Genetic variability of the SARS-CoV-2 JN.1 lineage

Genetic variability of the SARS-CoV-2 JN.1 lineag

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

Italian QX genotype population dynamics.

<p>Upper figure: Mean relative genetic diversity (Ne x t) of the Italian GI-19 population over time. The results of the ten independent runs have been color-coded. Lower Figure: Mean, median and upper and lower 95HPD values are reported for each run.</p

Phylogeographical mapping of CCHF S gene sequences .

<p>The bubblegrams show the frequency of gene flows (migrations) to/from ten European countries (same code as that used in Figure 1) . The surface of each circle is proportional to the percentage of observed migrations in the ML genealogy. The migrations were inferred using a modified version of the Slatkin and Maddison algorithm.</p

Italian QX genotype migration paths.

<p>Well supported migration paths (i.e. BF>20) among Italian regions, which have been colour coded) are depicted. The arrows indicate the directionality of the process while the edge colour is proportional to the base-10 logarithm of the migration rate.</p

Bayesian maximum clade credibility (MCC) tree of the 202 Italian influenza A(H3N2) virus HA gene sequences.

<p>Different clusters and the Italian clades are indicated by different colours. The numbers on the internal nodes represent posterior probabilities. Amino acid substitutions characterising a particular branch are indicated. The scale at the bottom of the tree represents the calendar months between the tMRCA of the tree root and the most recent samples (March 2012).</p

Significant non-zero CCHFV migration rates worldwide.

<p>Rates supported by a BF of >3 are highlighted: the relative strength of the support is indicated by the colour of the lines (from dark red = weak to light red = strong). Dotted lines indicate non-significant linkages. The map was reconstructed using SPREAD (see Methods). The numbers indicate the mean estimated year in which the virus entered the area. </p

QX genotype MRCA and evolutionary rate.

<p>Upper figure: Boxplot (left) and Densityplot of the MRCA posterior probability. Lower figure: Boxplot (left) and Densityplot of the mean evolutionary rate (expressed in base-10 logarithm) posterior probability. Results have been estimated performing ten independent runs based on sequences randomly sampled from the international database. The 95HPD intervals are reported for both figures.</p

The maximum clade credibility (MCC) tree of CCHFV S gene sequences.

<p>The branches are coloured on the basis of the most probable location of the descendent nodes (A=Africa, AL=Albania, ASC=Central Asia, BU=Bulgaria, CH=China, G=Greece, KO=Kosovo, MO=Middle East, PA=Pakistan, T=Turkey). The numbers on the internal nodes indicate significant posterior probabilities (pp>0.8), and the scale at the bottom of the tree represents the number of years before the last sampling time (2010). The main geographical clades (genotypes) have been highlighted.</p