Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

Bhatt, Samir; Flaxman, Seth

doi:10.1016/j.eclinm.2021.101064

Cited by 119 publications

(119 citation statements)

References 31 publications

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“…Novel VOCs 52 and increased population immunity due to vaccinations may affect overall NPI effectiveness. In addition, if new VOCs resulted in a higher initial , then stricter or more NPIs would be required to bring below 1.…”

Section: Resultsmentioning

confidence: 99%

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

et al. 2021

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European governments use non-pharmaceutical interventions (NPIs) to control resurging waves of COVID-19. However, they only have outdated estimates for how effective individual NPIs were in the first wave. We estimate the effectiveness of 17 NPIs in Europe’s second wave from subnational case and death data by introducing a flexible hierarchical Bayesian transmission model and collecting the largest dataset of NPI implementation dates across Europe. Business closures, educational institution closures, and gathering bans reduced transmission, but reduced it less than they did in the first wave. This difference is likely due to organisational safety measures and individual protective behaviours—such as distancing—which made various areas of public life safer and thereby reduced the effect of closing them. Specifically, we find smaller effects for closing educational institutions, suggesting that stringent safety measures made schools safer compared to the first wave. Second-wave estimates outperform previous estimates at predicting transmission in Europe’s third wave.

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Section: Resultsmentioning

confidence: 99%

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

et al. 2021

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“…The latter is successful ongoing with 66,43 % of the population over 12 who have completed the vaccination cycle at 2021.08.18 [34]. However, in the period July-August 2021 an increase of infections registered in Italy has been observed [35], probably due to the Delta variant, becoming the dominant variant in England by late May, due to partial immune escape [36]. In particular, a single dose vaccination is not sufficiently protective [37] and the Delta variant has a significantly higher transmission capacity than the Alpha variant [38].…”

Section: Discussionmentioning

confidence: 99%

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Ciccotti¹,

Pagliaro²,

Peluso³

et al. 2021

IJSSE

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The COVID-19 outbreak in Italy saturated the public hospitals' intensive care units in March 2020. The Ministry of Health asked for the Military Health Unit's intervention to deal with the emergency. The first COVID-19 Army field hospital in the world was thus built in Piacenza, Italy, to address the emergency. We describe the architecture of the hospital and the preventive measures adopted to reduce COVID-19 contagion among the medical personnel. The hospital project with the "H" shape divides the "dirty path" of entry for operators and patients from the "clean path" of exit for operators. Hypochloritebased and alcohol-based solutions were used for personal protective equipment (PPE) decontamination before reuse. Although exposed to 50 confirmed COVID-19 patients, all primary care personnel tested negative to COVID-19, before the operation, 14 days after the first patient and 30 days after the closure of the military field hospital. Due to the reported discomfort and its potential toxicity, the hypochlorite-based disinfection method was substituted with alcohol-based disinfection solution, which displayed comparable effective results. The results of the present study pave the way for the creation of a protocol for future validation in larger studies aimed at providing guidelines in emergency conditions.

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“…Ten wild-type samples were also chosen that did not contain any of these mutations ( Tables 1 , 2 ) and also presented similar coverage depth at the positions of interest after normalization. Lineage B.1.1.7, termed Variant of Concern (VOC) 202012/01 by Public Health England (PHE) ( Public Health England, 2021 ), 20I/501Y.V1 by Nextstrain ( Centers for Disease Control and Prevention [CDC], 2021 ) and alpha variant by the World Health Organization ( WHO, 2021 ), was first reported in the United Kingdom but became the dominant strain in many European countries until the emergence of the delta variant since mid-April 2021 ( Mishra et al, 2021 ). The B.1.1.7 variant was found to be more transmissible ( Davies et al, 2021 ) and may cause more severe infections ( SAGE-EMG, SPI-B, Tranmission Group, 2020 ; GOV.UK - Scientific Advisory Group for Emergencies, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…These samples contained the mutations assigned to the B.1.1.7 variant. Ten wild-type samples were also chosen that did not contain any of these mutations (Tables 1, 2 , 2021), was first reported in the United Kingdom but became the dominant strain in many European countries until the emergence of the delta variant since mid-April 2021 (Mishra et al, 2021). The B.1.1.7 variant was found to be more transmissible (Davies et al, 2021) and may cause more severe infections (SAGE-EMG, SPI-B, Tranmission Group, 2020; GOV.UK -Scientific Advisory Group for Emergencies, 2021).…”

Section: Employed Sequencing Data and Generation Of Consensus Genome Sequencesmentioning

confidence: 99%

Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing

et al. 2021

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The ongoing COVID-19 pandemic, caused by SARS-CoV-2, constitutes a tremendous global health issue. Continuous monitoring of the virus has become a cornerstone to make rational decisions on implementing societal and sanitary measures to curtail the virus spread. Additionally, emerging SARS-CoV-2 variants have increased the need for genomic surveillance to detect particular strains because of their potentially increased transmissibility, pathogenicity and immune escape. Targeted SARS-CoV-2 sequencing of diagnostic and wastewater samples has been explored as an epidemiological surveillance method for the competent authorities. Currently, only the consensus genome sequence of the most abundant strain is taken into consideration for analysis, but multiple variant strains are now circulating in the population. Consequently, in diagnostic samples, potential co-infection(s) by several different variants can occur or quasispecies can develop during an infection in an individual. In wastewater samples, multiple variant strains will often be simultaneously present. Currently, quality criteria are mainly available for constructing the consensus genome sequence, and some guidelines exist for the detection of co-infections and quasispecies in diagnostic samples. The performance of detection and quantification of low-frequency variants using whole genome sequencing (WGS) of SARS-CoV-2 remains largely unknown. Here, we evaluated the detection and quantification of mutations present at low abundances using the mutations defining the SARS-CoV-2 lineage B.1.1.7 (alpha variant) as a case study. Real sequencing data were in silico modified by introducing mutations of interest into raw wild-type sequencing data, or by mixing wild-type and mutant raw sequencing data, to construct mixed samples subjected to WGS using a tiling amplicon-based targeted metagenomics approach and Illumina sequencing. As anticipated, higher variation and lower sensitivity were observed at lower coverages and allelic frequencies. We found that detection of all low-frequency variants at an abundance of 10, 5, 3, and 1%, requires at least a sequencing coverage of 250, 500, 1500, and 10,000×, respectively. Although increasing variability of estimated allelic frequencies at decreasing coverages and lower allelic frequencies was observed, its impact on reliable quantification was limited. This study provides a highly sensitive low-frequency variant detection approach, which is publicly available at https://galaxy.sciensano.be, and specific recommendations for minimum sequencing coverages to detect clade-defining mutations at certain allelic frequencies. This approach will be useful to detect and quantify low-frequency variants in both diagnostic (e.g., co-infections and quasispecies) and wastewater [e.g., multiple variants of concern (VOCs)] samples.

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Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

Cited by 119 publications

References 31 publications

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

Understanding the effectiveness of government interventions against the resurgence of COVID-19 in Europe

Prevention Procedures to Contain COVID-19 Contagion in the First Italian Army Field Hospital

Strategy and Performance Evaluation of Low-Frequency Variant Calling for SARS-CoV-2 Using Targeted Deep Illumina Sequencing

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