Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Oct 25;9:15343. doi: 10.1038/s41598-019-51326-2

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Workflow to identify and select diagnostic lineage/sub-lineage SNP for the development of the molecular assays. (A) We used a publicly available variant list containing 34,167 SNPs from 219 MTBC global strains. (B) First, we performed a parsimony-based approach to map and obtain 2,056 specific SNPs markers for all lineages, and 1,337 for all L4 sub-lineages. In the figure, the specific SNPs for lineage 4 in the phylogeny are marked with a circle. (C) Then, candidate SNPs were selected according to their functional change (we used synonymous SNPs in essential genes, whenever possible), and tested in-silico against a global dataset of 4,495 MTCB strains. (D) Finally, we developed seven specific primers to implement in the real-time PCR-HRM molecular assay, and two genomic regions for Sanger sequencing approach.