First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

Carrazco-Montalvo, Andrés; Bruno, Alfredo; Mora, Doménica de; Olmedo, Maritza; Garcés, Jimmy; Paez, Michelle; Regato-Arrata, Mary; González, M Ajenjo; Romero, J. Delgado; Mestanza, Orson; Freire‐Paspuel, Byron; Gaviria, A.; Orlando, Solon-Alberto; García-Bereguiaín, Miguel Angel; Patiño, Leandro

doi:10.2147/idr.s319439

Cited by 5 publications

(3 citation statements)

References 9 publications

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“…In December 2020, a new variant was reported in the UK as SARS-CoV-2 variants of concern (VOC) 202,012/01, also named B.1.1.7 (Alpha) [ 16 ]. The new variant, which was detected during regular sampling, shows several mutations in the RBD that were never reported before and started to replace other virus lineages in the area.…”

Section: Genomic Variations Of Sars-cov-2mentioning

confidence: 99%

Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity

Alquraan

Alzoubi

Rababa'h

2023

Informatics in Medicine Unlocked

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Section: Genomic Variations Of Sars-cov-2mentioning

confidence: 99%

Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity

Alquraan

Alzoubi

Rababa'h

2023

Informatics in Medicine Unlocked

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“…VOC lines are characterized by biological properties that increase the contagiousness and pathogenicity or reduce the neutralizing activity of antibodies [ 4 ]. To date, there are several VOC lines: the α-line (PANGO B.1.1.7, clade 501.YV,1 69–70del, Y144del), first registered in the UK in September 2020 [ 5 ]; the β-line (PANGO B.1.351), first discovered in South Africa in May 2020, containing nucleotide substitutions N501Y, K417N, and E484K in the S-protein [ 6 ]; the γ-line (PANGO p.1, 484K.V2), containing the key mutation E484K in the S-protein, first isolated from samples of patients from the state of Rio de Janeiro (Brazil) in November 2020 [ 7 ]; the δ-line (PANGO B.1.617.2), containing mutations L452R and T478K in the S-protein, first discovered in India in October 2020 [ 8 ]; and the Omicron line (PANGO B.1.1.529), containing S477N mutations and first detected in South Africa and Botswana in November 2021 [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Secretory Phospholipase A2 and Interleukin-6 Levels as Predictive Markers of the Severity and Outcome of Patients with COVID-19 Infections

Urazov

Chernov

Попов

et al. 2023

IJMS

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Coronavirus disease (COVID-19) has become a global pandemic. COVID-19 patients need immediate diagnosis and rehabilitation, which makes it urgent to identify new protein markers for a prognosis of the severity and outcome of the disease. The aim of this study was to analyze the levels of interleukin-6 (IL-6) and secretory phospholipase (sPLA2) in the blood of patients regarding the severity and outcome of COVID-19 infection. The study included clinical and biochemical data obtained from 158 patients with COVID-19 treated at St. Petersburg City Hospital No. 40. A detailed clinical blood test was performed on all patients, as well as an assessment of IL-6, sPLA2, aspartate aminotransferase (AST), total protein, albumin, lactate dehydrogenase (LDH), APTT, fibrinogen, procalcitonin, D-dimer, C-reactive protein (CRB), ferritin, and glomerular filtration rate (GFR) levels. It was found that the levels of PLA2, IL-6, APTV, AST, CRP, LDH, IL-6, D-dimer, and ferritin, as well as the number of neutrophils, significantly increased in patients with mild to severe COVID-19 infections. The levels of IL-6 were positively correlated with APTT; the levels of AST, LDH, CRP, D-dimer, and ferritin; and the number of neutrophils. The increase in the level of sPLA2 was positively correlated with the levels of CRP, LDH, D-dimer, and ferritin, the number of neutrophils, and APTT, and negatively correlated with the levels of GFR and lymphocytes. High levels of IL-6 and PLA2 significantly increase the risk of a severe course by 13.7 and 2.24 times, and increase the risk of death from COVID-19 infection by 14.82 and 5.32 times, respectively. We have shown that the blood levels of sPLA2 and IL-6 increase in cases which eventually result in death and when patients are transferred to the ICU (as the severity of COVID-19 infection increases), showing that IL-6 and sPLA2 can be considered as early predictors of aggravation of COVID-19 infections.

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“…The SARS-CoV-2 S protein contains the receptor-binding domain (RBD), a region in which mutations are directly linked to the emergence of new variants ( 8 ) and whose function is to interact with the viral receptor ACE2 (angiotensin-converting enzyme 2) in humans ( 9 , 10 ). Genetic diversity in this viral domain has a variety of implications on virus phenotype, including increased ACE2 affinity, increased intracellular reproduction rate, decreased humoral neutralization efficacy, and even potential bias in diagnostic procedures (e.g., dropout) ( 11 – 13 ). Because of these characteristics, the RBD has been a priority target for drug development and mutation dynamics research ( 14 – 19 ).…”

Section: Introductionmentioning

confidence: 99%

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

Burgos,

Ambuludí,

Morales-Jadán

et al. 2023

Microbiol Spectr

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.

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First Report of SARS-CoV-2 Lineage B.1.1.7 (Alpha Variant) in Ecuador, January 2021

Cited by 5 publications

References 9 publications

Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity

Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity

Secretory Phospholipase A2 and Interleukin-6 Levels as Predictive Markers of the Severity and Outcome of Patients with COVID-19 Infections

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

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