left" valign="top">PRRSV-23983</td>
<td align="left" valign="top">moDCs</td>
<td align="center" valign="top">IFN-&#x03B1;&#x2191;</td>
<td align="center" valign="top">(<xref ref-type="bibr" rid="ref91">91</xref>)</td>
</tr>
</tbody>
</table>
</table-wrap>
<p>The adaptive immune system (including antigen-presenting cells) offers broader and more sophisticated recognition of antigens (<xref ref-type="bibr" rid="ref93">93</xref>). It relies on the specific recognition of antigens by T and B cells that are generated through gene rearrangements during lymphocyte development, resulting in unique but limited specificity (<xref ref-type="bibr" rid="ref93">93</xref>). The innate immune system is vital for eliminating viruses; however, it may not always be adequate for eradicating pathogens (<xref ref-type="bibr" rid="ref93">93</xref>). Acquired immune functions are responsible for eliminating viruses and providing long-term immunity.</p>
<p>The adaptive immune response to PRRSV involves the activation of T and B cells, resulting in the production of targeted antibodies and development of cellular immune responses (<xref ref-type="bibr" rid="ref94">94</xref>). These immune responses are crucial to eradicate the virus and protect against reinfection. The intricate mechanisms underlying the adaptive immune response to PRRSV were extensively explored in previous reviews (<xref ref-type="bibr" rid="ref94">94</xref>, <xref ref-type="bibr" rid="ref95">95</xref>).</p>
<p>Differences in immune responses were observed among various pig breeds infected with PRRSV (<xref ref-type="bibr" rid="ref14">14</xref>, <xref ref-type="bibr" rid="ref15">15</xref>, <xref ref-type="bibr" rid="ref17 ref18 ref19">17&#x2013;19</xref>, <xref ref-type="bibr" rid="ref47">47</xref>, <xref ref-type="bibr" rid="ref82">82</xref>, <xref ref-type="bibr" rid="ref96 ref97 ref98 ref99 ref100 ref101">96&#x2013;101</xref>). For instance, TC pigs demonstrate enhanced resistance to PRRSV with milder clinical symptoms, fewer lung lesions, and lower viremia levels when compared to other breeds, such as LW pigs. These distinctions can be attributed to genetic factors and variations in cytokine levels. TC pigs show higher serum levels of interferon-gamma (IFN-&#x03B3;) that is associated with a T cell-mediated cellular immune response, whereas LW pigs show elevated levels of interleukin-10 (IL-10) that can inhibit viral clearance and impede the immune response (<xref ref-type="bibr" rid="ref17">17</xref>, <xref ref-type="bibr" rid="ref18">18</xref>). These indicate the presence of genetic variations that influence viral resistance or susceptibility.</p>
<p>Further analysis of lymph nodes from TC and LW pigs infected with PRRSV revealed genetic differences in antigen presentation, metabolism, and immune activation; this suggests that genetic variations contribute to divergent immune responses (<xref ref-type="bibr" rid="ref17">17</xref>). Integrated analysis of transcriptomic and metabolomic data provides additional insights into the immune response to PRRSV infection by highlighting the importance of immune activation, antigen recognition capacity, cell metabolism, and the cell cycle in the clearance of PRRSV. This analysis reveals differences in lipid metabolism and amino acid pathways between resistant and susceptible pigs, and further illustrates the impact of genetic factors on immune response (<xref ref-type="bibr" rid="ref98">98</xref>).</p>
<p>A comparison of the innate immune responses of conventional and specific-pathogen-free (SPF) Yorkshire pigs to PRRSV shows that SPF pigs have elevated levels of pro-inflammatory cytokines, such as IL-1&#x03B2;, IL-6, and TNF-&#x03B2;, and higher IFN-&#x03B2; concentrations when compared to conventional pig breeds (<xref ref-type="bibr" rid="ref102">102</xref>). Furthermore, SPF pigs exhibit lower viral RNA levels and less severe clinical symptoms in response to PRRSV infections (<xref ref-type="bibr" rid="ref102">102</xref>). Meanwhile, a study of the innate immune responses of LW and Meishan pigs to PRRSV revealed that the Meishan breed produces a higher concentration of IFN-&#x03B1; and has lower viral loads when compared to the LW breed; this suggests a greater resistance to PRRSV owing to differences in their innate immune response (<xref ref-type="bibr" rid="ref16">16</xref>).</p>
