The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index; 1 of the 9 sources its claims cite were checked for support.
Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7
Open accessPublished version of a preprint
Abstract
SARS-CoV-2 lineage B.1.1.7, a variant that was first detected in the UK in September 2020 1, has spread to multiple countries worldwide. Several studies have established that B.1.1.7 is more transmissible than pre-existing variants, but have not identified whether it leads to any change in disease severity 2. Here we analyse a dataset that links 2,245,263 positive SARS-CoV-2 community tests and 17,452 deaths associated with COVID-19 in England from 1 November 2020 to 14 February 2021. For 1,146,534 (51%) of these tests, the presence or absence of B.1.1.7 can be identified because mutations in this lineage prevent PCR amplification of the spike (S) gene target (known as S gene target failure (SGTF)1). On the basis of 4,945 deaths with known SGTF status, we estimate that the hazard of death associated with SGTF is 55% (95% confidence interval, 39-72%) higher than in cases without SGTF after adjustment for age, sex, ethnicity, deprivation, residence in a care home, the local authority of residence and test date. This corresponds to the absolute risk of death for a 55-69-year-old man increasing from 0.6% to 0.9% (95% confidence interval, 0.8-1.0%) within 28 days of a positive test in the community. Correcting for misclassification of SGTF and missingness in SGTF status, we estimate that the hazard of death associated with B.1.1.7 is 61% (42-82%) higher than with pre-existing variants. Our analysis suggests that B.1.1.7 is not only more transmissible than pre-existing SARS-CoV-2 variants, but may also cause more severe illness.
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Claims the paper makes
26 Own result · 14 Own method · 11 Own interpretation · 5 Not checked yet · 5 No basis given · 1 Supported
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Infections with the B.1.1.7 variant are associated with higher viral concentrations in nasopharyngeal swabs, as measured by C t values using PCR testing (Extended Data Fig. 6).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Discussion
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This comparison suggests that S-gene dropout samples are not overrepresented in testing data relative to the prevalence of S-gene dropout in the community”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Sensitivity analyses
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The prevalence of SGTF increased steeply over time (Fig. 1a), from 5.8% during 1-21 November 2020 to 94.3% during 24 January-14 February 2021.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 271
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“On the basis of 4,945 deaths with known SGTF status, we estimate that the hazard of death associated with SGTF is 55% (95% confidence interval, 39-72%) higher than in cases without SGTF after adjustment for age, sex, ethnicity, deprivation, residence in a care home, the local authority of residence and test date.”
- Also stated in: § Cox regression analyses · hedged
“For the analysis of the complete cases, the estimated hazard ratio for SGTF was 1.55 (95% confidence interval, 1.39-1.72),indicating that the hazard of death in the 28 days after a positive test is 55% (39-72%) higher for SGTF than for non-SGTF cases.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- The authors state this as an assumption: In the complete-case analysis, death is independent of whether SGTF status is observed or missing, given the individual's other characteristics included in the survival model.
- Also stated in: § Cox regression analyses · hedged
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Correcting for misclassification of SGTF and missingness in SGTF status, we estimate that the hazard of death associated with B.1.1.7 is 61% (42-82%) higher than with pre-existing variants.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- The authors state this as an assumption: In the IPW analysis, whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Stratifying by broad age groups and by sex, residence type, ethnicity, IMD, region and specimen date, death rates within 28 days of a positive SARS-CoV-2 test were higher among SGTF than non-SGTF cases in 98 of the 104 strata assessed (94%; Fig. 1d-i and Supplementary Table 2).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 271
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Approximately 49% of individuals in the study sample are missing data on SGTF status, due to their test not having been processed at one of the three laboratories using the Thermo Fisher TaqPath COVID-19 assay or the test being inconclusive.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Although we caution that symptomatic screening status may lie on the causal pathway between SGTF status and death, we found that this adjustment had no effect on the relative hazard of SGTF (1.54 (1.39-1.71);analysis of complete cases).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Further investigations
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- The authors state this as an assumption: In the complete-case analysis, death is independent of whether SGTF status is observed or missing, given the individual's other characteristics included in the survival model.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This corresponds to the absolute risk of death for a 55-69-year-old man increasing from 0.6% to 0.9% (95% confidence interval, 0.8-1.0%)within 28 days of a positive test in the community.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Among those with known SGTF status, the crude death rate associated with COVID-19 was 1.86 deaths per 10,000 person-days of follow-up in the SGTF group, versus 1.42 deaths per 10,000 person-days in the non-SGTF group (Fig. 1c and Extended Data Table 2).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 271
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- Probably not a substantial claim. 26
- It may state two separate claims as one. 25
Every source the paper cites for this claim was checked and supports it.
