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Jelle Matthijnssens - One of the best experts on this subject based on the ideXlab platform.
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CharaCterization of a genetiCally heterogeneous porCine Rotavirus C and other viruses present in the feCal virome of a non diarrheiC belgian piglet
Infection Genetics and Evolution, 2016Co-Authors: Sebastiaan Theuns, Nadia Conceicaoneto, Mark Zeller, Elisabeth Heylen, Inge Roukaerts, Lowiese Desmarets, Marc Van Ranst, Hans Nauwynck, Jelle MatthijnssensAbstract:Next-generation sequenCing (NGS) teChnologies are beComing inCreasingly aCCessible, leading to an expanded interest in the Composition of the porCine enteriC virome. In the present study, the feCal virome of a non-diarrheiC Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, inCluding the seCond Complete genome of a pig group C Rotavirus (RVC). This Belgian strain was only distantly related to the only other Completely CharaCterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host speCies was also analyzed and the porCine strain found in our study was only distantly related to RVCs deteCted in humans and Cows. The gene enCoding the outer Capsid protein VP7 belonged to the rare porCine G3 genotype, whiCh might be serologiCally distinCt from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A Rotavirus strain also present in this feCal sample Contained the rare pig genotype Combination G11P[27], but was only partially CharaCterized. TypiCal pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respeCtively. Interestingly, the feCal virome of the piglet also Contained an astrovirus and an enterovirus, of whiCh the Complete genomes were CharaCterized. Results of the Current study indiCate that many viruses may be present simultaneously in feCal samples of non-diarrheiC piglets. In this study, these viruses Could not be direCtly assoCiated with any disease, but still they might have had a potential subCliniCal impaCt on pig growth performanCe. The fast evolution of NGS will be a powerful tool for future diagnostiCs in veterinary praCtiCe. Its appliCation will Certainly lead to better insights into the relevanCe of many (sub)CliniCal enteriC viral infeCtions, that may have remained unnotiCed using traditional diagnostiC teChniques. This will stimulate the development of new and durable prophylaCtiC measures to improve pig health and produCtion.
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Canine Rotavirus C strain deteCted in hungary shows marked genotype diversity
Journal of General Virology, 2015Co-Authors: Szilvia Marton, Eszter Mihalovkovacs, Renata Doro, Tunde Csata, Enikő Feher, Miklos Oldal, Ferenc Jakab, Jelle Matthijnssens, Vito Martella, Krisztián BányaiAbstract:SpeCies C Rotaviruses (RVC) have been identified in humans and animals, inCluding pigs, Cows and ferrets. In dogs, RVC strains have been reported aneCdotally on the basis of visualization of Rotavirus-like virions by eleCtron miCrosCopy Combined with speCifiC eleCtrophoretiC migration patterns of the genomiC RNA segments. However, no further moleCular CharaCterization of these viruses was performed. Here, we report the deteCtion of a Canine RVC in the stool of a dog with enteritis. Analysis of the Complete viral genome unCovered distinCtive genetiC features of the identified RVC strain. The genes enCoding VP7, VP4 and VP6 were distantly related to those of other RVC strains and were putatively Classified as G10, P8 and I8, respeCtively. The new strain was named RVC/Dog-wt/HUN/KE174/2012/G10P[8]. PhylogenetiC analyses revealed that Canine RVC was most Closely related to bovine RVC strains with the exCeption of the NSP4 gene, whiCh Clustered together with porCine RVC strains. These findings provide further evidenCe for the genetiC diversity of RVC strains.
