Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic

Yavarian, Jila; Nejati, Ahmad; Salimi, Vahid; Shafiei-Jandaghi, Nazanin Zahra; Sadeghi, Kaveh; Abedi, Adel; Sharifi-Zarchi, Ali; Gouya, Mohammad Mehdí; Mokhtari‐Azad, Talat

doi:10.1371/journal.pone.0267847

Cited by 29 publications

(36 citation statements)

References 54 publications

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“…Ligand binding, viral oligomerization and packaging, fusion and antibody sensitivity have been reported to be disturbed by these mutations ( Arya et al, 2021 ; Ahamad et al, 2022 ). Moreover, our findings stand in good agreement with the proposal that in addition to the D614G substitution, mutations in the N protein (R203K/G204R mutations) affect infectivity and virulence of SARS-CoV-2 ( Wu S. et al, 2021 ; Yavarian et al, 2022 ). Therefore, future vaccine development programs may also focus on regions other than the Spike protein.…”

Section: Discussionsupporting

confidence: 91%

Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India

et al. 2023

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The emergence and rapid evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a global crisis that required a detailed characterization of the dynamics of mutational pattern of the viral genome for comprehending its epidemiology, pathogenesis and containment. We investigated the molecular evolution of the SASR-CoV-2 genome during the first, second and third waves of COVID-19 in Uttar Pradesh, India. Nanopore sequencing of the SARS-CoV-2 genome was undertaken in 544 confirmed cases of COVID-19, which included vaccinated and unvaccinated individuals. In the first wave (unvaccinated population), the 20A clade (56.32%) was superior that was replaced by 21A Delta in the second wave, which was more often seen in vaccinated individuals in comparison to unvaccinated (75.84% versus 16.17%, respectively). Subsequently, 21A delta got outcompeted by Omicron (71.8%), especially the 21L variant, in the third wave. We noticed that Q677H appeared in 20A Alpha and stayed up to Delta, D614G appeared in 20A Alpha and stayed in Delta and Omicron variants (got fixed), and several other mutations appeared in Delta and stayed in Omicron. A cross-sectional analysis of the vaccinated and unvaccinated individuals during the second wave revealed signature combinations of E156G, F157Del, L452R, T478K, D614G mutations in the Spike protein that might have facilitated vaccination breach in India. Interestingly, some of these mutation combinations were carried forward from Delta to Omicron. In silico protein docking showed that Omicron had a higher binding affinity with the host ACE2 receptor, resulting in enhanced infectivity of Omicron over the Delta variant. This work has identified the combinations of key mutations causing vaccination breach in India and provided insights into the change of [virus’s] binding affinity with evolution, resulting in more virulence in Delta and more infectivity in Omicron variants of SARS-CoV-2. Our findings will help in understanding the COVID-19 disease biology and guide further surveillance of the SARS-CoV-2 genome to facilitate the development of vaccines with better efficacies.

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Section: Discussionsupporting

confidence: 91%

Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India

et al. 2023

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“…V and L clades were discovered during the first wave; G, GH and GR clades identified the second wave; GH and GR were circulating clades during the third wave; and GRY (α variant), GK (δ variant) and one GH clade (β variant) were discovered in the fourth wave. All of the viruses in the fifth wave belonged to the clade GK (δ variant) [ 28 ]. The genomes in the current study were mostly from the clades GH (25%), GR (23%), O (21%) and GRY (14%).…”

Section: Discussionmentioning

confidence: 99%

Variation Analysis of SARS-CoV-2 Complete Sequences from Iran

Moradi

Alvandi

et al. 2022

Future Virol.

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Aim: SARS-CoV-2 is an emerging coronavirus that was discovered in China and rapidly spread throughout the world. The authors looked at nucleotide and amino acid variations in SARS-CoV-2 genomes, as well as phylogenetic and evolutionary events in viral genomes, in Iran. Materials & methods: All SARS-CoV-2 sequences that were publicly released between the start of the pandemic and 15 October 2021 were included. Results: The majority of mutations were found in vaccine target proteins, Spike and Nucleocapsid proteins, and nonstructural proteins. The majority of the viruses that circulated in the early stages of the pandemic belonged to the B.4 lineage. Conclusion: We discovered the prevalence of viral populations in Iran. As a result, tracking the virus’s variation in Iran and comparing it with a variety of nearby neighborhoods may reveal a pattern for future variant introductions.

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“…In the last updates of SARS‐CoV‐2 from 54 sequencing of 5 waves in Iran, different mutations were found in various sections of the genomes. However, the most common mutants were found in the Spike‐D614G, N‐R203K, N‐G204R and NSP12‐P323L 8 . Further analysis of SARS‐CoV‐2 sequencing confirmed that multiple mutations in the genome concentrated in the open reading frame area and SPs 9–11 .…”

Section: Introductionmentioning

confidence: 94%

“…However, the most common mutants were found in the Spike‐D614G, N‐R203K, N‐G204R and NSP12‐P323L. 8 Further analysis of SARS‐CoV‐2 sequencing confirmed that multiple mutations in the genome concentrated in the open reading frame area and SPs. 9 , 10 , 11 The most important variants and mutations ( https://covariants.org/ ) regarding viral infectivity were found in SPs at the position of 614 (D614G) (see Figure 1 ).…”

Section: Introductionmentioning

confidence: 97%

Promising use of immune cell‐derived exosomes in the treatment of SARS‐CoV‐2 infections

Alahdal

Elkord

2022

Clinical & Translational Med

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Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) infection is persistently threatening the lives of thousands of individuals globally. It triggers pulmonary oedema, driving to dyspnoea and lung failure. Viral infectivity of coronavirus disease 2019 (COVID‐19) is a genuine challenge due to the mutagenic genome and mysterious immune‐pathophysiology. Early reports highlighted that extracellular vesicles (exosomes, Exos) work to enhance COVID‐19 progression by mediating viral transmission, replication and mutations. Furthermore, recent studies revealed that Exos derived from immune cells play an essential role in the promotion of immune cell exhaustion by transferring regulatory lncRNAs and miRNAs from exhausted cells to the active cells. Fortunately, there are great chances to modulate the immune functions of Exos towards a sustained repression of COVID‐19. Engineered Exos hold promising immunotherapeutic opportunities for remodelling cytotoxic T cells’ function. Immune cell‐derived Exos may trigger a stable epigenetic repression of viral infectivity, restore functional cytokine‐producing T cells and rebalance immune response in severe infections by inducing functional T regulatory cells (Tregs). This review introduces a view on the current outcomes of immunopathology, and immunotherapeutic applications of immune cell‐derived Exos in COVID‐19, besides new perspectives to develop novel patterns of engineered Exos triggering novel anti‐SARS‐CoV‐2 immune responses.

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Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic

Cited by 29 publications

References 54 publications

Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India

Molecular determinants associated with temporal succession of SARS-CoV-2 variants in Uttar Pradesh, India

Variation Analysis of SARS-CoV-2 Complete Sequences from Iran

Promising use of immune cell‐derived exosomes in the treatment of SARS‐CoV‐2 infections

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