Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil.

Élcio Leal,Adriana Luchs,Maria De Fátima Neves Dos Santos Abrão Abrão,Shirley Vasconcelos Komninakis,Flávio Augusto De Pádua Milagres,Rogério Togisaki Das Chagas,Fabiola Villanova,Antônio Charlys Da Costa,Danielle Elise Gill,Rafael Brustulin,Márcia Cristina Alves Brito Sayão Lobato,Cássia Vitória De Deus Alves Soares,Eric Delwart,Xutao Deng,Steven S Witkin,Ester Cerdeira Sabino

doi:10.3390/v11060488

Abstract

We characterized the 24 nearly full-length genomes of human parechoviruses (PeV) from children in the north of Brazil. The initial phylogenetic analysis indicated that 17 strains belonged to genotype 1, 5 to genotype 4, and 1 to genotype 17. A more detailed analysis revealed a high frequency of recombinant strains (58%): A total of 14 of our PeV-As were chimeric, with four distinct recombination patterns identified. Five strains were composed of genotypes 1 and 5 (Rec1/5); five strains shared a complex mosaic pattern formed by genotypes 4, 5, and 17 (Rec4/17/5); two strains were composed of genotypes 1 and 17 (Rec1/17); and two strains were composed of genotype 1 and an undetermined strain (Rec1/und). Coalescent analysis based on the Vp1 gene, which is free of recombination, indicated that the recombinant strains most likely arose in this region approximately 30 years ago. They are present in high frequencies and are circulating in different small and isolated cities in the state of Tocantins. Further studies will be needed to establish whether the detected recombinant strains have been replacing parental strains or if they are co-circulating in distinct frequencies in Tocantins.

Highlights

The Picornaviridae family, whose natural hosts are vertebrates [1,2,3], is currently divided into 47 genera
We found that some previously reported PeV-As are recombinant strains
In our survey of 238 individuals affected by acute gastroenteritis, we found PeV-A in 24 patients

Summary

Introduction

The Picornaviridae family, whose natural hosts are vertebrates [1,2,3], is currently divided into 47 genera (http://www.picornaviridae.com). PeV-A infections have been associated with gastroenteritis, most are thought to be asymptomatic or cause only mild illness [4,9,11,12,13]. PeV-A of genotype 3 has been associated with severe infections in neonates [4]. Phylogenetic analysis, based on the VP1 gene, identified at least 19 different genotypes distributed globally [3,10,14,15]. Some studies identified breakpoint clustering around the junction between the capsid and nonstructural genes [3,16]. This pattern of recombination appears to be common in many members of the Picornaviridae family [18,19]

Methods

Results

Conclusion