Volume 16, Number 5—May 2010
Dispatch
Unusual Assortment of Segments in 2 Rare Human Rotavirus Genomes
Table 1
Nucleotide identity of 11 genome segments of 2 human rotavirus strains, Italy, 1994 and 1996*
Gene encoding | Cutoff value | Genotype of PAH136/96 | Identity of PAH136/96 against indicated strains |
Genotype of PAI58/96 | Identity of PAI58/96 against indicated strains |
Identity between PAH136/96 and PAI58/96 | ||
---|---|---|---|---|---|---|---|---|
Prototypes† | GenBank strains‡ | Prototypes† | GenBank strains‡ | |||||
VP1 | 83 | R2 | 83.7 (RF) | 94.6 (Hun5) | R2 | 94.9 (RF) | 95.7 (NCDV) | 83.2 |
VP2 | 84 | C2 | 90.9 (RF) | 98 (Hun5) | C2 | 89.9 (RF) | 93.9 (Chubut) | 91.6 |
VP3 | 81 | M2 | 89.2 (RF) | 92.9 (PA169) | M2 | 90.2 (RF) | 95.8 (PA169) | 92.6 |
VP4 | 80 | P[9] | 95.6 (AU-1) | (AU-1) | P[9] | 95.3 (AU-1) | (AU-1) | 94.6 |
VP6 | 85 | I2 | 86.9 (RF) | 95.5 (Hun5) | I2 | 91.8 (RF) | 92.4 (UKtc) | 86 |
VP7 | 80 | G3 | 90.1 (AU-1) | 94.2 (Cat2) | G3 | 90.5 (AU-1) | 95.9 (Cat2) | 95.7 |
NSP1 | 79 | A3 | 93.6 (AU-1) | 94.8 (Chubut) | A3 | 92.9 (AU-1) | 94.1 (Chubut) | 92.1 |
NSP2 | 85 | N1 | 91.4 (Wa) | 99.1 (Cat2) | N2 | 90.1 (RF) | 91.4 (NCDV) | 79 |
NSP3 | 85 | T6 | 94.7 (RF) | 97 (MG6) | T6 | 95.9 (RF) | (RF) | 97.5 |
NSP4 | 85 | E2 | 87 (DS-1) | 92.5 (PA169) | E2 | 87.5 (DS-1) | 98 (PA169) | 92.3 |
NSP5 | 91 | H3 | 96.8 (RF) | 97.3 (111/05) | H3 | 98 (RF) | 98.8 (Cat2) | 96.3 |
*Numeric values given as % nt. Percentage nucleotide cutoff values and genotype proposed by Matthijnssens et al. (8). VP, structural protein; NSP, nonstructural protein.
†Prototype genotype strains used by Matthijnssens et al. (8).
‡ Strains that shared the highest nucleotide identity in the cognate genes with the Italian G3P[9] rotaviruses.
References
- Estes KM, Kapikian AZ. Rotaviruses. In: Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B, et al., editors. Fields virology. 5th ed. Philadelphia: Lippincott Williams and Wilkins; 2007. p. 1917–74.
- Iturriza-Gomara M, Desselberger U, Gray J. Molecular epidemiology of rotaviruses: genetic mechanisms associated with diversity. In: Desselberger U, Gray J, editors. Viral gastroenteritis. Amsterdam: Elsevier Science; 2003. p. 317–44.
- Martella V, Banyai K, Matthijnssens J, Buonavoglia C, Ciarlet M. Zoonotic aspects of rotaviruses. Vet Microbiol. 2010;140:246–55. DOIPubMedGoogle Scholar
- Matthijnssens J, Bilcke J, Martella V, Ciarlet M, Bànyai K, Rahman M, Rotavirus disease and vaccination: impact on genotype diversity. Future Microbiol. 2009;4:1303–13. DOIPubMedGoogle Scholar
- De Grazia S, Giammanco GM, Martella V, Ramirez S, Colomba C, Cascio A, Rare AU-1–like G3P[9] human rotaviruses with a Kun-like NSP4 gene detected in children with diarrhea in Italy. J Clin Microbiol. 2008;46:357–60. DOIPubMedGoogle Scholar
- Santos N, Hoshino Y. Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine. Rev Med Virol. 2005;15:29–56. DOIPubMedGoogle Scholar
- Nakagomi T, Matsuda Y, Ohshima A, Mochizuki M, Nakagomi O. Characterization of a canine rotavirus strain by neutralization and molecular hybridization assays. Arch Virol. 1989;106:145–50. DOIPubMedGoogle Scholar
- Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1–like and bovine rotavirus strains. J Virol. 2008;82:3204–19. DOIPubMedGoogle Scholar
- Matthijnssens J, Ciarlet M, Rahman M, Attoui H, Banyai K, Estes MK, Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol. 2008;153:1621–9. DOIPubMedGoogle Scholar
- Nakagomi O, Nakagomi T. Interspecies transmission of rotaviruses studied from the perspective of genogroup. Microbiol Immunol. 1993;37:337–48.PubMedGoogle Scholar
- Gollop R, Nakagomi O, Silberstein I, Shulman LM, Greenberg HB, Mendelson E, Three forms of AU-1 like human rotaviruses differentiated by their overall genomic constellation and by the sequence of their VP8*. Arch Virol. 1998;143:263–77. DOIPubMedGoogle Scholar
- Potgieter AC, Page NA, Liebenberg J, Wright IM, Landt O, van Dijk AA. Improved strategies for sequence-independent amplification and sequencing of viral double-stranded RNA genomes. J Gen Virol. 2009;90:1423–32. DOIPubMedGoogle Scholar
- Matthijnssens J, Potgieter CA, Ciarlet M, Parreno V, Martella V, Banyai K, Are human P[14] rotavirus strains the result of interspecies transmissions from sheep or other ungulates that belong to the mammalian order Artiodactyla? J Virol. 2009;83:2917–29. DOIPubMedGoogle Scholar
- Tsugawa T, Hoshino Y. Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans. Virology. 2008;380:344–53. DOIPubMedGoogle Scholar
- De Grazia S, Martella V, Colomba C, Cascio A, Arista S, Giammanco GM. Genetic characterization of G3 rotaviruses detected in Italian children in the years 1993–2005. J Med Virol. 2009;81:2089–95. DOIPubMedGoogle Scholar