Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2024.110361
Qiumei Wang , Heyou Yi , Anli Chen , Tao Tian , Zhiqing Yu , Lechen Lu , Ruirui Ye , Ermin Xie , Guoxin Zheng , Guihong Zhang , Heng Wang
Since its emergence, porcine reproductive and respiratory syndrome (PRRS) has caused enormous economic losses to the global swine industry. The pathogenesis of PRRS remains under investigation. The porcine reproductive and respiratory syndrome virus (PRRSV) causes reproductive disorders in pigs and respiratory in piglets, which is a 15 kb RNA virus that encodes 16 viral proteins, most of which exhibit multiple functions during the virus lifecycle. RAP1 (Ras-proximate-1), a small GTPase, is known to regulates cell adhesion across different cell types and is one of the most conserved telomere proteins. Thus, this study explored the effect of RAP1 after PRRSV infection.
In this study, RAP1 did not participate in the adsorption and internalization process of PRRSV, however, it promoted viral RNA synthesis and enhanced PRRSV replication. Additionally, we discovered that RAP1 interacted with Nsp10 and the N protein. Specifically, the Myb domain of RAP1 primarily bound to the viral genome interacted with the N-terminal structural domain of the N protein, which contains an RNA-binding domain. Additionally, the C-terminal region of RAP1 interacted with the N-terminal domain of Nsp10. These results suggested that RAP1 is a critical factor in the PRRSV infection process, particularly in the context of viral RNA synthesis. RAP1 could be a potential target for the prevention and control of PRRSV.
{"title":"RAP1 is essential for PRRSV replication and the synthesis of the viral genome","authors":"Qiumei Wang , Heyou Yi , Anli Chen , Tao Tian , Zhiqing Yu , Lechen Lu , Ruirui Ye , Ermin Xie , Guoxin Zheng , Guihong Zhang , Heng Wang","doi":"10.1016/j.vetmic.2024.110361","DOIUrl":"10.1016/j.vetmic.2024.110361","url":null,"abstract":"<div><div>Since its emergence, porcine reproductive and respiratory syndrome (PRRS) has caused enormous economic losses to the global swine industry. The pathogenesis of PRRS remains under investigation. The porcine reproductive and respiratory syndrome virus (PRRSV) causes reproductive disorders in pigs and respiratory in piglets, which is a 15 kb RNA virus that encodes 16 viral proteins, most of which exhibit multiple functions during the virus lifecycle. RAP1 (Ras-proximate-1), a small GTPase, is known to regulates cell adhesion across different cell types and is one of the most conserved telomere proteins. Thus, this study explored the effect of RAP1 after PRRSV infection.</div><div>In this study, RAP1 did not participate in the adsorption and internalization process of PRRSV, however, it promoted viral RNA synthesis and enhanced PRRSV replication. Additionally, we discovered that RAP1 interacted with Nsp10 and the N protein. Specifically, the Myb domain of RAP1 primarily bound to the viral genome interacted with the N-terminal structural domain of the N protein, which contains an RNA-binding domain. Additionally, the C-terminal region of RAP1 interacted with the N-terminal domain of Nsp10. These results suggested that RAP1 is a critical factor in the PRRSV infection process, particularly in the context of viral RNA synthesis. RAP1 could be a potential target for the prevention and control of PRRSV.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110361"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2025.110367
Meng Cui , Ming Qiu , Shuai Yang , Yuejia Qiu , Wenhao Qi , Hong Lin , Zhe Sun , Wanglong Zheng , Jianzhong Zhu , Nanhua Chen
NADC34-like porcine reproductive and respiratory syndrome virus 2 (NADC34-like PRRSV-2) is currently a major prevalent strain in Chinese swine industry. Within which, recombination events are frequently detected. Previous studies have shown that the pathogenicity of NADC34-like PRRSV-2 isolates is highly variable. However, the characteristics between NADC34-like PRRSV-2 recombinant and non-recombinant isolates are rarely compared. In this study, two PRRSV-2 strains (BJ1805–2 and SDLY23–1742) were isolated from samples collected at 2018 and 2023 in China. ORF5-based phylogenetic analysis supported that both isolates are clustered with ORF5 RFLP 1–7–4 (NADC34-like) strains. However, genome-based phylogenetic tree showed that BJ1805–2 is still grouped with NADC34-like isolates but SDLY23–1742 is clustered with NADC30-like viruses. Furthermore, fragment comparisons and recombination detections also supported that SDLY23–1742 was recombined from NADC30-like, NADC34-like, and JXA1-like isolates while no recombination event was detected in BJ1805–2. Noticeably, BJ1805–2 had higher replication efficacy than SDLY23–1742 both in PAMs and in piglets. However, SDLY23–1742 caused longer high fever period and more severe histopathological lung lesions than BJ1805–2, indicating that SDLY23–1742 has higher pathogenicity than BJ1805–2. Overall, this study provides the first evidence that the pathogenicity of NADC34-like PRRSV-2 is not directly correlated with viral replication efficacy.
