Multiple clades of Husavirus in South America revealed by next generation sequencing

Abstract

Husavirus (HuV) is an unclassified virus of the order Picornavirales that has already been identified worldwide in various locations. The genetic, epidemiological, and pathogenic characteristics are, however, little understood. In children with acute gastroenteritis, this study used next-generation sequencing to recognize unknown sources of viruses. In particular, 251 fecal samples obtained from individuals were sequenced in southern, northeastern, and northern Brazil. all samples were also analyzed using culture methods and parasitological tests to classify other enteric pathogens such as bacteria, parasites, and viruses. 1.9% of the samples tested positive for HuV, for a total of 5 positive children, with a mean age of 2 year, with three males and two females. Detailed molecular characterization of full genomes showed that Brazilian HuVs' nucleotide divergence is less than 11%. The genetic gap between Brazilian sequences and the closest HuV reported previously, on the other hand, is 18%. The study showed that Brazilian sequences are closely related to the HuV defined in Viet Nam in 2013, further characterization based on phylogenetics. At least two divergent clades of HuV in South America were also seen in the phylogenetic study.

Fig 1. Characteristics of HuV genomes.

(a) Nucleotide similarity matrix of HuV. The similarity of all pairs of sequences are indicated in colors according to the scale in the figure. (b) comparison between the polyprotein of KX673248 and TO-030. The diagram represents the genome of HuV (black line) and the main motifs detected by motif finder analysis (blue areas) using Pfam data base.

Fig 2. Maximum likelihood tree of genome of Posa and Posa-like viruses.

Tree was inferred in FastTree using GTR+ gamma correction and the proportion of invariable sites model as selected by the jModelTest software. Branch support was achieved by approximate likelihood ratio test (aLRT) and is shown in a color scale. HuV identified in this study are highlighted in gray. Hosts in which viruses were identified are indicated in colors (green = pig; brown = rat; pink = bovine; blue = human). Colored rectangles indicate clades of HuV sequences from distinct countries (red = China; Gray = Venezuela; Yellow = Brazil). The geographical location of HuV not included in the clades shown by the colored rectangles is indicated in the name of each sequence. This tree was rooted using the poliovirus sequence NC_002058. Numbers within parenthesis above some branches indicate the genetic divergence in phyloclades of HuV.