<p>Additionally, the viral genomic diversity of PRRSV (including differences in immune epitopes) contributes to its ability to evade the immune system (<xref ref-type="bibr" rid="ref22">22</xref>). Genetic variability among PRRSV strains affects the response of pig breeds to infections. Landrace, Large White, and Yorkshire breeds are more susceptible to PRRSV, whereas Pietrain, Meishan, and Hampshire breeds are relatively resistant owing to stronger innate immune responses (<xref ref-type="bibr" rid="ref82">82</xref>, <xref ref-type="bibr" rid="ref103">103</xref>). Dendritic cells derived from Pietrain pigs elicit a more potent T cell response; this underscores the significance of innate immunity in adaptive immunity (<xref ref-type="bibr" rid="ref104">104</xref>). The susceptibility of pig breeds to PRRSV infection is primarily determined by genetic factors rather than environmental or husbandry factors.</p>
<p>Variations in genes associated with the innate immune response and resistance to PRRSV are identified. For example, single-nucleotide polymorphisms (SNPs) in genes such as <italic>EIF2AK2</italic>, <italic>CD163</italic>, <italic>CD169</italic>, and <italic>RGS16</italic> are linked to increased resistance against PRRSV infection (<xref ref-type="bibr" rid="ref105">105</xref>).</p>
<p>The differences in innate immunity observed among various pig breeds suggest disparities in their genetic makeup. Implementing breeding initiatives aimed at enhancing innate immunity may be a valuable strategy to boost the health and productivity of swine herds. Breeders and researchers can identify the genetic markers responsible for heightened innate immunity and increased resistance to PRRSV by delving into the mechanisms that regulate innate immunity,</p>
</sec>
<sec id="sec10">
<label>5.</label>
<title>Differential alternative splicing events triggered by PRRSV invasion in different pig breeds</title>
<p>Alternative splicing (AS) is a crucial mechanism for post-transcriptional RNA processing and is responsible for significant modification of transcript sequences (<xref ref-type="bibr" rid="ref106">106</xref>, <xref ref-type="bibr" rid="ref107">107</xref>). It is a critical mechanism in the regulation of eukaryotic gene expression via transcriptional control that enhances the versatility and diversity of transcriptomes and proteomes (<xref ref-type="bibr" rid="ref108 ref109 ref110 ref111">108&#x2013;111</xref>). This results in various alternative splicing events (ASEs), including skipped exons (SE), retained introns (RI), alternative 5&#x2032; and 3&#x2032; splicing sites (A5SS and A3SS), and mutually exclusive events (ME) (<xref ref-type="bibr" rid="ref112">112</xref>, <xref ref-type="bibr" rid="ref113">113</xref>).</p>
<p>Porcine reproductive and respiratory syndrome virus infection profoundly affects alternative splicing in pigs. Specifically, immune response-related genes (such as interferon-stimulated genes) exhibit alternative splicing following PRRSV infection (<xref ref-type="bibr" rid="ref114">114</xref>). This suggests that alternative splicing may play a role in regulating the host response to viral infections, such as PRRSV. Additionally, PRRSV infection can trigger widespread AS events in the spleen and inguinal lymph nodes (ILN) of TC and LW pigs. PRRSV infection resulted in 373 and 595 genes displaying differential ASEs in the spleen and ILN in TC pigs, respectively (<xref ref-type="bibr" rid="ref114">114</xref>). Meanwhile, 458 and 560 genes exhibit differential ASEs in the spleen and ILN, respectively in LW pigs. Gene Ontology functional analysis revealed that these genes are important for immune responses, transcriptional regulation, metabolism, and apoptosis (<xref ref-type="bibr" rid="ref114">114</xref>). Furthermore, the response to PRRSV in terms of alternative splicing significantly differed between the TC and LW pigs. This suggests a possible link between PRRSV infection and genetic variation in these two pig breeds.</p>
</sec>
<sec id="sec11">
<label>6.</label>
<title>Functions of host non-coding RNAs in PRRSV infection and replication</title>
<p>Non-coding RNAs (ncRNAs) play diverse roles in PRRSV infection and replication. PRRSV is an RNA virus possessing a long untranslated region (UTR) downstream of its open reading frame, 1ab (<xref ref-type="bibr" rid="ref21">21</xref>). Research suggests that the 3&#x2019;-UTR plays a significant role in modulating targeted mRNAs in animals (<xref ref-type="bibr" rid="ref115">115</xref>, <xref ref-type="bibr" rid="ref116">116</xref>). This indicates that the extended UTR in PRRSV could potentially serve as a pool of targets for host miRNAs.</p>
