The Molecular epidemiology of SARS-COV-2: current scenario in Gilgit, Pakistan

Authors

  • Minhas Alam Department of Animal Sciences /Microbiology, Karakoram International University Gilgit Baltistan, Pakistan , Department of Eastern Medicine, Qarshi University, Lahore, Pakistan
  • Rizwan Asif Department of Eastern Medicine, Qarshi University Lahore, Pakistan
  • Rabbia Pervaiz Department of Biotechnology, Qarshi University, Lahore, Pakistan
  • Sumara Baig Department of Virology, Provincial Headquarter Hospital, Gilgit, Pakistan
  • Abdul Latif Department of Livestock, Gilgit Baltistan
  • Riffat Yasmin Department of Medical Laboratory and Technology, Riphah International University, Faisalabad, Pakistan

DOI:

https://doi.org/10.52461/ijnms.v4i2.2118

Abstract

The epidemic of SARS-CoV-2 emerged in China (Wuhan) at the end of 2019, which created

a global pandemic, subsequently causing a significant health crisis. Although this disease has

become prevalent worldwide, there is very limited data available on its epidemiology and its

molecular characteristics in Gilgit, Pakistan. The aims of this research to share a summary of

the current SARS-CoV-2 epidemiological landscape in Gilgit through epidemiological

surveillance and molecular characterization. A cross-sectional study involved collecting a total

of 117,986 nasopharyngeal swabs from symptomatic patients in Gilgit. The viral RNA was

extracted and amplified using the Thermo-Fisher Auto Extraction Kit and TaqPath

Amplification Kit on the Quant Studio™ 5 Real-Time RT-PCR Detection System,

respectively. Whole-genome sequencing of selected samples was also conducted. The results

showed an overall prevalence of SARS-CoV-2 of 6.89%; the percentage was higher in males

(59.27%) than in females (40.72%). Year-wise prevalence showed a much higher prevalence

of SARS-CoV-2 in 2020 (10.52%), followed by 2022 (10.33%) and 2021 (4.02%). Also, the

mortality rate was highest in 2020 (0.17%), followed by 2021 (0.06%) and 2022 (0.02%). The

results of whole-genome sequencing revealed the presence of the Delta variant (B.1.617.2)

variant of concern in all 2021 samples and the Omicron variant in the majority of 2022

samples. Our study highlights that the effective control measures taken during the pandemic

were the reason for the low prevalence.

Additional Files

Published

2025-12-31

Issue

Vol. 4 No. 2 (2025): International Journal of Natural Medicine and Health Sciences

Section

Articles

License

Copyright (c) 2026 Minhas Alam, Rizwan Asif, Rabbia Pervaiz, Sumara Baig, Abdul Latif ; Riffat Yasmin

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