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

Joshua O Amimo,Anastasia N Vlasova,Roger Pelle,Eunice M Machuka,Edward O Abworo

doi:10.3390/v12111262

Abstract

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 (<90%) indicate that novel genotypes of PoAstVs are circulating in the study area. Recombination analysis using whole genomes revealed evidence of multiple recombination events in PoAstV4, suggesting that recombination might have contributed to the observed genetic diversity. Linear antigen epitope prediction and a comparative analysis of capsid protein of our field strains identified potential candidate epitopes that could help in the design of immuno-diagnostic tools and a subunit vaccine. These findings provide new insights into the molecular epidemiology of porcine astroviruses in East Africa.

Highlights

Porcine astroviruses (PoAstVs) belong to the family Astroviridae consisting of two genera, Avastrovirus and Mamastrovirus, based on the host ranges of avian and mammalian species, respectively [1].Astroviruses (AstVs) have been isolated from fecal samples of a wide variety of mammals and birds [1,2,3,4].AstVs are known to be the second most prevalent cause of viral gastroenteritis in infantsViruses 2020, 12, 1262; doi:10.3390/v12111262 www.mdpi.com/journal/virusesViruses 2020, 12, 1262 and children [5], and they have been reported in water sources and sewage samples [6,7]
PoAstVs detected in this study showed the conserved tyrosine residue within the TEEEY motif in the viral protein genome-linked (VPg) putative protein at the 30 end of ORF1a (PoAstV3 contained SEEEY)
The discovery of novel PoAstV strains described in this study provides an example of how diverse these viruses are in the smallholder pig population in the study region, where there is close contact between pigs and humans

Summary

Introduction

Astroviruses (AstVs) have been isolated from fecal samples of a wide variety of mammals and birds [1,2,3,4]. Viruses 2020, 12, 1262 and children [5], and they have been reported in water sources and sewage samples [6,7]. The first AstVs were identified by electron microscopy in 1975 in Scotland in fecal samples from infants hospitalized with diarrhea [8]. The number of reports on AstV detection is relatively low, and only one exists for East African children [10]. Emergence of porcine–human AstV recombinants has been reported in regions where pigs and humans live closely, such as our study region, with suspected human to pig transmission, the reverse has not been reported [12]

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