{"title":"The replication efficacy of NADC34-like porcine reproductive and respiratory syndrome virus 2 is not directly associated with the pathogenicity","authors":"Meng Cui , Ming Qiu , Shuai Yang , Yuejia Qiu , Wenhao Qi , Hong Lin , Zhe Sun , Wanglong Zheng , Jianzhong Zhu , Nanhua Chen","doi":"10.1016/j.vetmic.2025.110367","DOIUrl":"10.1016/j.vetmic.2025.110367","url":null,"abstract":"<div><div>NADC34-like porcine reproductive and respiratory syndrome virus 2 (NADC34-like PRRSV-2) is currently a major prevalent strain in Chinese swine industry. Within which, recombination events are frequently detected. Previous studies have shown that the pathogenicity of NADC34-like PRRSV-2 isolates is highly variable. However, the characteristics between NADC34-like PRRSV-2 recombinant and non-recombinant isolates are rarely compared. In this study, two PRRSV-2 strains (BJ1805–2 and SDLY23–1742) were isolated from samples collected at 2018 and 2023 in China. ORF5-based phylogenetic analysis supported that both isolates are clustered with ORF5 RFLP 1–7–4 (NADC34-like) strains. However, genome-based phylogenetic tree showed that BJ1805–2 is still grouped with NADC34-like isolates but SDLY23–1742 is clustered with NADC30-like viruses. Furthermore, fragment comparisons and recombination detections also supported that SDLY23–1742 was recombined from NADC30-like, NADC34-like, and JXA1-like isolates while no recombination event was detected in BJ1805–2. Noticeably, BJ1805–2 had higher replication efficacy than SDLY23–1742 both in PAMs and in piglets. However, SDLY23–1742 caused longer high fever period and more severe histopathological lung lesions than BJ1805–2, indicating that SDLY23–1742 has higher pathogenicity than BJ1805–2. Overall, this study provides the first evidence that the pathogenicity of NADC34-like PRRSV-2 is not directly correlated with viral replication efficacy.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110367"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142955556","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2024.110353
P.P. Jayasekara , C. Jenkins , P.D. Kirkland , P.F. Gerber , L. Olmo , T. Xaikhue , K. Eamens , W. Theppangna , S.W. Walkden-Brown
Clinical signs of respiratory disease are common in Lao goats. To identify the causative agents involved in this clinical syndrome, a matched case-control study was conducted across 70 smallholder goat holdings in Savannakhet province. Fifty paired nasal swab samples were collected from goats with respiratory signs (cases) and unaffected (control) goats from 27 goat holdings. The majority of cases (84 %) were from goats < 12 months of age. Samples were tested using quantitative PCR assays targeting possible pathogens causing respiratory disease. Mycoplasma ovipneumoniae, the cause of atypical pneumonia, was prevalent in both case (94 %) and control (76 %) groups and was identified as the principal causative agent based on odds ratio of presence (4.9) and a significantly higher pathogen load in case goats. Prolonged close contact between goats during confinement in often poorly constructed goat houses, likely facilitates transmission and progression from carrier to clinical status under the Lao goat production system. Mannheimia haemolytica was detected in 60 % of case and 52 % of control samples with no significant difference in pathogen load, while Pasteurella multocida was detected in only 2 % of control samples indicating no major role in causation for these pathogens. Mycoplasma capricolum subsp. capripneumoniae, respiratory syncytial virus and bovine parainfluenza 3 virus were not detected in any samples. Phylogenetic analysis showed no genetic variation of M. ovipneumoniae in the study samples and close similarity to recent isolates from China, US and Turkey. Improved housing conditions may be helpful in controlling atypical pneumonia in Lao goats and antibiotic treatment of goats with severe signs of respiratory disease was found to be effective.
