NSU Genome Research Institute (NGRI) of North South University is the first private university in the country to sequence the genome of coronavirus samples from Bangladesh.
Their research, in which they completed the sequencing of eight SARS-CoV-2 samples, strongly suggests that the virus arrived in our country from the United States.
NGRI plans to sequence 100 more genomes.
Dr Muhammad Maqsud Hossain, the principal investigator of the team, said the research team has completed sequencing of eight SARS-CoV-2 isolates using their facilities. They are now in the process of submitting their findings to genome databases including GenBank and GISAID within this week.
Dr Maqsud said the samples they tested bear similarities to the ones from the US, as well as the ones sequenced by Bangladesh Council of Scientific and Industrial Research (BCSIR).
All data have been released in the genome database GISAID and available for public analysis. One of the genomes had six nucleotide insertions compared to the Wuhan reference genome, he said.
Genome sequencing can help identify genetic patterns related to the virulence of a disease, as well as genetic factors that contribute to immunity or a successful vaccine response, according to “The Genomic Revolution: Implications for Treatment and Control of Infectious Disease: Working Group Summaries”, a research article published by the National Academies Press.
Sequencing data from different places can speed up Bangladesh’s Covid-19 research activities including that of developing a vaccine.
Currently, several institutions including a team of physicians from Bangladesh Medical College led by Prof Dr Tarek Alam, Chinese company Sinovac Research and Development Co Ltd, and the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) are working on developing vaccines.
The Ministry of Health and Family Welfare will soon meet with Prime Minister Sheikh Hasina to decide on Covid-19 vaccine trials in the country.
NGRI’s research project
NGRI’s project was funded by the NSU. NGRI plans to sequence 100 more genomes and wants to do a thorough comparative analysis with sequences available from other institutes.
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 on Saturday.
The institute collected the samples from the Covid-19 diagnostic centre of Noakhali Science and Technology University, a government authorized Covid-19 testing centre.
Of the eight isolates sequenced, three isolates had the best match with genomes from Rangpur and Barisal (99.99%) which were more closely related to genomes from the US (99.99-99.98%), and Germany (99.97-99.98%).
Two genomes were more closely related to Chittagong isolates with 99.97% and 99.72% similarities respectively, and similar to isolates from Saudi Arabia (99.97% and 99.72% respectively).
One isolate was found to have the best match with one genome from Barisal (99.98%) which was more similar to genomes from USA/NY and Germany at 99.97%.
According to Dr Maqsud, the method used for the sequencing was “Enrichment workflow for detecting coronavirus using Illumina NGS systems” using the Illumina MiSeq platform at NGRI. They used a unique bioinformatics method — de novo assembly — to have a better picture of the genome sequences.
The methods they used are supposed to provide more accurate and unbiased results compared to other methods that use mapping to reference genomes for retrieving the genome sequences.
Preliminary analysis shows the genomes are very similar to those from the US. However, it is still too early to reach any conclusion based on that since they just received the data.
Further analysis will help provide insight into the genomes sequenced in the study.
The analysis of available genome sequences will help to determine the sources, clusters, transmission dynamics, and will help in developing a vaccine.
The research team also included Prof Abdul Khaleque, Prof Kazi Nadim Hasan, Aura Rahman, Tahrima Huq, Abdus Sadique, and Jahidul Alam.
Dr Maqsud is a renowned genome scientist who is involved with many national and international genome research projects.
He is also collaborating with Yale, and Stanford University, and the consortium has received a grant of $2 million from the Gates Foundation for Covid-19 research.
The research team at NSU is working on finding specific mutation(s) contributing to the fitness advantage of SARS-CoV-2 circulating in the country and their association with disease severity and outcome.
