First detection of SARS-CoV-2 variant B.1.1.529 (Omicron) in Ecuador

Carrazco-Montalvo, Andrés; Armendáriz‐Castillo, Isaac; Tello, Clara Lucia; Morales, Diego; Armas-Gonzalez, Rubén; Guizado-Herrera, David; León-Sosa, Ariana; Ramos-Sarmiento, Daniel; Fuertes, Byron; Patiño, Leandro; Cárdenas, Paúl; Márquez, Sully; Prado-Vivar, Belén; Guadalupe, Juan José; Gutiérrez, Bernardo; Becerra-Wong, Mónica; Grunauer, Michelle; Trueba, Gabriel; Rojas-Silva, Patricio; Barragán, Verónica

doi:10.1016/j.nmni.2022.100951

Cited by 10 publications

(10 citation statements)

References 7 publications

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“…13 In Denmark, L452 and 452R markers were putatively used to differentiate between Omicron and Delta variants, respectively. 13 Identifications of both Delta and Omicron variants, by using either rapid molecular methods or sequencing, have been investigated in many countries including the United States, [16][17][18][19] United Kingdom, 3,20 Germany, 21,22 Denmark, 13 Italy, 11,23 Ecuador, 24 China, 25 Taiwan, 6 Belgium, 1 Malaysia, 26 Iran, 27 and Japan. 28 Such rapid molecular methods are uncommon in Iraq and Kurdistan region.…”

Section: Who Labelmentioning

confidence: 99%

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Rasheed

Awrahman

Al-Jaf

et al. 2023

Immunity Inflam & Disease

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Background: Five variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) have been globally recorded including Alpha, Beta, Gamma, Delta, and Omicron. The Omicron variant has outcompeted the other variants including the Delta variant. Molecular screenings of VOCs are important for surveillance, treatment, and vaccination programs. This study aimed to identify VOCs by using rapid inexpensive methods and partial sequencing of the virus's spike gene.Methods: Mutation-specific rRT PCR probes were used for both D614G and K417N mutations to potentially discriminate between Delta and Omicron variants. These were followed by sequencing of a fragment of spike gene (748 nucleotides), which covers the most notable VOC mutations in the receptor binding domain of SARS CoV-2.Results: Rapid methods showed that out of 24 SARS CoV-2 positive samples, 19 carried the N417 mutation, which is present in the Omicron variant. Furthermore, 3 samples carried K417 wildtype, which is present in the Delta variant. Additionally, 2 samples containing both K417 and N417 suggested mixed infections between the two variants. The D614G mutation was present in all samples. Among the 4 samples sequenced, 3 samples carried 13 mutations, which are present in Omicron BA.1. The fourth sample contained the two common mutations (T478K and L452R) present in Delta, in addition to two more rare mutations (F456L and F490S), which are not commonly seen in Delta. Our data suggested that both Omicron variant BA.1 and a novel Delta variant might have circulated in this region that needs further investigations.

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Section: Who Labelmentioning

confidence: 99%

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Rasheed

Awrahman

Al-Jaf

et al. 2023

Immunity Inflam & Disease

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“…It has reached several countries. A high number of mutations were observed in the spike protein, which was more highly transmissible among populations than the previous known variants of coronavirus [ 42 , 43 ]. On 11 November 2021, Botswana reported a novel SARS-CoV-2 strain, B.1.1.529, known as Omicron, a variant of the concern strain, followed by South Africa on 14 November 2021 [ 43 , 44 , 45 ].…”

Section: Omicronmentioning

confidence: 99%

Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic

et al. 2023

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus diseases (COVID-19) in late 2019 in China created a devastating economical loss and loss of human lives. To date, 11 variants have been identified with minimum to maximum severity of infection and surges in cases. Bacterial co-infection/secondary infection is identified during viral respiratory infection, which is a vital reason for morbidity and mortality. The occurrence of secondary infections is an additional burden to the healthcare system; therefore, the quick diagnosis of both COVID-19 and secondary infections will reduce work pressure on healthcare workers. Therefore, well-established support from Artificial Intelligence (AI) could reduce the stress in healthcare and even help in creating novel products to defend against the coronavirus. AI is one of the rapidly growing fields with numerous applications for the healthcare sector. The present review aims to access the recent literature on the role of AI and how its subfamily machine learning (ML) and deep learning (DL) are used to curb the pandemic’s effects. We discuss the role of AI in COVID-19 infections, the detection of secondary infections, technology-assisted protection from COVID-19, global laws and regulations on AI, and the impact of the pandemic on public life.

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“…BA.2 is also known as the “stealth variant” because it lacks a deletion signature at positions 69-70 that was not detected by the spike (S) gene target failure assay; therefore, BA.2 was underestimated with the current reverse transcription polymerase chain reaction setup, and its detection is only possible via whole genome sequencing[ 6 , 7 ]. According to viral genome sequences uploaded to the global GISAID database, the United Kingdom, the United States, Denmark, Germany, and Canada are the five countries with the highest prevalence of BA.2 ( ).…”

Section: To the Editormentioning

confidence: 99%

Global challenge with the SARS-CoV-2 omicron BA.2 (B.1.1.529.2) subvariant: Should we be concerned?

Roohani¹,

Keikha²

2022

World J Virol

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BA.2 is a novel omicron offshoot of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has gone viral. There is limited knowledge regarding this variant of concern. Current evidence suggests that this variant is more contagious but less severe than previous SARS-CoV-2 variants. However, there is concern regarding the virus mutations that could influence pathogenicity, transmissibility, and immune evasion.

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First detection of SARS-CoV-2 variant B.1.1.529 (Omicron) in Ecuador

Cited by 10 publications

References 7 publications

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Identification of SARS CoV‐2 Omicron BA.1 and a novel Delta lineage by rapid methods and partial spike protein sequences in Sulaymaniyah Province, Iraq

Artificial Intelligence: A Next-Level Approach in Confronting the COVID-19 Pandemic

Global challenge with the SARS-CoV-2 omicron BA.2 (B.1.1.529.2) subvariant: Should we be concerned?

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