{"title":"Mycoplasma ovipneumoniae identified as the main aetiological agent of respiratory disease in goats from a case-control study in Savannakhet province of Lao PDR","authors":"P.P. Jayasekara , C. Jenkins , P.D. Kirkland , P.F. Gerber , L. Olmo , T. Xaikhue , K. Eamens , W. Theppangna , S.W. Walkden-Brown","doi":"10.1016/j.vetmic.2024.110353","DOIUrl":"10.1016/j.vetmic.2024.110353","url":null,"abstract":"<div><div>Clinical signs of respiratory disease are common in Lao goats. To identify the causative agents involved in this clinical syndrome, a matched case-control study was conducted across 70 smallholder goat holdings in Savannakhet province. Fifty paired nasal swab samples were collected from goats with respiratory signs (cases) and unaffected (control) goats from 27 goat holdings. The majority of cases (84 %) were from goats < 12 months of age. Samples were tested using quantitative PCR assays targeting possible pathogens causing respiratory disease. <em>Mycoplasma ovipneumoniae,</em> the cause of atypical pneumonia, was prevalent in both case (94 %) and control (76 %) groups and was identified as the principal causative agent based on odds ratio of presence (4.9) and a significantly higher pathogen load in case goats. Prolonged close contact between goats during confinement in often poorly constructed goat houses, likely facilitates transmission and progression from carrier to clinical status under the Lao goat production system. <em>Mannheimia haemolytica</em> was detected in 60 % of case and 52 % of control samples with no significant difference in pathogen load, while <em>Pasteurella multocida</em> was detected in only 2 % of control samples indicating no major role in causation for these pathogens. <em>Mycoplasma capricolum</em> subsp. <em>capripneumoniae</em>, respiratory syncytial virus and bovine parainfluenza 3 virus were not detected in any samples. Phylogenetic analysis showed no genetic variation of <em>M. ovipneumoniae</em> in the study samples and close similarity to recent isolates from China, US and Turkey. Improved housing conditions may be helpful in controlling atypical pneumonia in Lao goats and antibiotic treatment of goats with severe signs of respiratory disease was found to be effective.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110353"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142898354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2025.110368
Huiyuan Jing , Ying Liu , Yvzhen Song , Tao Song , Ting Wang , Zhen Ding , Jie Liu , Pandeng Zhao
Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious swine pathogen, causing respiratory problems in piglets and reproductive failure in sows. Palmitoylation, catalyzed by zinc finger Asp-His-His-Cys (ZDHHC) domain-containing palmitoyl acyltransferases, plays intricate roles in virus infection. However, whether palmitoylation regulates PRRSV replication is incompletely understood. Here, we report that inhibition of palmitoylation by 2-bromo palmitate (2-BP) promotes PRRSV multiplication. ZDHHC3 is identified as the key palmitoyl transferase regulating PRRSV replication in PAMs infection. Mechanistically, ZDHHC3 catalyzes nucleocapsid (N) protein palmitoylation at cysteine 90. This modification prevents the Nsp9-N protein interaction and subsequent viral RNA synthesis. Furthermore, LYPLA1 de-palmitoylates N protein, thus counteracting the ZDHHC3’s activity on PRRSV replication. Meanwhile, the administration of small-molecule inhibitor ML348 targeting LYPLA1 could hinder PRRSV-2 replication. In summary, our results underscore the critical role of reversible palmitoylation in PRRSV replication. These findings might provide potential new anti-PRRSV strategies.
{"title":"ZDHHC3-LYPLA1 regulates PRRSV-2 replication through reversible palmitoylation","authors":"Huiyuan Jing , Ying Liu , Yvzhen Song , Tao Song , Ting Wang , Zhen Ding , Jie Liu , Pandeng Zhao","doi":"10.1016/j.vetmic.2025.110368","DOIUrl":"10.1016/j.vetmic.2025.110368","url":null,"abstract":"<div><div>Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious swine pathogen, causing respiratory problems in piglets and reproductive failure in sows. Palmitoylation, catalyzed by zinc finger Asp-His-His-Cys (ZDHHC) domain-containing palmitoyl acyltransferases, plays intricate roles in virus infection. However, whether palmitoylation regulates PRRSV replication is incompletely understood. Here, we report that inhibition of palmitoylation by 2-bromo palmitate (2-BP) promotes PRRSV multiplication. ZDHHC3 is identified as the key palmitoyl transferase regulating PRRSV replication in PAMs infection. Mechanistically, ZDHHC3 catalyzes nucleocapsid (N) protein palmitoylation at cysteine 90. This modification prevents the Nsp9-N protein interaction and subsequent viral RNA synthesis. Furthermore, LYPLA1 de-palmitoylates N protein, thus counteracting the ZDHHC3’s activity on PRRSV replication. Meanwhile, the administration of small-molecule inhibitor ML348 targeting LYPLA1 could hinder PRRSV-2 replication. In summary, our results underscore the critical role of reversible palmitoylation in PRRSV replication. These findings might provide potential new anti-PRRSV strategies.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110368"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142955561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2024.110355
Aldair Martinez , Emma Lavergne , Clément Brauge , Emma Laveran , Stéphane Bertagnoli , Corine Boucraut-Baralon , Pierre Bessière
Feline coronavirus (FCoV) is a virus endemic in cat populations. Specific genomic mutations give it a strong tropism for macrophages, allowing systemic infection and the development of a disease known as feline infectious peritonitis. This disease takes various clinical presentations, and can manifest as uveitis. Two mutations in the spike protein have been identified as possibly associated with FIP: mutations M1058L and S1060A. 193 clinical samples of aqueous humor were collected, all PCR-positive for feline coronavirus. Samples were taken either from cats with a clinical picture compatible with an ocular form of FIP (with uveitis and general clinical signs), or from cats with uveitis only. We sequenced the region of the S gene coding for positions 1058 and 1060 for 77 samples. The aim of the study was to determine whether viruses from cats with clinical signs compatible with FIP were more likely to harbor the M1058L and S1060A mutations. Our results confirm that these mutations are associated with severe disease, and also show that ocular samples from cats with uveitis alone are more likely to contain FECV.