In the paper
“Several studies have established that B.1.1.7 is more transmissible than pre-existing variants, but have not identified whether it leads to any change in disease severity 2 .”
- Also stated in: § Discussion · plain
“We previously found that B.1.1.7 is substantially more transmissible than pre-existing SARS-CoV-2 variants, but could not robustly identify any associated change in disease severity using population-level analysis of early data 2 .”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
What the sources say
- Supportedcites [2] Davies, N. G. et al. Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science https://doi.org/10.1126/science.abg3055 (2021). source
The Discussion estimates that B.1.1.7 (VOC 202012/01) had a higher reproduction number than preexisting variants in England. It also says the authors could not determine from early population-level data whether the variant was associated with higher disease severity. No page numbers are provided in our copy. (LLM, conf=0.93)
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Also stated in: § Discussion · plain
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“There was strong evidence of non-proportionality of hazards (likelihood ratio test P χ ( =11) = 0.009 1 2 ) (Fig. 2a and Extended Data Fig. 3), with the estimated time-varying hazard ratio increasing over time: 1.14 (0.92-1.40) on day 1 after the positive test, 1.58 (1.42-1.75) on day 14 and 2.24 (1.75-2.87) on day 28.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Cox regression analyses
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“A small proportion (10.4%) of SGTF tests are inconclusive.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Just over half of those tested (1,146,534; 51.1%) had a conclusive SGTF reading and, of these, 58.8% had SGTF.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Characteristics of the study population
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“there were 17,913 age-0 individuals compared to 10,132 age-1 individuals in the dataset”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plainn = 17,913- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably not a substantial claim. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“For those samples for which SGTF status was measured, SGTF prevalence was similar in male and female individuals, but lower in the older age groups: 59.0% in 1-34-year-old individuals compared with 55.4% in those aged 85 years and older.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Characteristics of the study population
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Similar to the analysis of the complete cases, the IPW analysis recovered an increasing hazard ratio with time since a positive test, but the increase was less marked (Fig. 2b) and did not significantly differ from zero (Wald test P χ ( =1.4) = 0.23 1 2 ).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 273
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: In the IPW analysis, whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The IPW analysis gave similar results to the analysis of the complete cases, yielding a hazard ratio of 1.58 (1.40-1.78).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 273
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: In the IPW analysis, whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The full dataset used for the main analysis comprises 2,245,263 individuals, with SGTF status missing or inconclusive for 1,098,729 (48.9%).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plainn = 2,245,263- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Of the 57,750 deaths associated with COVID-19 in England during the study period, 17,642 deaths (30.5%) can be linked to a positive Pillar 2 test; among these, 4,945 have non-missing SGTF status.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Missingness in SGTF status also differed substantially between regions of NHS England, ranging from 21.2% in the North West to 71.1% in the South West, which is largely explained by proximity to a Lighthouse laboratory that is capable of producing an SGTF reading (Extended Data Fig. 1).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 271
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Again restricting the analysis to specimens from 1 November 2020 onward, we find a hazard ratio associated with p VOC of 1.58 (1.42-1.76)for the analysis of the complete cases and 1.61 (1.42-1.82)for the IPW analysis (Fig. 2c, d).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Misclassification analysis
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: In the IPW analysis, whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In keeping with these age patterns, SGTF prevalence was lower in individuals living in a care or nursing home (54.3%) than those in residential accommodation (58.8%).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Characteristics of the study population
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In total, 19,615 people in the study sample are known to have died (0.87% of 2,245,263).Crude death rates were substantially higher in the elderly and in those living in a care or nursing home (Supplementary Table 1).The standard definition of a death associated with COVID-19 in England is any death that occurred within 28 days of the first positive SARS-CoV-2 test of an individual; 17,452 of the”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Nature | Vol 593 | 13 May 2021 | 271
plainn = 19,615- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“P = 0.001 for SGTF (a); P = 0.039 for age (b); P = 0.101 for sex (c); P = 0.937 for IMD decile (d); P = 0.969 for ethnicity (e-g); P = 0.064 for residence type (h-i); and P = 0.027 globally.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Sensitivity analyses
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
In the paper
“SGTF prevalence was the lowest in the most-deprived quintile of the index of multiple deprivation 3 (IMD) (53.9%).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Characteristics of the study population
What the sources say
- Not checked yetcites [3] McLennan, D. et al. English Indices of Deprivation 2019. https://www.gov.uk/government/publications/english-indices-of-deprivation-2019-technical-report (Ministry of Housing, Communities & Local Government 2019).
