raw sanger sequencing data  (Mendeley Ltd)

Journal: Frontiers in Microbiology

Article Title: Genomic tools for post-elimination measles molecular epidemiology using Canadian surveillance data from 2018–2020

doi: 10.3389/fmicb.2024.1475144

Figure Lengend Snippet: Characteristics of specimens and success of whole genome sequencing. (A–D) Filled bars indicate whole genome sequences achieved, while open or diagonal bars indicate whole genome sequencing failure. Purple color: respiratory specimens; green color: urine. (C) The asterisks indicate a significant difference between mean crossing point (CP) values ( t -test) with a p value <0.0001. (E) Median coverage depth aggregated across 59 measles genomes (WGS-t) generated solely by Illumina sequencing. Depth coverage at each position was obtained through Galaxy using the tool SamTools depth for 59 genomes (samples with termini filled in and sanger patches were excluded from this). Sample termini were trimmed and proportions at each position were determined. Median (solid line) and 25th to 75th percentile (shaded area) values at each nucleotide position were plotted using ggPlot2 in R.

Article Snippet: Consensus sequences of Sanger sequencing data were generated with SeqManPro version 11 software (DNASTAR Lasergene, WI).

Techniques: Sequencing, Generated, Illumina Sequencing

Journal: Frontiers in Microbiology

Article Title: Genomic tools for post-elimination measles molecular epidemiology using Canadian surveillance data from 2018–2020

doi: 10.3389/fmicb.2024.1475144

Figure Lengend Snippet: Epidemiological curve of confirmed measles cases, 2018–2020, by genotype and sequencing coverage. Top panel: all confirmed cases ( n = 143). Middle panel: cases occurring in 2018 ( n = 29). Bottom panel: cases occurring in 2019 ( n = 113). All panels: blue-fill: genotype D8; yellow-fill: genotype B3; no fill: case without sequences. Bottom two panels: solid-fill: N-450, MF-NCR and WGS-t sequences obtained; diagonal pattern: N-450 and MF-NCR sequences obtained; horizontal pattern: N-450 sequence only. Letter indicates outbreak identifier; lack of a letter indicates isolated case. Check mark (√): case was imported. Asterisk (*): case with unknown source.

Article Snippet: Consensus sequences of Sanger sequencing data were generated with SeqManPro version 11 software (DNASTAR Lasergene, WI).

Techniques: Sequencing, Isolation

Journal: Frontiers in Microbiology

Article Title: Genomic tools for post-elimination measles molecular epidemiology using Canadian surveillance data from 2018–2020

doi: 10.3389/fmicb.2024.1475144

Figure Lengend Snippet: Phylogenetic analysis of measles genotype B3 strains detected in Canada, 2018–2020. (A,B) Maximum likelihood phylogenetic trees of the N450, 450 nucleotides, [(A) 27 sequences] and MF-NCR, 1018 nucleotides, [(B) 21 sequences] loci with 1,000 bootstrap replicates. Bold face indicates the genotype B3 reference sequence [N450 only (A)]. Italics are international sequences obtained from GenBank and for the N450 tree (A) represent WHO-named strains. Thick branch edges correspond to bootstrap values ≥0.7. (D) Maximum clade credibility phylogenetic tree of WGS-t sequences ( n = 21) inferred with BEAST2. The time scale, in years, is at the top. Thick branch edges correspond to posterior values ≥0.7. Brackets with letters correspond to outbreaks and/or phylogenetic clusters analyzed in depth. Meta-data is provided in four columns to the right of the trees. A star symbol in the first column indicates a sequence from a case without a source identified. A check mark in the second column indicates that the case was considered imported. The two color strips indicate association with an outbreak and the MeaNS distinct sequence ID (DSId) assigned to the N450 sequence (including named strain, where applicable) with the legend provided in panel (C). The bracket present in all trees indicates the clade including the MVi/Marikina City.PHL/10.18 N450 named strain. (D) Shades of grey are added to the outbreak strip to denote the identification of related cases as a result of the sequence analysis. High resolution, interactive versions are available at: https://itol.embl.de/shared/GzTsavRiNVS9 .

Article Snippet: Consensus sequences of Sanger sequencing data were generated with SeqManPro version 11 software (DNASTAR Lasergene, WI).

Techniques: Sequencing, Stripping Membranes