A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals a novel NS5 mutation.

Dengue virus currently causes 50-100 million infections annually. Comprehensive knowledge about the evolution of Dengue in response to selection pressure is currently unavailable, but would greatly enhance vaccine design efforts. In the current study, we sequenced 187 new dengue virus serotype 3 (DENV-3) genotype III whole genomes isolated from Asia and the Americas. We analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype. In order to analyze the phylogenetic dynamics of DENV-3 during outbreak periods; we incorporated datasets of 48 and 11 sequences spanning two major outbreaks in Venezuela during 2001 and 2007-2008, respectively. Our phylogenetic analysis of newly sequenced viruses shows that subsets of genomes cluster primarily by geographic location, and secondarily by time of virus isolation. DENV-3 genotype III sequences from Asia are significantly divergent from those from the Americas due to their geographical separation and subsequent speciation. We measured amino acid variation for the E protein by calculating the Shannon entropy at each position between Asian and American genomes. We found a cluster of seven amino acid substitutions having high variability within E protein domain III, which has previously been implicated in serotype-specific neutralization escape mutants. No novel mutations were found in the E protein of sequences isolated during either Venezuelan outbreak. Shannon entropy analysis of the NS5 polymerase mature protein revealed that a G374E mutation, in a region that contributes to interferon resistance in other flaviviruses by interfering with JAK-STAT signaling was present in both the Asian and American sequences from the 2007-2008 Venezuelan outbreak, but was absent in the sequences from the 2001 Venezuelan outbreak. In addition to E, several NS5 amino acid changes were unique to the 2007-2008 epidemic in Venezuela and may give additional insight into the adaptive response of DENV-3 at the population level.

Mosquito vectors of West Nile virus during an epizootic outbreak in Puerto Rico.

The purpose of this investigation was to identify the mosquito (Diptera: Culicidae) vectors of West Nile virus (WNV; family Flaviviridae, genus Flavivirus) during an epizootic WNV outbreak in eastern Puerto Rico in 2007. In June 2006, 12 sentinel chicken pens with five chickens per pen were deployed in six types of habitats: herbaceous wetlands, mangrove forests, deciduous forests, evergreen forests, rural areas, and urban areas. Once WNV seroconversion in chickens was detected in June 2007, we began trapping mosquitoes using Centers for Disease Control and Prevention (CDC) miniature (light/CO2-baited) traps, CMT-20 collapsible mosquito (CO2- and ISCA SkinLure-baited) traps, and CDC gravid (hay infusion-baited) traps. We placed the CDC miniature traps both 2-4 m and >30 m from the chicken pens, the collapsible traps 2-4 m from the pens, and the gravid traps in backyards of houses with sentinel chicken pens and in a wetland adjacent to an urban area. We found numerous blood-engorged mosquitoes in the traps nearest to the sentinel chickens and reasoned that any such mosquitoes with a disseminated WNV infection likely served as vectors for the transmission of WNV to the sentinels. We used reverse transcriptase-polymerase chain reaction and isolation (C636) on pools of heads, thoraxes/ abdomens, and legs of collected blood-engorged mosquitoes to determine whether the mosquitoes carried WNV. We detected WNV-disseminated infections in and obtained WNV isolates from Culex nigripalpus Theo (minimum infection rate [MIR] 1.1-9.7/1,000), Culex bahamensis Dyar and Knab (MIR 1.8-6.0/1,000), and Aedes taeniorhynchus (Wied.) (MIR 0.34-0.36/1,000). WNV was also identified in and isolated from the pool of thoraxes and abdomens of Culex quinquefasciatus Say (4.17/1,000) and identified in one pool of thoraxes and abdomens of Culex habilitator Dyar and Knab (13.39/1,000). Accumulated evidence since 2002 suggests that WNV has not become endemic in Puerto Rico.

Epidemic dynamics revealed in dengue evolution.

Dengue is an emerging tropical disease infecting tens of millions of people annually. A febrile illness with potentially severe hemorrhagic manifestations, dengue is caused by mosquito-borne viruses (DENV-1 to -4) that are maintained in endemic transmission in large urban centers of the tropics with periodic epidemic cycles at 3- to 5-year intervals. Puerto Rico (PR), a major population center in the Caribbean, has experienced increasingly severe epidemics since multiple dengue serotypes were introduced beginning in the late 1970s. We document the phylodynamics of DENV-4 between 1981 and 1998, a period of dramatic ecological expansion during which evolutionary change also occurs. The timescale of viral evolution is sufficiently short that viral transmission dynamics can be elucidated from genetic diversity data. Specifically, by combining virus sequence data with confirmed case counts in PR over these two decades, we show that the pattern of cyclic epidemics is strongly correlated with coalescent estimates of effective population size that have been estimated from sampled virus sequences using Bayesian Markov Chain Monte Carlo methods. Thus, we show that the observed epidemiologic dynamics are correlated with similar fluctuations in diversity, including severe interepidemic reductions in genetic diversity compatible with population bottlenecks that may greatly impact DENV evolutionary dynamics. Mean effective population sizes based on genetic data appear to increase prior to isolation counts, suggesting a potential bias in the latter and justifying more active surveillance of DENV activity. Our analysis explicitly integrates epidemiologic and sequence data in a joint model that could be used to further explore transmission models of infectious disease.

