Temporal and spatial alterations in mutant swarm size of St. Louis encephalitis virus in mosquito hosts

Abstract

St. Louis encephalitis virus (SLEV; Flaviviridae; Flavivirus) is a member of the Japanese encephalitis serocomplex and a close relative of West Nile virus (WNV). Although SLEV remains endemic to the US, both levels of activity and geographical dispersal are relatively constrained when compared to the widespread distribution of WNV. In recent years, WNV appears to have displaced SLEV in California, yet both viruses currently coexist in Texas and several other states. It has become clear that viral swarm characterization is required if we are to fully evaluate the relationship between viral genomes, viral evolution, and epidemiology. Mutant swarm size and composition may be particularly important for arboviruses, which require replication not only in diverse tissues but also divergent hosts. In order to evaluate temporal, spatial, and host-specific patterns in the SLEV mutant swarm, we determined the size, composition, and phylogeny of the intrahost swarm within primary mosquito isolates from both Texas and California. Results indicate a general trend of decreasing intrahost diversity over time in both locations, with recent isolates being highly genetically homogeneous. Additionally, phylogenic analyses provide detailed information on the relatedness of minority variants both within and among strains and demonstrate how both geographic isolation and seasonal maintenance have shaped the viral swarm. Overall, these data generally provide insight into how time, space, and unique transmission cycles influence the SLEV mutant swarm and how understanding these processes can ultimately lead to a better understanding of arbovirus evolution and epidemiology.

Fig. 1

Phylogenetic-tree reconstruction of intrahost variants of individual isolates, using RAxML. The isolate number is followed by either the mutant number or ‘con’, indicating the consensus sequence. Duplicate sequences have been removed for this analysis. (A) Texas isolates from the same sample cluster together. Numbers on the right indicate the year of sample collection. (B) California isolates from different samples (obtained at different time points and different locations) grouped together. Multiples following the year of sample collection indicate how many independent samples are part of the same group; i.e. the top group consists of three samples taken in 2003, two taken in 2001, two in 2000, and one in 1993.

Fig. 2

Nucleotide diversity vs. isolation year, not corrected for phylogeny. (A) Texas, (B) California.

Fig. 3

Phylogenetically independent contrasts (PICs) of nucleotide diversity vs. PICs of isolation year. The trees used to calculate PICs are shown in Fig. S1. (A) Texas, (B) California.