Purpose: The COVID-19 pandemic, caused primarily by the SARS-CoV-2 virus, has significant adverse effects on global health and economies. As the virus spread from China to countries worldwide, including Pakistan, there has been a need to understand the diversity of novel variants in the region. This study aimed to investigate the prevalence and characteristics of SARS-CoV-2 variants in Pakistan.
Methods: Through a random sample process, 1000 Oropharyngeal swabs were obtained from hospitalized patients who voluntarily agreed to take part in the study. RT-PCR, Whole Genome Sequencing, Variant calling and Phylogenetic analysis were performed on them.
Results: Out of 1000 samples, only 15 or 1.5% participants received positive RT-PCR results. It’s interesting to note that only 7 or 46.7%, of these positive cases involved male patients, whereas 8 or 53.3%, involved female patients. The whole genome sequencing of four randomly selected samples among positive cases revealed four novel COVID-19 variants with nucleotide substitutions at different points, although these variants were not included in the existing phylogenetic trees. Through variant calling and phylogenetic analysis, we identified sub-lineages with higher frequencies and broader geographic distributions, indicating their significant role as major drivers of the pandemic in Asia.
Conclusion: This study contributes significantly to our understanding of COVID-19’s evolutionary dynamics and lays a solid foundation for future research projects. The development of tailored therapies, the improvement of potent vaccinations, and the application of control measures aimed at reducing the effects of the ongoing epidemic will all be greatly influenced by our findings.
Keywords: Pandemic, Variant calling, RT-PCR, Oropharyngeal, Phylogenetic