Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
Houriiyah Tegally, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, Sureshnee Pillay, Emmanuel James San, Nokukhanya Msomi, Koleka Mlisana, Anne von Gottberg, Sibongile Walaza, Mushal Allam, Arshad Ismail, Thabo Mohale, Allison J Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Francesco Petruccione, Alex Sigal, Diana Hardie, Gert Marais, Marvin Hsiao, Stephen Korsman, Mary-Ann Davies, Lynn Tyers, Innocent Mudau, Denis York, Caroline Maslo, Dominique Goedhals, Shareef Abrahams, Oluwakemi Laguda-Akingba, Arghavan Alisoltani-Dehkordi, Adam Godzik, Constantinos Kurt Wibmer, Bryan Trevor Sewell, Jose Lourenco, Luiz Carlos Junior Alcantara, Sergei L Kosakovsky Pond, Steven Weaver, Darren Martin, Richard J Lessells, Jinal N Bhiman, Carolyn Williamson, View ORCID ProfileTulio de de Oliveira
This article is a preprint and has not been certified by peer review [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.
Abstract
Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
The health secretary also said two cases have been detected of another new variant of the coronavirus in the UK.
Both were contacts of cases who have travelled from South Africa over the past few weeks, he said.
He said: "This new variant is highly concerning because it is yet more transmissible and it appears to have mutated further than the new variant that has been discovered in the UK."
The health secretary said both cases and close contacts of the cases have been quarantined.
There are immediate restrictions on travel from South Africa and the government is telling those who have been in contact with anyone who has been in South Africa in the last fortnight that they must quarantine.
The measures were temporary, he said, while the new variant was analysed by scientists at the government's research centre at Porton Down.
video is grave!
Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
Status: report | First online: 23-12-2020 | Last update: 23-12-2020
Authors: Nicholas Davies*, Rosanna C Barnard1, Christopher I Jarvis1, Adam J Kucharski1, James D Munday1, Carl A.B. Pearson1, Timothy W Russell1, Damien C Tully1, Sam Abbott, Amy Gimma, William Waites, Kerry LM Wong, Kevin van Zandvoort, CMMID COVID-19 working group, Rosalind M Eggo, Sebastian Funk, Mark Jit, Katherine E Atkins & W John Edmunds.
* corresponding author1 contributed equally
This study has not yet been peer reviewed.
A novel SARS-CoV-2 variant, VOC 202012/01, emerged in southeast England in November 2020 and appears to be rapidly spreading towards fixation. We fitted a two-strain mathematical model of SARS-CoV-2 transmission to observed COVID-19 hospital admissions, hospital and ICU bed occupancy, and deaths; SARS-CoV-2 PCR prevalence and seroprevalence; and the relative frequency of VOC 202012/01 in the three most heavily affected NHS England regions (South East, East of England, and London). We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence, with COVID-19 hospitalisations and deaths projected to reach higher levels in 2021 than were observed in 2020, even if regional tiered restrictions implemented before 19 December are maintained. Our estimates suggest that control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.
Covid-19: Chaotic decision making and failure to communicate undermined government response, says report
Cite this as: BMJ 2020;371:m4940
Shaun Griffin Author affiliations Ministers must improve the way they use and communicate advice from scientists or risk repeating mistakes made earlier in the coronavirus pandemic, a think tank has warned.
A report from the Institute for Government outlined a series of errors it said the government made in the past 10 months: from the lack of a coherent strategy when lockdown restrictions were lifted in May to its failure to consult scientists on “epidemiologically illiterate” policies, such as the “Eat Out to Help Out” scheme, and its delay in consulting the Scientific Advisory Group for Emergencies on the return of students to universities.1
Many such problems had been seen in the government’s handling of past crises, such as the outbreaks of bovine spongiform encephalopathy, foot and mouth disease, and H1N1 “swine” flu, said the report. These included the blurring of policy decisions and expert advice, relying on uncertain modelling and “groupthink,” and a lack of transparency in explaining how evidence and advice were used.
Tom Sasse, associate director at the institute and an author of the report, said that the pandemic response had so far “too often been undermined by misunderstanding the role of science advice and using it inconsistently.” He added, “Looking to scientists to make judgments only politicians can make has contributed to the government delaying the first lockdown.
“Haphazard communication of key public health messages switched between alarm and reassurance while failing to drive home key points such as the risk of gathering indoors.” Furthermore, a lack of transparent evidence had undermined confidence in government policies, such as the plan to reopen schools in June, he said.
“Ministers repeatedly insisted they were ‘following the science.’ But the decision over Christmas bubbles is yet another example of the government delaying decision making and failing to use scientific advice well—or to communicate a consistent message to the public,” said Sasse. “There are difficult months of restrictions and vaccine rollout to come in 2021. Ministers must avoid repeating the damaging mistakes of this year.”
SAGE role praised The report noted that, despite being an ad hoc body, SAGE had responded well under pressure. Its co-chairs, Patrick Vallance and Chris Whitty, adapted the group in response to the crisis when it was not designed to take on such a prolonged role.
