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

1
Instituto de Ciências Biológicais, Universidade Federal do Pará, Pará 66075-000, Brazil
2
Laboratório de Doenças Entéricas, Centro de Virologia, Instituto Adolfo Lutz, São Paulo 01246-000, Brazil
3
LIM/46, Faculdade de Medicina, Universidade de São Paulo, São Paulo 01246-903, Brazil
4
Secretaria de Saúde do Tocantins, Tocantins 77453-000, Brazil
5
Instituto de Ciências Biológicais, Universidade Federal do Tocantins, Tocantins 77001-090, Brazil
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Laboratório Central de Saúde Pública do Tocantins (LACEN/TO), Tocantins 77016-330, Brazil
7
Faculdade de Medicina do ABC, Santo André 09060-870, Brazil
8
Laboratório de Retrovirologia, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
9
Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, Brazil
10
Department of Obstetrics and Gynecology, Weill Cornell Medicine, 1300 York Avenue New York, NY 10065, USA
11
Blood Systems Research Institute, San Francisco, CA 94143, USA
12
Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(6), 488; https://doi.org/10.3390/v11060488
Received: 7 April 2019 / Revised: 30 April 2019 / Accepted: 3 May 2019 / Published: 29 May 2019
(This article belongs to the Special Issue Human Picornaviruses)
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. View Full-Text
Keywords: parechovirus; picornavirus; virome; recombination; coalescent; Brazil parechovirus; picornavirus; virome; recombination; coalescent; Brazil
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Leal, É.; Luchs, A.; Milagres, F.A.P.; Komninakis, S.V.; Gill, D.E.; Lobato, M.C.A.B.S.; Brustulin, R.; Chagas, R.T.; Abrão, M.F.N.S.; Soares, C.V.D.A.; Villanova, F.; Witkin, S.S.; Deng, X.; Sabino, E.C.; Delwart, E.; Costa, A.C. Recombinant Strains of Human Parechovirus in Rural Areas in the North of Brazil. Viruses 2019, 11, 488.

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