Using an unbiased metagenomic sequencing approach, we report here the first complete genome sequence of ZIKV isolated from a clinical semen sample. Sequence data for the virus isolated from a clinical semen sample align well with other sequences of ZIKV from the outbreak, including those from the Caribbean region, where the patient acquired the infection. The characterization of ZIKV isolated from semen samples will help improve our understanding of possible viral polymorphisms resulting from infection in different cellular environments. The isolated virus will be available imminently from the National Collection of Pathogenic Viruses and the European Virus Archive.
In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n = 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods.
ZIKV encodes a polyprotein that is processed to produce three structural and seven nonstructural (NS) proteins. We investigated the evolution of the viral polyprotein in ZIKV and in related flaviviruses (DENV, Spondweni virus, and Kedougou virus). After accounting for saturation issues, alignment uncertainties, and recombination, we found evidence of episodic positive selection on the branch that separates DENV from the other flaviviruses. NS1 emerged as the major selection target, and selected sites were located in immune epitopes or in functionally important protein regions. Three of these sites are located in an NS1 region that interacts with structural proteins and is essential for virion biogenesis. Analysis of the more recent evolutionary history of ZIKV lineages indicated that positive selection acted on NS5 and NS4B, this latter representing the preferential target. All selected sites were located in the N-terminal portion of NS4B, which inhibits interferon response. One of the positively selected sites (26M/I/T/V) in ZIKV also represents a selection target in sylvatic DENV2 isolates, and a nearby residue evolves adaptively in JEV. Two additional positively selected sites are within a protein region that interacts with host (e.g. STING) and viral (i.e. NS1, NS4A) proteins. Notably, mutations in the NS4B region of other flaviviruses modulate neurovirulence and/or neuroinvasiveness. These results suggest that the positively selected sites we identified modulate viral replication and contribute to immune evasion. These sites should be prioritized in future experimental studies. However, analyses herein detected no selective events associated to the spread of the Asian/American ZIKV lineage.
The southern house mosquito Cx. quinquefasciatus from Rio de Janeiro was not competent to transmit local strains of ZIKV. Thus, there is no experimental evidence that Cx. quinquefasciatus likely plays a role in the ZIKV transmission. Consequently, at least in Rio, mosquito control to reduce ZIKV transmission should remain focused on Ae. aegypti.
Here, we report the crystal structure of the full‐length ZIKV nonstructural protein 1 (NS1), a major host‐interaction molecule that functions in flaviviral replication, pathogenesis, and immune evasion. Of note, a long intertwined loop is observed in the wing domain of ZIKV NS1, and forms a hydrophobic “spike”, which can contribute to cellular membrane association. For different flaviviruses, the amino acid sequences of the “spike” are variable but their common characteristic is either hydrophobic or positively charged, which is a beneficial feature for membrane binding. Comparative studies with West Nile and Dengue virus NS1 structures reveal conserved features, but diversified electrostatic characteristics on both inner and outer faces. Our results suggest different mechanisms of flavivirus pathogenesis and should be considered during the development of diagnostic tools.
Zika virus infection acquired during pregnancy was associated with congenital microcephaly. We describe two cases of ZIKV infection in the 36th week of pregnancy whose fetuses had preserved head circumference at birth and findings of subependymal cysts and lenticulostriate vasculopathy in postnatal imaging. These represent the first signs of congenital brain injury acquired due to ZIKV in the third trimester.
Showing the closest link yet between Zika virus and fetal brain injury in an animal model that closely resembles humans, researchers today described brain abnormalities in the fetus of a macaque experimentally infected during the late stage of her pregnancy.
In other developments, Thailand reported several more Zika cases, many of them linked to a cluster in Bangkok, as the number of infections in Singapore grew steadily. In Florida, health officials denied a newspaper report charging problems with Zika reporting, and Broward County began aerial spraying withan organic pesticide as a prevention step.
Given the huge burden that Chikungunya and Zika fevers impose to public health in the affected countries and the lack of effective interventions against them, the aim of this work was to evaluate the antiviral potential of bovine lactoferrin (bLf) – an iron-binding glycoprotein with broad-spectrum antimicrobial properties – in both CHIKV and ZIKV infections. The general antiviral activity of bLf was assessed by plaque assays, and the inhibitory effects of the protein on specific stages of virus infecion was evaluated by immunofluorescence and nucleic acid quantification assays. Our data show that bLf exerts a dose-dependent strong inhibitory effect on the infection of Vero cells by the aforementioned arboviruses, reducing their infection efficiency in up to nearly 80%, with no significant cytotoxicity, and such antiviral activity occurs at the levels of binding and replication of the virus particles. Taken together, these findings reveal that bLf antimicrobial properties are extendable to CHIKV and ZIKV, underlining a generic inhibition mechanism that can be explored to develop a potential strategy against their infections.
A rapid point-of-care test is needed to detect the virus, especially at low resource settings. Methodology/Principal Findings: In this report, we describe the development of a reverse transcription isothermal recombinase polymerase amplification (RT-RPA) assay for the identification of ZIKV. RT-RPA assay was portable, sensitive (21 RNA molecules), and rapid (3-15 minutes). No cross-reactivity was detected to other flaviviruses, alphaviruses and arboviruses. Compared to real-time RT-PCR, the diagnostic sensitivity was 92% while the specificity was 100%. Conclusions/Significance: The developed assay is a promising platform for rapid point of need detection of ZIKV in low resource settings and elsewhere (e.g. during mass gathering).
The full-length genome sequence including non-coding regions of a South American ZIKV isolate from a patient with classical symptoms will support efforts to develop genetic tools for this virus. Detection of sfRNA that counteracts interferon responses is likely to be important for further understanding of pathogenesis and virus-host interactions.