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Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains
•Evidence of RVA circulating in asymptomatic piglets at high rates.•Age, management and pig density influenced the incidence of RVA infections.•A striking genetic heterogeneity of the RVA circulating in East African pigs.•Genetic similarities between the pig P[6] and P[8] strains and corresponding h...
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| Published in: | Veterinary microbiology 2015-02, Vol.175 (2-4), p.195-210 |
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| creator | Amimo, J.O. Junga, J.O. Ogara, W.O. Vlasova, A.N. Njahira, M.N. Maina, S. Okoth, E.A. Bishop, R.P. Saif, L.J. Djikeng, A. |
| description | •Evidence of RVA circulating in asymptomatic piglets at high rates.•Age, management and pig density influenced the incidence of RVA infections.•A striking genetic heterogeneity of the RVA circulating in East African pigs.•Genetic similarities between the pig P[6] and P[8] strains and corresponding human strains A possible reassortment event between swine and human RVA strains.•Asymptomatic animals could serve as natural reservoirs/sources of new emerging genotypes in both animals and humans, especially in view of the close proximity between them in some geographic regions.
Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1–29.7%). This study revealed that age, management system and pig density significantly (p |
| doi_str_mv | 10.1016/j.vetmic.2014.11.027 |
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Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1–29.7%). This study revealed that age, management system and pig density significantly (p<0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811–1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4–91.3% and 95.1–96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6–100% to 92–100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6–91.7% and 89.3–96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H? In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs.</description><identifier>ISSN: 0378-1135</identifier><identifier>EISSN: 1873-2542</identifier><identifier>DOI: 10.1016/j.vetmic.2014.11.027</identifier><identifier>PMID: 25541378</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Africa, Eastern - epidemiology ; Animals ; Asymptomatic pigs ; Base Sequence ; Diarrhea - veterinary ; East Africa ; Genome, Viral ; Genotype ; Group a rotavirus ; Group A rotaviruses ; Phylogeny ; Prevalence ; Rotavirus ; Rotavirus - genetics ; Rotavirus Infections - epidemiology ; Rotavirus Infections - veterinary ; Rotavirus Infections - virology ; Swine ; Swine Diseases - epidemiology ; Swine Diseases - virology</subject><ispartof>Veterinary microbiology, 2015-02, Vol.175 (2-4), p.195-210</ispartof><rights>2014 Elsevier B.V.</rights><rights>Copyright © 2014 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c465t-2d82933019b89c9c3049eb1e659038be457cb5c57fc0a5b38cf2eec8115874393</citedby><cites>FETCH-LOGICAL-c465t-2d82933019b89c9c3049eb1e659038be457cb5c57fc0a5b38cf2eec8115874393</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25541378$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Amimo, J.O.</creatorcontrib><creatorcontrib>Junga, J.O.</creatorcontrib><creatorcontrib>Ogara, W.O.</creatorcontrib><creatorcontrib>Vlasova, A.N.</creatorcontrib><creatorcontrib>Njahira, M.N.</creatorcontrib><creatorcontrib>Maina, S.</creatorcontrib><creatorcontrib>Okoth, E.A.</creatorcontrib><creatorcontrib>Bishop, R.P.</creatorcontrib><creatorcontrib>Saif, L.J.</creatorcontrib><creatorcontrib>Djikeng, A.</creatorcontrib><title>Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains</title><title>Veterinary microbiology</title><addtitle>Vet Microbiol</addtitle><description>•Evidence of RVA circulating in asymptomatic piglets at high rates.•Age, management and pig density influenced the incidence of RVA infections.•A striking genetic heterogeneity of the RVA circulating in East African pigs.•Genetic similarities between the pig P[6] and P[8] strains and corresponding human strains A possible reassortment event between swine and human RVA strains.•Asymptomatic animals could serve as natural reservoirs/sources of new emerging genotypes in both animals and humans, especially in view of the close proximity between them in some geographic regions.
Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1–29.7%). This study revealed that age, management system and pig density significantly (p<0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811–1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4–91.3% and 95.1–96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6–100% to 92–100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6–91.7% and 89.3–96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H? In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs.</description><subject>Africa, Eastern - epidemiology</subject><subject>Animals</subject><subject>Asymptomatic pigs</subject><subject>Base Sequence</subject><subject>Diarrhea - veterinary</subject><subject>East Africa</subject><subject>Genome, Viral</subject><subject>Genotype</subject><subject>Group a rotavirus</subject><subject>Group A rotaviruses</subject><subject>Phylogeny</subject><subject>Prevalence</subject><subject>Rotavirus</subject><subject>Rotavirus - genetics</subject><subject>Rotavirus Infections - epidemiology</subject><subject>Rotavirus Infections - veterinary</subject><subject>Rotavirus Infections - virology</subject><subject>Swine</subject><subject>Swine Diseases - epidemiology</subject><subject>Swine Diseases - virology</subject><issn>0378-1135</issn><issn>1873-2542</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><recordid>eNqNkc1u1DAUhS0EotOWN0DISzYJdmznhwXSqD-AVKldwKpCluPczHgUx8F2RhoejOfDmSksUVeW7j3nHut8CL2lJKeElh92-R6iNTovCOU5pTkpqhdoReuKZYXgxUu0IqyqM0qZOEPnIewIIbwpyWt0VgjBaVqu0O9riKCjcSNWY4c3MEI0Guut8kpH8OaXOi5djyfntRkBb7ybJ7zG3kW1N34OELBJ9nCwU3RWLf7JbI7DYNUwbN3Qgce98vY4vFEh4nXvjVYf8YOHzlkzqlHDkvLwWP9YvuHiYQLsIYBtBzNu8Ha2Kh2MXpkxXKJXvRoCvHl6L9D325tvV1-yu_vPX6_Wd5nmpYhZ0dVFwxihTVs3utEsFQAthVI0hNUtcFHpVmhR9Zoo0bJa9wWArikVdcVZwy7Q-9PdybufM4QorQkahkGN4OYgaVkSTohg4hlSUXDCy3KR8pNUexeCh15O3ljlD5ISucCVO3mCKxe4klKZ4Cbbu6eEubXQ_TP9pZkEn04CSJXsDXgZtIFUbGd8giw7Z_6f8AdcrLro</recordid><startdate>20150225</startdate><enddate>20150225</enddate><creator>Amimo, J.O.</creator><creator>Junga, J.O.</creator><creator>Ogara, W.O.</creator><creator>Vlasova, A.N.</creator><creator>Njahira, M.N.</creator><creator>Maina, S.</creator><creator>Okoth, E.A.</creator><creator>Bishop, R.P.</creator><creator>Saif, L.J.</creator><creator>Djikeng, A.</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7U9</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20150225</creationdate><title>Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains</title><author>Amimo, J.O. ; Junga, J.O. ; Ogara, W.O. ; Vlasova, A.N. ; Njahira, M.N. ; Maina, S. ; Okoth, E.A. ; Bishop, R.P. ; Saif, L.J. ; Djikeng, A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c465t-2d82933019b89c9c3049eb1e659038be457cb5c57fc0a5b38cf2eec8115874393</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Africa, Eastern - epidemiology</topic><topic>Animals</topic><topic>Asymptomatic pigs</topic><topic>Base Sequence</topic><topic>Diarrhea - veterinary</topic><topic>East Africa</topic><topic>Genome, Viral</topic><topic>Genotype</topic><topic>Group a rotavirus</topic><topic>Group A rotaviruses</topic><topic>Phylogeny</topic><topic>Prevalence</topic><topic>Rotavirus</topic><topic>Rotavirus - genetics</topic><topic>Rotavirus Infections - epidemiology</topic><topic>Rotavirus Infections - veterinary</topic><topic>Rotavirus Infections - virology</topic><topic>Swine</topic><topic>Swine Diseases - epidemiology</topic><topic>Swine Diseases - virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Amimo, J.O.</creatorcontrib><creatorcontrib>Junga, J.O.</creatorcontrib><creatorcontrib>Ogara, W.O.</creatorcontrib><creatorcontrib>Vlasova, A.N.</creatorcontrib><creatorcontrib>Njahira, M.N.</creatorcontrib><creatorcontrib>Maina, S.</creatorcontrib><creatorcontrib>Okoth, E.A.</creatorcontrib><creatorcontrib>Bishop, R.P.</creatorcontrib><creatorcontrib>Saif, L.J.</creatorcontrib><creatorcontrib>Djikeng, A.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Veterinary microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Amimo, J.O.</au><au>Junga, J.O.</au><au>Ogara, W.O.</au><au>Vlasova, A.N.</au><au>Njahira, M.N.</au><au>Maina, S.</au><au>Okoth, E.A.</au><au>Bishop, R.P.</au><au>Saif, L.J.</au><au>Djikeng, A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains</atitle><jtitle>Veterinary microbiology</jtitle><addtitle>Vet Microbiol</addtitle><date>2015-02-25</date><risdate>2015</risdate><volume>175</volume><issue>2-4</issue><spage>195</spage><epage>210</epage><pages>195-210</pages><issn>0378-1135</issn><eissn>1873-2542</eissn><abstract>•Evidence of RVA circulating in asymptomatic piglets at high rates.•Age, management and pig density influenced the incidence of RVA infections.•A striking genetic heterogeneity of the RVA circulating in East African pigs.•Genetic similarities between the pig P[6] and P[8] strains and corresponding human strains A possible reassortment event between swine and human RVA strains.•Asymptomatic animals could serve as natural reservoirs/sources of new emerging genotypes in both animals and humans, especially in view of the close proximity between them in some geographic regions.
