By Muhammad Luqman
A team of researchers in Pakistan’s port city of Karachi has carried out whole genome sequencing of novel coronavirus (SARS-CoV-2) that has infected over a million people across the globe and killed over 54,000 in around 200 countries.
This is the first indigenously sequenced whole genome of coranavirus from Pakistan. Analysis of the sequence revealed 9 mutations in the different regions of genome, as compared to the sequence reported from Wuhan, China.
“This will be helpful in decision making at national level for the use of future therapeutic options and vaccinations, ” Prof.Dr. Iqbal Choudhary, Director of International Centre for Chemical and Biological Centre, University of Karachi said.
Dr.Chaudhary who is also Director of Pakistan Biotechology Information Centre (PABIC) said that the sequencing was carried out to understand the genetics of this pathogen in Pakistan.
The entire genome sequence of SARS-CoV-2 was mapped by a team of young scientists under the supervision of Dr. Ishtiaq Ahmed. The work was carried out using next generation DNA sequencing systems at the Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (International Center for Chemical and Biological Sciences, University of Karachi).
The sample for genomic analysis was collected from a patient having a travel history.
Mutation is change which appears in the DNA of all organisms and viruses, the researcher said, adding that comparison with genomes from other parts of the world revealed that this virus is more closely related to the virus from China, the point from where the pandemic was started.
He said that coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a grave health challenge globally with more than 800,049 confirmed cases and 38, 714 recorded deaths to date. Currently no drug or vaccine is available for the treatment and prevention of this disease, respectively.
COVID-19 cases are exponentially on rise and new territories and regions are constantly reporting new cases, Dr. Iqbal Choudhary.
The sequencing report reveals that this viral genome is slowly mutating and it is premature to say what will be the impact on virulence (severity of disease) due to these mutations, he added.
“In pandemic it becomes more important to monitor the way, rate and nature of mutations which may have impact on effectiveness of future therapies and vaccinations,” Dr. Choudhary explained.
In past a single mutation in Chikungunya virus affected vector specificity and epidemic potential and lead to more efficient viral dissemination.
Hundreds of SARS-CoV-2 genomes are being reported from different parts of world. University of Cambridge, UK is spearheading effort to massively map coronavirus genomes from UK population. “A total of £20 million have been allocated for the said project in UK alone, which reflects the importance of such studies,” Dr Iqbal Choudhary said.
Given the specific environmental conditions in our part of the world, it is strongly recommended that more genomes from Pakistani patents are sequenced to understand the full spectrum of genetic variations, and the way the virus is evolving here, he said.
This will be helpful in decision making at national level for the use of future therapeutic options and vaccinations, he mentioned, and added that this study was carried out in collaboration with the DOW University of Health Sciences, Karachi.
By Muhammad Luqman