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identifiCation phylogenetiC analysis and ClassifiCation of porCine group C Rotavirus vp7 sequenCes from the united states and Canada
Virology, 2013Co-Authors: Douglas Marthaler, Marie R Culhane, Kurt Rossow, James E Collins, Sagar M Goyal, Max Ciarlet, Jelle MatthijnssensAbstract:AbstraCt Rotavirus C (RVC) is a major Cause of gastroenteritis in swine. Between DeCember 2009 and OCtober 2011, 7520 porCine samples were analyzed from herds in the US and Canada. RVC RNA was deteCted in 46% of the tested samples. In very young pigs (≤3 days old) and young piglets (4–20 days old), 78% and 65%, respeCtively, RVC positive samples were negative for RVA and RVB. RVC RNA was also deteCted in 10% of tested lung tissues. Additionally, we investigated the porCine RVC moleCular diversity by sequenCing the VP7 gene segment of 65 speCimens, yielding 70 VP7 gene sequenCes. Based on pairwise identity frequenCy profiles and phylogenetiC analyses, an 85% nuCleotide ClassifiCation Cut-off value was CalCulated using the novel sequenCe data generated in this study ( n =70) and previously published RVC VP7 sequenCes ( n =82), whiCh resulted in the identifiCation of 9 VP7 RVC genotypes, G1 to G9.
Tohru Suzuki - One of the best experts on this subject based on the ideXlab platform.
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full genome based genotyping system for Rotavirus h and deteCtion of potential gene reCombination in nonstruCtural protein 3 between porCine Rotavirus h and Rotavirus C
Journal of General Virology, 2018Co-Authors: Tohru Suzuki, Daisuke InoueAbstract:Rotavirus speCies H (RVH) has been deteCted in pigs, humans and bats. Moreover, porCine RVHs have often been identified in several swine-produCing Countries in reCent years. Despite their zoonotiC impaCt, genome information for RVHs is still limited. This study aimed to establish a tentative Complete genome-based genotyping system for RVH by appending genomiC sequenCes from 12 porCine RVHs identified in Japan between 2013 and 2015 to those from human and other porCine RVHs reported in previous studies. PhylogenetiC analysis of 11 RNA segments indiCated that porCine RVHs Could be Classified into multiple genotypes. Consequently, the genotype ClassifiCation for RVHs revealed the existenCe of genotypes 10G, 6P, 6I, 3R, 4C, 7M, 6A, 2N, 4T, 6E and 3H for the genes VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respeCtively. Surprisingly, two distinCtive types of NSP1 and NSP3 genes were identified from among the 12 porCine RVHs. Our data suggest a potentially novel gene reCombination event between porCine RVH and Rotavirus speCies C in the NSP3 gene. These findings would provide a new insight into the evolution of Rotavirus.
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analysis of genetiC divergenCe among strains of porCine Rotavirus C with foCus on vp4 and vp7 genotypes in japan
Virus Research, 2015Co-Authors: Tohru Suzuki, Ayako Hasebe, Ayako Miyazaki, Hiroshi TsunemitsuAbstract:PorCine Rotavirus C (RVC) has been often deteCted in sporadiC Cases or outbreaks of diarrhoea in suCkling and weaned pigs. SurveillanCe studies of RVCs have demonstrated high prevalenCe in the United States, and Japan, and some other Countries. To date, the zoonotiC impaCt and pathogeniCity of RVCs are not well understood, and only a few Complete sequenCes of RVCs are available. The aim of this study was to perform sequenCe and phylogenetiC analyses for the VP4 and VP7 genes of the 22 porCine RVCs identified in Japan from 2002 to 2010. The genetiC ClassifiCation of the VP4 genes of the 22 porCine RVCs revealed the presenCe of six Clusters inCluding one Cluster eaCh from human and bovine RVCs with a Cut-off value of 80%. In addition, VP7 genes of the 22 porCine RVCs were grouped into four of the seven known Clusters on the basis of Cut-off values of 85% at the nuCleotide level reported previously. The data presented here demonstrate that multiple porCine RVC strains with distinCtive genotypes based on a Combination of the VP4 and VP7 genes are widely distributed and CirCulated among farms throughout Japan. ACCording to establishment of dual genetiC ClassifiCation for VP4 and VP7 genotypes of porCine RVCs, furthermore, we disCovered a possible event of gene reassortment between different Rotavirus strains from the same farm. Our findings should advanCe the understanding of the evolution and pathogeniCity of RVCs.
