Isolation and phylogenetic analysis of Mucambo virus (Venezuelan equine encephalitis complex subtype IIIA) in Trinidad

Abstract

In the 1950s and 1960s, alphaviruses in the Venezuelan equine encephalitis (VEE) antigenic complex were the most frequently isolated arboviruses in Trinidad. Since then, there has been very little research performed with these viruses. Herein, we report on the isolation, sequencing, and phylogenetic analyses of Mucambo virus (MUCV; VEE complex subtype IIIA), including 6 recently isolated from Culex (Melanoconion) portesi mosquitoes and 11 previously isolated in Trinidad and Brazil. Results show that nucleotide and amino acid identities across the complete structural polyprotein for the MUCV isolates were 96.6-100% and 98.7-100%, respectively, and the phylogenetic tree inferred for MUCV was highly geographically- and temporally-structured. Bayesian analyses suggest that the sampled MUCV lineages have a recent common ancestry of approximately 198 years (with a 95% highest posterior density (HPD) interval of 63-448 years) prior to 2007, and an overall rate of evolution of 1.28 x 10(-4) substitutions/site/yr.

Figure 1

Total number of mosquitoes collected per trap per month and total number of Cx. portesi mosquitoes collected per trap per month between July 2007 and July 2008 in the Aripo Savannah Scientific Reserve (ASSR). Graph labels indicate which viruses were isolated from the mosquito collections.

Figure 2

Midpoint rooted maximum likelihood phylogeny based on a 3,777 nt fragment of the 18 MUCV isolates used in the study. Taxon labels include date of isolation, location of isolation, and virus strain (pool number); accession numbers are shown in Table 1. Amino acid changes that defined each cluster are shown at the relevant nodes. Amino acids numbers shown refer to the complete structural polypeptide. Isolates that were derived in this study are shown in red. Bootstrap values above 95% are indicated on the tree, and the major clades are numbered 1–3. The scale bar indicates percent divergence. *positively selected amino acid changes.

Figure 3

Midpoint rooted maximum likelihood phylogeny based on a 3,435 nt fragment of all VEEV subtypes available from GenBank. Taxon labels include: subtype, date of isolation, location of isolation, and virus strain (pool number). GenBank accession numbers are shown in Table 1. Bootstrap values above 95% are indicated on the tree, and the scale bar indicates percent divergence. Subtype IIIA isolates that were sequenced during this study are shown in blue.