Wastewater genomic surveillance tracks the spread of the SARS-CoV-2 Omicron variant across England (preprint)

Background Many countries have moved into a new stage of managing the SARS-CoV-2 pandemic with minimal restrictions and reduced testing in the population, leading to reduced genomic surveillance of virus variants in individuals. Wastewater-based epidemiology (WBE) can provide an alternative means of tracking virus variants in the population but is lacking verifications of its comparability to individual testing data. Methods We analysed more than 19,000 samples from 524 wastewater sites across England at least twice a week between November 2021 and February 2022, capturing sewage from >70% of the English population. We used amplicon-based sequencing and the phylogeny based de-mixing tool Freyja to estimate SARS-CoV-2 variant frequencies and compared these to the variant dynamics observed in individual testing data from clinical and community settings. Findings We show that wastewater data can reconstruct the spread of the Omicron variant across England since November 2021 in close detail and aligns closely with epidemiological estimates from individual testing data. We also show the temporal and spatial spread of Omicron within London. Our wastewater data further reliably track the transition between Omicron subvariants BA1 and BA2 in February 2022 at regional and national levels. Interpretation Our demonstration that WBE can track the fast-paced dynamics of SARS-CoV-2 variant frequencies at a national scale and closely match individual testing data in time shows that WBE can reliably fill the monitoring gap left by reduced individual testing in a more affordable way.

The mental health of NHS staff during the COVID-19 pandemic: a two-wave cohort study (preprint)

BackgroundHealth and social care workers(HSCWs) are at risk of experiencing adverse mental health (MH) outcomes (e.g., higher levels of anxiety and depression) as a result of the COVID-19 pandemic. This can have a detrimental impact on quality of care, the national response to the pandemic and its aftermath. AimsA longitudinal design provided follow-up evidence on the MH(changes in the prevalence of disease over time) of NHS staff working in a remote health board in Scotland during the COVID-19 pandemic and investigated the determinants of MH outcomes over time. MethodA two-wave longitudinal study was conducted from July to September 2020. Participants self-reported levels of depression(PHQ-9), anxiety(GAD-7), and mental well-being(WEMWBS) at baseline and again 1.5 months later. ResultsThe analytic sample of 169 participants, working in community(43%) and hospital(44%) settings reported substantial levels of probable clinical depression, anxiety and low mental well-being(MWB) at baseline(depression:30.8%, anxiety:20.1%, low-MWB:31.9%). Whilst the MH of participants remained mostly constant over time, the proportion of participants meeting the threshold for clinical anxiety increased to 27.2% at follow-up. Multivariable modelling indicated that working with, and disruption due to COVID-19 were associated with adverse MH changes over time. ConclusionsHSCWs working in a remote area with low COVID-19 prevalence, reported similar levels of substantial anxiety and depression as those working in areas of the UK with high rates of COVID-19 infections. Efforts to support HSCW MH must remain a priority and should minimize the adverse effects of working with, and the disruption caused by the COVID-19 pandemic.

Beyond the Disease: Contextualized Implications of the COVID-19 Pandemic for Children and Young People Living in Eastern and Southern Africa.

The coronavirus disease 2019 (COVID-19) pandemic has created extraordinary challenges and prompted remarkable social changes around the world. The effects of COVID-19 and the public health control measures that have been implemented to mitigate its impact are likely to be accompanied by a unique set of consequences for specific subpopulations living in low-income countries that have fragile health systems and pervasive social-structural vulnerabilities. This paper discusses the implications of COVID-19 and related public health interventions for children and young people living in Eastern and Southern Africa. Actionable prevention, care, and health promotion initiatives are proposed to attenuate the negative effects of the pandemic and government-enforced movement restrictions on children and young people.