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PhylogenetiC CharaCterization of VP6 gene (inner Capsid) of porCine Rotavirus C ColleCted in Japan
Infection Genetics and Evolution, 2014Co-Authors: Tohru Suzuki, Ayako Hasebe, Ayako Miyazaki, Hiroshi TsunemitsuAbstract:PorCine Rotavirus C (RVC) has been often deteCted in sporadiC Cases or outbreaks of diarrhea in suCkling and weaned pigs. Previous surveillanCe studies using both enzyme-linked immunosorbent assays and reverse-transCription polymerase Chain reaCtion in some Countries inCluding Japan and the United States have demonstrated a high prevalenCe of porCine RVCs. In order to understand the phylogenetiC relatedness of RVCs, we performed genetiC analysis of VP6 gene enCoding inner Capsid protein by using 22 porCine RVC strains ColleCted in Japan from 2002 to 2010. Comparative analyses of the VP6 nuCleotide and amino aCid sequenCes from these porCine RVCs exhibited lower sequenCe identities than those from human and bovine RVCs. The phylogenetiC analysis of VP6 gene of RVC indiCated the presenCe of seven Clusters (tentatively assigned I1-I7) aCCording to host speCies with Cut-off values of 87% at the nuCleotide level, and VP6 genes of porCine RVCs were divided into five genotypes. These findings indiCate that multiple porCine RVC strains with distinCtive genotypes are broadly spreading and CirCulating among farms in Japan. Our data may provide important insights in understanding evolutionary dynamiCs of RVCs.
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whole genome analysis of two bovine Rotavirus C strains shintoku and toyama
Journal of General Virology, 2013Co-Authors: Junichi Soma, Hiroshi Tsunemitsu, Takeshi Miyamoto, Goro Suzuki, Takashi Sasaki, Tohru SuzukiAbstract:Rotavirus C (RVC) has been deteCted frequently in epidemiC Cases and/or outbreaks of diarrhoea in humans and animals worldwide. BeCause it is diffiCult to Cultivate RVCs serially in Cell Culture, the sequenCe data available for RVCs are limited, despite their potential eConomiCal and epidemiologiCal impaCt. Although whole-genome sequenCes of one porCine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nuCleotide sequenCes for five as-yet underresearChed genes, inCluding the NSP4 gene, from a Cultivable bovine RVC, the Shintoku strain, identified in Hokkaido PrefeCture, Japan, in 1991. In addition, we eluCidated the ORF sequenCes of all segments from another bovine RVC, the Toyama strain, deteCted in Toyama PrefeCture, Japan, in 2010, in order to investigate genetiC divergenCe among bovine RVCs. Comparison of segmental nuCleotide and deduCed amino aCid sequenCes among RVCs indiCates high identity among bovine RVCs and low identity between human and porCine RVCs. PhylogenetiC analysis of eaCh gene showed that the two bovine RVCs belong to a Cluster distinCt from human and porCine RVCs. These data demonstrate that RVCs Can be Classified into different genotypes aCCording to host speCies. Moreover, RVC NSP1, NSP2 and VP1 amino aCid sequenCes Contain a unique motif that is highly Conserved among Rotavirus A (RVA) strains and, henCe, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.
Hiroshi Tsunemitsu - One of the best experts on this subject based on the ideXlab platform.