Unusual productivity of Aedes aegypti in septic tanks and its implications for dengue control.

Increased DEN-2 virus transmission in Puerto Rico during 2005 prompted the implementation of a rapid intervention programme to suppress Aedes aegypti (L.) (Diptera: Culicidae) emergence, which in turn lead to the discovery of previously unknown breeding sites underground. Initially, the following control measures were applied in Playa/Playita (PP), a town of 1,400 households, to all areas where the number of pupae per person exceeded the expected threshold for dengue transmission; all containers likely to be aquatic habitats were turned over and containers too large to turn were treated with 1 p.p.m. methoprene. The impact of these interventions was evaluated by comparing the number of resting adult mosquitoes (by backpack aspiration and sweepnetting in bedrooms) pre-intervention, with numbers at 3 and 5 weeks post-intervention, and by evaluating pupal density at 4 weeks post-intervention in PP and in a nearby town, Coqui (CO; 1500 households), which was not treated. The pre-intervention and post-intervention densities of resting Ae. aegypti adults were significantly larger in the intervention town, although the density of pupae in surface containers was low and similar in both towns at 4 weeks post-intervention. At 3 weeks post-intervention, the density of resting adults decreased by only 18% of pre-intervention levels, but returned to pre-intervention levels 5 weeks after treatment. By contrast, the density of resting adults in CO steadily decreased to 48% and 61%, at 3 and 5 weeks after the initial surveys, respectively. Geographical Information Systems identified significant clustering of adult mosquitoes, which led to the discovery of underground aquatic habitats (septic tanks) that were producing large numbers of Ae. aegypti and Culex quinquefasciatus (Say) in the treated town. We calculated that septic tanks could produce > 18 000 Ae. aegypti and approximately 170 000 Cx quinquefasciatus adults per day. Septic tanks are likely to be common and widespread in suburban and rural Puerto Rico, where, apparently, they can contribute significantly to the maintenance of island-wide dengue virus endemicity.

Telomere shortening and cell cycle arrest in Trypanosoma brucei expressing human telomeric repeat factor TRF1.

Trypanosoma brucei has telomeres composed of 15 kb tracts of TTAGGG repeats that end in 3' overhangs and form t-loops. This structure is also present in mammalian cells and is thought to reflect the presence of telomere-binding proteins. The human TTAGGG repeat-binding factor TRF1 binds to telomeres and regulates their length. We attempted to interfere with the normal function of trypanosome telomeres by expressing human TRF1 in T. brucei. TRF1 localized to telomeres in cultured procyclic (midgut-stage) trypanosomes with great fidelity, but not in bloodstream-stage trypanosomes. Procyclic trypanosomes expressing high levels of TRF1 for extended periods of time exhibited shortening and increased size heterogeneity of their telomeres and the cell cycle was arrested in G1-S. These effects were not detected in cells expressing a TRF1 mutant incapable of binding to TTAGGG repeats. We argue that TRF1 displaces putative endogenous trypanosome telomere-binding proteins, not yet identified, and affects telomeres in ways that reflect its role as a negative regulator of telomere length in human cells.

t-loops at trypanosome telomeres.

Mammalian telomeres form large duplex loops (t-loops) that may sequester chromosome ends by invasion of the 3' TTAGGG overhang into the duplex TTAGGG repeat array. Here we document t-loops in Trypanosoma brucei, a kinetoplastid protozoan with abundant telomeres due to the presence of many minichromosomes. These telomeres contained 10-20 kb duplex TTAGGG repeats and a 3' TTAGGG overhang. Electron microscopy of psoralen/UV cross-linked DNA revealed t-loops in enriched telomeric restriction fragments and at the ends of isolated minichromosomes. In mammals, t-loops are large (up to 25 kb), often comprising most of the telomere. Despite similar telomere lengths, trypanosome t-loops were much smaller (approximately 1 kb), indicating that t-loop sizes are regulated. Coating of non-cross-linked minichromosomes with Escherichia coli single-strand binding protein (SSB) often revealed 3' overhangs at both telomeres and several cross-linked minichromosomes had t-loops at both ends. These results suggest that t-loops and their prerequisite 3' tails can be formed on the products of both leading and lagging strand synthesis. We conclude that t-loops are a conserved feature of eukaryotic telomeres.

Stable expression of mosaic coats of variant surface glycoproteins in Trypanosoma brucei.

The paradigm of antigenic variation in parasites is the variant surface glycoprotein (VSG) of African trypanosomes. Only one VSG is expressed at any time, except for short periods during switching. The reasons for this pattern of expression and the consequences of expressing more than one VSG are unknown. Trypanosoma brucei was genetically manipulated to generate cell lines that expressed two VSGs simultaneously. These VSGs were produced in equal amounts and were homogeneously distributed on the trypanosome surface. The double-expressor cells had similar population doubling times and were as infective as wild-type cells. Thus, the simultaneous expression of two VSGs is not intrinsically harmful.