The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

Pascall, David; Vink, Elen; Blacow, Rachel; Bulteel, Naomi; Campbell, Alasdair; Campbell, Robyn; Clifford, Sarah; Davis, Chris; Filipe, Ana da Silva; Sakka, Noha El; Fjodorova, Ludmila; Forrest, Ruth; Goldstein, Emily; Gunson, Rory; Haughney, John; Holden, Matthew T. G.; Honour, Patrick; Hughes, Joseph; James, Edward; Lewis, Tim; Lycett, Samantha; MacLean, Oscar A; McHugh, M.; Mollett, Guy; Onishi, Yusuke; Parcell, Ben; Ray, Surajit; Robertson, David L.; Shabaan, Sharif; Shepherd, James G.; Smollett, Katherine; Templeton, Kate; Wastnedge, Elizabeth; Wilkie, Craig; Williams, Thomas C; Thomson, Emma C.

doi:10.1371/journal.pone.0284187

Cited by 6 publications

(3 citation statements)

References 29 publications

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“…ICU/AMV severity and the case fatality rate also increased in Alpha and the other lineages in comparison to other VOCs groups. Comparably, other studies have found an association between the Alpha variant and an increase in hospitalization, ICU admission, and mortality [36,37]. Similarly, an increase in the clinical severity risk due to the Gamma and Alpha lineages was highlighted with a linear regression model.…”

Section: Discussionmentioning

confidence: 65%

SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population

Maldonado-Cabrera,

Colin-Vilchis,

Haque

et al. 2023

Infectious Disease Reports

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The emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VOCs) presents global heterogeneity, and their relative effect on pediatric severity is still limited. In this study, we associate VOCs with pediatric clinical severity outcomes in Mexico. Bioinformatics methods were used to characterize VOCs and single amino acid (aa) mutations in 75,348 SARS-CoV-2 genetic sequences from February 2020 to October 2022. High-predominance VOCs groups were calculated and subsequently associated with 372,989 COVID-19 clinical pediatric outcomes. We identified 21 high-frequency mutations related to Omicron lineages with an increased prevalence in pediatric sequences compared to adults. Alpha and the other lineages had a significant increase in case fatality rate (CFR), intensive critical unit (ICU) admission, and automated mechanical ventilation (AMV). Furthermore, a logistic model with age-adjusted variables estimated an increased risk of hospitalization, ICU/AMV, and death in Gamma and Alpha, in contrast to the other lineages. We found that, regardless of the VOCs lineage, infant patients presented the worst severity prognoses. Our findings improve the understanding of the impact of VOCs on pediatric patients across time, regions, and clinical outcomes. Enhanced understanding of the pediatric severity for VOCs would enable the development and improvement of public health strategies worldwide.

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Section: Discussionmentioning

confidence: 65%

SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population

Maldonado-Cabrera,

Colin-Vilchis,

Haque

et al. 2023

Infectious Disease Reports

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“…We can assume, in our patients, that better use of treatments may partially explain why the inflammatory parameters did not reach the levels of the first wave. In the UK, the increased severity of this wave was attributed to the emergence of the Alpha variant during winter 2021 [ 40 ], but this variant entered our country at a later time. In Japan or Congo, this wave, also during winter 2021, also had a higher percentage of patients and deaths [ 10 , 16 ].…”

Section: Discussionmentioning

confidence: 99%

Seven Epidemic Waves of COVID-19 in a Hospital in Madrid: Analysis of Severity and Associated Factors

San Martín-López,

Mesa,

Bernal-Bello

et al. 2023

Viruses

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(1) Background: COVID-19 has evolved during seven epidemic waves in Spain. Our objective was to describe changes in mortality and severity in our hospitalized patients. (2) Method: This study employed a descriptive, retrospective approach for COVID-19 patients admitted to the Hospital de Fuenlabrada (Madrid, Spain) until 31 December 2022. (3) Results: A total of 5510 admissions for COVID-19 were recorded. The first wave accounted for 1823 (33%) admissions and exhibited the highest proportion of severe patients: 65% with bilateral pneumonia and 83% with oxygen saturation under 94% during admission and elevated levels of CRP, IL-6, and D-dimer. In contrast, the seventh wave had the highest median age (79 years) and comorbidity (Charlson: 2.7), while only 3% of patients had bilateral pneumonia and 3% required intubation. The overall mortality rate was 10.3%. The first wave represented 39% of the total. The variables related to mortality were age (OR: 1.08, 1.07–1.09), cancer (OR: 1.99, 1.53–2.60), dementia (OR: 1.82, 1.20–2.75), the Charlson index (1.38, 1.31–1.47), the need for high-flow oxygen (OR: 6.10, 4.94–7.52), mechanical ventilation (OR: 11.554, 6.996–19.080), and CRP (OR: 1.04, 1.03–1.06). (4) Conclusions: The variables associated with mortality included age, comorbidity, respiratory failure, and inflammation. Differences in the baseline characteristics of admitted patients explained the differences in mortality in each wave. Differences observed between patients admitted in the latest wave and the earlier ones suggest that COVID-19 has evolved into a distinct disease, requiring a distinct approach.

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“…Delta for example was more virulent, in both humans and in experimental animal models, compared to previously circulating variants [36][37][38][39] . Omicron instead displayed a new preferred cell entry pathway, and predominantly infected the upper respiratory tract, resulting in a milder disease compared to Delta and the ancestral Wuhan strain 40,36,37,[41][42][43][44] .…”

Section: Introductionmentioning

confidence: 99%

Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic

Furnon,

Cowton,

De Lorenzo

et al. 2024

Preprint

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Variants of SARS-CoV-2, defined mainly by mutations in the spike glycoprotein, have emerged throughout the COVID-19 pandemic and will undoubtedly continue to emerge in the future. Spike strongly influences virus phenotype, and it is therefore critical to understand the evolution of this viral protein during distinct phases of the pandemic. Here, we generated a panel of recombinant viruses carrying spike from 27 of the most significant variants, circulating between 2020 and 2024, within an otherwise identical genomic backbone. We systematically assessed phenotypic traits of these viruses both in vitro and in vivo in hamsters. Overall, we determined distinct phenotypic trajectories of spike among and between the variants circulating before (“pre-Omicron") and after (“post-Omicron”) the emergence of Omicron. Spillover of SARS-CoV-2 in the human population was followed by a period of adaptation and fine-tuning to the host in the pre-Omicron variants. Omicron simultaneously “reset” several established phenotypes of previously circulating variants. Since then, spike of post-Omicron variants maintained its enhanced tropism for the nasal epithelium but displayed over time several phenotypic traits typical of the pre-Omicron variants. These data suggest that it may be possible for spike with phenotypic features of both pre- and post-Omicron variants to emerge in the future.

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The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

Cited by 6 publications

References 29 publications

SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population

SARS-CoV-2 Variants of Concern and Clinical Severity in the Mexican Pediatric Population

Seven Epidemic Waves of COVID-19 in a Hospital in Madrid: Analysis of Severity and Associated Factors

Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic

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