Genomic analysis of any emerging virus is important to understand its structure, pathogenicity and evolution (i.e. it’s change and adaption in new environmental conditions). Massive genome sequencing efforts are underway globally to document a comprehensive mutational spectrum of SARC-Car-2. In this context, scientists at the International Centre for Chemical and Biological Sciences (ICCBS), Karachi University, Karachi, Pakistan, have successfully carried out the sequencing and analysis of 48 genomes of SARS-CoV-2 from Karachi. Samples were collected in a time phased approach from May to August 2020 from the areas designated as COVID hot spots by the local administrative authorities.
The ICCBS analysis identified 109 mutations including 36 recurrent mutations. (Recurrent mutations are those which are observed in more than one sample). Few frequent mutations were found that are associated with increased infectivity and fatality while several mutations were found in the spike protein which is very important for entry of virus into host cells. This data depicts the first detailed mutational spectrum from Pakistan and an in-depth analysis is underway for further insights. With the current onset of the second wave of the virus, the scientists at ICCBS are collecting samples for genome analysis related to this second wave.
Whole genome sequencing of 48 SARS-CoV-2 samples was carried out by using Illumina MiSeq NGS sequencing system with reference genome sequence of SARS-CoV-2 from Wuhan. Notably, two missense mutations P4715L in ORF1ab and D614G in Spike protein gene were found in 25 cases each. These two mutations have been reported to be associated with higher fatality in BCG-vaccinated countries, while another study has reported that D614G mutation enhances replication on human lung epithelial cells and primary human airway tissues through an improved infectivity of virions.
The ICCBS intends to complete 1000 – genome SARS-CoV project in next 6 months.
Technical details of the analysis are provided in the footnote (https://www.cogconsortium.uk/)