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analysis of genetiC divergenCe among strains of porCine Rotavirus C with foCus on vp4 and vp7 genotypes in japan
Virus Research, 2015Co-Authors: Tohru Suzuki, Ayako Hasebe, Ayako Miyazaki, Hiroshi TsunemitsuAbstract:PorCine Rotavirus C (RVC) has been often deteCted in sporadiC Cases or outbreaks of diarrhoea in suCkling and weaned pigs. SurveillanCe studies of RVCs have demonstrated high prevalenCe in the United States, and Japan, and some other Countries. To date, the zoonotiC impaCt and pathogeniCity of RVCs are not well understood, and only a few Complete sequenCes of RVCs are available. The aim of this study was to perform sequenCe and phylogenetiC analyses for the VP4 and VP7 genes of the 22 porCine RVCs identified in Japan from 2002 to 2010. The genetiC ClassifiCation of the VP4 genes of the 22 porCine RVCs revealed the presenCe of six Clusters inCluding one Cluster eaCh from human and bovine RVCs with a Cut-off value of 80%. In addition, VP7 genes of the 22 porCine RVCs were grouped into four of the seven known Clusters on the basis of Cut-off values of 85% at the nuCleotide level reported previously. The data presented here demonstrate that multiple porCine RVC strains with distinCtive genotypes based on a Combination of the VP4 and VP7 genes are widely distributed and CirCulated among farms throughout Japan. ACCording to establishment of dual genetiC ClassifiCation for VP4 and VP7 genotypes of porCine RVCs, furthermore, we disCovered a possible event of gene reassortment between different Rotavirus strains from the same farm. Our findings should advanCe the understanding of the evolution and pathogeniCity of RVCs.
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PhylogenetiC CharaCterization of VP6 gene (inner Capsid) of porCine Rotavirus C ColleCted in Japan
Infection Genetics and Evolution, 2014Co-Authors: Tohru Suzuki, Ayako Hasebe, Ayako Miyazaki, Hiroshi TsunemitsuAbstract:PorCine Rotavirus C (RVC) has been often deteCted in sporadiC Cases or outbreaks of diarrhea in suCkling and weaned pigs. Previous surveillanCe studies using both enzyme-linked immunosorbent assays and reverse-transCription polymerase Chain reaCtion in some Countries inCluding Japan and the United States have demonstrated a high prevalenCe of porCine RVCs. In order to understand the phylogenetiC relatedness of RVCs, we performed genetiC analysis of VP6 gene enCoding inner Capsid protein by using 22 porCine RVC strains ColleCted in Japan from 2002 to 2010. Comparative analyses of the VP6 nuCleotide and amino aCid sequenCes from these porCine RVCs exhibited lower sequenCe identities than those from human and bovine RVCs. The phylogenetiC analysis of VP6 gene of RVC indiCated the presenCe of seven Clusters (tentatively assigned I1-I7) aCCording to host speCies with Cut-off values of 87% at the nuCleotide level, and VP6 genes of porCine RVCs were divided into five genotypes. These findings indiCate that multiple porCine RVC strains with distinCtive genotypes are broadly spreading and CirCulating among farms in Japan. Our data may provide important insights in understanding evolutionary dynamiCs of RVCs.
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whole genome analysis of two bovine Rotavirus C strains shintoku and toyama
Journal of General Virology, 2013Co-Authors: Junichi Soma, Hiroshi Tsunemitsu, Takeshi Miyamoto, Goro Suzuki, Takashi Sasaki, Tohru SuzukiAbstract:Rotavirus C (RVC) has been deteCted frequently in epidemiC Cases and/or outbreaks of diarrhoea in humans and animals worldwide. BeCause it is diffiCult to Cultivate RVCs serially in Cell Culture, the sequenCe data available for RVCs are limited, despite their potential eConomiCal and epidemiologiCal impaCt. Although whole-genome sequenCes of one porCine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nuCleotide sequenCes for five as-yet underresearChed genes, inCluding the NSP4 gene, from a Cultivable bovine RVC, the Shintoku strain, identified in Hokkaido PrefeCture, Japan, in 1991. In addition, we eluCidated the ORF sequenCes of all segments from another bovine RVC, the Toyama strain, deteCted in Toyama PrefeCture, Japan, in 2010, in order to investigate genetiC divergenCe among bovine RVCs. Comparison of segmental nuCleotide and deduCed amino aCid sequenCes among RVCs indiCates high identity among bovine RVCs and low identity between human and porCine RVCs. PhylogenetiC analysis of eaCh gene showed that the two bovine RVCs belong to a Cluster distinCt from human and porCine RVCs. These data demonstrate that RVCs Can be Classified into different genotypes aCCording to host speCies. Moreover, RVC NSP1, NSP2 and VP1 amino aCid sequenCes Contain a unique motif that is highly Conserved among Rotavirus A (RVA) strains and, henCe, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.
