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Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms

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Title Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms
 
Creator Amimo, Joshua O.
Machuka, Eunice M.
Okoth, Edward A.
Vlasova, Anastasia N.
Pellé, Roger
 
Subject analysis
farms
strains
 
Description Astroviruses (AstVs) are widely distributed and are associated with gastroenteritis in human and animals. The knowledge of the genetic diversity and epidemiology of AstVs in Africa is limited. This study aimed to characterize astroviruses in asymptomatic smallholder piglets in Kenya and Uganda. Twenty-four samples were randomly selected from a total of 446 piglets aged below 6 months that were initially collected for rotavirus study and sequenced for whole genome analysis. Thirteen (13/24) samples had contigs with high identity to genus Mamastrovirus. Analysis of seven strains with complete (or near complete) AstV genome revealed variable nucleotide and amino acid sequence identities with known porcine astrovirus (PoAstV) strains. The U083 and K321 strains had nucleotide sequence identities ranging from 66.4 to 75.4% with the known PoAstV2 strains; U460 strain had nucleotide sequence identities of 57.0 to 65.1% regarding the known PoAstV3; and K062, K366, K451, and K456 strains had nucleotide sequence identities of 63.5 to 80% with the known PoAstV4 strains. The low sequence identities (
 
Date 2020-11-05
2023-03-10T14:38:15Z
2023-03-10T14:38:15Z
 
Type Journal Article
 
Identifier Amimo, Joshua O.; Machuka, Eunice M.; Okoth, Edward A.; Vlasova, Anastasia N.; Pellé, Roger. 2020. Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Strains Circulating in East African Smallholder Pig Farms. Viruses 12: 1262
1999-4915
https://hdl.handle.net/10568/129535
https://doi.org/10.3390/v12111262
 
Rights CC-BY-4.0
Open Access
 
Format 1262
 
Publisher MDPI AG
 
Source Viruses