SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study)

Hajazadeh, Faezeh; Khanizadeh, Sayyad; Khodadadi, Hamidreza; Mokhayeri, Yaser; Ajorloo, Mehdi; Malekshahi, Asra; Heydari, Ezatoallah

doi:10.1016/j.micpath.2022.105595

Cited by 19 publications

(18 citation statements)

References 30 publications

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“…For instance, in Iran, nested PCR and sequencing were used to amplify the RBD of the spike protein that has found mutations (D614G, L452R, and T478K) in the Delta variant, and (D614G, T478K, G496S, and T547K) in Omicron variant. 27 Furthermore, in Japan and Iraq studies sequenced the whole spike protein gene using several pairs of primers and PCR reactions that identified mutations of VOCs. 28,30 In the current study, 13 mutations (K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, and D614G) in the Omicron BA.1 subvariants and five mutations (D614G, L452R, T478K, F456L, F490S) in the novel Delta variant were found using only a pair of primer and a single reaction that is less expensive and more time-saving than previous methods.…”

Section: Discussionmentioning

confidence: 99%

“…Sequencing of the SARS CoV‐2 spike gene has been used to identify the most common mutations. For instance, in Iran, nested PCR and sequencing were used to amplify the RBD of the spike protein that has found mutations (D614G, L452R, and T478K) in the Delta variant, and (D614G, T478K, G496S, and T547K) in Omicron variant 27 . Furthermore, in Japan and Iraq studies sequenced the whole spike protein gene using several pairs of primers and PCR reactions that identified mutations of VOCs 28,30 .…”

Section: Discussionmentioning

confidence: 99%

“…13 In Denmark, L452 and 452R markers were putatively used to differentiate between Omicron and Delta variants, respectively. 13 Identifications of both Delta and Omicron variants, by using either rapid molecular methods or sequencing, have been investigated in many countries including the United States, [16][17][18][19] United Kingdom, 3,20 Germany, 21,22 Denmark, 13 Italy, 11,23 Ecuador, 24 China, 25 Taiwan, 6 Belgium, 1 Malaysia, 26 Iran, 27 and Japan. 28 Such rapid molecular methods are uncommon in Iraq and Kurdistan region.…”

Section: Who Labelmentioning

confidence: 99%

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Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Rasheed

Awrahman

Al-Jaf

et al. 2023

Immunity Inflam & Disease

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Background: Five variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) have been globally recorded including Alpha, Beta, Gamma, Delta, and Omicron. The Omicron variant has outcompeted the other variants including the Delta variant. Molecular screenings of VOCs are important for surveillance, treatment, and vaccination programs. This study aimed to identify VOCs by using rapid inexpensive methods and partial sequencing of the virus's spike gene.Methods: Mutation-specific rRT PCR probes were used for both D614G and K417N mutations to potentially discriminate between Delta and Omicron variants. These were followed by sequencing of a fragment of spike gene (748 nucleotides), which covers the most notable VOC mutations in the receptor binding domain of SARS CoV-2.Results: Rapid methods showed that out of 24 SARS CoV-2 positive samples, 19 carried the N417 mutation, which is present in the Omicron variant. Furthermore, 3 samples carried K417 wildtype, which is present in the Delta variant. Additionally, 2 samples containing both K417 and N417 suggested mixed infections between the two variants. The D614G mutation was present in all samples. Among the 4 samples sequenced, 3 samples carried 13 mutations, which are present in Omicron BA.1. The fourth sample contained the two common mutations (T478K and L452R) present in Delta, in addition to two more rare mutations (F456L and F490S), which are not commonly seen in Delta. Our data suggested that both Omicron variant BA.1 and a novel Delta variant might have circulated in this region that needs further investigations.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Who Labelmentioning

confidence: 99%

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Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Rasheed

Awrahman

Al-Jaf

et al. 2023

Immunity Inflam & Disease

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“…Curiously, this depends on its set of mutations; there are 15 mutations in the receptor-binding domain (the part of the spike that mediates the binding of the virus to the cell) and there are also 3 mutations near the furin cleavage site that may be involved in making the variant more transmissible. By the same token, a group of four new mutations could create additional obstacles for antibodies [ 37 , 38 ]. Despite it being such a feared variant, strictly because of the characteristics belonging to it, our study showed that it was associated in a reductive way with the emergence of anosmia and dysgeusia.…”

Section: Discussionmentioning

confidence: 99%

Risk Factors for Persistent Anosmia and Dysgeusia in Children with SARS-CoV-2 Infection: A Retrospective Study

