Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study

Sallam, Malik; Ababneh, Nidaa A.; Dababseh, Deema; Bakri, Faris G.; Mahafzah, Azmi

doi:10.1101/2020.08.24.20176792

Cited by 3 publications

(7 citation statements)

References 61 publications

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“…Another mutation was S477I detected in Tangerang, western border of Jakarta. Other studies reported this S477 substitution but in different residue S477G ( 20 ) and S477R in Egypt ( 19 ).…”

Section: Discussionmentioning

confidence: 64%

“…This mutation tends to increase in many countries, as also reported by Sallam et al that D614G mutation predominates in the Middle East and North Africa. It was noticed the escalation percentage from 63.0% in February to 98.5% in four months later ( 19 ).…”

Section: Discussionmentioning

confidence: 99%

“…In Egypt, the Q677H mutation, was detected as the most frequent mutation after D614G. It was recorded in 8 samples from total 553 samples from Middle East and North Africa (MENA) ( 19 ). Since this mutation frequently appeared in MENA region, it may indicate that this substitution spread worldwide from Middle East.…”

Section: Discussionmentioning

confidence: 99%

“…The study of variation in Spike Receptor Binding Domain protein had been reported ( 19 , 20 , 23 ). In MENA there are at least 8 different Spike Receptor Binding Domain variants ( 19 ).…”

Section: Discussionmentioning

confidence: 99%

“…The study of variation in Spike Receptor Binding Domain protein had been reported ( 19 , 20 , 23 ). In MENA there are at least 8 different Spike Receptor Binding Domain variants ( 19 ). The multiple point mutations even reported in China, India, Australia, Taiwan, Malaysia, Canada, Spain, and UK ( 23 ).…”

Section: Discussionmentioning

confidence: 99%

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Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia

Ulfah¹,

Helianti²

2021

IJM

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Background and Objectives: In first May 2020, Indonesia has been successfully submitted the first three full-length sequence of SARS-CoV-2 to GISAID database. Until September 10th , 2020, Indonesia had submitted 54 WGS. In this study, we have analyzed and annotated SARS-CoV-2 mutations in spike protein and main proteases. Materials and Methods: The Whole Genome Sequence (WGS) of Indonesia were obtained from GISAID data base. The 54 data were taken from March to September 10th, 2020. The sequences corresponded to Spike Protein (SP), 3-chymotrypsin like protease (3CLpro), and papain like protease (PLpro) were selected. The Wuhan genome was used as reference. Results: In total WGS from Indonesia, we found 5 major clades, which dominated as G clade, where the mutation of D614G was found. This D614G was identified as much as 59%, which mostly reported in late samples submitted. Beside D614G mutation, we report three unique mutations: A352S, S477I, and Q677H. Besides, some mutations were also detected in two domains that were expected to be conserved region, the main viral proteases: PLpro (P77L and V205I), 3CLpro (M49I and L50F). Conclusion: The analysis of SARS-CoV-2 from WGS Indonesia showed a high genetic variation. The diversity in SARSCoV-2 may epidemiologically enhance virulence and transmission of this virus. The prevalence of D614G over the time in different locations, indicating that changes in this mutation may related to host infection and the viral transmission. However, some mutations that have been reported in this study were not eligible for the most stable conformation.

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“…Another mutation was S477I detected in Tangerang, western border of Jakarta. Other studies reported this S477 substitution but in different residue S477G ( 20 ) and S477R in Egypt ( 19 ).…”

Section: Discussionmentioning

confidence: 64%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…The study of variation in Spike Receptor Binding Domain protein had been reported ( 19 , 20 , 23 ). In MENA there are at least 8 different Spike Receptor Binding Domain variants ( 19 ).…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 3 more Smart Citations

Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia

Ulfah¹,

Helianti²

2021

IJM

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Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country

Al-Mahruqi

Wahaibi

Khan

et al. 2021

International Journal of Infectious Diseases

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Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. Methods: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The wholegenome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. Findings: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Interpretation: Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.

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SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia

Obeid

Alsanea

Alnemari

et al. 2021

J Infect Dev Ctries

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Introduction: In December 2019, a new severe acute respiratory syndrome coronavirus, SARS-CoV-2, emerged in China, causing coronavirus disease 2019. The present study investigated genetic profiles and variations of SARS-CoV-2 distributed in different regions of Saudi Arabia to begin to understand the pathogenesis and transmission of SARS-CoV-2 in this country and analyzed associations of these variations with host factors. Methodology: In total, 774 SARS-CoV-2 genomic sequences obtained and annotated by the Global Initiative on Sharing All Influenza Data (GISAID) were captured and analyzed. Results: The most common SARS-CoV-2 clades in Saudi Arabia were GH followed by O, GR, G, and S. Statistically significant associations were detected between clades and patient outcome. Age, as a host factor, was significantly associated with many variables, including virus geographical location, clade, and patient outcome. The most common variants detected were the NSP12_P323L mutation 94.9%, followed by the D614G mutation (76%) and the NS3_Q57H mutation (71.4%). The concerned variants B.1.1.7, B.1.351, and P.1 were not detected in our population. D614G was associated with higher morbidities than the wild-type virus, including higher rates of death and hospitalization. The NS3_Q57H mutation was the only variant associated with better patient outcome than the wild type. Risk of death was highest with the NSP12_P323L mutation (OR = 1.84; 95% CI = 0.37-9.30) and lowest with the NS3_Q57H mutation (OR = 0.43; 95% CI = 0.25-0.727). Conclusions: SARS-CoV-2 has evolved uniquely and independently in Saudi Arabia. Our findings provide evidence to begin linking the evolutionary implications to host factors and their effects on the virus severity and transmission.

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Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study

Cited by 3 publications

References 61 publications

Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia

Bioinformatic analysis of the whole genome sequences of SARS-CoV-2 from Indonesia

Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country

SARS-CoV-2 genetic diversity and variants of concern in Saudi Arabia

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