NSU-NGRI finds rare mutation in Spike Proteins of SARS-CoV-2

NSU Live: North South University (NSU) is the first and only private university in the country to sequence SARS-CoV-2 genomes using their own facilities at NSU Genome Research Institute (NGRI). Researchers at NGRI, under the leadership of Prof. Hasan Mahmud Reza, Dean of the School of Health and Life Sciences, NSU and Dr. Muhammad Maqsud Hossain, Director of NGRI, NSU have completed sequencing of fifty eight SARS-CoV-2 isolates using Illumina MiSeq platform. Prof. Firoz Ahmed and Prof. Aminul Islam of Noakhali Science and Technology University assisted in providing samples.

The SARS-CoV-2 virus consists of 29 proteins, of which the four structural proteins have been the subject of much investigation as potential therapeutic targets. Among these, the spike protein has by far been the most studied one. Spike proteins protrude out of the viral membrane and facilitate its entry into host cells through interacting with surface receptor ACE2. Mutations in spike protein can therefore impact how efficiently the virus is able to penetrate and infect host cells.

NGRI, Bangladesh has reported some rare mutations in these four structural proteins that have not been found commonly across the globe. Of these, one mutation in the crucial spike protein is hereby being reported for the first time Bangladesh and thereby in the world.

This is the substitution of the amino acid tyrosine (Y) by the amino acid phenylalanine (F) in position 204 of the spike protein (Y204F). This is also to be noted that genome harboring this mutation belongs to the lineage B.1.36. Whether or not this mutation has any downstream effects on the structure and function of the SARS-CoV-2 spike protein as well as the virus’s infectivity is sure to be a topic of further investigation. The same mutation was found in 2 samples sequenced by NGRI as part of a mass sequencing project. 

The team identifies this lineage as one of the most virulent isolates and it is mutating for its better fitness in the community. The observation is based on the genome sequences available in GISAID for deceased patients from the India and Saudi Arabia who were infected with this lineage. Among the 52 Indian genomes available for deceased, 10 were infected by this lineage, whereas, in Saudi Arabia among the 121 available genomes, almost 50% were affected by this lineage. Other countries where this lineage has been found include UK (45%), Denmark (9%), and Canada.

Other members of the team included Prof. Abdul Khaleque, Prof. Kazi Nadim Hasan, Aura Rahman, Tahrima Huq, Naushin, Abdus Sadique, and Jahidul Alam from NGRI, NSU.

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