Comparative Analysis of NS3 Sequences of Temporally Separated Dengue 3 Virus Strains Isolated from Southeast Asia

Abstract

By a combination of PCR and direct-cycle sequencing using consensus primers, we analyzed approximately 400-bp fragments within the NS3 genes of twenty-one dengue virus type 3 strains isolated from five neighboring Southeast Asian countries at different time intervals from 1956 to 1992. The majority of base disparities were silent mutations, with few predicted amino acid substitutions, thus emphasizing the strict conservation of the NS3 gene. Phylogenetic trees constructed on the basis of these nucleotide differences revealed distinct but related clusters of strains from the Philippines, Indonesia, and strains from Singapore and Malaysia of the 1970s and early 1980s, while the Thai cluster was relatively more distant. This genetic relationship was compatible with that proposed by other workers who have studied other dengue 3 virus genes such as E, M and prM. However, we observed that the more recent, epidemic-associated dengue 3 strains from Singapore and Malaysia of the late 1980s and early 1990s were more closely related to the Thai cluster, implying their evolution from the latter, and emphasizing the importance of viral spread via increasing travel within the Southeast Asian area and elsewhere. Nucleotide sequence analysis of the NS3 genes of dengue viruses can serve to advance the understanding of the epidemiology and evolution of these viruses.

Phylogenetic relationship of dengue virus type 3 isolated in Brazil and Paraguay and global evolutionary divergence dynamics

“…Previous studies analyzing the C, PrM, E and NS3 genes have shown that DENV-3 segregated into four genotypes [13,14,24,25]. In this study, we have found that DENV-3 segregated in the same genotypes I, II and III as shown in the previous studies mentioned above, analyzing either the entire ORF or each protein gene sequence.…”

Microevolution and virulence of dengue viruses

“…The tree also supports the previous hypothesis (Wang et al, 2000) that sylvatic strains, one from Malaysia in this case, evolved earlier from a hypothetical ancestor shared by all dengue viruses, which is why most sylvatic viruses are basal (branch off first) in all ML-estimated trees. However, only one dengue type 1 virus has been isolated under these ecological conditions (from a sentinel monkey) (Rudnick, 1965); it is also unclear if this virus cycle still exists, as field work has ceased and other isolates from Malaysia are now from urban epidemics and involve other genotypes (Chow et al, 1994). It is clear, however, that this sylvatic genotype, albeit represented by one isolate, is of low epidemiological importance to humans, as it is not causing detectable disease in humans and there is no evidence that reintroduc-tion from a sylvatic cycle is required for persistence of dengue transmission year-round.…”

Differential display RT‐PCR analysis of ECV304 endothelial‐like cells infected with dengue virus type 2 reveals messenger RNA expression profiles of multiple human genes involved in known and novel roles

“…In addition to this immune enhancement theory, viral virulence factors such as the envelope protein display considerable divergence within each of the four serotypes, in turn subdivided into several subtypes and numerous strains [Worobey et al, 1999]. This heterogeneity is attributed to the high mutation rate of RNA viruses as well as genetic recombination when different virus strains co-infect and replicate within the same host cell [Chow et al, 1994[Chow et al, , 1998]. The appearance of DHF in the Americas has been linked to the introduction of virulent genotypes of dengue virus type 2 [Rico-Hesse et al, 1997].…”