Genetic Analysis and Epidemiological Impact of SARS-CoV-2: A Multinational Study of 1000 Samples Using RT-PCR

• Published in: Applied Microbiology (Basel) 2024-03, Vol.4 (1), p.133-146
• Main Authors: Banser, Talib, Abduljaleel, Zainularifeen, Alzabeedi, Kamal H., Alzahrani, Adil A., Khogeer, Asim Abdulaziz, Qabbani, Fadel Hassan, Almutairi, Ahmed T., Melebari, Sami, Shahzad, Naiyer
• Format: Article
• Language: English
• Subjects: coronavirus disease; COVID-19; pandemic; RT-PCR; SARS-CoV-2
• ISSN: 2673-8007; 2673-8007
• DOI: 10.3390/applmicrobiol4010010

The ongoing global public health challenge posed by the COVID-19 pandemic necessitates continuous research and surveillance efforts. In this study, we comprehensively analyzed over 1000 COVID-19 RT-PCR tests conducted on a cohort of 1200 patients in Saudi Arabia. Our primary goal was to investigate mutations in specific genes RdRp, N, and E different infection and recovery stages in Saudi patients with SARS-CoV-2. We also extended our analysis to include patients of various nationalities residing in Saudi Arabia, with the overarching objective of assessing these genes as markers for COVID-19 presence and progression. To diagnose and investigate potential genetic variations in COVID-19, we engaged RT-PCR. Our study primarily focused on detecting mutations in the RdRp, N, and E genes in Saudi patients with SARS-CoV-2, as well as individuals from various national residing in Saudi Arabia. This molecular technique provided valuable insights into the virus’s genetic makeup during infection and recovery. In our analysis of 671 positive COVID-19 cases, diverse gene involvement patterns were observed. Specifically, 55.91% had mutations in all three genes (RdRp, N, and E), 62.33% in both N and E genes, and 67.16% in RdRp and N genes. Additionally, 30.75% exhibited mutations exclusively in the RdRp gene, and 51.58% had mutations in the N gene. The N gene, in particular, showed high sensitivity as a marker for identifying active viral circulation. Regarding the temporal dynamics of the disease, the median duration between a positive and a subsequent negative COVID-19 RT-PCR test result was approximately 33.86 days for 44% of cases, 14.31 days for 30%, and 22.67 days for 4%. The insights from this study hold significant implications for managing COVID-19 patients during the ongoing pandemic. The N gene shows promise as a marker for detecting active viral circulation, potentially improving patient care and containment strategies. Establishing a defined positive threshold for diagnostic methods and correlating it with a low risk of infection remains a challenge. Further research is needed to address these complexities and enhance our understanding of COVID-19 epidemiology and diagnostics.