Partial nucleotide sequence at the 3′ end of 1D (VP1-encoding) gene of 90 foot-and-mouth
disease virus type O isolates recovered from field outbreaks in India between 1993–9 were
determined. The sequences were compared with each other and reference viruses. The published
sequences of 15 type O isolates recovered from different parts of Asia and one isolate (O1BFS)
from Europe and one from Egypt (O1/Sharquia/Egypt/72) were also included in the analysis
for comparison. On the basis of phylogenetic analysis the viruses could be grouped into four
distinct genotypes (genotypes I–IV). All 90 isolates from India were genotype-I, as were the
reference isolates from Bangladesh, China, Egypt, Iran, Saudi Arabia, Syria and Turkey.
Genotype-I isolates were further subdivided into 16 sub-genotypes. The Indian isolates were
found to be extremely heterogeneous in nature and clustered into 12 different genetic groups.
In genotype-I, the nucleotide sequence difference seen between the isolates was 0–11·6%, while
among the Indian isolates it is 0–8·8%. Viruses of similar genetic groups are circulating in
India, Bangladesh and countries of the Middle East. Genotype-II and -III are represented by
isolates from Lebanon (O1/South Lebanon) and Europe (O1-BFS), respectively. Genotype-IV
is formed by isolates from China, Hong Kong and Taiwan. The present study reveals the
occurrence of viruses belonging to multiple genetic groups over a short period of time and
persistence of single genetic group in the same geographical area over several years. This is
consistent with the endemic nature of the disease in the country.