KARACHI: Researchers at the Jamil-ur-Rahman Centre for Genome Research (JCGR) at Karachi University (KU) have carried out ‘whole genome sequencing of the coronavirus’ infecting a local patient and found nine mutations in the ‘different regions’ of its genome during analysis.

The procedure could help develop treatment, diagnostic and preventive tools, if financial support was available for sequencing at least 50 genomes, they said.

“This is the first indigenous whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, perhaps, also the first WGS of a pathogen in Pakistan,” said Prof Mohammad Iqbal Choudhary, the director of International Centre for Chemical and Biological Sciences (ICCBS) at the KU.

The centre has two wings — the JCGR and Dr Panjwani Centre for Molecular Medicine and Drug Research.

Sharing how the analysis was done, he said a team headed by Dr Ishtiaq Ahmed acquired the sample for the procedure from a patient (who had a travel history to Iran) admitted to the Dow University of Health Sciences and then analysed it at the KU centre.

“A big task in carrying out the analysis was to carefully separate human genomes from viral genomes. It took the team less than a week to complete the job and then it compared the findings with the international data,” he said, adding the team found nine mutations (changes in the DNA) in the different regions of genome when compared to the sequence reported from Wuhan (China).

“But, even then, the virus was found to be more closely related to the virus in Wuhan when we studied data from other countries. No mutation was identified in the protein and enzyme, though, which helped the virus make [its] way into the respiratory tract of a human body,” he explained.

The coronavirus, according to Dr Choudhary, is slowly mutating and it’s premature to say what will be the impact of these changes on disease severity.

“In a 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. For instance, in case of Chikungunya virus, we know that a single mutation had affected vector specificity and helped the virus to transmit more easily,” he said.

About global efforts in this field, Prof Choudhary pointed out that hundreds of SARS-CoV-2 genomes were being reported from different parts of world and that the University of Cambridge, UK, was spearheading efforts to massively map coronavirus genomes from the UK population.

“Given the specific environmental conditions in our part of the world, it is strongly recommended that more genomes from the different affected areas of Pakistan are sequenced to understand the full spectrum of variations and the way the virus is evolving here. This will help build capacity of our young scientists and develop therapeutic options and vaccinations,” he said.

Published in Dawn, April 1st, 2020

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