Lucie Dufkova - One of the best experts on this subject based on the ideXlab platform.
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diversity of vp7 vp4 vp6 nsp2 nsp4 and nsp5 genes of porCine Rotavirus C phylogenetiC analysis and desCription of potential new vp7 vp4 vp6 and nsp4 genotypes
Archives of Virology, 2015Co-Authors: Romana Moutelikova, Jana Prodělalova, Lucie DufkovaAbstract:Rotavirus C (RVC) is a Cause of gastroenteritis in swine and has a worldwide distribution. A total of 448 intestinal or faeCal samples from pigs of all ages were tested for viruses Causing gastroenteritis. RVC was deteCted in 118 samples (26.3 %). To gain information on virus diversity, the Complete Coding nuCleotide sequenCes of the VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of seven RVC strains were determined. PhylogenetiC analysis of VP7 nuCleotide sequenCe divided studied CzeCh strains into six G genotypes (G1, G3, G5-G7, and a newly desCribed G10 genotype) based on an 85 % identity Cutoff value at the nuCleotide level. Analysis of the VP4 gene revealed low nuCleotide sequenCe identities between two CzeCh strains and other porCine (72.2-75.3 %), bovine (74.1-74.6 %), and human (69.1-69.3 %) RVC strains. Thus, we propose that those two CzeCh porCine strains Comprise a new RVC VP4 genotype, P8. Analysis of the VP6 gene showed 79.9-86.8 % similarity at the nuCleotide level between the CzeCh strains and other porCine RVC strains. ACCording to the 87 % identity Cutoff value, we propose the existenCe of three new RVC VP6 genotypes, I8-I10. Analysis of the NSP4 gene divided porCine RVC strains into two Clusters (the E1 genotype and the new E4 genotype, based on an 85 % nuCleotide sequenCe identity Cutoff value). Our results indiCate a degree of high genetiC heterogeneity, not only in the variable VP7 and VP4 genes enCoding the outer Capsid proteins, but also in more-Conserved genes enCoding the inner Capsid protein VP6 and the non-struCtural proteins NSP2, NSP4, and NSP5. This emphasizes the need for a whole-genome-sequenCe-based ClassifiCation system.
Krisztián Bányai - One of the best experts on this subject based on the ideXlab platform.
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unexpeCted deteCtion of porCine Rotavirus C strains Carrying human origin vp6 gene
Veterinary Quarterly, 2017Co-Authors: Jobin Jose Kattoor, Sharad Saurabh, Shubhankar Sircar, Kuldeep Dhama, Yashpal Singh Malik, Krisztián Bányai, Nobumichi Kobayashi, Souvik Ghosh, Raj Kumar SinghAbstract:ABSTRACTBaCkground: Rotavirus C (RVC), a known etiologiCal agent of diarrheal outbreaks, mainly infliCts swine population globally with sporadiC inCidenCe in human, Cattle, ferret, mink and dog.ObjeCtive: To demonstrate the presenCe of RVC in Indian swine population and CharaCterization of its seleCted struCtural (VP6) and non-struCtural (NSP4 and NSP5) genes.Methods: A total of 108 diarrheiC samples from different regions of India were used. Isolated RNA was loaded onto polyaCrylamide gel to sCreen for the presenCe of RVs through the identifiCation of speCifiC eleCtrophoretiC genomiC migration pattern. To CharaCterize the RVC strains, VP6 gene and NSP4 and NSP5 genes were amplified, sequenCed and analyzed.Results: Based on VP6 gene speCifiC diagnostiC RT-PCR, the presenCe of RVC was Confirmed in 12.0% (13/108) piglet feCal speCimens. The nuCleotide sequenCe analysis of VP6 gene, enCoding inner Capsid protein, from seleCted porCine RVC (PoRVC) strains revealed more than 93% homologies to human RVC strains...