Viral enteritis is a serious problem accounting for deaths in neonatal animals and humans worldwide. The absence of surveillance programs and diagnostic laboratory facilities have resulted in a lack of data on rotavirus associated diarrheas in pigs in East Africa. Here we describe the incidence of group A rotavirus (RVA) infections in asymptomatic young pigs in East Africa. Of the 446 samples examined, 26.2% (117/446) were positive for RVA. More nursing piglets (78.7%) shed RVA than weaned (32.9%) and grower (5.8%) pigs. RVA incidence was higher in pigs that were either housed_free-range (77.8%) or tethered_free-range (29.0%) than those that were free-range or housed or housed-tethered pigs. The farms with larger herd size (>10 pigs) had higher RVA prevalence (56.5%) than farms with smaller herd size (24.1–29.7%). This study revealed that age, management system and pig density significantly (p<0.01) influenced the incidence of RVA infections, with housed_free-range management system and larger herd size showing higher risks for RVA infection. Partial (811–1604nt region) sequence of the VP4 gene of selected positive samples revealed that different genotypes (P[6], P[8] and P[13]) are circulating in the study area with P[8] being predominant. The P[6] strain shared nucleotide (nt) and amino acid (aa) sequence identity of 84.4–91.3% and 95.1–96.9%, respectively, with known porcine and human P[6] strains. The P[8] strains shared high nt and aa sequence identity with known human P[8] strains ranging from 95.6–100% to 92–100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6–91.7% and 89.3–96.4%, respectively, only with known porcine P[13] strains. No P[8] strains yielded RNA of sufficient quality/quantity for full genome sequencing. However analysis of the full genome constellation of the P[6], two P[13] and one untypeable strains revealed that the P[6] strain (Ke-003-5) genome constellation was G26-P[6]-I5-R1-C1-M1-A8-N1-T1-E1-H1, P[13] strains (Ug-049 and Ug-453) had G5-P[13]-I5-R1-C1-M1-A8-N1-T7-E1-H1 while the untypeable strain (Ug-218) had G5-P[?]-I5-R1-C1-M1-A8-N1-T1-E1-H? In conclusion, P[6] and P[8] genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission. Further studies are required to determine the role of RVA in swine enteric disease burden and to determine the genetic/antigenic heterogeneity of the circulating strains for development of accurate diagnostic tools and to implement appropriate prophylaxis programs.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>25541378</pmid><doi>10.1016/j.vetmic.2014.11.027</doi><tpages>16</tpages></addata></record> |
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| subjects | Africa, Eastern - epidemiology Animals Asymptomatic pigs Base Sequence Diarrhea - veterinary East Africa Genome, Viral Genotype Group a rotavirus Group A rotaviruses Phylogeny Prevalence Rotavirus Rotavirus - genetics Rotavirus Infections - epidemiology Rotavirus Infections - veterinary Rotavirus Infections - virology Swine Swine Diseases - epidemiology Swine Diseases - virology |
| title | Detection and genetic characterization of porcine group A rotaviruses in asymptomatic pigs in smallholder farms in East Africa: Predominance of P[8] genotype resembling human strains |
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