General genome features of the <i>V. cholerae</i> strain IEC224.

<p>General genome features of the <i>V. cholerae</i> strain IEC224.</p

Genome of the Latin American epidemic <i>Vibrio cholerae</i> marker phage.

<p>Graphical representation of the genes that correspond to the genome of a bacteriophage that is present in all the Latin American epidemic strains tested in this study. The CDS are the blue arrows that are pointed towards the direction they are coded in the genome. The putative protein functions are listed below, with a corresponding number to its localization in the image. (Images generated in the Geneious software – reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Drummond1" target="_blank">[24]</a>)</p

The altered sucrose phenotype of the strain IEC224 is due to a frame-shift mutation.

<p>The characteristic phenotype of <i>Vibrio cholerae</i> is to produce shiny gold colonies after 48 h incubation on TCBS agar (as pictured on the right side). The strain IEC224 fails to ferment sucrose and colonies remain green (pictured on the left). The only genomic difference between a functioning sucrose fermenter and the IEC224 strain is an insertion in the gene coding for the sucrose-specific IIB domain of the PTS system, which is shown above in the aligned fragments of the mutated IEC224 gene and the functioning N16961 gene. A diagram with the metabolic role of this protein is illustrated in the center, showing that it is a carrier that selectively transports sucrose into the cell and phosphorylates it to signal downstream reactions. A model of the functioning protein structure is shown on the top left, as well as a model for the altered structure can be seen in the top right. (Model generated by PHYRE², following the pipeline of reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Kelley1" target="_blank">[25]</a>)</p

Classification of the <i>V. cholerae</i> Latin American epidemic phage in the dsDNA Phage Proteomic Tree.

<p>Neighbor Joining comparison of all the proteins of 733 dsDNA phages grouped the Latin American epidemic phage with the genus of LUZ24-Like viruses. These are phages from the Podoviridae family that conform a separate cluster, which is different from all other phages classified in the tree. The group containing these phages is highlighted pink. On the right is a table with the color keys of the phages that are colored in the tree according to their ICTV classification <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-King1" target="_blank">[36]</a>.</p

Variants of the Latin American epidemic phage in sequenced V. cholerae genomes.

<p>The assembly of sequencing reads from 16 other El Tor <i>V. cholerae</i> genomes from Latin America, and their putative ancestor strain from Angola, revealed the presence of the Latin American epidemic phage in all strains. The genomic variations were in 8 sites numbered from bases 0 through 49,291 (right). Collectively these strains formed 10 variants of the phage, with the variant A being the most abundant. This variant is shared with the putative ancestor strain. All strains accumulated at least one SNP after 1992.</p

Circular plot of the IEC224 genome.

<p>The green arrow of ring I represents chromosome I, while the blue arrow represents chromosome II. Red and yellow traces on ring II represent, respectively rRNAs and tRNAs. Rings III and V show the predicted CDS, respectively clockwise and counter-clockwise. Ring IV represents putative mobile regions – elements associated with virulence and pandemic strains are colored red: <i>Vibrio</i> pathogenicity island I and II (VPI-1 and VPI-2); cholera toxin phage (CTX), <i>Vibrio</i> seventh pandemic islands I and II (VSP-1, and VSP2). Genomic islands predicted by the study in reference 38 (GI I-X) are blue, the O antigen gene cluster is black, the Latin American marker phage is orange, and the super integron is green. The Ring VI contains the GC plot, where areas with GC above range are dark green, while GC below range is light green. Ring VII contains the GC skew (G−C/G+C), in which regions above average are colored yellow, while below average are colored green. (Image generated in the DNA Plotter software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Carver1" target="_blank">[38]</a>)</p

A similar bacteriophage is present in strains of two other Vibrio species.

<p>The <i>Vibrio vulnificus</i> strain MO6 24/O and the <i>Vibrio parahaemolyticus</i> AN-503 both contain a similar bacteriophage inserted in the same repeat sequence of the membrane alanine aminopeptidase (pepN) gene which is shown in the center of the top figure. The Artemis Comparison Tool (ACT) alignment shows nucleotide matches as red lines, inverted repeats as blue lines, and gaps as white spaces. The lower image shows alignments were the corresponding genes are represented as blue arrows. Above these alignments, there is a pair-wise similarity representation, showing identical matches as dark vivid green and similarity grades down into lighter green tones. Mismatches are red. (Images generated in ACT <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Carver2" target="_blank">[39]</a>, and Geneious <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037283#pone.0037283-Drummond1" target="_blank">[24]</a> softwares)</p

Epidemiological Data: Numbers of suspected ZIKV cases and suspected microcephaly cases per state and per epidemiological week.

Contains 1) CSV file with number suspected ZIKV cases from January 2015 to the end of December 2015; 2) CSV file with number of suspected microcephaly cases from January 2015 to the first week of January 2016. Numbers correspond to suspected microcephaly cases at week 20 of pregnancy; 3) CSV file with codes of state of residence and municipality of residence in Brazil; and 4) R scripts for correlation analysis described in SI Section 1.5

Sequence data details and alignments for dataset A and B.

Contains (1) table with accession numbers, isolate names, cell passage history, publication details, country/location of sampling, sampling dates and (2) Fasta format sequence alignments of datasets A and B

BEAST XML input file used for genetic analysis.

BEAST XML input file used to generate Figure 3 under a strict clock model, a Bayesian skyline coalescent prior and a CTMC prior on the clock rate