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Molecular detection, genetic characterization and zoonotic potenial of porcine rotaviruses
  • Joshua O Amimo, University of Nairobi
Virus induced enteritis is one of the serious problems accounting for maximum deaths in neonatal animals and human throughout the world. The absence of appropriate surveillance programs and laboratory facilities have resulted in a scarcity of accessible data on virus associated diarrheas (especially rotavirus) in pigs in the East African region. The aim of this study was to provide detailed molecular epidemiological information on the prevalence and genetic diversity of rotaviruses (RVs) and also the distribution of genotypes of group A RVs (RVA) circulating in high intensive commercial pig production systems in the USA and smallholder pig production systems (1-25 pigs per farm) in Kenya and Uganda. Fecal samples obtained from the state of Ohio, USA (n=380), western Kenya (n=239) and eastern Uganda (n=207) from nursing and weaned piglets were screened for the presence of RVs (USA and East Africa) and other enteric viruses (kobuviruses and astroviruses in East African pig fecal samples). Of the 380 samples obtained from 5 swine herds in Ohio, USA, 371 samples were examined for the presence of RVA of which 9.4% (35/371) were positive. A total of 23 positive samples were analyzed for RVA G and P genotypes. The dominant G-P combination was G9P[13] found in 60.9% of sequenced strains. The other combinations were G9P[7] (8.7%), G4P[13] (8.7%), G11P[13] (4.3%) and G11P[7] (4.3%). Sequence analysis of partial VP7 genes of selected strains revealed that the G4 strains were closely related to one another (95%) and to a lower extent to human (82-84%) and porcine (84-86%) G4 strains. The G11 strains detected shared identical VP7 gene sequence (100%) and were closely related to human (85-86%) and other porcine (83%) G11 strains. The G9 strains identified were closely related to one another, human and other porcine strains (96-97%, 89-91% and 89-91% nucleotide identities, respectively). The VP4 gene analysis revealed that P[7] strains were closely related to each other and to P[7] strains isolated from porcine, bovine and panda (91-99%, 92-99% and 92-99%, respectively). The P[13] strains showed a higher diversity among themselves and with other porcine P[13] strains ranging from 83% to 99% and 82-97%, respectively. A total of 380 USA samples were also tested for group C rotavirus (RVC) and 19.5% were positive. Of the 128 samples collected in 2012, 23.5% from nursing piglets and 8.5% from weaned piglets were RVC positive, with a higher RVC frequency in diarrheic (28.4%) than in non-diarrheic (6.6%) piglets. Two strains (RVC/Pig-wt/USA/RV0104/2011/G3PX and RVC/Pig-wt/USA/RV0143/2012/G6Px) from two different farms were characterized genetically to gain information on virus diversity based on full length sequences of the inner capsid VP6, enterotoxin NSP4 and the outer capsid VP7 and VP4 genes. The results of this study indicate high genetic heterogeneity in RVA and RVC genes and the concurrent co-circulation of different RV genogroups and genotypes at the same time in the USA. The RVA genotyping results suggest the possibility of genetic reassortment between different RVA genotypes within these US farms. These findings are useful for the development of more accurate diagnostic tools and to provide information for vaccine development. Of the 446 samples obtained from East Africa, 31.6% (141/446) were positive for RVs, of which 73.8% (104/141) were positive for RVA alone, and 17% (24/141) were positive for RVC alone and 9.2% (13/141) were of RVA/RVC mixed infection. 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% and 92-100%, respectively. The P[13] strains shared nt and aa sequence identity of 83.6-91.7% and 89.3-96.4%, respectively, with known porcine P[13] strains. The study in Kenya and Uganda demonstrates that infection with RV is frequent in East African piggeries. The P[6] and P[8] RVA genotypes detected were genetically closely related to human strains suggesting the possibility of interspecies transmission and zoonotic potential. Additionally, of the 446 samples from East Africa, 251 samples were screened for the presence of other enteric viruses (caliciviruses and kobuviruses), of which 12.7% were positive for caliciviruses and 13.1% positive for kobuviruses. Genetic analysis of the kobuvirus RdRp partial sequence revealed that they are more diverse, sharing nucleotide identity ranging from 89.7-99.1% among them. We also detected porcine astroviruses in few samples belonging to type 2 and type 3 Mamastroviruses. To our knowledge this study reports the first detection and molecular analysis of group A RVs, kobuviruses and astroviruses in the African swine population. The presence of these gastroenteritis-producing viruses in clinically healthy pigs represents a source of infection of pigs, and possibly to humans, and hence further studies are required to determine their role in gastrointestinal infections of pigs in this region and to determine their genetic diversity in-order to develop accurate diagnostic tools and implement appropriate control strategies to improve pig health. Improved pig health will lead to improved production and ultimately improved livelihood.
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Citation Information
Joshua O Amimo. "Molecular detection, genetic characterization and zoonotic potenial of porcine rotaviruses" (2014)
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