Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

O’Toole, Áine; Hill, Verity; Pybus, Oliver G.; Watts, Alexander; Bogoch, Isaac I; Khan, Kamran; Messina, Jane P.; Tegally, Houriiyah; Lessells, Richard; Giandhari, Jennifer; Pillay, Sureshnee; Tumedi, Kefentse A.; Nyepetsi, Gape; Kebabonye, Malebogo; Matsheka, Maitshwarelo Ignatius; Mine, Madisa; Tokajian, Sima; Hassan, Hamad; Salloum, Tamara; Merhi, Georgi; Koweyes, Jad; Geoghegan, Jemma L.; Ligt, Joep de; Ren, Xiaoyun; Storey, Matthew; Freed, Nikki E.; Pattabiraman, Chitra; Prasad, Pramada; Desai, Anita; Ravi, Vasanthapuram; Schulz, Thomas F.; Steinbrück, Lars; Stadler, Tanja; Parisi, Antonio; Bianco, Angelica; Viedma, Darı́o Garcı́a de; Buenestado‐Serrano, Sergio; Borges, Vítor; Isidro, Joana; Duarte, Sílvia; Gomes, João Paulo; Zuckerman, Neta S.; Mandelboim, Michal; Mor, Orna; Seemann, Torsten; Arnott, Alicia; Draper, Jenny; Gall, Mailie; Rawlinson, William D.; Deveson, Ira W.; Schlebusch, Sanmarié; McMahon, Jamie; Leong, Lex; Lim, Chuan Kok; Chironna, Maria; Loconsole, Daniela; Bal, Antonin; Josset, Laurence; Holmes, Edward C.; George, Kirsten St.; Lasek‐Nesselquist, Erica; Sikkema, Reina S.; Munnink, Bas B. Oude; Koopmans, Marion; Brytting, Mia; Rani, Vannavada Sudha; Pavani, S.; Smura, Teemu; Heim, Albert; Kurkela, Satu; Umair, Massab; Salman, Muhammad; Bartolini, Barbara; Rueca, Martina; Drosten, Christian; Wolff, Thorsten; Silander, Olin K.; Eggink, Dirk; Reusken, Chantal; Vennema, Harry; Park, Aekyung; Carrington, Christine V. F.; Sahadeo, Nikita; Carr, Michael J.; Gonzalez, Gabo; Diego, Search Alliance San; SeqCOVID-Spain,; Oliveira, Túlio de; Faria, Nuno Rodrigues; Rambaut, Andrew; Kraemer, Moritz U. G.

doi:10.12688/wellcomeopenres.16661.1

Cited by 148 publications

(91 citation statements)

References 14 publications

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“…Infectivity and pathogenicity differ between virus variants in humans [ 64 ]. Since all dogs were sampled before other variants of concern were confirmed in Croatia [ 65 ], additional studies should address potential strain-dependent differences in epidemiology and clinical manifestation of SARS-CoV-2 infections in dogs.…”

Section: Discussionmentioning

confidence: 99%

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

Stevanović

Tabain

Vilibić-Čavlek

et al. 2021

Viruses

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Over a year into the COVID-19 pandemic, there is growing evidence that SARS-CoV-2 infections among dogs are more common than previously thought. In this study, the prevalence of SARS-CoV-2 antibodies was investigated in two dog populations. The first group was comprised of 1069 dogs admitted to the Veterinary Teaching Hospital for any given reason. The second group included dogs that shared households with confirmed COVID-19 cases in humans. This study group numbered 78 dogs. In COVID-19 infected households, 43.9% tested ELISA positive, and neutralising antibodies were detected in 25.64% of dogs. Those data are comparable with the secondary attack rate in the human population. With 14.69% of dogs in the general population testing ELISA positive, there was a surge of SARS-CoV-2 infections within the dog population amid the second wave of the pandemic. Noticeably seroprevalence of SARS-CoV-2 in the dog and the human population did not differ at the end of the study period. Male sex, breed and age were identified as significant risk factors. This study gives strong evidence that while acute dog infections are mostly asymptomatic, they can pose a significant risk to dog health. Due to the retrospective nature of this study, samples for viral isolation and PCR were unavailable. Still, seropositive dogs had a 1.97 times greater risk for developing central nervous symptoms.

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Section: Discussionmentioning

confidence: 99%

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

Stevanović

Tabain

Vilibić-Čavlek

et al. 2021

Viruses

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“…SARS-CoV-2 variants of concern (VOC) in the cohort of 62,211 sequences (viral isolates) were detected with the tool pangolin (https://github.com/cov-lineages/pangolin), according to the 'cov-lineages.org' lineage report [31] and the PANGO nomenclature [32].…”

Section: Variant Calling and Annotationmentioning

confidence: 99%

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts

Tasakis

Samaras

Jamison³

et al. 2021

PLoS ONE

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Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year and a half has caused 3.56 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for effectively controlling the pandemic and informing vaccine platform development. Our study explores evolution of SARS-CoV-2 in a representative cohort of sequences covering the entire genome in the United States, through all of 2020 and early 2021. Strikingly, we detected many accumulating Single Nucleotide Variations (SNVs) encoding amino acid changes in the SARS-CoV-2 genome, with a pattern indicative of RNA editing enzymes as major mutators of SARS-CoV-2 genomes. We report three major variants through October of 2020. These revealed 14 key mutations that were found in various combinations among 14 distinct predominant signatures. These signatures likely represent evolutionary lineages of SARS-CoV-2 in the U.S. and reveal clues to its evolution such as a mutational burst in the summer of 2020 likely leading to a homegrown new variant, and a trend towards higher mutational load among viral isolates, but with occasional mutation loss. The last quartile of 2020 revealed a concerning accumulation of mostly novel low frequency replacement mutations in the Spike protein, and a hypermutable glutamine residue near the putative furin cleavage site. Finally, end of the year data and 2021 revealed the gradual increase to prevalence of known variants of concern, particularly B.1.1.7, that have acquired additional Spike mutations. Overall, our results suggest that predominant viral genomes are dynamically evolving over time, with periods of mutational bursts and unabated mutation accumulation. This high level of existing variation, even at low frequencies and especially in the Spike-encoding region may become problematic when super-spreader events, akin to serial Founder Events in evolution, drive these rare mutations to prominence.

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“…4 This variant has been identified in 154 countries and was until recently the most prevalent lineage in Europe and North America. 5 …”

Section: Introductionmentioning

confidence: 99%

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Twohig

Nyberg

Zaidi

et al. 2022

The Lancet Infectious Diseases

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714

526

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Background The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes. Methods This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status. Findings Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low. Interpretation This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant. Funding Medical Research Council; UK Research and Innovati...

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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

Cited by 148 publications

References 14 publications

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

The Emergence of SARS-CoV-2 within the Dog Population in Croatia: Host Factors and Clinical Outcome

SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts

Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

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