Analysis of SARS-CoV-2 genomic surveillance data during the Delta and Omicron waves at a Saudi tertiary referral hospital

Obeid, Dalia; Al‐Qahtani, Ahmed; Almaghrabi, Reem S.; Alghamdi, Sarah M.; Alsanea, Madain; Alahideb, Basma; Almutairi, Saeedah Musaed; Alsuwairi, Feda; Al-Abdulkareem, M.; Asiri, M.; Alshukairi, Abeer N.; Alkahtany, J.; Altamimi, S.; Mutabagani, Maysoon S.; Althawadi, Sahar; Alanzi, F.; Al-Hamlan, F.

doi:10.1016/j.jiph.2022.12.007

Cited by 5 publications

(4 citation statements)

References 35 publications

(36 reference statements)

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“…Furthermore, the association between mutations in the S protein and vaccination status was studied. N440K was mostly detected in unvaccinated patients, whereas L452R and P681R were mostly found in vaccinated patients [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia

Alsuwairi,

Alsaleh,

Obeid

et al. 2024

Microorganisms

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The genome of severe acute respiratory coronavirus-2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has undergone a rapid evolution, resulting in the emergence of multiple SARS-CoV-2 variants with amino acid changes. This study aimed to sequence the whole genome of SARS-CoV-2 and detect the variants present in specimens from Saudi Arabia. Furthermore, we sought to analyze and characterize the amino acid changes in the various proteins of the identified SARS-CoV-2 variants. A total of 1161 samples from patients diagnosed with COVID-19 in Saudi Arabia, between 1 April 2021 and 31 July 2023, were analyzed. Whole genome sequencing was employed for variant identification and mutation analysis. The statistical analysis was performed using the Statistical Analytical Software SAS, version 9.4, and GraphPad, version 9.0. This study identified twenty-three variants and subvariants of SARS-CoV-2 within the population, with the Omicron BA.1 (21K) variant (37.0%) and the Delta (21J) variant (12%) being the most frequently detected. Notably, the Omicron subvariants exhibited a higher mean mutation rate. Amino acid mutations were observed in twelve proteins. Among these, the spike (S), ORF1a, nucleocapsid (N), and ORF1b proteins showed a higher frequency of amino acid mutations compared to other the viral proteins. The S protein exhibited the highest incidence of amino acid mutations (47.6%). Conversely, the ORF3a, ORF8, ORF7a, ORF6, and ORF7b proteins appeared more conserved, demonstrating the lowest percentage and frequency of amino acid mutations. The investigation of structural protein regions revealed the N-terminal S1 subunit of the S protein to frequently harbor mutations, while the N-terminal domain of the envelope (E) protein displayed the lowest mutation frequency. This study provides insights into the variants and genetic diversity of SARS-CoV-2, underscoring the need for further research to comprehend its genome evolution and the occurrence of mutations. These findings are pertinent to the development of testing approaches, therapeutics, and vaccine strategies.

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Section: Discussionmentioning

confidence: 99%

Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia

Alsuwairi,

Alsaleh,

Obeid

et al. 2024

Microorganisms

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“…During this period, the virus mutated. Many variants have emerged, among which the main lineages pose the greatest global threat ( 36 ). Emerging Omicron variants and their lineages have led to a rapid and substantial increase in COVID-19 cases globally while adversely affecting the protective efficacy of existing vaccines and antibody-based therapies ( 37 ).…”

Section: Discussionmentioning

confidence: 99%

Global trends in COVID-19 Alzheimer's related research: a bibliometric analysis

Cao

Zhou

et al. 2023

Front. Neurol.

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BackgroundThe COVID-19 pandemic has significantly impacted public health, putting people with Alzheimer's disease at significant risk. This study used bibliometric analysis method to conduct in-depth research on the relationship between COVID-19 and Alzheimer's disease, as well as to predict its development trends.MethodsThe Web of Science Core Collection was searched for relevant literature on Alzheimer's and Coronavirus-19 during 2019–2023. We used a search query string in our advanced search. Using Microsoft Excel 2021 and VOSviewer software, a statistical analysis of primary high-yield authors, research institutions, countries, and journals was performed. Knowledge networks, collaboration maps, hotspots, and regional trends were analyzed using VOSviewer and CiteSpace.ResultsDuring 2020–2023, 866 academic studies were published in international journals. United States, Italy, and the United Kingdom rank top three in the survey; in terms of productivity, the top three schools were Harvard Medical School, the University of Padua, and the University of Oxford; Bonanni, Laura, from Gabriele d'Annunzio University (Italy), Tedeschi, Gioacchino from the University of Campania Luigi Vanvitelli (Italy), Vanacore, Nicola from Natl Ctr Dis Prevent and Health Promot (Italy), Reddy, P. Hemachandra from Texas Tech University (USA), and El Haj, Mohamad from University of Nantes (France) were the authors who published the most articles; The Journal of Alzheimer's Disease is the journals with the most published articles; “COVID-19,” “Alzheimer's disease,” “neurodegenerative diseases,” “cognitive impairment,” “neuroinflammation,” “quality of life,” and “neurological complications” have been the focus of attention in the last 3 years.ConclusionThe disease caused by the COVID-19 virus infection related to Alzheimer's disease has attracted significant attention worldwide. The major hot topics in 2020 were: “Alzheimer' disease,” COVID-19,” risk factors,” care,” and “Parkinson's disease.” During the 2 years 2021 and 2022, researchers were also interested in “neurodegenerative diseases,” “cognitive impairment,” and “quality of life,” which require further investigation.

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“…The B.1.1.529 lineage was also recognized as GR/484A or 21 K. The Omicron variant was the most prevalent lineage during 2022. It possesses five sub-lineages with BA.1 being the initial subtype that appeared in South Africa during winter 2021–2022 [ 4 ].…”

Section: Sars-cov-2 Genetic Diversity and Their Clinical Implicationsmentioning

confidence: 99%

“…They are zoonotic infections with animal origin and have the largest non-segmented RNA viral genome (∼ 30 kb). CoVs belong to the order Nidovirales in the family Coronaviridae and sub-family Orthocoronavirinae and include four genera: alpha-, beta-, gamma-, and delta-coronaviruses [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression

Hussein,

Thabet,

Wardany

et al. 2024

Virol J

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The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.

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Analysis of SARS-CoV-2 genomic surveillance data during the Delta and Omicron waves at a Saudi tertiary referral hospital

Cited by 5 publications

References 35 publications

Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia

Genomic Surveillance and Mutation Analysis of SARS-CoV-2 Variants among Patients in Saudi Arabia

Global trends in COVID-19 Alzheimer's related research: a bibliometric analysis

SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression

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