Novel West Nile virus lineage 1a full genome sequences from human cases of infection in north-eastern Italy, 2011

Abstract

During 2008-2009, several human cases of WNV disease caused by an endemic lineage 1a strain were reported in areas surrounding the Po river in north-eastern Italy. Since 2010, cases have been recorded in nearby northern areas, where, in 2011, both lineage 1a and 2 were detected. We describe here two new WNV complete genome sequences from human cases of WNV infection occurring in 2011 in the Veneto Region. Phylogenetic analysis showed that both genome sequences belonged to lineage 1a and were related to WNV strains of the Western Mediterranean subtype. The novel WNV genomes had high nucleotide and amino acid sequence divergence from each other and from the WNV strain circulating in Italy in 2008-2009. The presence of different WNV strains in a relatively small geographical area is a novel finding with unpredictable impact on human disease that requires further investigation.

Large Human Outbreak of West Nile Virus Infection in North-Eastern Italy in 2012

“…In 2012, most human cases of WNV infection occurred in north-eastern Italy, in areas that had been affected also in 2010 and 2011 (Figure 1) [13,23,35]. However, in 2012, a markedly higher incidence of WNV infection was observed than in previous years, with 25 cases of WNND, 17 cases of WNF, 14 WNV RNA-positive blood donors, and further two cases of asymptomatic WNV infection identified by active surveillance of subjects at risk of WNV exposure.…”

“…Whole genome sequencing of these two isolates (GenBank accession numbers JX556213.1 and KC954092, respectively) demonstrated 99.9% nucleotide sequence identity with each other and with the WNV Livenza strain that was fully sequenced in the same area in 2011 (GenBank accession number JQ928174.1) [23]. Comparison among viral polyprotein amino acid sequences demonstrated only neutral changes (e.g., Val118Ile and Val113Ile in the capsid and Val45Ile in the NS5 protein) that probably did not affect viral fitness or pathogenicity.…”

“…In Italy, circulation of different WNV genotypes of both lineage 1 and lineage 2 has been documented, even in the same area [23,24,25], and outbreaks in humans have been reported since 2008, when the first human cases of WNND were identified in areas surrounding the Po river in Northern Italy [26,27]. In the following years, cases of WNND were diagnosed in a larger area near the Po river [28,29,30], while sero-prevalence studies in blood and organ donors [31,32] and veterinary and entomological investigation indicated viral activity also in other regions [33].…”

“…In addition, based on the evidence of widespread WNV circulation in its territory, Veneto region implemented a special surveillance program for WNF [34], besides surveillance for WNND according to the national plan. While in 2008–2010 human cases of infection were detected only in northeastern Italy and were caused by WNV lineage 1 genotypes [28,29,30,35], in 2011, in addition to northeastern Italy [23], cases were notified for the first time also in Marche region (Central Italy) and in Sardinia island and included infections with WNV lineage 2 [25,36]. …”

Isolation of West Nile Virus from Urine Samples of Patients with Acute Infection

“…This laboratory diagnosis is challenging because the WNV load in blood is generally very low or undetectable at the time of symptom onset and because WNV antibodies crossreact with other flaviviruses, thus requiring confirmation by neutralization assays. A relevant improvement to the diagnosis of WNV infection was recently provided by WNV RNA testing in urine, since viral RNA is detectable in urine at a higher load and for a longer time than in blood or CSF (3)(4)(5)(6)(7)(8)(9)(10)(11). In addition, the isolation of infectious WNV in cell cultures from urine samples has been reported in some patients with acute infection (8)(9)(10).…”