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Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan.
PLoS One. 2021; 16(8):e0256451.Plos

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.

Authors+Show Affiliations

Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Biological and Biomedical Sciences, AKU, Karachi, Pakistan.Department of Medicine, AKU, Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pediatrics and Child Health, AKU, Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Health, Government of Sindh, Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan.Department of Pathology and Laboratory Medicine, The Aga Khan University (AKU), Karachi, Pakistan. Faculty of Infectious and Tropical Disease, London School of Hygiene and Tropical Medicine, London, United Kingdom.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

34464419

Citation

Ghanchi, Najia Karim, et al. "Higher Entropy Observed in SARS-CoV-2 Genomes From the First COVID-19 Wave in Pakistan." PloS One, vol. 16, no. 8, 2021, pp. e0256451.
Ghanchi NK, Nasir A, Masood KI, et al. Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. PLoS One. 2021;16(8):e0256451.
Ghanchi, N. K., Nasir, A., Masood, K. I., Abidi, S. H., Mahmood, S. F., Kanji, A., Razzak, S., Khan, W., Shahid, S., Yameen, M., Raza, A., Ashraf, J., Ansar, Z., 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. https://doi.org/10.1371/journal.pone.0256451
Ghanchi NK, et al. Higher Entropy Observed in SARS-CoV-2 Genomes From the First COVID-19 Wave in Pakistan. PLoS One. 2021;16(8):e0256451. PubMed PMID: 34464419.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Higher entropy observed in SARS-CoV-2 genomes from the first COVID-19 wave in Pakistan. AU - Ghanchi,Najia Karim, AU - Nasir,Asghar, AU - Masood,Kiran Iqbal, AU - Abidi,Syed Hani, AU - Mahmood,Syed Faisal, AU - Kanji,Akbar, AU - Razzak,Safina, AU - Khan,Waqasuddin, AU - Shahid,Saba, AU - Yameen,Maliha, AU - Raza,Ali, AU - Ashraf,Javaria, AU - Ansar,Zeeshan, AU - Dharejo,Mohammad Buksh, AU - Islam,Nazneen, AU - Hasan,Zahra, AU - Hasan,Rumina, Y1 - 2021/08/31/ PY - 2021/03/25/received PY - 2021/08/09/accepted PY - 2021/8/31/entrez PY - 2021/9/1/pubmed PY - 2021/9/10/medline SP - e0256451 EP - e0256451 JF - PloS one JO - PLoS One VL - 16 IS - 8 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/34464419/Higher_entropy_observed_in_SARS_CoV_2_genomes_from_the_first_COVID_19_wave_in_Pakistan_ L2 - https://dx.plos.org/10.1371/journal.pone.0256451 DB - PRIME DP - Unbound Medicine ER -