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Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa-1.pdf
Archives of Virology (2016)
  • Joshua O Amimo
Pigs harbor a variety of viruses that are closely
related to human viruses and are suspected to have zoonotic
potential. Little is known about the presence of
viruses in smallholder farms where pigs are in close contact
with humans and wildlife. This study provides insight into
viral communities and the prevalence and characteristics of
enteric viral co-infections in smallholder pigs in East
Africa. Sequence-independent amplification and highthroughput
sequencing were applied to the metagenomics
analysis of viruses in feces collected from asymptomatic
pigs. A total of 47,213 de novo-assembled contigs were
constructed and compared with sequences from the Gen-
Bank database. Blastx search results revealed that 1039
contigs ([200 nt) were related to viral sequences in the
GenBank database. Of the 1039 contigs, 612 were not
assigned to any viral taxa because they had little similarity
to known viral genomic or protein sequences, while 427
contigs had a high level of sequence similarity to known
viruses and were assigned to viral taxa. The most frequent
contigs related to mammalian viruses resembling members
of the viral genera Astrovirus, Rotavirus, Bocavirus, Circovirus,
and Kobuvirus. Other less abundant contigs were
related to members of the genera Sapelovirus, Pasivirus,
Posavirus, Teschovirus and Picobirnavirus. This is the first
report on the diversity of the fecal virome of pig populations
in East Africa. The findings of the present study help
to elucidate the etiology of diarrheal diseases in pigs and
identify potential zoonotic and emerging viruses in the
region. Further investigations are required to compare the
incidence of these viruses in healthy and diseased pigs in
order to better elucidate their pathogenic role.
Publication Date
Citation Information
Joshua O Amimo. "Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa-1.pdf" Archives of Virology (2016)
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