<p>miRNAs play a critical role in regulating viral replication and the host immune response infection during PRRSV. For example, miR-181 inhibits PRRSV <italic>in vivo</italic> and <italic>in vitro</italic>, and therapeutic delivery of miR-181 alleviates symptoms and prolongs the survival of highly pathogenic PRRSV-infected pigs (<xref ref-type="bibr" rid="ref117">117</xref>). Furthermore, it downregulates the PRRSV receptor CD163, effectively hindering PRRSV infection. The construction of an miR-181 target site-mutated PRRSV demonstrated that miR-181 effectively blocked wild-type PRRSV invasion in the late stage, suggesting its significant impact on PRRSV infection and replication <italic>in vivo</italic>. Additionally, cellular miR-23 inhibits PRRSV replication by directly targeting PRRSV RNA and potentially upregulating type I interferon (<xref ref-type="bibr" rid="ref118">118</xref>). MiR-378 and miR-505 suppress PRRSV replication by directly targeting PRRSV RNA (<xref ref-type="bibr" rid="ref118">118</xref>), whereas miR-10a-5p inhibits PRRSV replication by suppressing SRP14 expression (<xref ref-type="bibr" rid="ref119">119</xref>).</p>
<p>In contrast, PRRSV-induced miR-142-5p significantly promotes viral replication by directly targeting FAM134B (<xref ref-type="bibr" rid="ref120">120</xref>). Conversely, let-7 family miRNAs inhibit PRRSV replication by targeting the 3&#x2019;-UTR of the PRRSV-2 genome and porcine IL-6 (<xref ref-type="bibr" rid="ref121">121</xref>). MiR-146a expression increases in macrophages during PRRSV infection, and positively affects the immune response by regulating the expression of genes, such as <italic>C1QTNF3</italic> and <italic>MAFB</italic> (<xref ref-type="bibr" rid="ref122">122</xref>). Notably, neither PRRSV-infected target cells nor host pigs induce the production of type I interferon (IFN) proteins <italic>in vivo</italic> or <italic>in vitro</italic> (<xref ref-type="bibr" rid="ref123">123</xref>). MiRNAs can be induced or repressed by type I IFN, although they can also play key roles in regulating innate immune responses by modulating the production of type I IFN and other important molecular pathways (<xref ref-type="bibr" rid="ref124">124</xref>). In particular, miR-331-3p/miR-210 is involved in lung inflammation by targeting ORF1b and downregulating STAT1/TNF-&#x03B1; (<xref ref-type="bibr" rid="ref16">16</xref>).</p>
<p>Let-7b, miR-26a, miR-34a, and miR-145 directly target sequences within the porcine IFN-&#x03B2; 3 &#x03B2;-UTR regions at positions 160&#x2013;181, 9&#x2013;31, 27&#x2013;47, and 12&#x2013;32&#x2009;bp, respectively, to inhibit the expression of IFN-&#x03B2; protein in primary PAMs (<xref ref-type="bibr" rid="ref125">125</xref>). Moreover, it is suggested that PRRSV can suppress the post-transcriptional expression of IFN-&#x03B2; protein by upregulating these four miRNAs in cultured PAMs (<xref ref-type="bibr" rid="ref126">126</xref>). MiR-199a-3p downregulates the protein expression of CD151, a receptor utilized by PRRSV (<xref ref-type="bibr" rid="ref125">125</xref>). Additionally, miR-199a-3p is differentially expressed in the lung tissues of different pig breeds (such as, Tongcheng and Landrace) in the control and infection groups; this suggests its crucial role in regulating PRRSV infection in pigs (<xref ref-type="bibr" rid="ref127">127</xref>). Furthermore, miR-378 and miR-10a-5p are upregulated in the control group of Tongcheng pigs when compared to those in the control group of Landrace pigs, and both miRNAs showed inhibitory effects on PRRSV replication (<xref ref-type="bibr" rid="ref126">126</xref>).</p>
<p>Numerous studies have explored the role of miRNAs in the PRRSV process, shedding light on their regulatory mechanisms in viral infection, and revealing variations in miRNA expression among different pig breeds. These findings provide novel insights into the interaction between PRRSV and the host, and present promising avenues to develop antiviral strategies against PRRSV infection.</p>
</sec>
<sec id="sec12">
<label>7.</label>
<title>Future perspectives</title>
<p>Future research should focus on several key areas to advance our understanding of PRRSV infections and drive the development of effective control strategies.</p>
