GenBank accession numbers for each of the gene segments of strains Dhaka6, KTM368, Dhaka22 01, Matlab36 02, YM, OSU, and Gottfried are shown in Technical Appendix 1. Complete genome sequences of 3 human rotavirus strains (Dhaka6, KTM368, and Matlab36 02) were determined.
Complete nucleotide sequences of all 11 RNA segments of strain J19 have been determined (9 ).
Phylogenetic analyses showed that all 11 genome segments of strain 17237 were most closely related to strains of either feline-like human or feline origin.
The VP1, VP6, NSP2, and NSP4 genome segments of strain 17237 were closely related to BA222, clustering in the R2, I2, N1, and E2 genotypes, respectively.
In addition, for the VP1 VP2 and NSP1 NSP5 gene segments of strain Dhaka22 01, high identities (range 97.9%–100%) at the nucleotide level were found between strain Dhaka22 01 and the other human Wa-like G11 strains.
The second source of support comes from the fact that our phylogenetic analyses confirmed that each of the 11 gene segments of strain 17237 was more closely related to BA222-like RVA strains than to bovine or bovine-like RVA strains.
To clarify the host-dependent characteristics of influenza A virus sequences with BLSOM, di-, tri-, or tetranucleotide frequencies in eight genome segments of virus strains were summed up for each strain, and BLSOM was constructed with the summed frequency for each strain.
The NSP2 gene segment of strain 17237 clustered in the N1 genotype and was distantly related to typical human Wa-like RVA strains.
Because the sequence of the VP6 gene segment of strain KTM368 did not belong to any of the established VP6 I genotypes, it was submitted to the RCWG for appropriate genotype assignment.
For the VP3 gene segment, identities between strain Dhaka22 01 and strains KTM368, Dhaka6, and Matlab36 02 were low (range 86.3% 86.7%), and the VP3 gene segment of strain Dhaka22 01 was closely related to strains in the human M1 subcluster (99.6% identity with strain Dhaka12 03).
Because the genes located in this segment of strain Lai (and Fiocruz L1-130) were predicted to encode glycosyltransferases and enzymes catalyzing sugar activation, the genetic variations of this segment is likely to cause the variations in LPS composition/structure of the tested strains.