{"title":"Feline coronavirus-associated uveitis: The eye as a gateway to systemic spread and feline infectious peritonitis?","authors":"Aldair Martinez , Emma Lavergne , Clément Brauge , Emma Laveran , Stéphane Bertagnoli , Corine Boucraut-Baralon , Pierre Bessière","doi":"10.1016/j.vetmic.2024.110355","DOIUrl":"10.1016/j.vetmic.2024.110355","url":null,"abstract":"<div><div>Feline coronavirus (FCoV) is a virus endemic in cat populations. Specific genomic mutations give it a strong tropism for macrophages, allowing systemic infection and the development of a disease known as feline infectious peritonitis. This disease takes various clinical presentations, and can manifest as uveitis. Two mutations in the spike protein have been identified as possibly associated with FIP: mutations M1058L and S1060A. 193 clinical samples of aqueous humor were collected, all PCR-positive for feline coronavirus. Samples were taken either from cats with a clinical picture compatible with an ocular form of FIP (with uveitis and general clinical signs), or from cats with uveitis only. We sequenced the region of the S gene coding for positions 1058 and 1060 for 77 samples. The aim of the study was to determine whether viruses from cats with clinical signs compatible with FIP were more likely to harbor the M1058L and S1060A mutations. Our results confirm that these mutations are associated with severe disease, and also show that ocular samples from cats with uveitis alone are more likely to contain FECV.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110355"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2025.110376
Anna Vilaró , Kasper T. Karstensen , Laia Serra , Emma Solé , Ingrid Seró , Elena Novell , Vicens Enrique-Tarancón , Lina M. Cavaco , Narjol Gonzalez-Escalona , Lourdes Migura-Garcia , Lorenzo Fraile
Streptococcus suis (S. suis) is a major pathogen for pigs, causing large economic losses to the swine industry. Moreover, this bacterium has a zoonotic potential, being capable of infecting humans in close contact with pigs or, less frequently, through contact with pork products. Given its importance in both veterinary and public health, S. suis remains a key topic of research. This study explores the genetic characteristics of 154 S. suis isolates obtained from clinical samples collected from pigs between 2018 and 2022. Whole genome sequencing (WGS) allowed a comprehensive analysis of the S. suis population in Spain, including detection of serotype, sequence type (ST), antimicrobial resistance genes, and virulence-associated genes. This approach also explored the vertical transmission of this pathogen through vertically integrated pyramids, as evidenced by associations between grandmother and mother sow farms, and phylogenetic groups, serotypes, and STs. Our analysis revealed that serotype 9 was the most prevalent in our strain collection, predominantly associated with ST123. Notably, the three most significant virulence genes, encoding the extracellular protein factor (EPF), the muramidase-release protein (MRP), and suilysin (SLY), were not consistently present in all clinical isolates. Regarding antimicrobial resistance, no phenotypic resistance was observed to ceftiofur or florfenicol, while observing low resistance to ampicillin (0.6 %) and enrofloxacin (2.6 %), intermediate resistance to penicillin (22.1 %), and high percentage of non-wild-type isolates to trimethoprim-sulfamethoxazole (57.1 %), and doxycycline (96.1 %). The most prevalent antimicrobial resistance genes (ARGs) were tet(O) (85.1 %) and erm(B) (86.4 %), conferring resistance to tetracyclines and macrolides, respectively, although macrolides were not included in the phenotypic testing. Overall, this study provides key epidemiological insights into this significant systemic pathogen within the Spanish swine population. The findings underscore the importance of understanding sample origins, such as grandmother and mother sow farms, to develop an effective antimicrobial stewardship program for managing S. suis-associated diseases.
