Genomics and Bioinformatics approach to Study of the SARS-COV-2 (COVID-19) Mutations: Variant analysis and detection

7 min readApr 24, 2021

Genomics and Bioinformatics approach to Study of the SARS-COV-2 (COVID-19) Mutations: Variant analysis and detection Pine biotech Mohit Mazumder Omicslogic — Genomics and Bioinformatics approach to Study of the SARS-COV-2 (COVID-19) Mutations: Variant analysis and detection

Seeing the weekly and the monthly global infection & death rate it seems like we are into the “Lockdown year-2”. In this era, where the people of the world are more connected than ever, the challenges that we have faced are entirely new!

Viruses are unique among all living creatures — parasites that are not even alive without a host. Viral infections can go on undetected or bring a lethal outcome to a complex host like a human in a matter of days. Looking at the devastating effect of recent pandemics, it’s evident that our understanding of these biological entities is still limited. A community of scientists, researchers, clinicians, and doctors are working every day to help us understand more and develop ways to tackle the outbreak.

Even though with many advances we are still struggling to unlock all the mysteries that this coronavirus has brought to us and one of the major reasons is the access as well as the scale. However not all is lost, the fastest ever vaccine initiatives and seeing so many successful strategies has made us realize that maybe we can outsmart this new threat. Like any other cells, the virus undergoes evolution and natural selection, and being an outsider facing challenges encountering the immunity system it mutates or “evolves”, let's find out more.

To learn more about the variant and to understand the three well-characterized variants, please take a look at the article posted by visual capitalists from where the text and images are adopted.

What is a Variant?

To infect someone, a virus takes over a host cell and uses it to replicate itself. But nature isn’t perfect, and sometimes, mistakes are made during the replication process — those mistakes are called mutations. A virus with one or more mutations is referred to as a variant. Most of the time, variants do not affect a virus’s physical structure, and in those instances, they eventually disappear. However, there are certain cases when a mutation impacts part of a virus’s genetic makeup that does change its behavior.

what are the covid-19 variants pine biotech mohit mazumder south Africa Britain India West Bengal New Delhi — Visit: https://www.visualcapitalist.com/the-3-major-covid-19-variants/

According to the U.S. Centers for Disease Control (CDC) a change in behavior can alter:

Rate of transmission
Mortality
Ability to potentially infect someone with natural or vaccine-induced immunity

Preliminary research has detected some of these changes in the three major COVID-19 variants — B.1.1.7, B.1.351, and P.1.

There are approximately 48 countries with reported cases, and research suggests several of the existing COVID-19 vaccines may not be as effective against this variant. Being a Bioinformatics company and having experience working on similar projects over the last few years, we have started to work on samples that have been collected for patients and wastewater plants.

After being able to complete those projects, we thought about all of the researchers and students, and faculty who might benefit from this research and by learning the analysis and interpretation could scientifically contribute. Please find the details of this specialization workshop designed as an initiative to help the research community.

*Hands-on training to understand the logic behind the analysis of variants of concern and develop a workflow for variant reporting using curated data from clinical and environmental sequencing.*

Who is this program for?

This hands-on workshop series (Omicslogic program) is designed for Students & faculty and beginners, biologists, clinicians, and researchers who are interested in advancing their understanding of the logic behind the analysis of variants of concern and develop a workflow for variant reporting using curated data from clinical and environmental sequencing. The program will not require any background in coding, bioinformatics, or biostatistics, however, we will speak about topics related to cell and molecular biology and utilize terminology coming from biostatistics and data science domains.

https://edu.tbioinfo.com/genomic-analysis-of-sars-cov-2-hands-on-training

Program Overview:

In this program, we will learn about the way the SARS-COV-2 pandemic has transformed our appreciation of genomics and bioinformatics. understand how genomic data analysis tools can help identify specific viral strains, understand multiple sequence alignment, phylogenetic analysis, and the significance of mutations in the context of viral protein structure and function. We will further discuss the viral genomes of Covid-19, genes, proteins, and the virology of the disease. We will discuss how the data and the various analysis tools can help in the detection of viral genomes, compare and distinguish between viral strains, identify the impact of mutations on the functionality of viral proteins, and discuss the virology from the standpoint of data.

For free resources and webinars and to learn about training program pre-registration form: https://edu.tbioinfo.com/genomic-analysis-of-sars-cov-2-hands-on-training

Topics

NGS data processing and quality control
Genomic Sequence analysis for Viral Genomes
Analysis of phylogenetic relationships by strain, population, host
Analysis of variants — functional, structural, and association
Structural analysis to understand the function of variants

This online program includes:

As a participant of this program, you will have access to instructor support, access to asynchronous training resources, curated datasets for hands-on practice. You will also have the chance to evaluate our big data analysis platform (T-BioInfo) which enables our participants to go through online materials and do the analysis without having to invest in high-end computational infrastructure.

Bioinformatics pipelines and workflows are essential in the analysis of genomic data generated by next-generation sequencing (NGS) using the analytical and coding platform and utilizing R statistical language that has a rich library, tools, and functions available at Bioconductor and Github we have prepared tutorials and omics logic training resources to guide participants to create a report to analyze variants using genomic sequencing data, cloud processing, and custom R scripts.

Sequence to Structure -> Function and Future directions (Vaccination & monitoring)

Interpretation of the molecular-level effect of missense variants is challenging and requires an investigation of amino acid substitutions in the context of protein structure and function. Answers to questions like ‘Is a variant changing a site involved in key molecular interactions that has a key correlation with the change in function?’, or ‘Is a variant changing an amino acid located at the protein core or part of a cluster of known pathogenic mutations in 3D?’ are crucial (4). In the last session we will learn to visualize and analyze missense variants in protein sequence and structural space using molecular visualization tools such as chimera (5) and pymol (6).

In early February, U.S. laboratories were only sequencing about 8,000 COVID-19 strains per week. Since then, the rate of sequencing has increased substantially, strengthening the country’s ability to detect and respond to emerging and more contagious COVID-19 strains, like the variants currently sweeping through the Midwest and parts of the East Coast.

The Biden Administration has already made a nearly $200 million investment to help increase genomic sequencing to 29,000 samples per week. Thanks to today’s funding from the American Rescue Plan, states and the CDC will expand that even further and, importantly, provide states with more resources to expand their own efforts to increase geographic coverage of sequencing to better detect emerging threats like variants. This will mean that both existing and any new COVID variants could be detected faster before they grow prevalent (4).

Research and innovation continue to be crucial in fighting the continuing challenges of this pandemic. The Hera Incubator and the reinforcement of European infrastructures and networks, supported by additional funding from Horizon 2020 and Horizon Europe, will help us deal with any variants and be better prepared for future outbreaks (7–10).

Pre-register to receive the registration links: https://edu.tbioinfo.com/genomic-analysis-of-sars-cov-2-hands-on-training

Registration link (if you are interested in mentor guidance for bioinformatics project for the bioinformatics analysis of infectious diseases): https://drug-discovery.omicslogic.com/

References

Genomics and Bioinformatics approach to Study of the SARS-COV-2 (COVID-19) Mutations: Variant analysis and detection

What is a Variant?

Program Overview:

This online program includes:

Written by Mohit Mazumder, Ph.D.