Track Omicron’s spread with molecular data

Scott, Lesley; Hsiao, Nei-yuan; Moyo, Sikhuline; Singh, Lavanya; Tegally, Houriiyah; Dor, Graeme; Maes, Piet; Pybus, Oliver G.; Kraemer, Moritz U. G.; Semenova, Elizaveta; Bhatt, Samir; Flaxman, Seth; Faria, Nuno R.; Oliveira, Túlio de

doi:10.1126/science.abn4543

Cited by 118 publications

(101 citation statements)

References 6 publications

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“…But omicron has spread rapidly through the world and is fueling waves in other countries. S-gene target failure (SGTF) as a proxy for omicron, is allowing rapid identification of probable omicron cases pending genomic sequencing [ 8 ]. UK is severely affected with more than 100,000 cases per day; in London more than 90% of the patients are infected with omicron [ 9 ].…”

Section: Omicron—an Overviewmentioning

confidence: 99%

The Emergence of Omicron: Challenging Times Are Here Again!

Singhal

2022

Indian J Pediatr

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COVID-19 has been reported to have caused more than 286 million cases and 5.4 million deaths till date. COVID variants have appeared at regular intervals—alpha, beta, gamma, delta and now omicron. ‘Omicron’ is driving the current surge of cases in most countries including India and is poised to replace ‘delta’ the world over. This variant with more than 50 mutations is phylogenetically very different from other variants. The omicron variant spreads rapidly with an average doubling time of two days. The disease so far has been mild as compared with delta. Though previous infection and vaccination offer little or no protection against infection with omicron, they do seem to partially protect against hospitalization and severe disease. Booster vaccinations have not made any notable impact on the spread of omicron and have further worsened global vaccine equity. The indirect consequences of omicron from lockdowns, restrictions, travel bans, economic losses, health care worker infections and overwhelming of health care facilities are likely to be enormous. The direct effects of omicron on children are expected to be mild like with the previous variants. However, the indirect effects on child mental, physical, and social health may be considerable owing to school closures, missed vaccinations, neglect of other diseases, etc. It is, therefore, imperative that governments take rational decisions to navigate the world through this latest crisis.

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Section: Omicron—an Overviewmentioning

confidence: 99%

The Emergence of Omicron: Challenging Times Are Here Again!

Singhal

2022

Indian J Pediatr

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“…DATCOV-Gen 4 is a prospective surveillance network linking real-time SARS-CoV-2 genome data to detailed epidemiologic and clinical data on hospitalised cases to allow rapid assessment of severity and clinical presentation of emerging SARS-CoV-2 VOCs. We aimed to assess the severity of Omicron infections compared to Delta variant using SGTF as a proxy 5 .…”

Section: Introductionmentioning

confidence: 99%

Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

Wolter

Jassat

Walaza

et al. 2021

Preprint

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127

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Background The SARS-CoV-2 Omicron variant of concern (VOC) almost completely replaced other variants in South Africa during November 2021, and was associated with a rapid increase in COVID-19 cases. We aimed to assess clinical severity of individuals infected with Omicron, using S Gene Target Failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy. Methods We performed data linkages for (i) SARS-CoV-2 laboratory tests, (ii) COVID-19 case data, (iii) genome data, and (iv) the DATCOV national hospital surveillance system for the whole of South Africa. For cases identified using Thermo Fisher TaqPath COVID-19 PCR, infections were designated as SGTF or non-SGTF. Disease severity was assessed using multivariable logistic regression models comparing SGTF-infected individuals diagnosed between 1 October to 30 November to (i) non-SGTF in the same period, and (ii) Delta infections diagnosed between April and November 2021. Results From 1 October through 6 December 2021, 161,328 COVID-19 cases were reported nationally; 38,282 were tested using TaqPath PCR and 29,721 SGTF infections were identified. The proportion of SGTF infections increased from 3% in early October (week 39) to 98% in early December (week 48). On multivariable analysis, after controlling for factors associated with hospitalisation, individuals with SGTF infection had lower odds of being admitted to hospital compared to non-SGTF infections (adjusted odds ratio (aOR) 0.2, 95% confidence interval (CI) 0.1-0.3). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ between SGTF-infected individuals compared to non-SGTF individuals diagnosed during the same time period (aOR 0.7, 95% CI 0.3-1.4). Compared to earlier Delta infections, after controlling for factors associated with severe disease, SGTF-infected individuals had a lower odds of severe disease (aOR 0.3, 95% CI 0.2-0.6). Conclusion Early analyses suggest a reduced risk of hospitalisation among SGTF-infected individuals when compared to non-SGTF infected individuals in the same time period, and a reduced risk of severe disease when compared to earlier Delta-infected individuals. Some of this reducton is likely a result of high population immunity.

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“…It is expected to become dominant in the coming weeks 2 , probably due to enhanced transmissibility. A striking feature of this variant is the large number of spike mutations 3 that pose a threat to the efficacy of current COVID-19 vaccines and antibody therapies 4 . This concern is amplified by the findings from our study.…”

Section: Introductionmentioning

confidence: 99%

Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2

Liu

Iketani

Guo

et al. 2021

Preprint

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The Omicron (B.1.1.529) variant of SARS-CoV-2 was only recently detected in southern Africa, but its subsequent spread has been extensive, both regionally and globally1. It is expected to become dominant in the coming weeks2, probably due to enhanced transmissibility. A striking feature of this variant is the large number of spike mutations3 that pose a threat to the efficacy of current COVID-19 vaccines and antibody therapies4. This concern is amplified by the findings from our study. We found B.1.1.529 to be markedly resistant to neutralization by serum not only from convalescent patients, but also from individuals vaccinated with one of the four widely used COVID-19 vaccines. Even serum from persons vaccinated and boosted with mRNA-based vaccines exhibited substantially diminished neutralizing activity against B.1.1.529. By evaluating a panel of monoclonal antibodies to all known epitope clusters on the spike protein, we noted that the activity of 18 of the 19 antibodies tested were either abolished or impaired, including ones currently authorized or approved for use in patients. In addition, we also identified four new spike mutations (S371L, N440K, G446S, and Q493R) that confer greater antibody resistance to B.1.1.529. The Omicron variant presents a serious threat to many existing COVID-19 vaccines and therapies, compelling the development of new interventions that anticipate the evolutionary trajectory of SARS-CoV-2.

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Track Omicron’s spread with molecular data

Cited by 118 publications

References 6 publications

The Emergence of Omicron: Challenging Times Are Here Again!

The Emergence of Omicron: Challenging Times Are Here Again!

Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa

Striking Antibody Evasion Manifested by the Omicron Variant of SARS-CoV-2

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