{"title":"New insights into the epidemiology of Streptococcus suis in pig production systems using whole genome sequencing","authors":"Anna Vilaró , Kasper T. Karstensen , Laia Serra , Emma Solé , Ingrid Seró , Elena Novell , Vicens Enrique-Tarancón , Lina M. Cavaco , Narjol Gonzalez-Escalona , Lourdes Migura-Garcia , Lorenzo Fraile","doi":"10.1016/j.vetmic.2025.110376","DOIUrl":"10.1016/j.vetmic.2025.110376","url":null,"abstract":"<div><div><em>Streptococcus suis</em> (<em>S. suis</em>) is a major pathogen for pigs, causing large economic losses to the swine industry. Moreover, this bacterium has a zoonotic potential, being capable of infecting humans in close contact with pigs or, less frequently, through contact with pork products. Given its importance in both veterinary and public health, <em>S. suis</em> remains a key topic of research. This study explores the genetic characteristics of 154 <em>S. suis</em> isolates obtained from clinical samples collected from pigs between 2018 and 2022. Whole genome sequencing (WGS) allowed a comprehensive analysis of the <em>S. suis</em> population in Spain, including detection of serotype, sequence type (ST), antimicrobial resistance genes, and virulence-associated genes. This approach also explored the vertical transmission of this pathogen through vertically integrated pyramids, as evidenced by associations between grandmother and mother sow farms, and phylogenetic groups, serotypes, and STs. Our analysis revealed that serotype 9 was the most prevalent in our strain collection, predominantly associated with ST123. Notably, the three most significant virulence genes, encoding the extracellular protein factor (EPF), the muramidase-release protein (MRP), and suilysin (SLY), were not consistently present in all clinical isolates. Regarding antimicrobial resistance, no phenotypic resistance was observed to ceftiofur or florfenicol, while observing low resistance to ampicillin (0.6 %) and enrofloxacin (2.6 %), intermediate resistance to penicillin (22.1 %), and high percentage of non-wild-type isolates to trimethoprim-sulfamethoxazole (57.1 %), and doxycycline (96.1 %). The most prevalent antimicrobial resistance genes (ARGs) were <em>tet</em>(O) (85.1 %) and <em>erm</em>(B) (86.4 %), conferring resistance to tetracyclines and macrolides, respectively, although macrolides were not included in the phenotypic testing. Overall, this study provides key epidemiological insights into this significant systemic pathogen within the Spanish swine population. The findings underscore the importance of understanding sample origins, such as grandmother and mother sow farms, to develop an effective antimicrobial stewardship program for managing <em>S. suis</em>-associated diseases.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110376"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142967093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.vetmic.2024.110365
René van den Brom , Inge Santman-Berends , Mark G. van der Heijden , Frank Harders , Marc Engelsma , Rene G.P. van Gennip , Mieke A. Maris-Veldhuis , Arno-Jan Feddema , Karianne Peterson , Natalia Golender , Marcel Spierenburg , Piet A. van Rijn , Melle Holwerda
Bluetongue (BT) is a viral vector borne disease primarily affecting ruminants such as sheep, cattle, and goats. On 3 September 2023, the Netherlands reported the first case of bluetongue virus serotype 3 (BTV-3/NET2023)), after being BTV free for eleven years. Vaccination with inactivated BT vaccines for serotype 3 has been applied in the Netherlands since May 2024. Nonetheless, in late June/July 2024, BTV-3 re-emerged and spread over large parts of Europe. In October 2024, BTV-12 was identified by follow-up diagnostics after a BTV-3 vaccinated sheep with signs of BT was tested positive for BTV but negative for serotype 3. This marks a significant event, as BTV-12 had never been reported in Europe. Screening of farms in close proximity to the sheep farm and retrospective analysis of samples from clinically affected animals that were panBTV PCR positive resulted in the detection of nine BTV-12 affected farms in total. The emergence of BTV-12 in the Netherlands raises important questions about the route of introduction of BT in the Netherlands and mechanisms of viral spread of this specific serotype. Possible adaptation of new BTV serotypes to the European climatic and husbandry conditions prompts reconsideration of prevention, surveillance, and control strategies in relation to changing ecological conditions and vector dynamics. The initial findings, respective studies as well as the initial attempts to trace the origin of BTV-12/NET2024 are described.
