Mutations in SARS-CoV-2 structural proteins: a global analysis

Abavisani, Mohammad; Rahimian, Karim; Mahdavi, Bahar; Tokhanbigli, Samaneh; Siasakht, Mahsa Mollapour; Farhadi, Amin; Kodori, Mansoor; Mahmanzar, Mohammadamin; Meshkat, Zahra

doi:10.1186/s12985-022-01951-7

Cited by 46 publications

(53 citation statements)

References 57 publications

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“…Their mutational burden is by comparison much lower than that of the S protein. Hence, using these virus structural proteins could lead to more robust and durable immune responses without the need for regularly changing the S protein strain in vaccine formulations [ 126 ].…”

Section: Discussionmentioning

confidence: 99%

mRNA Vaccines against SARS-CoV-2: Advantages and Caveats

Echaide

Chocarro

Bocanegra

et al. 2023

IJMS

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The application of BNT162b2 and mRNA-1273 vaccines against SARS-CoV-2 infection has constituted a determinant resource to control the COVID-19 pandemic. Since the beginning of 2021, millions of doses have been administered in several countries of North and South America and Europe. Many studies have confirmed the efficacy of these vaccines in a wide range of ages and in vulnerable groups of people against COVID-19. Nevertheless, the emergence and selection of new variants have led to a progressive decay in vaccine efficacy. Pfizer–BioNTech and Moderna developed updated bivalent vaccines—Comirnaty and Spikevax—to improve responses against the SARS-CoV-2 Omicron variants. Frequent booster doses with monovalent or bivalent mRNA vaccines, the emergence of some rare but serious adverse events and the activation of T-helper 17 responses suggest the need for improved mRNA vaccine formulations or the use of other types of vaccines. In this review, we discuss the advantages and limitations of mRNA vaccines targeting SARS-CoV-2 focusing on the most recent, related publications.

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Section: Discussionmentioning

confidence: 99%

mRNA Vaccines against SARS-CoV-2: Advantages and Caveats

Echaide

Chocarro

Bocanegra

et al. 2023

IJMS

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“…Omicron has 40 mutations including more than 30 mutations in protein S, one mutation in protein E, three mutations in protein M, and six mutations in protein N. 33 …”

Section: Discussionmentioning

confidence: 99%

Genomic surveillance of SARS‐CoV‐2 strains circulating in Iran during six waves of the pandemic

Sadeghi

Zadheidar

Zebardast

et al. 2023

Influenza Resp Viruses

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Background SARS‐CoV‐2 genomic surveillance is necessary for the detection, monitoring, and evaluation of virus variants, which can have increased transmissibility, disease severity, or other adverse effects. We sequenced 330 SARS‐CoV‐2 genomes during the sixth wave of the COVID pandemic in Iran and compared them with five previous waves, for identifying SARS‐CoV‐2 variants, the genomic behavior of the virus, and understanding its characteristics. Methods After viral RNA extraction from clinical samples collected during the COVID‐19 pandemic, next generation sequencing was performed using the Nextseq and Nanopore platforms. The sequencing data were analyzed and compared with reference sequences. Results In Iran during the first wave, V and L clades were detected. The second wave was recognized by G, GH, and GR clades. Circulating clades during the third wave were GH and GR. In the fourth wave, GRY (alpha variant), GK (delta variant), and one GH clade (beta variant) were detected. All viruses in the fifth wave were in GK clade (delta variant). In the sixth wave, Omicron variant (GRA clade) was circulating. Conclusions Genome sequencing, a key strategy in genomic surveillance systems, helps to detect and monitor the prevalence of SARS‐CoV‐2 variants, monitor the viral evolution of SARS‐CoV‐2, identify new variants for disease prevention, control, and treatment, and also provide information for and conduct public health measures in this area. With this system, Iran could be ready for surveillance of other respiratory virus diseases besides influenza and SARS‐CoV‐2.

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“…These proteins are involved in the host cell recognition, entry and uncoating, replication and transcription, assembly, and release, among other functions (details below). In particular, the four genes coding for structural proteins, from 5′to 3′, are the gene S (nucleotide positions 21563-25384, encoding the spike glycoprotein [16]), the gene E (nucleotide positions 26245-26472, which produces the viral envelope proteins [17]), the gene M (nucleotide positions 26523-27191, leading to the membrane M protein [17]), and the gene N (nucleotide positions 28274-29533, encoding nucleocapsid N proteins [18]). Briefly (see also Figure 1), the spike glycoprotein binds the virus to the cell receptor; thus, its diversity should be considered in studies on the transmissibility of the virus and the design of certain therapies [19].…”

Section: The Sars-cov-2 Genome and Proteinsmentioning

confidence: 99%

Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic

González-Vázquez

Arenas

2023

Genes

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10−3–10−4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.

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Mutations in SARS-CoV-2 structural proteins: a global analysis

Cited by 46 publications

References 57 publications

mRNA Vaccines against SARS-CoV-2: Advantages and Caveats

mRNA Vaccines against SARS-CoV-2: Advantages and Caveats

Genomic surveillance of SARS‐CoV‐2 strains circulating in Iran during six waves of the pandemic

Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic

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