Context: Recently, The Council of Scientific and Industrial Research (CSIR) is working on developing “mega labs” to ramp up testing for COVID-19 as well as improve the accuracy rate. Next-Generation Sequencing machines (NGS) will be used in these labs. 

• The machines will be repurposed to sequence 1,500-3,000 viral genomes at a go for detecting the SARS-CoV-2 novel coronavirus in the mega labs 

About Next-Generation Sequencing machines (NGS)

• Next-Generation Sequencing is massively parallel or deep sequencing are related terms that describe a DNA sequencing technology which has revolutionised genomic research. NGS is normally used for sequencing human genomes.

Benefits of using NGS machines 

• Using NGS an entire human genome can be sequenced within a single day.
• The genome sequencing (NGS) machines when used optimally and with appropriate modifications, can substantially detect the possible presence of the virus even in several instances where the traditional RT-PCR tests miss out on them. 
• The genome method can read a bigger chunk of the virus genome and thereby provide more certainty, unlike the RT-PCR test that identifies the SARS-CoV-2 virus by exploring only specific sections of the virus. 
• NGS identified cases as either positive and negative when RT-PCR found them to be ‘inconclusive’. So this can also be used as a confirmatory test. 
• It can also trace the evolutionary history of the virus and track mutations more reliably and it can help identify more places where SARS-COv-2 viruses differ from other related viruses. 
• The NGS does not need primers and probes and only needs custom reagents, unlike the RT-PCR that needs primers and probes, which is a key hurdle in the scaling of tests. 
• Primers are short sequences of DNA used to amplify a particular DNA sequence. A probe is a small radioactively or fluorescently labelled DNA sequence used to identify a particular DNA sequence.
• Reagent for DNA is designed to easily prepare DNA extracts from animal tissues that can be used directly in PCR.

Other uses of the machine

• Establishing “hubs” capable of whole-genome sequencing would help track significant mutations in the virus and can be repurposed for any kind of outbreak, be they of viral or bacterial origin.
• Due to the limited accuracy and capacity of existing tests, a sizeable population is falsely negative. NGS can help in serving a larger purpose of continuous surveillance of large pools like industrial hubs, commercial establishments or places where an outbreak is likely.
• NGS can also be used to develop new diagnostic tests for Covid-19 in future for more fast and accurate testing. 

Additional Information
About Genome

• A genome is all the genetic matter in an organism.
• It is defined as an organism’s complete set of DNA, including all of its genes.
• Each genome contains all of the information needed to build and maintain that organism.
• Human Genome is made up of 23 chromosome pairs with more than 3 billion DNA base pairs, contained in all cells that have a nucleus.

About Genome sequencing

• It is a process to figure out order of DNA nucleotides or bases in a genome.
• This means the order of As, Cs, Gs, and Ts, a unique combination of which makes up an organism’s DNA.
• After the genome is sequenced, the data is analysed to understand the genetic information of an entire species.