{"title":"Bluetongue virus serotype 12 in sheep and cattle in the Netherlands in 2024 – A BTV serotype reported in Europe for the first time","authors":"René van den Brom , Inge Santman-Berends , Mark G. van der Heijden , Frank Harders , Marc Engelsma , Rene G.P. van Gennip , Mieke A. Maris-Veldhuis , Arno-Jan Feddema , Karianne Peterson , Natalia Golender , Marcel Spierenburg , Piet A. van Rijn , Melle Holwerda","doi":"10.1016/j.vetmic.2024.110365","DOIUrl":"10.1016/j.vetmic.2024.110365","url":null,"abstract":"<div><div>Bluetongue (BT) is a viral vector borne disease primarily affecting ruminants such as sheep, cattle, and goats. On 3 September 2023, the Netherlands reported the first case of bluetongue virus serotype 3 (BTV-3/NET2023)), after being BTV free for eleven years. Vaccination with inactivated BT vaccines for serotype 3 has been applied in the Netherlands since May 2024. Nonetheless, in late June/July 2024, BTV-3 re-emerged and spread over large parts of Europe. In October 2024, BTV-12 was identified by follow-up diagnostics after a BTV-3 vaccinated sheep with signs of BT was tested positive for BTV but negative for serotype 3. This marks a significant event, as BTV-12 had never been reported in Europe. Screening of farms in close proximity to the sheep farm and retrospective analysis of samples from clinically affected animals that were panBTV PCR positive resulted in the detection of nine BTV-12 affected farms in total. The emergence of BTV-12 in the Netherlands raises important questions about the route of introduction of BT in the Netherlands and mechanisms of viral spread of this specific serotype. Possible adaptation of new BTV serotypes to the European climatic and husbandry conditions prompts reconsideration of prevention, surveillance, and control strategies in relation to changing ecological conditions and vector dynamics. The initial findings, respective studies as well as the initial attempts to trace the origin of BTV-12/NET2024 are described.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"301 ","pages":"Article 110365"},"PeriodicalIF":2.4,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143012543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-30DOI: 10.1016/j.vetmic.2025.110419
Sofia Kozak , Déborah Merda , Virginie Chesnais , Marie-France Breuil , Megan Harrison , Irena Zdovc , Majda Golob , Sandrine Petry , Fabien Duquesne
Taylorella equigenitalis is the causative agent of contagious equine metritis, an internationally regulated sexually-transmitted infection in horses, which is of great concern as it usually results in temporary infertility. Taylorella asinigenitalis, the second member of the genus, is mainly found in donkeys and is considered non-pathogenic, although a first natural outbreak was reported in 2019 in the United Arab Emirates. Multilocus sequence typing (MLST) is currently used to study the epidemiology of Taylorella spp. but, while highly transposable and reproducible, it only focuses on < 0.5 % of the genome (seven genes). We therefore aimed to develop a robust core genome MLST (cgMLST) based on the analysis of 370 T. equigenitalis and 68 T. asinigenitalis genomes belonging to 46 and 18 sequence types (STs), respectively. Typing results based on 1333 loci (84.0 % of the genome) from T. equigenitalis genomes and 1255 loci (80.3 %) from T. asinigenitalis genomes showed that the discriminatory power of both species-specific cgMLSTs was greater than that of MLST, with 368 and 68 distinct core genome STs (cgSTs), respectively. Clustering was congruent between the cgMLST and MLST methods, with few inconsistencies for T. equigenitalis. Maximum allelic distance between epidemiologically-related strains was used to define cgMLST clustering thresholds, set at ≤ 15 and 20 allelic distances for T. equigenitalis and T. asinigenitalis, respectively. These parameters grouped the cgSTs into 47 and 11 clonal groups (CGs), respectively. Overall, the cgMLST method outperformed conventional MLST in distinguishing clonal strains from epidemiologically-linked strains, supporting the hypothesis that typing based on a few housekeeping genes does not always accurately reflect genomic relatedness between strains, and making cgMLST more suitable for outbreak investigations.
