Exploring Novel Genetic Mutations in SARS-CoV-2: Insights into Viral Genetic Diversity and Evolutionary Dynamics

 The study aimed to detect SARS-CoV-2 using custom-designed primers in conventional PCR, targeting RdRp, E, and N genes, and assess regional isolate genetic diversity compared to global strains.

 In Sulaimani City, Iraq, from September 2020 to September 2021, 200 positive nasopharyngeal samples were collected, and 17 known variants with the S gene were randomly selected for whole RdRp, E, and N gene sequencing. To facilitate sequencing, six primer sets were designed for the RdRp gene (RdRp1, RdRp2, RdRp3), two for the N gene (N1, N2), and one for the E gene.

 Twelve mutations in the RdRp gene were identified, with the most common mutation being 14408C>T (P323L). In the N gene, a unique mutation, 28977C>T (S235F), was detected in eight samples of various variants alongside other amino acid-altering point mutations (28280-2GAT>CTA and 2881-3GGG>AAC). The E gene exhibited amino acid-altering mutations (S68F and I13L) in two samples. The most frequent mutation, 28977C>T (S235F), was identified in eight samples representing alpha, gamma, and cluster 5 variants.

 A novel mutation, specifically 28280-2GAT>CTA, resulting in D3L, along with three other mutations (28484G>A, 29129T>G, 29131T>C) causing amino acid substitutions (G70S, N284K, F285L) were identified in the N gene. Additionally, a unique mutation at 26281 A>T in the E gene was observed in the Wuhan variant.