GENOMIC SURVEILLANCE OF SARS-COV-2: WHOLE-GENOME CHARACTERIZATION OF AN ALPHA VARIANT

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequencing remains essential for monitoring viral evolution, disease progression, control strategies, vaccine design, and therapeutic development. Balochistan, the largest province of Pakistan, shares borders with Iran and Afghanistan and experiences frequent cross-border movement, creating a strong need to characterize circulating regional variants. In this study, a nasopharyngeal swab from an adult male patient visiting the Public Health Laboratory, Quetta, in November 2021 was processed for whole-genome sequencing using the Illumina NextSeq500 next-generation sequencing platform. The isolate was assigned to the Alpha lineage and deposited under accession number OQ983908.1. Comparative analysis against the reference genome identified 20 mutations. Ten spike-protein mutations were detected, including three deletions and seven missense changes: H69, H70, Y144, A570D, N501Y, D614G, P681H, T716I, S982A, and D1118H. Six missense mutations occurred in ORF1ab, including N460Y, T1001I, A1708D, K1763N, I2230P, and P314L. Two mutations were identified in the nucleocapsid protein, G204R and S235F, and two occurred in ORF8, Q27- and Y73C. Phylogenetic analysis clustered the isolate with sequences from the USA, Italy, and Austria. These findings expand the epidemiological and evolutionary record of SARS-CoV-2 in Pakistan.