{"title":"Core genome multilocus sequence typing schemes for epidemiological investigation of Taylorella equigenitalis and Taylorella asinigenitalis","authors":"Sofia Kozak , Déborah Merda , Virginie Chesnais , Marie-France Breuil , Megan Harrison , Irena Zdovc , Majda Golob , Sandrine Petry , Fabien Duquesne","doi":"10.1016/j.vetmic.2025.110419","DOIUrl":"10.1016/j.vetmic.2025.110419","url":null,"abstract":"<div><div><em>Taylorella equigenitalis</em> is the causative agent of contagious equine metritis, an internationally regulated sexually-transmitted infection in horses, which is of great concern as it usually results in temporary infertility. <em>Taylorella asinigenitalis</em>, the second member of the genus, is mainly found in donkeys and is considered non-pathogenic, although a first natural outbreak was reported in 2019 in the United Arab Emirates. Multilocus sequence typing (MLST) is currently used to study the epidemiology of <em>Taylorella</em> spp. but, while highly transposable and reproducible, it only focuses on < 0.5 % of the genome (seven genes). We therefore aimed to develop a robust core genome MLST (cgMLST) based on the analysis of 370 <em>T. equigenitalis</em> and 68 <em>T. asinigenitalis</em> genomes belonging to 46 and 18 sequence types (STs), respectively. Typing results based on 1333 loci (84.0 % of the genome) from <em>T. equigenitalis</em> genomes and 1255 loci (80.3 %) from <em>T. asinigenitalis</em> genomes showed that the discriminatory power of both species-specific cgMLSTs was greater than that of MLST, with 368 and 68 distinct core genome STs (cgSTs), respectively. Clustering was congruent between the cgMLST and MLST methods, with few inconsistencies for <em>T. equigenitalis</em>. Maximum allelic distance between epidemiologically-related strains was used to define cgMLST clustering thresholds, set at ≤ 15 and 20 allelic distances for <em>T. equigenitalis</em> and <em>T. asinigenitalis</em>, respectively. These parameters grouped the cgSTs into 47 and 11 clonal groups (CGs), respectively. Overall, the cgMLST method outperformed conventional MLST in distinguishing clonal strains from epidemiologically-linked strains, supporting the hypothesis that typing based on a few housekeeping genes does not always accurately reflect genomic relatedness between strains, and making cgMLST more suitable for outbreak investigations.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"302 ","pages":"Article 110419"},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143145622","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-30DOI: 10.1016/j.vetmic.2025.110413
Wannarat Yim-im , Tavis K. Anderson , Jan Böhmer , Jordi Baliellas , Tomasz Stadejek , Phillip C. Gauger , Karen M. Krueger , Cornelis J. Vermeulen , Rianne Buter , Aliaksandr Kazlouski , Tongqing An , Jianqiang Zhang
Porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) primarily circulates in Europe but is also detected in North America and Asia. Based on ORF5 sequences, previous studies classified PRRSV-1 into four subtypes. Subtype 1 was further classified into 12 clades (A-L) or into three lineages with lineage 1 including clades 1A-1G and lineage 3 including clades 3A–3G, but the systems are inconsistent and have not been adopted. In this study, we proposed a statistically supported PRRSV-1 genetic classification system based on 10,446 global PRRSV-1 ORF5 sequences spanning 1991–2023. We replaced the colloquial “subtype” designation with “lineage” to reflect evolutionary history and, subsequently, PRRSV-1 was classified into four lineages (L1-L4) with L1 including 18 sublineages (L1.1 to L1.18). The proposed classification system is flexible and may be amended if additional lineages, sublineages, or more granular classifications are needed to reflect contemporary PRRSV-1 detections and evolution. Geographic distributions of PRRSV-1 at lineage and sublineage levels were distinct, with L1 globally distributed and L2, L3 and L4 more restricted. Temporal dynamic changes in some countries were quantified. Classification and ORF5 nucleotide identity of six commercial PRRSV-1 vaccines to each lineage and sublineage and detection frequency of vaccine-like viruses were determined. The phylogenies based on whole-genome and ORF5 sequences demonstrated slightly different tree topologies. Recombination of PRRSV-1 was observed at within-sublineage and between-sublineage levels. A set of ORF5 reference sequences representing the refined classification is available for future diagnostic and epidemiological applications. This study provides a benchmark delineating the current genetic diversity of PRRSV-1 and introduces a refined classification system to support the global standardization and application of ORF5-based genetic classification for PRRSV-1.
