Genome composition and genetic characterization of SARS-CoV-2

Al-Qaaneh, Ayman M.; Alshammari, Thamer; Aldahhan, Razan; Al-Dossary, Hanan A.; Alkhalifah, Zahra; Borgio, J. Francis

doi:10.1016/j.sjbs.2020.12.053

Cited by 27 publications

(33 citation statements)

References 126 publications

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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%

“…In spite of high homology, each study pointed few different mutations which were either specific or coexist with other mutations. The genetic variation in SARS-CoV-2 genomes could be due to geographical distributions and intra-host viral evolution after infection ( Al-Qaaneh et al, 2021 , Ceraolo and Giorgi, 2020 ). Abduljalil and Abduljalil (2020) stated that the genomic signature studies reveal a strong relation between the time of sampling, location of sample and genetic diversity.…”

Section: Discussionmentioning

confidence: 99%

“…These results are in congruence with Das et al (2021) , who studied 469 SARS-CoV-2 genome sequences, and specified that the susceptible proteins are ORF1ab, spike, nucleocapsid, ORF3a and ORF7a. The ORF1ab is the largest viral segment covering 2/3 of the viral genome ( Koyama et al, 2020 ), contributing important non-structural proteins such as polyprotein, leader protein, 3C-like proteinase, RNA-dependent RNA polymerase, helicase, 3′-to-5′ exonuclease, and endoRNAse, as these proteins influence viral replication and host immune response ( Al-Qaaneh et al, 2021 ). Consequently, many reports stated that the majority of mutations occurred in ORF1ab gene ( Khailany et al, 2020 , Shishir et al, 2021 ).…”

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%

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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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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

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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“…As a member of the Nidovirales order in the Coronaviridae family, SARS-CoV-2 is one of the largest positive-stranded RNA viruses with an approximately 30 kb genome in length with a 5′ cap and a 3′ poly A tail (Wang et al 2020 ; Clark et al 2021 ). The ORF1a and ORF1ab locate in the 5′ terminal viral genomes coding for polyproteins, including pp1a and pp1ab by ribosome shifting, and then the proteases hydrolyze and cleave polyproteins into 16 distinct nonstructural proteins (nsps) (Al-Qaaneh et al 2021 ). The nsps that participate in viral genome replication and transcription are essential for the survival of the SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Chen

et al. 2021

Virol. Sin.

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SARS-CoV-2 has become a global pandemic threatening human health and safety. It is urgent to find effective therapeutic agents and targets with the continuous emergence of novel mutant strains. The knowledge of the molecular basis and pathogenesis of SARS-CoV-2 in host cells requires to be understood comprehensively. The unknown structure and function of nsp2 have hindered our understanding of its role in SARS-CoV-2 infection. Here, we report the crystal structure of the N-terminal of SARS-CoV-2 nsp2 to a high resolution of 1.96 Å. This novel structure contains three zinc fingers, belonging to the C2H2, C4, and C2HC types, respectively. Structure analysis suggests that nsp2 may be involved in binding nucleic acids and regulating intracellular signaling pathways. The binding to single or double-stranded nucleic acids was mainly through the large positively charged region on the surface of nsp2, and K111, K112, K113 were key residues. Our findings lay the foundation for a better understanding of the relationship between structure and function for nsp2. It is helpful to make full use of nsp2 as further research and development of antiviral targets and drug design. Supplementary Information The online version contains supplementary material available at 10.1007/s12250-021-00431-6.

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Genome sequencing reveals molecular epidemiological characteristics and new recombinations of adenovirus in Beijing, China, 2014−2019

Li,

Kang

et al. 2023

Journal of Medical Virology

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To investigate the molecular epidemiological characteristics and genetic variations of human adenovirus (HAdV) in acute respiratory tract infections in Beijing. Whole‐genome sequencing and phylogenetic analyses were performed for 83 strains of HAdV with different types in Beijing from 2014 to 2019. The clinical characteristics of HAdV infection were analyzed statistically. HAdV‐B was divided into four genotypes, including B3 (n = 11), B7 (n = 13), B14 (n = 4), and B55 (n = 2). HAdV‐C was divided into three genotypes, including C1 (n = 14), C2 (n = 13), and C5 (n = 10). In HAdV‐C, nine recombinant adenovirus strains were identified in type 1, and seven recombinant strains were found in type 2. In type 1, we found three newly emerged intraspecific recombinant strains (A47, A48, and A52) collected in 2017, 2018, and 2019, respectively. In addition, the previously reported recombinant strains of HAdV‐C1 showed more severe disease than other strains of HAdV‐C, causing severe community‐acquired pneumonia in both the elderly and children. Continuous population‐wide molecular epidemiological surveillance of HAdV is essential for the prevention and control of respiratory infectious diseases.

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Genome composition and genetic characterization of SARS-CoV-2

Cited by 27 publications

References 126 publications

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

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

Structure and Function of N-Terminal Zinc Finger Domain of SARS-CoV-2 NSP2

Genome sequencing reveals molecular epidemiological characteristics and new recombinations of adenovirus in Beijing, China, 2014−2019

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