Pan-Virome of Third Wave SARS-CoV-2 Strains in Pakistan Reveals Higher Entropy

Abstract

Background: Pakistan faced five distinct waves of COVID-19 caused by unique SARS-CoV-2 strains. Of these, the third wave, which started in March 2021 and ended in June 2021, proved worst causing 335,728 reported infections and 7849 deaths. During the third wave SARS-CoV-2 alpha variant remained dominant causing more than seventy percent of infections. Hence, the current study aimed to investigate the entropy rate in SARS-CoV-2 through pan-virome analysis during the third wave of COVID-19 in Pakistan. Methods: Whole-genome sequencing of five viral isolates (three from female and two from male patients) was performed and in-silico analysis was carried out by taking into account other reported worldwide sequences. Bioinformatics analysis was done, and a phylogenetic tree was constructed to find out the clustering. Prokka was utilized to predict the genes and annotate all the viromes. The pan-genome of SARS-CoV-2 was inferred with Snippy. Results: The phylogenetic analysis reveals that most of the genomes were identical. It was discovered that the most common change was C > T, whereas T > A substitutions were the rarest. There was a total of nine different types of mutations and four types of mutations had a significant impact on phenotypes. The four specific types of mutations identified in our study have been observed to lead to notable changes in the genetic makeup of the SARS-CoV-2 virus. Such mutations suggested a high entropy in the pan-virome of third wave SARS-CoV-2 strains. Conclusion: This research provides valuable insights into unique SARS-CoV-2 strains and dominant variants during the third wave in the country. The phylogenetic tree and virome annotation revealed in tracking transmission patterns. These research efforts contribute to global endeavors in controlling the COVID-19 pandemic and preparing for future viral outbreaks.