Two different <i>Xylella fastidiosa</i> strains circulating in Italy: phylogenetic and evolutionary analyses

<p><i>Xylella fastidiosa</i>, a bacterial species infecting a broad range plants, includes five subspecies, <i>fastidiosa, multiplex, pauca, mulberry and sandyi.</i> In Europe, <i>Xylella</i> was isolated in olive trees in southern Italy (Apulia region) during the year 2013. The aim of the present study was to apply phylogenetic and evolutionary analysis to trace the possible origin and way of the entrance of <i>Xylella fastidiosa</i> in Italy. All the genomes available for <i>Xylella fastidiosa</i> spp were downloaded from NCBI. A phylogeographic analysis was performed using BEAST. <i>X. fastidiosa</i> strains belonging to <i>X. fastidiosa</i> subsp. <i>pauca</i> and subsp. <i>sandyi</i> have been reported to infect olive trees and coffee plants, respectively. The phylogeographic analysis also revealed and confirmed these two different ways of provenience <i>X. fastidiosa</i> subsp. <i>pauca</i> from Costa Rica and <i>X. fastidiosa</i> subsp <i>sandyi</i> from California Phylogeny have been an important tool to validate and support the recent hypothesis for <i>X. fastidiosa pauca</i> provenience.</p

Phylogenesys and homology modeling in Zika virus epidemic: food for thought

<p>Zika virus (ZIKV) is an emerging Flavivirus that have recently caused an outbreak in Brazil and rapid spread in several countries. In this study, the consequences of ZIKV evolution on protein recognition by the host immune system have been analyzed. Evolutionary analysis was combined with homology modeling and T-B cells epitope predictions. Two separate clades, the African one with the Uganda sequence, as the most probable ancestor, and the second one containing all the most recent sequences from the equatorial belt were identified. Brazilian strains clustered all together and closely related to the French Polynesia isolates. A strong presence of a negatively selected site in the envelope gene (<i>Env</i>) protein was evidenced, suggesting a probable purging of deleterious polymorphisms in functionally important genes. Our results show relative conservancy of ZIKV sequences when envelope and other non-structural proteins (NS3 and NS5) are analyzed by homology modeling. However, some regions within the consensus sequence of NS5 protein and to a lesser extent in the envelope protein, show localized high mutation frequency corresponding to a considerable alteration in protein stability. In terms of viral immune escape, envelope protein is under a higher selective pressure than NS5 and NS3 proteins for HLA class I and II molecules. Moreover, envelope mutations that are not strictly related to T-cell immune responses are mostly located on the surface of the protein in putative B-cell epitopes, suggesting an important contribution of B cells in the immune response as well.</p

Additional file 1 of MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

The user guide for MISSEL software, which is a pdf file with all the instructions for the user to run the software. (PDF 891 KB

Phylogenetic tree of the 63 HEV genotype 3 isolates from Bulgaria.

<p>A red circle marks Bulgarian sequences; for each sequence, the town/village (Dup: Dupnica; Jam: Jambol; Iht: Ihtiman; Karl: Karlovo; Paz: Pazardzhik; Plev: Pleven; Plov: Plovdiv; Sam: Samokov; Sof: Sofia; Var: Varna) and the isolation year (2013, 2014, 2015) are reported after the sequence ID. Reference genotype 3 strains with known subtype were included in the analysis and are marked as shown in the box. For each reference sequence, genotype and subtype (e.g. 3e), Accession number, host (hu: human; sw: swine), country and year of detection are reported. Significant bootstrap values (>70) are reported.</p

Geographical localization of the characterized HEV genotype 3 strains in Bulgarian towns/villages.

<p>Cases are represented by a colour coded square, according to the box included in the figure. The Haskovo town, in which a patient infected by HEV genotype 1 was identified, is also reported.</p

Phylogenetic tree of the 64 Bulgarian HEV sequences.

<p>A red circle marks Bulgarian sequences; for each sequence, the town/village (Dup: Dupnica; Jam: Jambol; Iht: Ihtiman; Karl: Karlovo; Paz: Pazardzhik; Plev: Pleven; Plov: Plovdiv; Sam: Samokov; Sof: Sofia; Var: Varna) and the isolation year (2013, 2014, 2015) are reported after the sequence ID. Reference strains with known genotype (1, 2, 3 and 4) were included in the analysis and are marked as shown in the box. For each reference sequence, genotype/subtype (e.g. 3e), Accession number, host (hu: human; sw: swine), country and year of detection are reported. Significant bootstrap values (>70) are reported.</p

Onset date of cases, from Plovdiv and Pazardzhik, harbouring cluster A and cluster B sequences, 3e subtype.

<p>Cases from cluster A and B (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198045#pone.0198045.g002" target="_blank">Fig 2</a>) are indicated according to the box included in the figure.</p

Virus-specific CPE in simian kidney cell line LLC-MK2.

<p>Non-inoculated cells (A) and cells inoculated with plasma specimen 1225/2014, 8 days post-inoculation (B). Perinuclear vacuoles are evident. Original images taken at 400x magnification; insets at approx. 800X.</p

Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data - Fig 2

<p><b>A) Transmission electron micrograph detail of a ZIKV-infected LLC-MK2 cell.</b> The large arrow points out an area containing typical flavivirus-induced paracrystalline arrays/convoluted membranes in a ZIKV-infected LLC-MK2 cell. (B) Transmission electron micrograph detail of ZIKV-infected LLC-MK2 cell. Crystalline arrays of virus cores (large arrow) are shown in association with membrane vesicles.</p

Maximum-Likelihood tree of ZIKV complete genome sequences.

<p>The tree was obtained using the best fitting nucleotide substitution model (TN93+G) selected by a hierarchical likelihood ratio test. Branches are drawn to scale in nucleotide substitutions per site according to the bar at the bottom of the tree. Percentage bootstrap (out of 1000 replicates) support values are given along branches. The Haiti sequence is in bold.</p