Sars COV2Genome Sequencing
Prevalence
- In 2019, the world was affected by a global pandemic SARS COVID-19 viruse
- Millions of people have been affected by COVID-19 and many have lost their lives as well
- In the second wave of COVID-19 in 20721 in India the positivity rate <20%
- India is second worst affected country in terms of active covid cases
Variant of concern (VOC)
There are currently six known VOCs which are in circulation in India. These VOCs have few mutations in spike protein of the virus which are matter of concern since they are known to cause increased transmissibility and immune escape. It is very essential to identify these in the population along with newer variants which could be emerging. The variants are as follows:
- B.1.1.7 – UK variant
- B.1.351 – South African variant
- P.1 – Brazilian variant
- B.1.427 and B.1.429 – California variant
- B.1.617-Indian variant with double mutation (E484Q and L452R) which is currently responsible for second wave in India
Why do you Need for whole genome sequencing of SARS COV2
Understand the ability to spread in people
Ability to cause either milder or more severe detection in people
Ability to evade detection by specific diagnostic tests
Provides information about decreased susceptibility to medical therapies
Ability to evade natural or vaccine-induced immunity
Virus variant identification
Antigen evolution tracking for vaccine development
Why MedGenome
- Targeted sequencing of the complete viral ssRNA genome
- Processing of any number of samples, starting with one sample
- Target enrichment by using a Primer Panel which is multiplexed to cover the whole-genome of SARS-CoV2
- Adaptable sequencing output in multiples of b M read pairs (2x 150 bp)
- Mapping of high-quality sequencing reads to reference SARS-CoV2 genome
- Alignment-based consensus virus genome sequence generation for samples with a genome coverage > 90%
- Identification of Variant of concerns and SNP table
- Phylogenetic analysis to determine the lineage and clade
- Sequencing platform: Illumina high throughput
Sars COV2 whole Genome sequencing offered by Medgenome
Test
SARS-CoV2 Sequencing
Test Code
MGM1825
TAT
10 working days
Sample
Nasopharyngeal and Oropharyngeal Swab
Methedology
NGS
Location
Bangalore
Deliverables
- Sequence raw reads (FastQ)
- Consensus SARS-CoV-2 genome sequence of isolates (Fasta)
- Analysis report (HTML|PDF)
References
- Genomic Surveillance for SARS-CoV-2 Variants. May 17th 2021.
- V’kovski, P., Kratzel, A., Steiner, S. et al. Coronavirus biology and replication: implications for SARS-CoV-2.Nat Rev Microbiol 19, 155–170 (2021). https://doi.org/10.1038/s41579-020-00468-6
- Genomic sequencing of SARS-CoV-2: a guide to implementation for maximum impact on public health. 8th January 2021.
- As on 10 May ’20
- Aarogya setu
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