Pharma Focus Asia

Unravelling the Link Between SARS-CoV-2 Mutation Frequencies, Patient Comorbidities, and Structural Dynamics

Amirah Azzeri, Nurul Azmawati Mohamed, Saarah Huurieyah Wan Rosli, Muttaqillah Najihan Abdul Samat, Zetti Zainol Rashid, Muhamad Arif Mohamad Jamali, Muhammad Zarul Hanifah Md Zoqratt, Muhammad Azamuddeen Mohammad Nasir, Harpreet Kaur Ranjit Singh, Liyana Azmi.

Abstract

Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance.

Introduction:

The coronavirus disease-2019 (COVID-19) was first isolated from Wuhan City, Hubei Province, China in December 2019. It is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2,) a novel betacoronavirus (β-CoV). The SARS-CoV-2 genome showed 79% homology to SARS-CoV, therefore possesses similarities of its pathogenesis, epidemiology, viral origin, and mechanism of action to SARS-CoV. Symptoms of SARS-CoV-2 infection vary widely in humans, ranging from mild flu-like symptoms such as fever, fatigue, and dry cough to complete respiratory failure.

Discussion:

Our genomic analysis of 99 samples revealed a prominent prevalence of the Pango AY.59 lineage during Malaysia’s third wave of COVID-19. Interestingly, another study noted a dominance of AY.79 in West Coast areas of Malaysia, indicating the infection patterns of the infected patients between June–December 2021 [22]. Notably, the Delta variant is notable for its heightened virulence and prompted us to explore the correlation between patient comorbidity levels and the manifestation of SARS-CoV-2 mutations.

Acknowledgments:

We gratefully acknowledge all SARS-CoV-2 data contributors, i.e., the Authors, their originating and submitting laboratories responsible for obtaining the specimens, including Mohd Noor Mat Isa from Malaysia Genome and Vaccine Institute (MGVI), Universiti Kebangsaan Malaysia, and Nor Azila Muhammad Azami from Universiti Kebangsaan Malaysia Institute Molecular Biology for generating the genetic sequence, metadata and sharing via the GISAID Initiative, on which this research is based. We would also like to acknowledge Dr. Azima Abdul Aziz from Universiti Putra Malaysia for the proof reading of this manuscript. Finally, we would like to extend our appreciation to Associate Professor Dr. Amir Syahir Amir Hamzah from Universiti Putra Malaysia for his assistance in providing the server for our molecular dynamic simulations. This research was funded by USIM Internal Grant, grant number PPPI/FPSK/0122/USIM/14622 and PPPI/FPSK/0122/USIM/14322. Ethics approval by Research Ethics Committee, Universiti Kebangsaan Malaysia (JEP-2022-805).

Citation: Azzeri A, Mohamed NA, Wan Rosli SH, Abdul Samat MN, Rashid ZZ, Mohamad Jamali MA, et al. (2024) Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics. PLoS ONE 19(3): e0291892. https://doi.org/10.1371/journal.pone.0291892

Editor: Ahmed A. Al-Karmalawy, Ahram Canadian University, EGYPT

Received: September 14, 2023; Accepted: February 23, 2024; Published: March 14, 2024.

Copyright: © 2024 Azzeri et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: This study was funded by two the Universiti Sains Islam Malaysia Internal Research Grants: AA - Grant number PPPI/FPSK/0122/USIM/14622 and LA - Grant number PPPI/FPSK/0122/USIM/14322). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

 

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