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
![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 .](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_1582/pmc11611582/pmc11611582__fmicb-15-1475144-g003.jpg)