Emergence and fast spread of B.1.1.7 lineage in Lebanon

Younes, Mahmoud; Hamze, Kassem; Nassar, Hassan; makki, mohammad; Ghaddar, Mayssa; Nguewa, Paul; Abdel-Sater, Fadi

doi:10.1101/2021.01.25.21249974

Cited by 8 publications

(5 citation statements)

References 4 publications

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“…In the UK, B.1.1.7 is now the predominant lineage, accounting for >90 % of infections [95]. In many countries, initially imported B.1.1.7 is rapidly outcompeting local strains and becoming the major circulating strain [96–99]. B.1.1.7 contains seven non-synonymous mutations in the spike glycoprotein and a total of 23 mutations across the whole genome (see ).…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Peacock

Penrice-Randal

Hiscox

et al. 2021

Journal of General Virology

149

118

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SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral ‘genetic drift’ or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.

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Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Peacock

Penrice-Randal

Hiscox

et al. 2021

Journal of General Virology

149

118

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“…Genome sequencing is the gold method to confirm the new variant, but observational studies provide also stronger evidence if similar models are observed in multiple countries, especially when randomized studies are not possible. In Lebanon, surveillance data from Beirut Medical Center and Bahman Hospital showed a rapid and dramatic increase in S-negative profile in PCR testing for SARS-CoV-2 in the first twelve days in January, reaching approximately 60% of positive cases and 95% in February [9,10].…”

Section: Introductionmentioning

confidence: 99%

A rapid and low-cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-based RT-qPCR

Abdel-Sater

Younes

Nassar³

et al. 2021

Mol Biol Rep

Self Cite

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BackgroundThe new SARS-CoV-2 variant VOC (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit). Methods To control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to the VOC (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, detected by using the Applied Biosystems TaqPath RT-PCR COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile. Results Our results emphasized that all S-negative samples harbored the mutations Δ69/Δ70 and Δ106/Δ107/Δ108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene. Conclusions This technique may allow to identify patients carrying the VOC (202012/01) or a closely related variant, in case of shortage in sequencing.

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“…Studies conducted in different countries, including the US, Germany, Spain, Denmark, and the United Kingdom, found that the B.1.1.7 lineage is more likely than the original virus to send infected patients to the hospital and is also more deadly [111][112][113] [115]. Furthermore, over a 12-day period in January, the number of patients with B.1.1.7 grew rapidly at a hospital and cardiac center in Lebanon, and the proportion of COVID-19 cases with "spike gene target failure" or "spike gene drop out" (SGTF increased from 16 to 60% [116]; SGTF refers to positive test with a non-detectable S gene Ct value and Ct ≤ 30 for N and ORF1ab targets [117]. A Swedish research group revealed that Alpha-positive persons had considerably greater rates of hospitalization (2.6% vs. 1.2%) and severe illness than negative individuals, although the numbers were too small to assess differences in severity rates among hospitalized individuals [118].…”

Section: Disease Severitymentioning

confidence: 99%

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

Hoteit

Yassine

2022

Vaccines

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus’s transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.

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Emergence and fast spread of B.1.1.7 lineage in Lebanon

Cited by 8 publications

References 4 publications

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

A rapid and low-cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-based RT-qPCR

Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences

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