The surveillance of spike protein mutations of SARS-COV-2 omicron subvariant isolated from Duhok province, Iraq

Abstract

Background: In 2020, many fast-spreading SARS-CoV-2 variants emerged with significant spike protein mutations. Understanding these genetic changes revealed that variants of concern (VOC) increased virus replication and immune system evasion. 

Methods: This study involved sequencing the entire genome of the SARS-CoV-2 virus from forty cases in Duhok, Iraq. RNA was extracted using the QIAamp Viral RNA Mini Kit (Qiagen, MD). The extracted RNA underwent reverse transcription with SuperScript IV VILO (ThermoFisher Scientific, Waltham, MA). The virus cDNA was then amplified in two multiplexed PCR reactions using Q5 DNA High-fidelity Polymerase (New England Biolabs, Ipswich, MA). The complete genome sequencing was performed on this sample at the Scripps Research Institute (TSRI) in California, USA. Sequencing was conducted using the NovaSeq 6000 SP Reagent Kit v1.5 (Illumina, USA). TSRI subsequently uploaded the sequence to the GISAID database.

Results: The viral sequence was analyzed in comparison to the SARS-CoV-2 variant from Wuhan, China (accession number: NC 045512.2), utilizing Illumina sequencing technology (Illumina, CA). This examination identified 25 unique mutations. The SARS-CoV-2 genome was aligned and mutation analysis performed using the NextClade software tool available at clades.nextstrain.org. The sequencing investigation concluded that the spike glycoprotein (S) exhibited a total of 25 mutations.

Conclusion: A continuous genetic surveillance system is crucial. This method would improve the prompt detection of mutations that could increase the virus's infectivity and those selected by the virus to evade immune responses.