Bangladeshi scientists crack virus genome

A team from Child Health Research Foundation (CHRF) yesterday successfully completed the genome sequencing of the SARS-CoV-2 virus in Bangladesh.

The announcement came late on Tuesday evening in a press release distributed by CHRF. SARS-CoV-2 is the coronavirus that causes Covid-19.

"We completed genome sequencing of the virus a few hours ago," confirmed Dr Senjuti Saha, the scientist who led the team of three. The others were Roly Malaker and Md Saiful Islam Shajib.

Dr Senjuti's father, eminent microbiologist and Executive Director of CHRF Dr Samir Kumar Saha also played a leadership role.

"The entire CHRF Covid-19 response team of more than 80 people has directly or indirectly helped us make this possible," Dr. Senjuti Saha said.

Genome sequencing is the process of identifying what nucleotides -- the basic building block of DNA and RNA -- are present in a certain cell and in what order.

"The SARS-CoV-2 virus cells contain RNA. RNA is made of four bases or 'letters' -- A (adenine), U (uracil), G (guanine), and C (cytosine). The SARS-CoV-2 virus is made up of almost 30,000 letters and we had to figure out what the sequence was," explained Dr Senjuti.

As of now, they have only finished the genome sequencing of one sample, and plan to do around 80, she added.

"We have been working on this for over a month, but the actual work of sequencing was done over 4 days of non-stop work," said an excited Dr Senjuti.

"In addition, the biologists working on the genome sequencing also had a full eight-hour shift of testing samples from patients. We did not want patients to suffer while we tried to do genome sequencing. So, all the work was done after hours," she said, speaking to this correspondent from Cambridge in England in the early hours yesterday, where she has been stuck because of the closing of the borders in the wake of the pandemic.

"To make things harder, because I had come to Cambridge in mid-March, and gotten stuck here, the collaboration had to be remote. My team in CHRF literally had to set up a camera in the space where they were doing the sequencing, so that I could see what was happening," described Dr Senjuti.

While scientists in Bangladesh have done genome sequencing of Jute and Hilsa (both of which have DNA), genome sequencing of cells containing RNA is a rare feat.

"Up until now, we have usually had to send our samples abroad for sequencing and analysis. But with help from the Bill and Melinda Gates Foundation and Chan-Zuckerberg Initiative/Biohub, we were able to purchase a sequencer and since before the pandemic hit we had been practising and teaching our staff to sequence dengue, RSV and influenza viruses," said Dr Senjuti.

WHAT THIS MEANS FOR THE FUTURE

Doing genome sequencing of the virus means that scientists can begin to understand which type it is, which country it came from, and when it came to Bangladesh.

"This will help us make predictions for the future -- when will we hit the peak?" said Dr Senjuti.

Genome sequencing of this virus has already been done worldwide around 16,000 times, which Bangladesh can compare against, she explained.

In addition, this means that vaccines can be explored. "Vaccines are being built in other countries, but how do we know it will work for Bangladesh unless we know the type of virus we have?" added Dr Senjuti.

Vaccines will be injecting RNA of the virus into the body of the patient to help it build antibodies against the disease. The RNA in the vaccine needs to match the RNA of the virus strain hitting our country right now.

"We have also uploaded the results to an open-access database and hope that vaccine-makers will also be able to see it and incorporate that into their vaccine design," said Dr Senjuti.

The scientist has also made the sequencing protocol public and hopes that other laboratories around the country can train themselves and start sequencing samples.

"We assume that each month two 'letters' in the RNA mutate, which means this virus is constantly mutating. Therefore, sequencing too, needs to be a constant process."

Besides, having a group trained in genome sequencing can prevent the next pandemic in Bangladesh. 

Dr Senjuti said that this would not have been possible if the Directorate General of Health Services( DGHS) and IEDCR had not given them samples and the persmission to test.

Previously, during the chikungunya outbreak of 2018, Dr Senjuti Saha had completed the metagenomic sequencing to discover that chikungunya is causing meningitis in children.