Genomic characterization of SARS‐CoV‐2 isolates from patients in Turkey reveals the presence of novel mutations in spike and nsp12 proteins

Abstract

Novel mutations have been emerging in the genome of severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2); consequently, the evolving of more virulent and treatment resistance strains have the potential to increase transmissibility and mortality rates. The characterization of full‐length SARS‐CoV‐2 genomes is critical for understanding the origin and transmission pathways of the virus, as well as identifying mutations that affect the transmissibility and pathogenicity of the virus. We present an analysis of the mutation pattern and clade distribution of full‐length SARS‐CoV‐2 genome sequences obtained from specimens tested at Gazi University Medical Virology Laboratory. Viral RNA was extracted from nasopharyngeal specimens. Next‐generation sequencing libraries were prepared and sequenced on Illumina iSeq 100 platform. Raw sequencing data were processed to obtain full‐length genome sequences and variant calling was performed to analyze amino acid changes. Clade distribution was determined to understand the phylogenetic background in relation to global data. A total of 293 distinct mutations were identified, of which 152 missense, 124 synonymous, 12 noncoding, and 5 deletions. The most frequent mutations were P323L (nsp12), D614G (ORF2/S), and 2421C>T (5′‐untranslated region) found simultaneously in all sequences. Novel mutations were found in nsp12 (V111A, H133R, Y453C, M626K) and ORF2/S (R995G, V1068L). Nine different Pangolin lineages were detected. The most frequently assigned lineage was B.1.1 (17 sequences), followed by B.1 (7 sequences) and B.1.1.36 (3 sequences). Sequence information is essential for revealing genomic diversity. Mutations might have significant functional implications and analysis of these mutations provides valuable information for therapeutic and vaccine development studies. Our findings point to the introduction of the virus into Turkey through various sources and the subsequent spread of several key variants.

Severity, Pathogenicity and Transmissibility of Delta and Lambda Variants of SARS-CoV-2, Toxicity of Spike Protein and Possibilities for Future Prevention of COVID-19

“…According to the NCBI annotation, (NC_045512), SARS-CoV-2 has 14 functional open reading frames (ORFs), which encode up to 31 proteins, shown schematically in Figure 1 [ 3 , 10 ]. The first ORFs, ORF1a and ORF1b, are the longest ORFs and occupy more than two thirds of the whole genome [ 3 , 11 ]. Polyproteins 1a and 1b are encoded by ORFs 1a and 1b.…”

The emergence and epidemic characteristics of the highly mutated SARS‐CoV‐2 Omicron variant

“…23 NSPs, particularly NSP12 and NSP14, of CoVs are indispensable for viral replication and transcription. It has been shown that the P323 L mutation in NSP12 can reduce the fidelity of viral gene replication, 40 , 41 the Δ105–107 mutation in NSP6 may affect the innate immune response and T cell immunity, 42 and the R203K/G204R mutation in the N protein can enhance the virulence of variants. 43 …”

Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant lineages (BA.1, BA.2, BA.3 and BA.1.1)

“…1.9 Mutations in NSP12 At least in Turkey this mutation has been found in a large number of samples [111] and presumably in combination with D614G mutation in the spike protein may have a correlation with severity of the disease [112].…”