et al. 2023

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Background: Olfactory and gustative dysfunctions are two of the most common post-acute sequelae of SARS-CoV-2 infection in children, which can have a negative impact on the routines of children and families. As several children have had COVID-19 since the Omicron variant, it is important to investigate if this increase in infections is reflected in higher olfactory/taste disfunctions. The primary aim of this study was to characterize the presence of olfactory/gustative problems in a cohort of children, its evolution, and its association with risk factors such as COVID-19 variant, hospitalization, presence of olfactory/gustative dysfunction during the acute phase, and vaccination. Methods: This was a retrospective analysis of children with microbiologically confirmed SARS-CoV-2 infection evaluated in person at a referral pediatric post-COVID-19 clinic in Rome, Italy. We included children younger than 19 years old, evaluated from the beginning of the pandemic up to October 2022. At specific timepoints, we investigated the presence of olfactory/taste disfunctions and evaluated them according to the SARS-CoV-2 variants circulating at the time of infection. Results: A total of 1250 children (650 females; 52.0%) with a mean age of 6.77 (±4.12) years were included in the study. At 3, 6, 12, and 18 months, 12 (9.6%), 7 (5.6%), 2 (1.6%), and 1 (0.8%) of the children reported anosmia and dysgeusia post-COVID-19 infection, respectively. The presence of anosmia and dysgeusia during the acute phase of infection and being infected with a pre-Omicron variant were found to be significant risk factors for persistent olfactory and gustatory dysfunction during all follow-up periods. Conclusions: anosmia and dysgeusia symptoms tended to decrease gradually over time, but not all children recovered quickly.

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“…During the pandemic, the intermittent emergence of multiple variants of concern (VOC) was observed, which played a primary role in maintaining the pandemic across various countries worldwide (Mlcochova et al 2021;Tao et al 2021). The mutation profiles in previous VOCs have been primarily evaluated and categorized based on single nucleotide substitutions (i.e., point mutations), especially in the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) gene S1 subunit (SeyedAlinaghi et al 2021;Hajizadeh et al 2022). Recently, hotspots of insertions/deletions (indels) have been reported in the open reading frame 1a (ORF1a) polyprotein-encoding gene and N-terminal domain (NTD) of the S1 gene in various SARS-related coronaviruses (Akaishi 2022a), suggesting the importance of mutations in these genomic sites that are different from S1 RBD in the subgenus Sarbecovirus.…”

Section: Introductionmentioning

confidence: 99%

Trinucleotide Substitutions at Two Locations in the SARS-CoV-2 Nucleocapsid (<i>N</i>) Gene

Akaishi

Fujiwara

Ishii

2023

Tohoku J. Exp. Med.

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The genomes of sarbecoviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), incorporate mutations with short sequence exchanges based on unknown processes. Currently, the presence of such short-sequence exchanges among the genomes of different SARS-CoV-2 lineages remains uncertain. In the present study, multiple SARS-CoV-2 genome sequences from different clades or sublineages were collected from an international mass sequence database and compared to identify the presence of short sequence exchanges. Initial screening with multiple sequence alignments identified two locations with trinucleotide substitutions, both in the nucleocapsid (N) gene. The first exchange from 5´-GAT-3´ to 5´-CTA-3´ at nucleotide positions 28280-28282 resulted in a change in the amino acid from aspartic acid (D) to leucine (L), which was predominant in clade GRY (Alpha).The second exchange from 5´-GGG-3´ to 5´-AAC-3´ at nucleotide positions 28881-28883 resulted in an amino acid change from arginine and glycine (RG) to lysine and arginine (KR), which was predominant in GR (Gamma), GRY (Alpha), and GRA (Omicron). Both trinucleotide substitutions occurred before June 2020. The sequence identity rate between these lineages suggests that coincidental succession of single-nucleotide substitutions is unlikely. Basic local alignment search tool sequence search revealed the absence of intermediating mutations based on single-base substitutions or overlapping indels before the emergence of these trinucleotide substitutions. These findings suggest that trinucleotide substitutions could have developed via an en bloc exchange. In summary, 8The present study was approved by the institutional review board of Tohoku University Graduate School of Medicine (approval number: 2022-1-720). The findings of this study are based on metadata associated with 14,329,052 sequences, which were sampled from humans and available on GISAID up to December 22, 2022, via gisaid.org/EPI_SET_230112cr. RESULTS Sites with an exchange of ≥ 3 consecutive nucleotidesTwo sets of multiple sequence alignments with different sets of 25 sequences identified two sites with base exchanges in three consecutive nucleotides, both in the N gene. The first site was located at the N-terminal domain of the coding region of the N gene corresponding to the nucleotide positions of 28280-28282 nt in the SARS-CoV-2 genome sequence, and a change in the nucleotide sequence from "GAT" to "CTA" was observed. The coded amino acid was changed from aspartic acid (D) to leucine (L). This first trinucleotide exchange site was identified in both evaluated sequences from clade GRY (Alpha). The second site was located at the nucleotide positions of 28881-28883 nt in the middle of the SARS-CoV-2 N gene, and a change in the nucleotide sequence from "GGG" to "AAC" was observed. The coded amino acids were changed from the succession of arginine and glycine (203-204 amino acids: RG) to lysine and arginine (KR). This second trinucleotide exchange site was identified

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SARS-COV-2 RBD (Receptor binding domain) mutations and variants (A sectional-analytical study)

Cited by 19 publications

References 30 publications

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Risk Factors for Persistent Anosmia and Dysgeusia in Children with SARS-CoV-2 Infection: A Retrospective Study

Trinucleotide Substitutions at Two Locations in the SARS-CoV-2 Nucleocapsid (<i>N</i>) Gene

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