Researchers from North South University (NSU) have detected a rare mutation in spike proteins of SARS-Cov-2.
NSU Genome Research Institute (NGRI) sequenced SARS-CoV-2 genomes, using their own facilities. NSU, which also funded the project, is the first and only private university in the country to achieve such a feat.
Dr Muhammad Maqsud Hossain, principal investigator of the team, said the research team had completed the sequencing of 58 SARS-CoV-2 isolates by using their facilities.
They are now in the process of publishing and submitting their findings to genome databases, including GenBank and Global Initiative on Sharing All Influenza Data (GISAID) within this week, Dr Maqsud said.
Researchers at NGRI, under the leadership of Prof Hasan Mahmud Reza, dean of the School of Health and Life Sciences, and Dr Muhammad Maqsud Hossain, director of NGRI, completed the project.
The institute collected the samples from the Covid-19 diagnostic centre of Noakhali Science and Technology University, a government authorized Covid-19 testing centre.
The SARS-CoV-2 virus consists of 29 proteins, of which the 4 structural proteins were investigated as potential therapeutic targets. Among these, the spike protein was studied the most by far.
Spike proteins protrude out of the viral membrane and facilitate its entry into host cells by interacting with receptors on the surface of these cells. Mutations in this protein can therefore affect how efficiently the virus is able to penetrate and infect host cells.
Rare mutation
NGRI reported that some rare mutations in these 4 structural proteins had been found to be uncommon across the globe.
Of these, one mutation in the crucial spike protein is being reported for the first time globally. This is the substitution of the amino acid tyrosine (Y) into the amino acid phenylalanine (F) in position 204 of the spike protein (Y204F).
As both the amino acids are grouped as aromatic amino acids, they have structural similarities. However, there have been studies where the substitution of F for Y has had effects on the functions of other proteins.
Whether or not this mutation has any downstream effects on the structure and function of the SARS-CoV-2 spike protein and thus the virus’s infectivity is a topic of further investigation.
This mutation was found in 2 variants sequenced by NGRI as part of a mass sequencing project where a total of 58 variants from Noakhali were collected and sequenced in the lab.
The mutational analysis of the variants also showed mutations that were only reported a handful of times across the world, and several mutations that were found in Bangladesh for the first time, according to researchers.
However, Dr Maqsud told Dhaka Tribune: “As there is no Level-3 Biosafety Lab in the country, it is not possible to determine the effectiveness of this newly identified protein and what kind of impact it may have on vaccine development.”
The government and its health wings organization should set up such a lab to identify its effectiveness to curb the spread of the new variant of the virus across the country, he suggested.
Dr Maqsud identified this lineage as one of the most virulent isolates and its mutating for its better fitness in the community.
The major reason for his hypothesis is the observation based on the genome sequences available from deceased patients in GISAID.
Among the 52 Indian genomes available, 10 were infected with this lineage. In Saudi Arabia, almost 50% were infected with this lineage out of 121 available genomes.Other countries where this lineage has been found include the UK (45%), Denmark (9%), and Canada.
Young researchers Tahrima Huq and Aura Rahman from NGRI made significant contributions in carrying out the research activities and bioinformatics analysis to find unique mutations of the virus.
The research team also included Prof Abdul Khaleque, Prof Kazi Nadim Hasan, Naushin, Abdus Sadique and Jahidul Alam.