<p>First, extensive studies are required to investigate the genetic factors underlying the varied responses to PRRSV infection among different pig breeds. Identifying specific genes and genetic markers associated with PRRSV resistance or susceptibility will provide valuable insights into targeted breeding programs and the development of precision medicine approaches. Through genetic improvement and selective breeding methods, it is possible to rear pig breeds that exhibit enhanced resistance to PRRSV. Leveraging modern genetic engineering technologies and selective breeding methods, individuals with robust immune responses can be selected for reproduction, thereby gradually improving the overall PRRSV resistance within the entire pig population.</p>
<p>Second, rapid advancements in single-cell transcriptome sequencing and spatial transcriptomics present opportunities to gain in-depth molecular insights into PRRSV infection. Further research in these areas can provide a comprehensive understanding of viral spread within tissues, the dynamics of host-virus interactions, and how various host cell types contribute to the pathogenesis and immune response against PRRSV.</p>
<p>Furthermore, the functional roles of ncRNAs in PRRSV infection and replication should be explored. Additional investigations into the regulatory mechanisms of host ncRNAs in modulating viral replication, immune responses, and disease outcomes could lead to the development of novel therapeutic interventions and identification of potential biomarkers for diagnostic purposes.</p>
<p>Additionally, incorporating multi-omics approaches (such as transcriptomics, genomics, proteomics, and epigenomics) will provide a more comprehensive understanding of the complex molecular interplay between PRRSV and the host. The integration of these omics datasets could uncover crucial interactions, pathways, and networks involved in PRRSV infection and host responses that ultimately lead to more effective preventive and therapeutic strategies.</p>
<p>Lastly, efforts should continue to focus on sustainable pig farming practices that reduce reliance on antibiotics and mitigate environmental impacts. This includes integrating genetic information into breeding programs to select disease resistance traits, advancing precision farming technologies for early detection and intervention, and promoting biosecurity measures to minimize the risk of pathogen transmission.</p>
<p>In conclusion, future PRRSV studies should advance our understanding of the genetic and molecular mechanisms underlying host-virus interactions, develop targeted control strategies, and promote sustainable pig farming practices. Harnessing these insights will facilitate more effective prevention, management, and control of PRRSV that benefit swine health and productivity.</p>
</sec>
<sec sec-type="conclusions" id="sec13">
<label>8.</label>
<title>Conclusion</title>
<p>Overall, the findings of this review contribute to a comprehensive understanding of the genetic factors underlying the varied responses to PRRSV in different pig breeds to PRRSV infection. This knowledge can be used to formulate more effective control measures for PRRSV, such as designing breeding programs to select resistance traits and developing targeted vaccines. Additionally, exploring the potential of genetic-based interventions and further research into host-virus interactions at the molecular level holds promise for future developments in PRRSV control and prevention.</p>
</sec>
<sec sec-type="author-contributions" id="sec14">
<title>Author contributions</title>
<p>YP: Writing &#x2013; original draft, Writing &#x2013; review &#x0026; editing. CL: Writing &#x2013; original draft. HL: Writing &#x2013; review &#x0026; editing. ZF: Writing &#x2013; original draft, Writing &#x2013; review &#x0026; editing.</p>
</sec>
</body>
<back>
<sec sec-type="funding-information" id="sec15">
<title>Funding</title>
<p>The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was funded by the Guangdong Basic and Applied Basic Research Foundation (2020B1515120016), Key Technologies R&#x0026;D Program of Guangdong Province (2022B0202090001).</p>
</sec>
<sec sec-type="COI-statement" id="sec16">
<title>Conflict of interest</title>
<p>The 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="sec100" 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>
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