SARS-CoV-2: Finally, India shares genome sequence data with GISAID

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A day after I reported that India has not shared genome sequence data of the novel coronavirus (SARS-CoV-2) with GISAID, NIV shared two sequences on March 5.

India has finally shared two whole genome sequence data of the novel coronavirus (SARS-CoV-2) with the Global Initiative on Sharing All Influenza Data (GISAID). The two sequences were shared by the Pune-based National Institute of Virology. This news comes after I reported on March 4 that India has not shared any genome sequence data with the GISAID.

“We shared the two sequences with GISAID on March 5 evening,” said Dr. Priya Abraham, Director of NIV. “We had shared the sequences with GenBank about two weeks ago.”

When were the sequences shared with GenBank

However, the GenBank website clearly mentions that whole genome sequences of two oronasopharynx (mouth, nose, throat) samples collected on January 27 and January 31 from two COVID-19 patients in Kerala were deposited in GenBank only on March 6 and not two weeks ago as the NIV Director claims.

Genome sequences - GenBank

The accession number of the two sequences is MT012098 (collected on January 27) and MT050493 (collected on January 31).

The two sequences were shared by Dr. Varsha Potdar and others from NIV. Dr. Potdar heads the Influenza Group and her “major interest is molecular epidemiology of influenza and other respiratory viruses”.

Indian sequences are different from others

In tweet on March 6 evening, GISAID said it has “updated” the database with “two SARS-CoV-2 sequences from Kerala sampled at the end of January”. It added: “These sequences do not link very closely to other sequences in the tree.”

The three adults in Kerala who were found to be infected with the novel virus had returned from Wuhan. The first COVID-19 patient in India, a medical student who had returned from Wuhan, was laboratory confirmed by NIV on January 30. Two more adults from Kerala were laboratory confirmed by NIV within a couple of days.

At this point, it is not clear why the sequences appear to differ from the rest in the phylogenetic tree. A virologist who did not want to be named said that it could possibly be due to sequencing errors.

“NIV should rule out sequencing errors or contact Chinese CDC to find out if these sequences are linked to other sequences in Wuhan and not deposited in GISAID,” says Dr Shahid Jameel, CEO of the Wellcome Trust/DBT India Alliance.

Referring to the Indian genome sequences not closely linked to other sequences in the tree, Dr. Chitra Pattabiraman from the National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru says: “There are at least two possibilities — sequences could reflect the variations of the virus in China or they could be errors in sequencing, which can be corrected over time. The former is more likely and this can be resolved by adding more sequences.”

Why study genome sequences

Studying viral genome sequences immensely helps in epidemiological investigations. “Sequencing the genome of novel coronavirus will help us to know where the virus came from and how the virus has spread. For instance, by sequencing the genome of the virus isolated from an Indian patient, it will become possible to know if the virus had come from China or any other country,” Dr. Gautam Menon, professor of physics and biology at Ashoka University, Sonepat, Haryana and the Chennai-based Institute of Mathematical Sciences had earlier told me.

So far, 26 countries, including India, have shared 178 SARS-CoV-2 genome sequences with the GISAID. At 70, China has shared the highest number of sequences. The other countries that have shared higher number of sequences are the U.S. (22), Australia and Japan (10 each), and Singapore and South Korea (eight each). Nepal, Vietnam and Cambodia have also shared one sequence each.

Published in The Hindu on March 7, 2020

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