MicroRNA levels are modulated in Aedes aegypti after exposure to Dengue-2.

To define microRNA (miRNA) involvement during arbovirus infection of Aedes aegypti, we mined deep sequencing libraries of Dengue type 2 (DENV2)-exposed mosquitoes. Three biological replicates for each timepoint [2, 4 and 9 days post-exposure (dpe)] and treatment group allowed us to remove the outliers associated with sample-to-sample variability. Using edgeR (R Bioconductor), designed for use with replicate deep sequencing data, we determined the log fold-change (logFC) of miRNA levels [18-23 nucleotides (nt)]. The number of significantly modulated miRNAs increased from ≤ 5 at 2 and 4 dpe to 23 unique miRNAs by 9 dpe. Putative miRNA targets were predicted by aligning miRNAs to the transcriptome, and the list was reduced to include the intersection of hits found using the Miranda, PITA, and TargetScan algorithms. To further reduce false-positives, putative targets were validated by cross-checking them with mRNAs reported in recent DENV2 host response transcriptome reports; 4076 targets were identified. Of these, 464 gene targets have predicted miRNA-binding sites in 3' untranslated regions. Context-specific target functional groups include proteins involved in transport, transcriptional regulation, mitochondrial function, chromatin modification and signal transduction processes known to be required for viral replication and dissemination. The miRNA response is placed in context with other vector host response studies by comparing the predicted targets with those of transcriptome studies. Together, these data are consistent with the hypothesis that profound and persistent changes to gene expression occur in DENV2-exposed mosquitoes.

Partial genetic characterization of West Nile virus strains, New York State, 2000.

We analyzed nucleotide sequences from the envelope gene of 11 West Nile (WN) virus strains collected in New York State during the 2000 transmission season to determine whether they differed genetically from each other and from the initial strain isolated in 1999. The complete envelope genes of these strains were amplified by reverse transcription-polymerase chain reaction. The resulting sequences were aligned, the genetic distances were computed, and a phylogenetic tree was constructed. Ten (0.7%) of 1,503 positions in the envelope gene were polymorphic in one or more sequences. The genetic distances were 0.003 or less. WN virus strains circulating in 2000 were homogeneous with respect to one another and to a strain isolated in 1999.

High-throughput detection of West Nile virus RNA.

The recent outbreaks of West Nile virus (WNV) in the northeastern United States and other regions of the world have made it essential to develop an efficient protocol for surveillance of WNV. In the present report, we describe a high-throughput procedure that combines automated RNA extraction, amplification, and detection of WNV RNA. The procedure analyzed 96 samples in approximately 4.5 h. A robotic system, the ABI Prism 6700 Automated Nucleic Acid workstation, extracted RNA and set up reactions for real-time reverse transcription (RT)-PCR in a 96-well format. The robot extracted RNA with a recovery as efficient as that of a commercial RNA extraction kit. A real-time RT-PCR assay was used to detect and quantitate WNV RNA. Using in vitro transcribed RNA, we estimated the detection limit of the real-time RT-PCR to be approximately 40 copies of RNA. A standard RT-PCR assay was optimized to a sensitivity similar to that of the real-time RT-PCR. The standard assay can be reliably used to test a small number of samples or to confirm previous test results. Using internal primers in a nested RT-PCR, we increased the sensitivity by approximately 10-fold compared to that of the standard RT-PCR. The results of the study demonstrated for the first time that the use of an automated system for the purpose of large-scale viral RNA surveillance dramatically increased the speed and efficiency of sample throughput for diagnosis.

Enzootic transmission of deer tick virus in New England and Wisconsin sites.

To determine whether rodents that are intensely exposed to the deer tick-transmitted agents of Lyme disease, human granulocytic ehrlichiosis, and human babesiosis are also exposed to deer tick virus (DTV), we assayed serum samples from white-footed mice (Peromyscus leucopus) and meadow voles (Microtus pennsylvanicus) in sites densely infested by deer ticks. To conduct serosurveys, we developed an enzyme-linked immunosorbent assay (ELISA) and Western blot assay by cloning, expressing, and purifying a portion of the DTV envelope glycoprotein (DTV rE) for use as test antigen. Sera from mice and voles trapped in Massachusetts, Rhode Island, and Wisconsin were screened by ELISA for IgG reactive to DTV rE. Samples that were positive or borderline by ELISA were subsequently analyzed by immunoblotting. Samples reactive in both assays were considered to be positive. Three percent of 264 mouse samples collected from sites in Rhode Island, 3.8% of 52 samples from mice trapped in Wisconsin, and 3.9% of 282 samples collected from mice trapped on Nantucket Island, MA were positive. No samples from either Great Island, MA, or voles from any study site were reactive. A reverse transcriptase-polymerase chain reaction yielded molecular evidence of DTV infecting questing adult deer ticks in sites where seroreactive mice were trapped, but not from ticks collected where serologic evidence of virus perpetuation was absent. White-footed mice appear to be exposed to DTV in certain sites where other deer tick-borne agents perpetuate. This virus may be maintained in the same enzootic cycle.

A focus of deer tick virus transmission in the northcentral United States.

We screened salivary glands from adult deer ticks collected near Spooner and Hayward, Wisconsin, to determine whether deer tick virus, a recently described flavivirus, occurs with other tickborne agents in the upper Midwest. Intraacinar inclusions suggestive of replicating virus were detected in 4 (4.6%) of 87 ticks. The virus was isolated by suckling-mouse inoculation.