All known field isolates of enterovirus 71 (EV71) can be divided into three distinct genogroups (A,
B, C) and 10 subgenogroups (A, B1-5, C1-4) based on VP1 gene sequences. We examined VP1
gene sequences of 10, 12 and 11 EV71 strains isolated in peninsular Malaysia during the outbreaks
of hand, foot and mouth disease in 1997, 2000 and 2005 respectively. Four EV71 strains isolated in
the hand, foot and mouth disease outbreak of 2006 in Sarawak (Malaysian Borneo) were included
to describe their genetic relationship.
Four subgenogroups (C1, C2, B3 and B4) of EV71 co-circulated and caused the outbreak of hand,
foot and mouth disease in peninsular Malaysia in 1997. Two subgenogroups (C1 and B4) were noted
to cause the outbreak in 2000. In the 2005 outbreak, besides EV71 strains of subgenogroup C1,
EV71 strains belonged to subgenogroup B5 were isolated but formed a cluster which was distinct
from EV71 strains of the subgenogroup B5 isolated in 2003. The four EV71 strains isolated from
clinical specimens of patients with hand, foot and mouth disease in the Sarawak outbreak in early
2006 also belonged to subgenogroup B5. Phylogenetic analysis of the VP1 gene sequences showed
that the four Sarawak EV71 isolates belonged to the same cluster as the EV71 strains that were
isolated in peninsular Malaysia as early as May 2005. The data suggested that the EV71 strains
causing the outbreak in Sarawak could have originated from peninsular Malaysia.