COVID-19 Notes
By Dr. Satish K Gupta*
In India, INSACOG was set up with the aim to sequence at least 5% of COVID-19 samples. But only 1% has been achieved yet.
The Delhi Government reported that 81 per cent of the samples sequenced on the New Year’s weekend were of the Omicron variant. Once it was clear that the new variant was driving the surge in cases, the Government stopped sequencing all samples.
World over, Genome testing is controlled by respective governments. Presently no government is able to meet the rising demand of the testing.
Genome testing framework in India
- The Omicron pandemic has unearthed the importance of genomic sequencing and made it a popular and commonly requested test.
- For genome testing, RTPCR positive samples are sent to the designated lab of INSACOG- the apex body for Genome sequencing in India.
- The Indian SARS-CoV-2 Genomic Consortia (INSACOG) was launched on December 20, 2020 with aim to monitor the genomic variations in the SARS-CoV-2. INSACOG is a consortium of 10 manor labs and 28 satellite labs in various parts of the country. (After 20 UK returnees test positive with new COVID-19 strain, a consortium will ascertain strain’s current status in India)
How many samples have been processed by INSACOG?
INSACOG was set up with the aim to sequence at least 5% of COVID-19 samples. But only 1% has been achieved yet. Although more than 100,000 samples have been processed till date.
Does INSACOG convey results of Omicron testing to patients?
No, INSACOG works within the Central Government’s control. Results of samples are not communicated to individuals rather used for research and policy making decisions.
Case load of Omicron testing in India?
Till now, Omicron has been detected in more than 29 states of India.
As of January 18, 2022, 8,891 Omicron cases have been reported across India. While India reported 2,38,018 lakh new cases of Covid-19 on January 18, 2021. Major circulating variant in India presently being Omicron, Omicron case numbers represent just the tip of iceberg because not more than 1% samples are being processed for Genome testing.
Previously Delhi was doing Genome analysis of all positive case, why did the Government change its policy?
Till December-end, Delhi sequenced all its positive samples when the number of COVID-19 cases was low. The Delhi Government reported that 81 per cent of the samples sequenced on the New Year’s weekend were of the Omicron variant. Once it was clear that the new variant was driving the surge in cases, the Government stopped sequencing all samples.
World scenario of Omicron!
Omicron has spread to more than 140 nations starting from Botswana since mid November, 2021.
As of January 17, 2022, the United Kingdom had reported the highest number of SARS-CoV-2 Omicron cases, with over 161 thousand cases. Next in Omicron reporting is USA
Genome testing in other countries including USA and UK
World over, Genome testing is controlled by respective Governments. Presently no government is able to meet the rising demand of the testing. All Governments share their data with GISAID which is global science initiative and primary source established in 2008 with headquarters in Munich. Now GISAID database has become the world’s largest repository for SARS-CoV-2 sequences.
Do we have better Genome sequencers to process thousands of samples?
Yes, Genomic sequencing has now evolved to a stage where large sequencers can process even thousands of samples simultaneously. However, Genome sequencing is a technically demanding job where experts must purify the samples appropriately and get them ready to be used in sequencers. Currently turn around time for a Genome sequencing report is 5 to 7 days.
Nanopore technology- road to mass sequencing. How does it work?
Various technologies can be used for gene sequencing but a particularly important one in taking us to where we are is nanopore sequencing. Ten years ago this technology wasn’t available as it is today.
Here’s how it works:
- The Sars Cov-2 virus’s genome consists of RNA, and each of its 30,000 characters is one of four building blocks, represented by the letters A, G, C and U. Sequencing is the process of identifying their unique order.
- First the RNA is converted to DNA. Then, like a long thread of cotton being pulled through a pinhole in a sheet of fabric, the DNA is pulled through a pore in a membrane. This nanopore is a million times smaller than a pin head. As each building block of DNA passes through the nanopore, it gives off a unique signal. A sensor detects the signal changes, and a computer program decrypts this to reveal the sequence.
Nano sequencing, the new affordable hallmark!
Amazingly, the flagship machine for doing nanopore sequencing – the MinION, released by Oxford Nanopore Technologies (ONT) in 2014 – is only the size of a stapler; other sequencing techniques (such as those developed by Illumina and Pacific BioSciences) generally require bulky equipment and a well-stocked lab.
Experience with Nano tech
Using the technology scientist could set up Pop up labs even in areas lacking scientific infrastructure, during the 2013-16 Ebola outbreak and then during the Zika epidemic of 2015-16. These make shift labs helped scientists to identify where each outbreak originated.
Nanopore sequencing of Zika and Ebola laid the foundation for sequencing the coronavirus today. Govts just need to utilize it on never-before-seen scale.
Once pandemic ends, will genome labs become idle?
Genome sequencing also has a role to play in the future of healthcare and medicine. It has the potential to diagnose rare genetic disorders, gene therapy inform personalised medicine, and monitor the ever-increasing threat of drug resistance. Labs set up today will unlock unseen frontiers in future and benefit the mankind. With so much demand for Genome testing let this opportunity not be lost.
What are the risks involved with Genome analysis?
There are a lot of fears and concerns. Routine genome sequencing could overwhelm doctors and patients with confusing and sometimes alarming information, leading to anxiety and stress, as well as expensive and sometimes dangerous follow-up testing.
Privacy concerns and family suits might increase. But Goverments can always exercise control by legislations and strict punishments.
Various other potentially dangerous but beneficial programmes like organ transportation, IVF, child surrogacy, prenatal diagnostics, ultrasounds and genetics have shown the way that responsible citizen behavior and strict legislative control can yield good results while protecting society from misuse of scientific advancements.
What are the way ahead to increase foot print of Genome analysis in India?
Public private partnership is the only plausible answer. Government should be permit Genome testing in Private Labs with result sharing on commercial basis. Genome testing set up are already available in many corporate hospitals. Many of them are allowed to do Genetic analysis for research purposes but not permitted to issue reports on commercial basis. When allowed many more labs would be ready to set up Genome testing facility using equipment which is available from $1000 to >$50000.
During pandemic tests like IL-6 descended from research labs to next door street laboratory. RTPCR became a common name. Similarly expanding Gene Testing Network for nation, could be a Golden Opportunity, let it not become an opportunity lost.
Latest updates as per Ministry of Health and Family Welfare, Government of India
2,38,018 new cases recorded in the last 24 hours till 9 am on January 18, 2021
8,891 total Omicron cases detected so far; an increase of 8.31% since yesterday
Daily positivity rate (14.43%)
Weekly positivity rate (14.92%)
Also read: Understanding COVID-19: Genome Sequencing
*Dr. Satish K Gupta is an MD in Medicines, a Visiting Senior Consultant Physician and Internist at Max Super Speciality Hospital, and a Clinical Assistant Professor at GS Medical College, Chaudhary Charan Singh University, Meerut. He is the author of Journey of COVID in India: A Doctor’s Perspective.
