Abstract
West Nile virus (WNV) appeared in the U.S. in 1999 and has since become endemic, with yearly summer epidemics causing tens of thousands of cases of serious disease over the past 14 years. Analysis of WNV strains isolated during the 2006–2007 epidemic seasons demonstrates that a new genetic variant had emerged coincidentally with an intense outbreak in Idaho during 2006. The isolates belonging to the new variant carry a 13 nt deletion, termed ID-Δ13, located at the variable region of the 3′UTR, and are genetically related. The analysis of deletions and insertions in the 3′UTR of two major lineages of WNV revealed the presence of conserved repeats and two indel motifs in the variable region of the 3′UTR. One human and two bird isolates from the Idaho 2006–2007 outbreaks were sequenced using Illumina technology and within-host variability was analyzed. Continued monitoring of new genetic variants is important for public health as WNV continues to evolve.
Highlights
West Nile virus (WNV; family Flaviviridae, genus Flavivirus) is a mosquito-borne virus that is maintained in a bird-mosquito enzootic cycle, with occasional infections of humans, horses and other animals [1]
We have found that some WNV isolates from Idaho and North Dakota collected during the 2006–2007 outbreaks form a separate cluster within genotype SW/WN03, termed MW/WN06 [20]
Twelve isolates from the 2006–2007 outbreaks were completely sequenced and demonstrated nucleotide divergence in the range of 0.35–0.44% compared to NY99 (AF196835)
Summary
West Nile virus (WNV; family Flaviviridae, genus Flavivirus) is a mosquito-borne virus that is maintained in a bird-mosquito enzootic cycle, with occasional infections of humans, horses and other animals [1]. The WNV positive RNA genome is about 11 kb in length, containing a single open reading frame (ORF) encoding one polyprotein processed into three structural and seven nonstructural viral proteins by cellular and viral proteases. It is flanked by 5′- and 3′-untranslated regions (UTR). Which are involved in translation and viral RNA replication, and play an important role in genome packaging [2] Both the 5′ and 3′UTR in the WNV genome form highly conserved secondary and tertiary structures, some elements of which are similar among mosquito-borne flaviviruses. Different functional regions have been described inside both the 5′ and 3′UTR of flaviviruses based on factors such as nucleotide content, degree of sequence conservation, occurrence of repeated sequence motifs, and predicted secondary structure [2,3,4].
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