Full genomic analysis of human rotavirus strain B4106 and lapine rotavirus strain 30/96 provides evidence for interspecies transmission

Abstract

The Belgian rotavirus strain B4106, isolated from a child with gastroenteritis, was previously found to have VP7 (G3), VP4 (P[14]), and NSP4 (A genotype) genes closely related to those of lapine rotaviruses, suggesting a possible lapine origin or natural reassortment of strain B4106. To investigate the origin of this unusual strain, the gene sequences encoding VP1, VP2, VP3, VP6, NSP1, NSP2, NSP3, and NSP5/6 were also determined. To allow comparison to a lapine strain, the 11 double-stranded RNA segments of a European G3P[14] rabbit rotavirus strain 30/96 were also determined. The complete genome similarity between strains B4106 and 30/96 was 93.4% at the nucleotide level and 96.9% at the amino acid level. All 11 genome segments of strain B4106 were closely related to those of lapine rotaviruses and clustered with the lapine strains in phylogenetic analyses. In addition, sequence analyses of the NSP5 gene of strain B4106 revealed that the altered electrophoretic mobility of NSP5, resulting in a super-short pattern, was due to a gene rearrangement (head-to-tail partial duplication, combined with two short insertions and a deletion). Altogether, these findings confirm that a rotavirus strain with an entirely lapine genome complement was able to infect and cause severe disease in a human child.

FIG. 1.

Analysis of rearranged NSP5 gene of HRV strain B4106. (A) Dot plot analysis, comparing the nucleotide sequence of the LRV 30/96 NSP5 gene with the duplicated NSP5 gene of B4106. (B) Schematic representation of the duplication, the hypothetical intermediate, and the subsequent insertion and deletion events. For further details, see the text. (C) Comparison of the duplicated region with the homologous coding sequence of B4106.

FIG. 2.

Phylogenetic dendrograms constructed with the structural rotaviral protein sequences of VP1, VP2, VP3, VP4, VP6, and VP7. Accession numbers can be found in in the supplemental material. Bootstrap values (2,000 replicates) greater than 50 are shown. The size of the triangles is an indication for the amount of sequences they represent. Hu, human; La, lapine; Bo, bovine; Po, porcine; Si, simian; Eq, equine; Ca, canine; Fe, feline; Capr, caprine; Rh, rhesus; Mu, murine; Av, avian. For the construction of the VP4 amino acid dendrogram representatives of all known P-types were used, except P[22], P[23], and P[25] because no complete amino acid sequences of these P-genotypes are available. For the VP7 amino acid dendrogram, the sequence of B4106, and representatives of all known G-types were used. For simplicity, not all G3 rotaviruses are depicted completely, one G3 subcluster containing only murine rotaviruses was designated G3/Mu, and a second subcluster (G3/Hu-Po-Bo) contained human, porcine, and bovine rotavirus strains. Lapine subclusters, including those containing HRV strain B4106, are boxed.

FIG. 3.

Phylogenetic dendrograms of the nonstructural rotaviral protein sequences of NSP1, NSP2, NSP3, NSP4, and NSP5. Accession numbers can be found in supplemental data. Bootstrap values (2,000 replicates) above 50 are shown. The size of the triangles is an indication for the amount of sequences they represent. For the NSP4 amino acid dendrograms, the sequence of B4106, and strains representing the six (A to F) established genogroups were used. Hu, human, La, lapine; Bo, bovine; Po, porcine; Si, simian; Eq, equine; Ca, canine; Fe, feline; Capr, caprine; Rh, rhesus; Mu, murine; Av, avian. Lapine subclusters, including those containing HRV strain B4106, are boxed.