SC2 Mutation Frequency Calculator (SMFC)

A covSonar Utility tool to detect characteristic and signature mutations based on mutation profiles. This tool allows the calculation of mutation frequencies for a user-defined timeframe for specific lineages.

1. Setup

1.1 Prerequisites

Conda and python are necessary. CovSonar is the key tool to extract mutation profiles from. It has a database with consensussequences sequenced in the course of the pandemic assigned to lineages which can be queried.

1.2 Install

Proceed as follows to install SMFC:

# download the repository to the current working directory using git 
git clone https://github.com/rki-mf1/sc2-mutation-frequency-calculator.git
# build the custom software environment using conda [recommended]
conda env create -n sonar -f sc2-mutation-frequency-calculator/smfc.env.yml
# activate the conda evironment if built 
conda activate smfc

1.3 Options/--help

option	value(s)	note
--acc	one or more genome accessions (e.g. NC_045512.2)
--lineage	one or more pangolin lineages (e.g. B.1.1.7)
--zip	one or more zip codes (e.g. 10627)	zip codes are dynamically extended to the right side, e.g. 033 matches to all zip codes starting with 033
--date	one or more dates or date ranges (e.g. 2021-01-01)	single dates are formatted as YYYY-MM-DD while date ranges can be defined by YYYY-MM-DD:YY-MM-DD (from:to)
--submission_date	one or more dates or date ranges (e.g. 2021-01-01)	single dates are formatted as YYYY-MM-DD while date ranges can be defined by YYYY-MM-DD:YY-MM-DD (from:to)
--lab	one or more labs (e.g. L1)
--source	one or more data sources (e.g. DESH)
--collection	one or more data collections (e.g. RANDOM)
--technology	one or more sequencing technologies (e.g. Illumina)
--platform	one or more sequencing platforms (e.g. MiSeq)
--chemistry	one or more sequencing chemistries (e.g. Cleanplex)
--software	one software tool used for genome reconstruction (e.g. covPipe)
--version	one software tool version used for genome reconstruction (e.g. 3.0.5)	needs --software defined
--material	one or more sample materials (e.g. 'nasal swap')
--min_ct	minimal ct value (e.g. 20)
--max_ct	maximal ct value (e.g. 20)

1.4 Default

Mutation frequency matrix (figure)

*Parent Lineage: *Number of sequences detected: *Labdiversity:

How a frequency matrix can be created:

# download the repository to the current working directory using git 
git clone https://github.com/rki-mf1/sc2-mutation-frequency-calculator.git
# build the custom software environment using conda [recommended]
conda env create -n sonar -f sc2-mutation-frequency-calculator/smfc.env.yml
# activate the conda evironment if built 
conda activate smfc

2. Examples

2.1 variant-specific pcr test-design

signature mutations can be used to determine which mutations acuretly define a lineage (nothing else) which can be used to test for specific lineage in a variant-specific pcr test-design: (figure)

How signature mutations can be calculated:

# download the repository to the current working directory using git 
git clone https://github.com/rki-mf1/sc2-mutation-frequency-calculator.git
# build the custom software environment using conda [recommended]
conda env create -n sonar -f sc2-mutation-frequency-calculator/smfc.env.yml
# activate the conda evironment if built 
conda activate smfc

2.2 consensus^2 for representing a lineage

How signature mutations can be calculated:

# download the repository to the current working directory using git 
git clone https://github.com/rki-mf1/sc2-mutation-frequency-calculator.git
# build the custom software environment using conda [recommended]
conda env create -n sonar -f sc2-mutation-frequency-calculator/smfc.env.yml
# activate the conda evironment if built 
conda activate smfc

3. Best practice

3.1 Inputformat

Lineage
BA.5.2.1
BA.4.6
BE.1

Mutation
S:D46Y
ORF1ab:S367G
N:A679D

3.2 Presence of overlap in the data

See #4 (comment)

4. Contribution

covSonar has been very carefully programmed and tested, but is still in an early stage of development. You can contribute to this project by reporting problems or writing feature requests to the issue section under https://github.com/rki-mf1/sc2-mutation-frequency-calculator/issues

Your feedback is very welcome!

5. FAQ

characteristic vs signature mutations?

figure

consensus^2?

Other then the conventional consensus method consensus^2 is used to build a robust and represenative consensus of a number of samples for a lineage by introducing the most frequent mutations (default cut-off:10) in a timeframe in a reference genome (default: Wuhan).

Could be used for primer selection (and building phylogenetic trees): figure