The representative Covid-19 strain in Qatar is very similar to the strains found in Guangdong (China), Philippines and India, according to an analysis by two officials from Hamad Bin Khalifa University (HBKU).
Expressing their views in their personal capacity, Dr Mounir Hamdi, dean of the College of Science and Engineering, Dr Tanvir Ala, an assistant professor at the college noted that although these countries do not share a geographical border with Qatar, there are many expats from China, Philippines, and India who are residents of Qatar.
According to their analysis, “Though Qatar’s initial case was reported from Iran, subsequent cases might have originated from these countries. Our estimated phylogenetic tree places the representative strain of Qatar very close to England, Hong Kong, and Wales as well. Interestingly, strains from other Gulf countries were under the same clade of the phylogenetic tree but proved quite far from the clade of the representative strain of Qatar.”
The analysis was formed leveraging the power of machine learning techniques along with the alignment-free methods to identify the most representative strain from multiple locations across the world including Qatar. The phylogenetic analysis reveals intriguing relationships among the strains across the world including the Gulf countries.
As of July 26, Qatar has had the second-highest number of patients for Covid-19 in the Middle-East after Saudi Arabia, with more than 109,000 affected people. The first case of the novel coronavirus in Qatar was reported on February 27, and the Qatari government’s first measure was to evacuate all Qatari nationals from Iran. Then, as an extension of its precautionary steps, Qatar introduced a temporary travel restriction on several international destinations in mid-March .
Currently, no antiviral drugs exist that show confirmed clinical efficacy, nor any vaccines for its prevention (though multiple vaccines are at different stages of clinical trials).These efforts are hindered by limited knowledge we have of the molecular details and evolutionary relationship among the strains of novel coronavirus. To fill this gap, different laboratories across the world have produced a huge number of sequences from viral strains. As of July, 2020, more than 75,000 high-quality complete sequences of novel coronavirus have been identified , which encompass more than two billion sequence bases for multiple strains of this novel coronavirus.
“We analysed SARS-CoV-2 strains from nearly 150 locations across the world, including multiple locations in China. Traditionally, alignment-based methods are used to understand the phylogenetic relationship of the viral strains. However, calculating the phylogenetic relationship based on genomic sequences is computationally expensive and requires a lot of memory. Consequently, alignment-free methods are getting attention in the scientific community to compare viral sequences as well as in constructing the phylogenetic relationship,” expalined, the officials.
“As part of this study, an alignment-free phylogenetic analysis was carried out to uncover the evolutionary relationship among the strains of SARS-CoV-2 in all countries in the world. We leveraged the power of machine learning techniques to identify the most representative strain from multiple locations across the world. Based on our computational workflow, we identified a single representative strain from each location and built the phylogenetic tree to discover their evolutionary relationship,” they added.