Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Almubaid, Zaid; Al-Mubaid, Hisham

doi:10.1016/j.genrep.2021.101064

Cited by 31 publications

(31 citation statements)

References 24 publications

(56 reference statements)

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“…Mutations are an inherent feature of all viruses; however, RNA viruses present higher mutation rates than DNA viruses [ 3 , 4 ]. The mutability magnitude of RNA in comparison to some DNA viruses can exceed by up to five orders [ 5 ].…”

Section: Introductionmentioning

confidence: 99%

The Emerging Concern and Interest SARS-CoV-2 Variants

et al. 2021

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 2019 (COVID-19) was discovered in December 2019 in Wuhan, China. Since that time, the virus has spread around the world, which resulted in an announcement of the World Health Organization (WHO), dated in March 2020, that COVID-19 was a worldwide pandemic, and since then, the world has been struggling with this disease. SARS-CoV-2, similar to other RNA viruses, continually mutates, and new variants are appearing. Among large numbers of detected SARS-CoV-2 variants, only an insignificant amount of them are able to pose a risk to public health, as they are more contagious and cause more severe conditions. The emerged variants were classified by the Centers for Disease Control and Prevention (CDC) in collaboration with SARS-CoV-2 Interagency Group (SIG) according to strictly defined pattern. Variants were classified as variants of concern, variants of interest, and variants of high consequence. In the last few months, three variants of concern (B.1.1.7, B.1.351, and P.1) and four variants of interests (B.1.526, B.1.525, B.1.427/B.1.429, and P.2) were distinguished and are essential for close monitoring. This analysis summarizes the principal information concerning SARS-CoV-2 variants, such as their infectivity, severity, mutations, and immune susceptibility.

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Section: Introductionmentioning

confidence: 99%

The Emerging Concern and Interest SARS-CoV-2 Variants

et al. 2021

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“…Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, local confirmed cases had risen exponentially with up to nearly 900 newly registered cases daily which represents almost 0.5% of daily registered cases worldwide (Almubaid and Al-Mubaid, 2021). Summertime holidays, with the regional movement of tourists between Serbia and countries that had left borders open, had permitted expansion of the epicenter of the epidemic and made an impact on distribution dynamics of virus lineages and clades.…”

Section: Discussionmentioning

confidence: 99%

“…One of them, ORF1ab, is proteolytically cleaved into 16 non-structural proteins (nsp1-nsp16) that are essential for viral replication and immune evasion (Snijder et al, 2003;Cagliani et al, 2020). Other open reading frames, located in between genes for structural proteins, define accessory proteins: ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 (Almubaid and Al-Mubaid, 2021).…”

Section: Introductionmentioning

confidence: 99%

The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

Miljanovic

Milićević

Lončar³

et al. 2021

Front. Microbiol.

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March 6, 2020 is considered as the official date of the beginning of the COVID-19 epidemic in Serbia. In late spring and early summer 2020, Europe recorded a decline in the rate of SARS-CoV-2 infection and subsiding of the first wave. This trend lasted until the fall, when the second wave of the epidemic began to appear. Unlike the rest of Europe, Serbia was hit by the second wave of the epidemic a few months earlier. Already in June 2020, newly confirmed cases had risen exponentially. As the COVID-19 pandemic is the first pandemic in which there has been instant sharing of genomic information on isolates around the world, the aim of this study was to analyze whole SARS-CoV-2 viral genomes from Serbia, to identify circulating variants/clade/lineages, and to explore site-specific mutational patterns in the unique early second wave of the European epidemic. This analysis of Serbian isolates represents the first publication from Balkan countries, which demonstrates the importance of specificities of local transmission especially when preventive measures differ among countries. One hundred forty-eight different genome variants among 41 Serbian isolates were detected in this study. One unique and seven extremely rare mutations were identified, with locally specific continuous dominance of the 20D clade. At the same time, amino acid substitutions of newly identified variants of concern were found in our isolates from October 2020. Future research should be focused on functional characterization of novel mutations in order to understand the exact role of these variations.

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“…The rapid transmission and world wide spread of SARS-CoV-2 reflect its ability to adapt to different environments and conditions. The nucleotides changes during the course of transmission drive the genome variability and viral evolution in a way that affects the transmission, pathogenesis, diagnosis, disease course, and treatment outcome ( Almubaid and Al-Mubaid, 2021 , Al-Qaaneh et al, 2021 , Islam et al, 2020 ). Therefore the present study determined the nucleotides changes in SARS-CoV-2 variants isolated in KSA.…”

Section: Discussionmentioning

confidence: 99%

“…The outbreak dynamics of Covid 19 varies among regions and countries; this may be due to several factors such environment, cultural practices and public health system that comprises testing rate and surveillance policies ( Bandoy and Weimer, 2021 ). Recently several studies were conducted regionally and globally to determine the mutations of SARS-CoV-2 ( Almubaid and Al-Mubaid, 2021 , Al-Qaaneh et al, 2021 ). Considering the history of MERS-CoV which was first identified in Saudi Arabia in 2012, ( WHO, 2021 ) the population dynamics of Saudi Arabia as center of Islamic world and the great numbers of overseas workers, the determination of the nucleotide changes of SARS-CoV-2 in Saudi Arabia (KSA) may be of great interest.…”

Section: Introductionmentioning

confidence: 99%

Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study

Ullah

Alnour

Elssaig

et al. 2021

Saudi Journal of Biological Sciences

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SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico , cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5′UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.

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Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Cited by 31 publications

References 24 publications

The Emerging Concern and Interest SARS-CoV-2 Variants

The Emerging Concern and Interest SARS-CoV-2 Variants

The First Molecular Characterization of Serbian SARS-CoV-2 Isolates From a Unique Early Second Wave in Europe

Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study

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