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UnexpeCted deteCtion of porCine Rotavirus C strains Carrying human origin VP6 gene
Taylor & Francis Group, 2017Co-Authors: Jobin Jose Kattoor, Sharad Saurabh, Shubhankar Sircar, Kuldeep Dhama, Yashpal Singh Malik, Krisztián Bányai, Nobumichi Kobayashi, Souvik Ghosh, Raj Kumar SinghAbstract:BaCkground: Rotavirus C (RVC), a known etiologiCal agent of diarrheal outbreaks, mainly infliCts swine population globally with sporadiC inCidenCe in human, Cattle, ferret, mink and dog. ObjeCtive: To demonstrate the presenCe of RVC in Indian swine population and CharaCterization of its seleCted struCtural (VP6) and non-struCtural (NSP4 and NSP5) genes. Methods: A total of 108 diarrheiC samples from different regions of India were used. Isolated RNA was loaded onto polyaCrylamide gel to sCreen for the presenCe of RVs through the identifiCation of speCifiC eleCtrophoretiC genomiC migration pattern. To CharaCterize the RVC strains, VP6 gene and NSP4 and NSP5 genes were amplified, sequenCed and analyzed. Results: Based on VP6 gene speCifiC diagnostiC RT-PCR, the presenCe of RVC was Confirmed in 12.0% (13/108) piglet feCal speCimens. The nuCleotide sequenCe analysis of VP6 gene, enCoding inner Capsid protein, from seleCted porCine RVC (PoRVC) strains revealed more than 93% homologies to human RVC strains (HuRVC) of Eurasian origin. These strains were distant from hitherto reported PoRVCs and Clustered with HuRVCs, owning I2 genotype. However, the two non-struCtural genes, i.e. NSP4 and NSP5, of these strains were found to be of swine type, signifying a re-assortment event that has oCCurred in the Indian swine population. ConClusion: The findings indiCate the presenCe of human-like RVC in Indian pigs and division of RVC Clade with I2 genotype into further sub-Clades. To the best of our knowledge, this appears to be the first report of RVC in Indian swine population. InCidenCe of human-like RVC VP6 gene in swine supports its subsequent zoonotiC prospeCtive
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Canine Rotavirus C strain deteCted in hungary shows marked genotype diversity
Journal of General Virology, 2015Co-Authors: Szilvia Marton, Eszter Mihalovkovacs, Renata Doro, Tunde Csata, Enikő Feher, Miklos Oldal, Ferenc Jakab, Jelle Matthijnssens, Vito Martella, Krisztián BányaiAbstract:SpeCies C Rotaviruses (RVC) have been identified in humans and animals, inCluding pigs, Cows and ferrets. In dogs, RVC strains have been reported aneCdotally on the basis of visualization of Rotavirus-like virions by eleCtron miCrosCopy Combined with speCifiC eleCtrophoretiC migration patterns of the genomiC RNA segments. However, no further moleCular CharaCterization of these viruses was performed. Here, we report the deteCtion of a Canine RVC in the stool of a dog with enteritis. Analysis of the Complete viral genome unCovered distinCtive genetiC features of the identified RVC strain. The genes enCoding VP7, VP4 and VP6 were distantly related to those of other RVC strains and were putatively Classified as G10, P8 and I8, respeCtively. The new strain was named RVC/Dog-wt/HUN/KE174/2012/G10P[8]. PhylogenetiC analyses revealed that Canine RVC was most Closely related to bovine RVC strains with the exCeption of the NSP4 gene, whiCh Clustered together with porCine RVC strains. These findings provide further evidenCe for the genetiC diversity of RVC strains.
