Reassortment in vivo: driving force for diversity of human rotavirus strains isolated in the United Kingdom between 1995 and 1999

Abstract

The G and P genotypes of 3,601 rotavirus strains collected in the United Kingdom between 1995 and 1999 were determined (M. Iturriza-Gómara et al., J. Clin. Microbiol. 38:4394-4401, 2000). In 95.4% of the strains the most common G and P combinations, G1P[8], G2P[4], G3P[8], and G4P[8], were found. A small but significant number (2%) of isolates from the remaining strains were reassortants of the most common cocirculating strains, e.g., G1P[4] and G2P[8]. Rotavirus G9P[6] and G9P[8] strains, which constituted 2.7% of all viruses, were genetically closely related in their G components, but the P components of the G9P[8] strains were very closely related to those of cocirculating strains of the more common G types (G1, G3, and G4). In conclusion, genetic interaction by reassortment among cocirculating rotaviruses is not a rare event and contributes significantly to their overall diversity.

FIG. 1

Phylogenetic tree constructed from nucleotide sequences of the VP7 gene (nt 417 to 784) of the rotavirus strains G1P[8] and possible reassortants G1P[4] using Clustal and neighbor-joining methods. Laboratory number, rotavirus season, G/P combination, and geographical origin of the strains are indicated. Prototype strains KU and Wa were included (GenBank accession numbers D16343 and K02033, respectively). VP7 sequences derived from G1P[4] strains are underlined. Bootstrap values are indicated in the dendrogram. The calibration bar indicates percent homology.

FIG. 2

Phylogenetic tree constructed from partial nucleotide sequences of the VP7 gene (nt 166 to 782) of the G9 rotavirus strains using the maximum-likelihood method. Nomenclature of the sequences indicates the laboratory number, season of isolation, the G and P types of the strains, and the geographical origin, OB indicates outbreak strains. The VP7 sequence of strain US1205 was provided by C. Kirkwood and that of strain 116E was obtained from GenBank (accession number L14072). Brackets indicate lineages I-A, I-B, II, and III. The calibration bar indicates percent homology. Strains from the United States and India are underlined. Sequences of Mysore strains were obtained from G. Kang, Vellore, India.

FIG. 3

Phylogenetic tree constructed from partial nucleotide sequences of the VP8* fragment of VP4 genes (nt 11 to 887) of the rotavirus strains G1P[8], G3P[8], and G4P[8] and of possible reassortants G2P[8], G8P[8], and G9P[8] using the Clustal method and Megalign. Laboratory number, rotavirus season, G/P combination, and geographical origin of the strains are indicated. Representative strains of the different VP7 G1 lineages (Fig. 2) are indicated (∗). Strains Wa and KU (GenBank/EMBL accession no. M96825 and M2114, respectively) and a P[6] strain (GenBank/EMBL accession no. AF076925) were included for comparisons. Strains whose sequences were obtained from GenBank/EMBL are shaded. The calibration bar indicates percent divergence.

FIG. 4

Phylogenetic tree constructed from nucleotide sequences of VP8* regions of the VP4 genes (nt 11 to 887) of rotavirus strain G2P[4] and possible reassortants G1P[4] and G4P[4], using the Clustal method and Megalign. Laboratory number, rotavirus season, G/P combination, and geographical origin of the strains are indicated. VP4 sequences of two P[4] strains (GenBank/EMBL accession no. U07753 and M32559) and a P[8] strain (Wa, GenBank/EMBL accession no. M96825) were included for comparison (shaded). Possible reassortant strains are underlined. The calibration bar indicates percent divergence.

FIG. 5

Phylogenetic tree constructed from partial nucleotide sequences (nt 232 to 822) of the VP4 gene (corresponding to the hypervariable region of VP8*) of the P[9] rotavirus strains found in the United Kingdom (underlined) and reference human and feline rotavirus P[9] strains, using the Clustal method and Megalign. Nomenclature of the strains indicates the laboratoy number followed by the G/P type and the geographical origin of the isolates for the United Kingdom strains. Sequences of P[9] strains and of a P[8] strain (Wa) were used for comparison. Accession numbers, strains, and hosts from which the P[9] strains were isolated are indicated. The calibration bar indicates percent divergence.