SAGE has met more than 70 times to discuss covid, whereas in previous crises it met no more than five times. After the first few weeks the Department of Health and Social Care for England and Public Health England, and their devolved equivalents, would have been expected to take over the ongoing response, but this did not happen. Instead, Number 10 opted to retain greater control and keep SAGE running, even after the high level Cabinet Office group stopped meeting.
Sasses said that although there were “valid criticisms about the range of disciplines represented in [SAGE’s] membership . . . the greater problem has been chaotic decision making from the top of government.” This has repeatedly created problems in how SAGE’s work is commissioned and how its members understand the way their advice is used.
Recommendations The institute called on covid cabinet committees to better integrate scientific, economic, and other advice in making decisions in the coming months and for ministers to explain clearly how trade-offs are made. The government must also make more use of scientist led briefings to explain to the public the reasons for its measures.
The institute also said that the Treasury should publish economic analyses of the costs and effects on wellbeing of implementing, or not implementing, public health restrictions.
In the longer term the government should strengthen science capability across the civil service, develop strong working relations with ministerial scientific advisers, and make more consistent use of groups tasked with finding weaknesses in crisis response plans.
Science advice in a crisis
Published: 18 December 2020
Ministers must improve the way they use and communicate science advice or risk repeating mistakes made during the coronavirus crisis.
This paper draws on interviews with key players including current and former officials, scientific advisers and SAGE members.
While ministers have faced extraordinarily difficult choices, the government’s response to the pandemic has too often been undermined by misunderstanding the role of science advice and using it inconsistently. Looking to scientists to make judgements only politicians can make – captured in ministers’ misleading mantra that they were “following the science” – contributed to the government delaying the first lockdown.
The government failed to bring different strands of advice together to form a coherent strategy when restrictions were lifted from May. Scientists were not consulted about policies including the Eat Out to Help Out scheme and thought they were epidemiologically illiterate, and SAGE was consulted too late about the return of university students to offer useful advice.
Haphazard communication of key public health messages has switched between alarm and reassurance, while failing to drive home key points such as the risk of gathering indoors. The government has also failed to explain the trade-offs behind its policies, while a lack of transparent evidence undermined confidence in specific policies, such as the plan to reopen schools in June.
SAGE itself has responded well under substantial pressure and despite being designed as an ad-hoc body. While there are valid criticisms about the range of disciplines represented in its membership, with discussion often dominated by epidemiologists and modellers and a lack of external public health experts, the greater problem has been chaotic decision making from the top of government. This has repeatedly created problems in how SAGE work is commissioned and how its members understand the way their advice is used by government.
As it rolls out a vaccine, the government will continue to face difficult decisions about how to control the virus in the coming months. The report sets out how it can make immediate improvements to the way it uses science advice and makes recommendations for future crises.
Science Advice in a Crisis December 2020
covid Galveston County Texas DEATHS 204 to date
Galveston County:
Confirmed Cases 17,945
Probable Cases 935
Fatalities 204
Active Cases (Estimated) 2,971
Recovered (Estimated) 14,802
Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations
Report written by: Andrew Rambaut1, Nick Loman2, Oliver Pybus3, Wendy Barclay4, Jeff Barrett5, Alesandro Carabelli6, Tom Connor7, Tom Peacock4, David L Robertson8, Erik Volz4, on behalf of COVID-19 Genomics Consortium UK (CoG-UK)9.
University of Edinburgh University of Birmingham University of Oxford Imperial College London Wellcome Trust Sanger Institute University of Cambridge Cardiff University MRC-University of Glasgow Centre for Virus Research https://www.cogconsortium.uk 1.2k
Summary
Recently a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset. This cluster has been growing rapidly over the past 4 weeks and since been observed in other UK locations, indicating further spread.
Several aspects of this cluster are noteworthy for epidemiological and biological reasons and we report preliminary findings below. In summary:
The B.1.1.7 lineage accounts for an increasing proportion of cases in parts of England. The number of B.1.1.7 cases, and the number of regions reporting B.1.1.7 infections, are growing.
B.1.1.7 has an unusually large number of genetic changes, particularly in the spike protein.
Three of these mutations have potential biological effects that have been described previously to varying extents:
Mutation N501Y is one of six key contact residues within the receptor-binding domain (RBD) and has been identified as increasing binding affinity to human and murine ACE2.
The spike deletion 69-70del has been described in the context of evasion to the human immune response but has also occurred a number of times in association with other RBD changes.
Mutation P681H is immediately adjacent to the furin cleavage site, a known location of biological significance. The rapid growth of this lineage indicates the need for enhanced genomic and epidemiological surveillance worldwide and laboratory investigations of antigenicity and infectivity.
Background
The two earliest sampled genomes that belong to the B.1.1.7 lineage were collected on 20-Sept-2020 in Kent and another on 21-Sept-2020 from Greater London. B.1.1.7 infections have continued to be detected in the UK through early December 2020. Genomes belonging to lineage B.1.1.7 form a monophyletic clade that is well supported by a large number of lineage-defining mutations (Figure 1). As of 15th December, there are 1623 genomes in the B.1.1.7 lineage. Of these 519 were sampled in Greater London, 555 in Kent, 545 in other regions of the UK including both Scotland and Wales, and 4 in other countries...
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Coronavirus (COVID-19) Infection Survey, UK Statistical bulletins
to be continued...tss