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“So, although our study includes 1,098,729 Pillar 2 tests with non-missing SGTF status, which represents 51.1% of the 2,245,263 Pillar 2 tests over this period and 40.2% of the 2,736,806 combined Pillar 1 (hospital) and Pillar 2 (community) SARS-CoV-2 tests over this period, we can only assess SGTF status for 8.6% (4,945/57,750) of the individuals who died from COVID-19 over the study period.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“SGTF prevalence by self-identified ethnicity was 58.0% in the white group, 57.6% in the Asian group, 69.6% in the Black group and 64.8% in the other, mixed or unknown ethnicity group.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Characteristics of the study population
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We assessed whether the association between SGTF and the hazard was modified by age, sex, IMD, ethnicity and residence type.Models with and without interactions were compared using likelihood ratio tests for the analyses of the complete cases.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Area of residence and specimen date were expected to be potentially strong confounding factors.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For our main analysis, we included only tests from after 1 November 2020 to avoid including an excess of tests with SGTF not resulting from infection by lineage B.1.1.7.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, we find no clear difference in SGTF frequency among community tests relative to a random sample of SARS-CoV-2 infections in the population (Extended Data Fig. 7), which suggests that variant-associated changes in test-seeking propensity do not explain our findings.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Discussion
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Unfortunately, we were unable to account for vaccination status in this analysis.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Discussion
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“For IPW analyses, the standard errors accounted for the weights, although the fact that the weights were estimated was not accounted for; this results in conservative standard errors.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This is explained by differing mortality rates among individuals who first test positive in a hospital compared to those who are tested in the community, as the former group are much more likely to have a severe illness, as well as by missingness in the SGTF data.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Misclassification of an exposure can result in bias in its estimated association with the outcome.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Misclassification analysis
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The baseline hazard in the Cox model was stratified by both specimen date and LTLA, therefore finely controlling for these variables.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“Our findings are consistent with earlier reports by ourselves and other groups 7 and with contemporaneous studies [8][9][10][11] assessing the risk of severe outcomes among individuals with B.1.1.7 infection.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Discussion
What the sources say
- Not checked yetcites [7] Scientific Advisory Group for Emergencies. NERVTAG: Update Note on B.1.1.7 Severity, 11 February 2021. https://www.gov.uk/government/publications/nervtag-update-note-on-b117-severity-11-february-2021 (2021).
- Not checked yetcites [8] Challen, R. et al. Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study. BMJ 372, n579 (2021). source
- Not checked yetcites [9] Grint, D. J. et al. Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England. Euro Surveill. 26, 21002 (2021).
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The assumption of proportional hazards was assessed by including in the model an interaction between each covariate and time, which was performed separately for SGTF and for each other covariate.Schoenfeld residual plots were also obtained for each covariate (Extended Data Fig. 3).”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These estimates reflect a substantial increase in absolute risk among older age groups, but the risk of death associated with COVID-19 after a positive test in the community remains below 1% in most individuals who are younger than 70 years old.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Absolute risks
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The baseline risk of death among individuals tested in the community between August and October 2020 is illustrative of the case fatality ratio associated with pre-existing SARS-CoV-2 variants.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The stratification gives a large number of strata matched by specimen date and LTLA.Only those strata that contain individuals who died and individuals who survived contribute to the analysis.The analysis is therefore similar to the analysis that would be performed had we created a matched nested case-control sample.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We do not identify any mechanism for the increased mortality here.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Discussion
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“The fit of the missingness model was assessed using a Q-Q plot (Extended Data Fig. 4), and Hosmer-Lemeshow and Hinkley tests were used to choose the most appropriate model.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“The following variables were also identified as potential confounding factors: sex, age, residence type (residential, care or nursing home, or other or unknown), ethnicity (white, Asian, Black or other, mixed or unknown) and IMD.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“There was a small amount of missing data for sex (n = 14, <0.01%), age (n = 171, <0.01%), and IMD and regional covariates (n = 3,817, 0.16%).There were no missing specimen dates.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
plainn = 2,245,263- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our analysis suggests that B.1.1.7 is not only more transmissible than pre-existing SARS-CoV-2 variants, but may also cause more severe illness.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“the administrative censoring date, which we chose as the date of the most recent death linkable to SGTF status minus 10 days (that is, 14 February 2021) to minimize any potential bias due to late reporting of deaths.”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Statistical methods
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
The authors state this as an assumption.
In the complete-case analysis, death is independent of whether SGTF status is observed or missing, given the individual's other characteristics included in the survival model.
“The analysis of the complete cases assumes that whether an individual dies is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the survival model”
The authors state this as an assumption.
In the IPW analysis, whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights.
“whereas the IPW analysis assumes that whether an individual has SGTF is independent of whether their SGTF status is observed or missing, given the individual's other characteristics included in the model used to derive weights for IPW 5 .”
