COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Kläser, Kerstin; Molteni, Erika; Graham, Mark S.; Canas, Liane S; Österdahl, Marc F.; Antonelli, Michela; Chen, Liyuan; Deng, Jie; Murray, Benjamin; Kerfoot, Eric; Wolf, Jonathan; May, Anna; Fox, Ben; Capdevila, Joan; Modat, Marc; Hammers, Alexander; Spector, Tim D.; Steves, Claire J.; Sudre, Carole H.; Ourselin, Sébastien; Duncan, Emma L.

doi:10.1038/s41598-022-14016-0

Cited by 49 publications

(35 citation statements)

References 34 publications

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“…6 The UK has experienced multiple waves of SARS-CoV-2 infections since March 2020, often following the emergence and rapid spread of new variants, including alpha in November 2020, delta in April 2021 and omicron in November 2021. Delta was more transmissible than alpha, 7 but, unlike in adults, 8 was not associated with more severe disease in children and adolescents. 9 The ability of the omicron BA.1 variant identified in England late November 2021 and, subsequently, the BA.2 variant identified late December 2021, to evade both natural and vaccine-induced immunity was associated with the highest case numbers across all age-groups, although hospitalisation rates and fatalities remained low, 10 likely due to prior immunity from a combination of previous infections and vaccination, 11 along with a predilection of the omicron variant to infect the upper rather than lower airway, thus causing less severe disease.…”

Section: Introductionmentioning

confidence: 72%

Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England

Powell¹,

Kirsebom²,

Stowe³

et al. 2022

Preprint

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Background Little is known about the protection following prior infection with different SARS-CoV-2 variants, COVID-19 vaccination, and a combination of the two (hybrid immunity) in adolescents. Methods We used national SARS-CoV-2 testing and COVID-19 mRNA vaccination data in England to estimate protection following previous infection and vaccination against symptomatic PCR-confirmed delta and omicron (BA.1 or BA.2) variants in 11-17-year-olds using a test-negative case-control design. Findings By 31 March 2022, 63.6% of 16-17-year-olds and 48.2% of 12-15-year-olds had received more than one COVID-19 mRNA vaccine dose. Between 08 August 2021 and 31 March 2022, 1,161,704 SARS-CoV-2 PCR-tests were successfully linked to COVID-19 vaccination status. In unvaccinated adolescents, prior infection with wildtype, alpha or delta provided greater protection against subsequent delta infection than subsequent omicron; prior omicron infection provided had the highest protection against omicron reinfection (59.3%; 95%CI: 46.7-69.0). In infection-naive adolescents, vaccination provided lower protection against symptomatic omicron infection than delta, peaking at 64.5% (95%CI; 63.6-65.4) 2-14 days after dose two and 62.9% (95%CI; 60.5-65.1) 2-14 weeks after dose three, with rapidly waning protection after each dose. Previously infected and vaccinated adolescents had the highest protection, irrespective of primary infecting SARS-CoV-2 strain. The highest protection against omicron was observed in vaccinated adolescents with prior omicron infection, reaching 96.4% (95%CI, 84.4-99.1) at 15-24 weeks post dose two. Interpretation All variants provide some protection against symptomatic reinfection and vaccination adds to protection. Vaccination provides low-to-moderate protection against symptomatic omicron infection, with waning protection after each dose, while hybrid immunity provides the most robust protection.

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Section: Introductionmentioning

confidence: 72%

Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England

Powell¹,

Kirsebom²,

Stowe³

et al. 2022

Preprint

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“…A peak's ascent reflects the accumulating momentum of a variant of concern, while the descent suggests this new variant's primacy. Alpha swept the population in March 2021 (27), Delta by July 2021 (28), and Omicron by January 2022 (29) 1), this within wave signal tracks the information complexity of steady evolution following a selective sweep.…”

Section: Resultsmentioning

confidence: 96%

“…A peak’s ascent reflects the accumulating momentum of a variant of concern, while the descent suggests this new variant’s primacy. Alpha swept the population in March 2021 (27), Delta by July 2021 (28), and Omicron by January 2022 (29). In each case, KHILL settles into a local minimum of about 1.03 effective genomes highlighting the near clonality of the viral population after a variant achieves dominance.…”

Section: Resultsmentioning

confidence: 99%

Hill numbers at the edge of a pandemic: rapid SARS-COV2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

Narechania

Bobo

Deitz

et al. 2022

Preprint

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The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control strategies. Timeliness is key, but rapid deployment of existing surveillance is difficult because current approaches are based in sequence alignment and phylogeny. Millions of SARS-CoV-2 genomes have been assembled, the largest collection of sequence data in history. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pan-genomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of sequenced genomes. Quantifying diversity is central to ecology. Studies that measure the diversity of various environments increasingly use the concept of Hill numbers, or the effective number of species in a sample, to provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pan-genome of the species. Applying Hill numbers in this way allows us to summarize the temporal trajectory of pandemic variants by collapsing each day's assemblies into genomic equivalents. We do this quickly, without alignment or trees, using modern genome sketching techniques to accommodate millions of genomes in one condensed view of pandemic dynamics. Using data from the UK, USA, and South Africa, we trace the ascendence of new variants of concern as they emerge in local populations. This history of emerging variants uses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID19 pandemic.

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“…In February 2021 the alpha variant was detected in Kenya [ 18 ]. The alpha variant has been reported to be less transmissible than other variants such as the delta variant but associated with a higher risk of acute respiratory distress syndrome [ 19 , 20 ].…”

Section: Discussionmentioning

confidence: 99%

Management of Multisystem Inflammatory Syndrome in Children (MIS-C) in resource limited settings: The Kenyan Experience

et al. 2022

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Background Since the onset of the recent COVID-19 pandemic, there have been growing concerns regarding multisystem inflammatory syndrome in children (MIS-C). This study aims to describe the clinico-epidemiological profile and challenges in management of MIS-C in low-middle income countries by highlighting the Kenyan experience. Methods A retrospective study at the Aga Khan University Hospital Nairobi, Avenue Hospital Kisumu and Kapsabet County Referral Hospital was undertaken to identify cases of MIS-C. A detailed chart review using the World Health Organization (WHO) data collection tool was adapted to incorporate information on socio-demographic details and treatment regimens. Findings Twenty children with MIS-C were identified across the three facilities between August 1st 2020 and August 31st 2021. Seventy percent of the children were male (14 of 20). COVID-19 PCR testing was done for five children and only one was positive. The commonest clinical symptoms were fever (90%), tachycardia (80%), prolonged capillary refill (80%), oral mucosal changes (65%) and peripheral cutaneous inflammation (50%). Four children required admission into the critical care unit for ventilation support and inotropic support. Cardiac evaluation was available for six patients four of whom had myocardial dysfunction, three had valvulitis and one had pericarditis. Immunoglobulin therapy was availed to two children and systemic steroids provided for three children. There were no documented mortalities. Interpretation We describe the first case series of MIS-C in East and Central Africa. Majority of suspected cases of MIS-C did not have access to timely COVID-19 testing and other appropriate evaluations which highlights the iniquity in access to diagnostics and treatment.

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COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

Cited by 49 publications

References 34 publications

Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England

Protection against symptomatic disease with the delta and omicron BA.1/BA.2 variants of SARS-CoV-2 after infection and vaccination in adolescents: national observational test-negative case control study, August 2021 to March 2022, England

Hill numbers at the edge of a pandemic: rapid SARS-COV2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change

Management of Multisystem Inflammatory Syndrome in Children (MIS-C) in resource limited settings: The Kenyan Experience

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