Variation in reported SARS-CoV-2 cases after testing policy changes

Halford, Florence; Nash, Sophie; Tessier, Elise; Kall, Meaghan; Dabrera, Gavin

doi:10.1016/s1473-3099(22)00572-2

Cited by 5 publications

(8 citation statements)

References 1 publication

(1 reference statement)

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“…This analysis demonstrates that sequenced cases of COVID-19 between March 2020 and August 2021 in England were generally representative of all cases by key socio-economic characteristics, such as the most deprived who were disproportionately affected by the pandemic, providing important utility for these sequencing data. Future work will be needed to explore sequencing trends in later time periods and to consider the effects on representativeness from changes to SARS-CoV-2 testing approaches in England [22], particularly in relation to deprivation and ethnicity. This study has provided evidence to support the use of sequencing data for rigorous epidemiological analyses, including, but not limited to, assessing variant severity, vaccine effectiveness, and household transmission, which have been crucial in understanding health inequalities and informing the national COVID-19 pandemic response [23][24][25][26][27].…”

Section: Discussionmentioning

confidence: 99%

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Twohig,

Harman,

Zaidi

et al. 2023

Epidemiol. Infect.

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Whole-genome sequencing (WGS) information has played a crucial role in the SARS-CoV-2 (COVID-19) pandemic by providing evidence about variants to inform public health policy. The purpose of this study was to assess the representativeness of sequenced cases compared with all COVID-19 cases in England, between March 2020 and August 2021, by demographic and socio-economic characteristics, to evaluate the representativeness and utility of these data in epidemiological analyses. To achieve this, polymerase chain reaction (PCR)-confirmed COVID-19 cases were extracted from the national laboratory system and linked with WGS data. During the study period, over 10% of COVID-19 cases in England had WGS data available for epidemiological analysis. With sequencing capacity increasing throughout the period, sequencing representativeness compared to all reported COVID-19 cases increased over time, allowing for valuable epidemiological analyses using demographic and socio-economic characteristics, particularly during periods with emerging novel SARS-CoV-2 variants. This study demonstrates the comprehensiveness of England’s sequencing throughout the COVID-19 pandemic, rapidly detecting variants of concern, and enabling representative epidemiological analyses to inform policy.

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Section: Discussionmentioning

confidence: 99%

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Twohig,

Harman,

Zaidi

et al. 2023

Epidemiol. Infect.

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“… 8 We extracted data for positive COVID‐19 cases (polymerase chain reaction or lateral flow test) from 02 February 2020 to 31 March 2022, when free community testing was discontinued. 9 For individuals with more than one COVID‐19 episode, each diagnosis occurring ≥90 days from the last episode was counted as a new episode. For each individual, data on age, sex, ethnicity, index of multiple deprivation (IMD) deciles, address and region were collected from the first episode extracted from SGSS.…”

Section: Methodsmentioning

confidence: 99%

“…The UK Health Security Agency (UKHSA) is responsible for collecting data on all notifications of COVID‐19 infection in England via the Second Generation Surveillance System (SGSS) 8 . We extracted data for positive COVID‐19 cases (polymerase chain reaction or lateral flow test) from 02 February 2020 to 31 March 2022, when free community testing was discontinued 9 . For individuals with more than one COVID‐19 episode, each diagnosis occurring ≥90 days from the last episode was counted as a new episode.…”

Section: Methodsmentioning

confidence: 99%

The impact of COVID‐19 on residents of long‐term care facilities with learning disabilities and/or autism

Tessier¹,

Webster²,

Aziz³

et al. 2023

Influenza Resp Viruses

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Background The COVID‐19 pandemic has had disproportionate impact on vulnerable populations including those with learning disabilities. Assessing the incidence and risk of death in such settings can improve the prevention of COVID‐19. We describe individuals who tested positive for SARS‐CoV‐2 while residing in care homes for learning disabilities and/or autism and investigate the risk of death compared with individuals living in their own homes. Methods Surveillance records for COVID‐19 infections in England from 02 February 2020 to 31 March 2022 were extracted. Data on property type, variant wave, vaccination, hospitalisation and death were derived through data linkage and enrichment. Care home residents with learning disabilities and/or autism and diagnosed with COVID‐19 were identified and analysed, and logistic regression analyses compared the risk of death of individuals living in private residence. We assessed interaction parameters by post‐estimation analyses. Results A total of 3501 individuals were identified as diagnosed with SARS‐CoV‐2 whilst living in 632 care home properties for learning disabilities and/or autism. Of the 3686 episodes of infection, 80.4% were part of an outbreak. The crude case fatality rate was 2.6% and 0.6% among care home residents with autism and/or learning disabilities and their counterparts in households, respectively. The post‐estimation analyses found over eight times the odds of death among care home residents in 60 years old compared with their counterparts living in private homes. Conclusions Care home residents with learning disabilities and/or autism have a greater risk of death from COVID‐19. Optimising guidance to meet their needs is of great importance.

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“…During the spring and summer of 2022, mass testing for COVID-19, as well as sequencing capacity, was reduced in many countries where the pandemic appeared to recede [27][28][29][30]. As data on cases and the virus variants become less available, collaborative international efforts will become more important.…”

Section: Introductionmentioning

confidence: 99%

A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022

Nyberg,

Bager,

Svalgaard

et al. 2023

Eurosurveillance

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Several SARS-CoV-2 variants that evolved during the COVID-19 pandemic have appeared to differ in severity, based on analyses of single-country datasets. With decreased testing and sequencing, international collaborative studies will become increasingly important for timely assessment of the severity of new variants. Therefore, a joint WHO Regional Office for Europe and ECDC working group was formed to produce and pilot a standardised study protocol to estimate relative case-severity of SARS-CoV-2 variants during periods when two variants were co-circulating. The study protocol and its associated statistical analysis code was applied by investigators in Denmark, England, Luxembourg, Norway, Portugal and Scotland to assess the severity of cases with the Omicron BA.1 virus variant relative to Delta. After pooling estimates using meta-analysis methods (random effects estimates), the risk of hospital admission (adjusted hazard ratio (aHR) = 0.41; 95% confidence interval (CI): 0.31−0.54), admission to intensive care unit (aHR = 0.12; 95% CI: 0.05−0.27) and death (aHR = 0.31; 95% CI: 0.28−0.35) was lower for Omicron BA.1 compared with Delta cases. The aHRs varied by age group and vaccination status. In conclusion, this study demonstrates the feasibility of conducting variant severity analyses in a multinational collaborative framework and adds evidence for the reduced severity of the Omicron BA.1 variant.

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Variation in reported SARS-CoV-2 cases after testing policy changes

Cited by 5 publications

References 1 publication

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

Representativeness of whole-genome sequencing approaches in England: the importance for understanding inequalities associated with SARS-CoV-2 infection

The impact of COVID‐19 on residents of long‐term care facilities with learning disabilities and/or autism

A standardised protocol for relative SARS-CoV-2 variant severity assessment, applied to Omicron BA.1 and Delta in six European countries, October 2021 to February 2022

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