The authors state this as an assumption.
The baseline risk of death among individuals tested in the community between August and October 2020 is illustrative of the case fatality ratio associated with pre-existing SARS-CoV-2 variants.
“applying hazard ratios for SGTF to the baseline risk of death among individuals tested in the community between August and October 2020 (assumed to be illustrative of the case fatality ratio associated with pre-existing variants of SARS-CoV-2)”
The authors state this as an assumption.
The complete-case analysis assumes that missing SGTF status is independent of the outcome given the variables in the models, a type of missing-not-at-random assumption that may depend on the underlying SGTF value.
“This analysis of complete cases assumes that for each analysis, the missing data-in this case missing SGTF status-are independent of the outcome of interest given the variables included in the models.This is a specific type of 'missing not at random' assumption, as in particular it is allowed to depend on the underlying value of SGTF.”
The authors state this as an assumption.
The IPW analysis assumes that SGTF status is missing at random.
“We also performed an analysis of the complete cases using inverse probability weights 5 (IPW) to address the missing data on SGTF, under a 'missing at random' assumption.”
The authors state this as an assumption.
The analysis assumes that censoring is uninformative.
“The analysis assumes that censoring is uninformative, which is plausible as all censoring is administrative.”
The authors state this as an assumption.
A negative SGTF test is assumed to indicate absence of B.1.1.7 infection.
“A negative test of SGTF is assumed to be indicative of an absence of infection with B.1.1.7.”
The authors state this as an assumption.
Poisson confidence intervals for mortality rates assume constant rates.
“Exact Poisson confidence intervals are used for mortality rates, assuming constant rates.”
The authors state this as an assumption.
The Cox model assumes proportional hazards for SGTF and the covariates.
“We began by assuming the proportionality of the hazards for SGTF and the covariates included in the model.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“and an estimated 50% increased mortality 194,195,202 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [194]
In the citing paper
“Other studies have assessed the relative mortality of the VOC with similar conclusions [7-10], however, our results are the first to include detailed information on the presence of comorbidities.”
From Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England, 16 November to 5 February (2021) · cites this paper as [9]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
“So, although our study includes 1,098,729 Pillar 2 tests with non-missing SGTF status, which represents 51.1% of the 2,245,263 Pillar 2 tests over this period”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Data sources
Reported 51.1 · recomputed 48.935425
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Misclassification analysis
“downloaded from the Microreact platform 15 (https://microreact.org/) on 11 January 2020 to estimate p VOC .”
§ Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 > Abstract
“SARS-CoV-2 lineage B.1.1.7,a variant that was first detected in the UK in September 2020 1 , has spread to multiple countries worldwide.”
Citations
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Metadata
- Authors
- CMMID COVID-19 Working Group, Davies, N. G., Jarvis, C. I., Edmunds, W. J., Jewell, N. P., Diaz-Ordaz, K., & Keogh, R. H.
- Affiliations
- London School of Hygiene & Tropical Medicine (GB)
- Corresponding author
- Davies, Nicholas G.
- Venue
- Nature
- Published
- 2021-03-15
- Volume
- 593
- Issue
- 7858
- Pages
- 270-274
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9170116
- OpenAlex
- W3137149656
- Cited by
- 921
- References
- 12
- Citations by year
- 2026: 12 · 2025: 37 · 2024: 74 · 2023: 130 · 2022: 303 · 2021: 362
- FWCI
- 68.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
- Funders
- Wellcome Trust (208812/Z/17/Z, 206471/Z/17/Z, 218554/Z/19/Z)
- UK Research and Innovation (ES/P010873/1, MR/S017968/1, ES/P010873)
- National Institute for Health Research Health Protection Research Unit (NIHR200908, NIHR200929)
- National Institute for Health and Care Research ((NIHR200929), (NIHR200908), NIHR-INF-1846)
- Research Councils UK (ES/P010873/1)
- European Commission (101003688)
- Public Health England
- National Institutes of Health
- Medical Research Council (NIHR200908, MR/S017968/1, MC_PC_19065)
- Economic and Social Research Council (ES/P010873/1)
- National Institute of Allergy and Infectious Diseases (R01AI148127)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Keywords
- COVID-19 mortality, S-gene target failure, spike gene mutations, disease severity, SARS-CoV-2 variants, England
- MeSH terms
- COVID-19, SARS-CoV-2, Adolescent, Adult, Aged, Aged, 80 and over, Child, Child, Preschool, England, Ethnicity, Female, Homes for the Aged, Humans, Infant, Male, Middle Aged, Phylogeny, Time Factors, Proportional Hazards Models, Survival Analysis, Risk Assessment, Evolution, Molecular, Young Adult
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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