Typing of human rotaviruses: nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure.
BACKGROUND
Rotavirus genotyping is performed by using reverse transcription PCR with type-specific-primers. Because the high rotavirus mutation rate generates an extensive genomic variation, different G-type-specific primer sets are applied in different geographical locations. In Bangladesh, a significant proportion (36.9%) of the rotavirus strains isolated in 2002 could not be G-typed using the routinely used primer set. To investigate the reason why the strains were untypeable, nucleotide sequencing of the VP7 genes was performed.


RESULTS
Four nucleotide substitutions at the G1 primer-binding site of the VP7 gene of Bangladeshi G1 rotaviruses rendered a major proportion of circulating strains untypeable using the routine primer set. Using an alternative primer set, we could identify G1 rotaviruses as the most prevalent genotype (44.8%), followed by G9 (21.7%), G2 (15.0%) and G4 (13.8%).


CONCLUSIONS
Because of the natural variation in the rotaviral gene sequences, close monitoring of rotavirus genotyping methods is important.
Rahman
Mustafizur
M
ICDDR,B: Centre for Health and Population Research, Mohakhali, Dhaka-1212, Bangladesh. mustafizur.rahman@uz.kuleuven.ac.be
Sultana
Rasheda
R
Podder
Goutam
G
Faruque
Abu S G
AS
Matthijnssens
Jelle
J
Zaman
Khalequz
K
Breiman
Robert F
RF
Sack
David A
DA
Van Ranst
Marc
M
Azim
Tasnim
T
D000956:Antigens, Viral / Q000235:genetics*; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D017931:DNA Primers; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D008969:Molecular Sequence Data; D012401:Rotavirus / Q000235:genetics*
D000956:Antigens, Viral; D036022:Capsid Proteins; D017931:DNA Primers; C050779:VP7 protein, Rotavirus