Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan

Authors

Najia Karim Ghanchi, Aga Khan UniversityFollow
Asghar Nasir, Aga Khan UniversityFollow
Kiran I. Masood, Aga Khan UniversityFollow
Syed Hani Abidi, Aga Khan UniversityFollow
Syed Faisal Mahmood, Aga Khan UniversityFollow
Akber Kanji, Aga Khan UniversityFollow
Safina Abdul Razzak, Aga Khan UniversityFollow
Waqasuddin Khan, Aga Khan UniversityFollow
Saba Shahid, Aga Khan University
Maliha Yameen, Aga Khan UniversityFollow
Ali Raza, Aga Khan UniversityFollow
Javaria Ashraf, Aga Khan UniversityFollow
Zeeshan Ansar Ahmed, Aga Khan UniversityFollow
Mohammad Buksh Dharejo, Government of Sindh, Karachi, Pakistan
Nazneen Islam, Aga Khan UniversityFollow
Zahra Hasan, Aga Khan UniversityFollow
Rumina Hasan, Aga Khan UniversityFollow

Document Type

Article

Department

Biological and Biomedical Sciences; Department of Medicine; Paediatrics and Child Health; Pathology and Laboratory Medicine

Abstract

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.
Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The highest diversity of clades was present in Sindh and Islamabad Capital Territory and the least in Punjab province. Initial introductions of SARS-CoV-2 GH (B.1.255, B.1) and S (A) clades were associated with overseas travelers. Additionally, GH (B.1.255, B.1, B.1.160, B.1.36), L (B, B.6, B.4), V (B.4) and S (A) clades were transmitted locally. SARS-CoV-2 genomes clustered with global strains except for ten which matched Pakistani isolates. RNA substitution rates were estimated at 5.86 x10-4. The most frequent mutations were 5' UTR 241C > T, Spike glycoprotein D614G, RNA dependent RNA polymerase (RdRp) P4715L and Orf3a Q57H. Strains up until June 2020 exhibited an overall higher mean and site-specific entropy as compared with sequences after June. Relative entropy was higher across GH as compared with GR and L clades. More sites were under selection pressure in GH strains but this was not significant for any particular site.
Conclusions: The higher entropy and diversity observed in early pandemic as compared with later strains suggests increasing stability of the genomes in subsequent COVID-19 waves. This would likely lead to the selection of site-specific changes that are advantageous to the virus, as has been currently observed through the pandemic.

Comments

Pagination are not provided by the author/publisher

Publication (Name of Journal)

PLoS One

Recommended Citation

Ghanchi, N. K., Nasir, A., Masood, K. I., Abidi, S. H., Mahmood, S., Kanji, A., Razzak, S. A., Khan, W., Shahid, S., Yameen, M., Raza, A., Ashraf, J., Ahmed, Z. A., Dharejo, M. B., Islam, N., Hasan, Z., Hasan, R. (2021). Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. PLoS One, 16(8), e0256451.
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_pathol_microbiol/1345

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.