{"title":"Refining genetic classification of global porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) and investigating their geographic and temporal distributions","authors":"Wannarat Yim-im , Tavis K. Anderson , Jan Böhmer , Jordi Baliellas , Tomasz Stadejek , Phillip C. Gauger , Karen M. Krueger , Cornelis J. Vermeulen , Rianne Buter , Aliaksandr Kazlouski , Tongqing An , Jianqiang Zhang","doi":"10.1016/j.vetmic.2025.110413","DOIUrl":"10.1016/j.vetmic.2025.110413","url":null,"abstract":"<div><div>Porcine reproductive and respiratory syndrome virus type 1 (PRRSV-1) primarily circulates in Europe but is also detected in North America and Asia. Based on ORF5 sequences, previous studies classified PRRSV-1 into four subtypes. Subtype 1 was further classified into 12 clades (A-L) or into three lineages with lineage 1 including clades 1A-1G and lineage 3 including clades 3A–3G, but the systems are inconsistent and have not been adopted. In this study, we proposed a statistically supported PRRSV-1 genetic classification system based on 10,446 global PRRSV-1 ORF5 sequences spanning 1991–2023. We replaced the colloquial “subtype” designation with “lineage” to reflect evolutionary history and, subsequently, PRRSV-1 was classified into four lineages (L1-L4) with L1 including 18 sublineages (L1.1 to L1.18). The proposed classification system is flexible and may be amended if additional lineages, sublineages, or more granular classifications are needed to reflect contemporary PRRSV-1 detections and evolution. Geographic distributions of PRRSV-1 at lineage and sublineage levels were distinct, with L1 globally distributed and L2, L3 and L4 more restricted. Temporal dynamic changes in some countries were quantified. Classification and ORF5 nucleotide identity of six commercial PRRSV-1 vaccines to each lineage and sublineage and detection frequency of vaccine-like viruses were determined. The phylogenies based on whole-genome and ORF5 sequences demonstrated slightly different tree topologies. Recombination of PRRSV-1 was observed at within-sublineage and between-sublineage levels. A set of ORF5 reference sequences representing the refined classification is available for future diagnostic and epidemiological applications. This study provides a benchmark delineating the current genetic diversity of PRRSV-1 and introduces a refined classification system to support the global standardization and application of ORF5-based genetic classification for PRRSV-1.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"302 ","pages":"Article 110413"},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143145621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-29DOI: 10.1016/j.vetmic.2025.110411
Julia P. Baker , Albert Rovira , Kimberly VanderWaal
Clinical re-breaks of PRRSV on sow farms are a frustrating reality for producers and practitioners. The underlying mechanisms allowing for a single viral variant to persist and cause repeated clinical outbreaks within a herd that should have strong immunity, through recent exposure to a highly similar genetic variant (≥%97 homology), are poorly understood. This study systematically identified clinical re-breaks on sow farms and performed whole genome sequencing on viral isolates available from each outbreak event to evaluate the hypothesis that such re-breaks may be associated with evolution on glycoprotein ectodomains. Pairwise comparisons between re-break isolates revealed multiple amino acid sites in structural proteins that frequently differed between re-break pairs. For sites identified on GP5, several sites were found to be changed in a higher proportion of re-breaks than expected from background variability. Intriguingly, 4 of 13 re-break events had no changes on GP5 but numerous changes in other structural protein ectodomains; GP2, E, GP3, and GP4 all contained several sites that were substituted in a high proportion of rebreak pairs, highlighting the multigenic nature of immune evasion. Across all structural proteins, most sites were located on ectodomains (15/22; 68 %). Several GP5 sites (6/8; 75 %) have been associated with escape from antibody neutralization in in vivo and in vitro experiments. To conclude, identification of suspected immune escape events from production and surveillance data resulted in detection of crucial amino acid positions on structural proteins that potentially underly antigenic diversity. Such micro-evolutionary change could result in escape from antibody neutralization, complicating interventions such as herd closures and leading to persistence of clinical outbreaks on sow farms.
{"title":"Repeat offenders: PRRSV-2 clinical re-breaks from a whole genome perspective","authors":"Julia P. Baker , Albert Rovira , Kimberly VanderWaal","doi":"10.1016/j.vetmic.2025.110411","DOIUrl":"10.1016/j.vetmic.2025.110411","url":null,"abstract":"<div><div>Clinical re-breaks of PRRSV on sow farms are a frustrating reality for producers and practitioners. The underlying mechanisms allowing for a single viral variant to persist and cause repeated clinical outbreaks within a herd that should have strong immunity, through recent exposure to a highly similar genetic variant (≥%97 homology), are poorly understood. This study systematically identified clinical re-breaks on sow farms and performed whole genome sequencing on viral isolates available from each outbreak event to evaluate the hypothesis that such re-breaks may be associated with evolution on glycoprotein ectodomains. Pairwise comparisons between re-break isolates revealed multiple amino acid sites in structural proteins that frequently differed between re-break pairs. For sites identified on GP5, several sites were found to be changed in a higher proportion of re-breaks than expected from background variability. Intriguingly, 4 of 13 re-break events had no changes on GP5 but numerous changes in other structural protein ectodomains; GP2, E, GP3, and GP4 all contained several sites that were substituted in a high proportion of rebreak pairs, highlighting the multigenic nature of immune evasion. Across all structural proteins, most sites were located on ectodomains (15/22; 68 %). Several GP5 sites (6/8; 75 %) have been associated with escape from antibody neutralization in <em>in vivo</em> and <em>in vitro</em> experiments. To conclude, identification of suspected immune escape events from production and surveillance data resulted in detection of crucial amino acid positions on structural proteins that potentially underly antigenic diversity. Such micro-evolutionary change could result in escape from antibody neutralization, complicating interventions such as herd closures and leading to persistence of clinical outbreaks on sow farms.</div></div>","PeriodicalId":23551,"journal":{"name":"Veterinary microbiology","volume":"302 ","pages":"Article 110411"},"PeriodicalIF":2.4,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143207995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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