Mutant spectrum of dengue type 1 virus in the plasma of patients from the 2006 epidemic in South China

Summary The aim of the present study was to explore the mutant spectrum of dengue type 1 virus (DENV-1) within individuals during the 2006 dengue epidemic in South China. A 513-bp fragment including most of domain III of the envelope (E) gene was amplified directly from clinical samples, then cloned and sequenced. A total of 89 clones from six patients (range 11–17 clones per patient) were sequenced. Genetic diversity was calculated using MEGA 4 package. The total number of nucleotide mutations was 113 (3.7%) within the sequenced 513-bp E gene, with a range of 15 (3%) to 24 (4.7%) within individual viral populations, harboring more non-synonymous than synonymous mutations. The extent of sequence diversity varied among patients, with the mean diversity ranging from 0.19% to 0.32%, and the mean pairwise p-distance ranging from 0.34% to 0.65%. No genome-defective virus was detected in any clone in this study. Purifying selection may be the main driving force for the intrahost evolution: the mean dN/dS ratio was 0.532. Our findings contribute to the understanding of the genetic variation of DENV-1 in South China.