ABSTRACT
The ongoing pandemic of COVID-19 caused by the SARS-COV2 virus has triggered millions of deaths around the globe. Emerging several variants of the virus with increased transmissibility, the severity of disease, and the ability of the virus to escape from the immune system has a cause for concerns. Here, we compared the spike protein sequence of 91 human SARS CoV2 strains of Iraq to the first reported sequence of SARS-CoV2 isolate from Wuhan Hu-1/China. The strains were isolated between June 2020 and March 2021. Twenty-two distinct mutations were identified within the spike protein regions which were: L5F, L18F, T19R, S151T, G181A, A222V, A348S, L452 (Q or M), T478K, N501Y, A520S, A522V, A570D, S605A, D614G, Q675H, N679K, P681H, T716I, S982A, A1020S, D1118H. The most frequently mutations occurred at the D614G (87/91), followed by S982A (50/91), and A570D (48/91), respectively. In addition, a distinct shift was observed in the type of SARS-COV2 variants present in 2020 compared to 2021 isolates. In 2020, B.1.428.1 lineage was appeared to be a dominant variant (85%). However, the diversity of the variants increased in 2021, and the majority (73%) of the isolated were appeared to belong to B.1.1.7 lineage (VOC/alpha variants). To our knowledge, this is the first major genome analysis of SARS-CoV2 in Iraq. The data from this research could provide insights into SARS-CoV2 evolution, and can be potentially used to recognize the effective vaccine against the disease.
ABSTRACT
SARS-CoV-2 is mutating and creating divergent variants by altering the composition of essential constituent proteins. Pharmacologically, it is crucial to understand the diverse mechanism of mutations for stable vaccine or anti-viral drug design. Our current study concentrates on all the constituent proteins of 469 SARS-CoV-2 genome samples, derived from Indian patients. However, the study may easily be extended to the samples across the globe. We perform clustering analysis towards identifying unique variants in each of the SARS-CoV-2 proteins. A total of 536 mutated positions within the coding regions of SARS-CoV-2 proteins are detected among the identified variants from Indian isolates. We quantify mutations by focusing on the unique variants of each SARS-CoV-2 protein. We report the average number of mutation per variant, percentage of mutated positions, synonymous and non-synonymous mutations, mutations occurring in three codon positions and so on. Our study reveals the most susceptible six (06) proteins, which are ORF1ab, Spike (S), Nucleocapsid (N), ORF3a, ORF7a, and ORF8. Several non-synonymous substitutions are observed to be unique in different SARS-CoV-2 proteins. A total of 57 possible deleterious amino acid substitutions are predicted, which may impact on the protein functions. Several mutations show a large decrease in protein stability and are observed in putative functional domains of the proteins that might have some role in disease pathogenesis. We observe a good number of physicochemical property change during above deleterious substitutions.