“This is the first indigenously sequenced whole genome of the coronavirus in Pakistan. Analysis of the sequence revealed nine mutations in the different regions of the genome, as compared to the sequence reported from Wuhan, China. This will be helpful in decision making at a national level for the use of future therapeutic options and vaccinations,” noted Prof Dr M Iqbal Choudhary, Director of International Center for Chemical and Biological Sciences (ICCBS), University of Karachi.
He 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), he said, adding that the sample for genomic analysis was collected from a patient with relevant travel history.
Mutation refers to any changes in the DNA of any organism, including viruses, he 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, where the pandemic started.
He said that the 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 rising, and new territories and regions are consistently reporting new cases, he said. Understanding the genetic repository of any infectious agent is vital for its prevention and clinical management, and viruses are no exceptions.
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, Prof Choudhary said.
"During pandemics, it is more important to monitor the way, rate, and nature of mutations that may have an impact on the effectiveness of future therapies and vaccinations."
In the past, a single mutation in the Chikungunya virus affected vector specificity and epidemic potential and lead to more efficient viral dissemination, he said, adding that this has important implications with respect to how viruses may establish a transmission cycle when introduced into a new area.
Hundreds of SARS-CoV-2 genomes are being reported from different parts of the world. The University of Cambridge, UK is spearheading efforts to massively map coronavirus genomes from the UK population, he said. "A total of £20 million have been allocated for the said project in the UK alone, which reflects the importance of such studies.”
Given the specific environmental conditions in our part of the world, it is strongly recommended that more genomes from Pakistani patients 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 a national level for the use of future therapeutic options and vaccinations, he noted. This study was carried out in collaboration with the DOW University of Health Sciences, Karachi.