2 results
Replacement dynamics and the pathogenesis of the Alpha, Delta and Omicron variants of SARS-CoV-2
- Thomas Ward, Alex Glaser, Christopher E. Overton, Bob Carpenter, Nick Gent, Anna C. Seale
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- Journal:
- Epidemiology & Infection / Volume 151 / 2023
- Published online by Cambridge University Press:
- 20 December 2022, e32
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New SARS-CoV-2 variants causing COVID-19 are a major risk to public health worldwide due to the potential for phenotypic change and increases in pathogenicity, transmissibility and/or vaccine escape. Recognising signatures of new variants in terms of replacing growth and severity are key to informing the public health response. To assess this, we aimed to investigate key time periods in the course of infection, hospitalisation and death, by variant. We linked datasets on contact tracing (Contact Tracing Advisory Service), testing (the Second-Generation Surveillance System) and hospitalisation (the Admitted Patient Care dataset) for the entire length of contact tracing in the England β from March 2020 to March 2022. We modelled, for England, time delay distributions using a Bayesian doubly interval censored modelling approach for the SARS-CoV-2 variants Alpha, Delta, Delta Plus (AY.4.2), Omicron BA.1 and Omicron BA.2. This was conducted for the incubation period, the time from infection to hospitalisation and hospitalisation to death. We further modelled the growth of novel variant replacement using a generalised additive model with a negative binomial error structure and the relationship between incubation period length and the risk of a fatality using a Bernoulli generalised linear model with a logit link. The mean incubation periods for each variant were: Alpha 4.19 (95% credible interval (CrI) 4.13β4.26) days; Delta 3.87 (95% CrI 3.82β3.93) days; Delta Plus 3.92 (95% CrI 3.87β3.98) days; Omicron BA.1 3.67 (95% CrI 3.61β3.72) days and Omicron BA.2 3.48 (95% CrI 3.43β3.53) days. The mean time from infection to hospitalisation was for Alpha 11.31 (95% CrI 11.20β11.41) days, Delta 10.36 (95% CrI 10.26β10.45) days and Omicron BA.1 11.54 (95% CrI 11.38β11.70) days. The mean time from hospitalisation to death was, for Alpha 14.31 (95% CrI 14.00β14.62) days; Delta 12.81 (95% CrI 12.62β13.00) days and Omicron BA.2 16.02 (95% CrI 15.46β16.60) days. The 95th percentile of the incubation periods were: Alpha 11.19 (95% CrI 10.92β11.48) days; Delta 9.97 (95% CrI 9.73β10.21) days; Delta Plus 9.99 (95% CrI 9.78β10.24) days; Omicron BA.1 9.45 (95% CrI 9.23β9.67) days and Omicron BA.2 8.83 (95% CrI 8.62β9.05) days. Shorter incubation periods were associated with greater fatality risk when adjusted for age, sex, variant, vaccination status, vaccination manufacturer and time since last dose with an odds ratio of 0.83 (95% confidence interval 0.82β0.83) (P value < 0.05). Variants of SARS-CoV-2 that have replaced previously dominant variants have had shorter incubation periods. Conversely co-existing variants have had very similar and non-distinct incubation period distributions. Shorter incubation periods reflect generation time advantage, with a reduction in the time to the peak infectious period, and may be a significant factor in novel variant replacing growth. Shorter times for admission to hospital and death were associated with variant severity β the most severe variant, Delta, led to significantly earlier hospitalisation, and death. These measures are likely important for future risk assessment of new variants, and their potential impact on population health.
Assessing the role of imported cases on the establishment of SARS-CoV-2 Delta variant of concern in Bolton, UK
- Joseph Shingleton, Thomas Finnie, Nick Gent, Emma Bennett
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- Journal:
- Epidemiology & Infection / Volume 150 / 2022
- Published online by Cambridge University Press:
- 12 May 2022, e100
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This paper presents a method used to rapidly assess the incursion and the establishment of community transmission of suspected SARS-CoV-2 variant of concern Delta (lineage B.1.617.2) into the UK in April and May 2021. The method described is independent of any genetically sequenced data, and so avoids the inherent lag times involved in sequencing of cases. We show that, between 1 April and 12 May 2021, there was a strong correlation between local authorities with high numbers of imported positive cases from India and high COVID-19 case rates, and that this relationship holds as we look at finer geographic detail. Further, we also show that Bolton was an outlier in the relationship, having the highest COVID-19 case rates despite relatively few importations. We use an artificial neural network trained on demographic data, to show that observed importations in Bolton were consistent with similar areas. Finally, using an SEIR transmission model, we show that imported positive cases were a contributing factor to persistent transmission in a number of local authorities, however they could not account for increased case rates observed in Bolton. As such, the outbreak of Delta variant in Bolton was likely not a result of direct importation from overseas, but rather secondary transmission from other regions within the UK.