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England has been heavily affected by the SARS-CoV-2 pandemic, with severe 'lockdown' mitigation measures now gradually being lifted. The real-time pandemic monitoring presented here has contributed to the evidence informing this pandemic management throughout the first wave. Estimates on the 10 May showed lockdown had reduced transmission by 75%, the reproduction number falling from 2.6 to 0.61. This regionally varying impact was largest in London with a reduction of 81% (95% credible interval: 77-84%). Reproduction numbers have since then slowly increased, and on 19 June the probability of the epidemic growing was greater than 5% in two regions, South West and London. By this date, an estimated 8% of the population had been infected, with a higher proportion in London (17%). The infection-to-fatality ratio is 1.1% (0.9-1.4%) overall but 17% (14-22%) among the over-75s. This ongoing work continues to be key to quantifying any widespread resurgence, should accrued immunity and effective contact tracing be insufficient to preclude a second wave. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

The tracking and projection of emerging epidemics is hindered by the disconnect between apparent epidemic dynamics, discernible from noisy and incomplete surveillance data, and the underlying, imperfectly observed, system. Behavior changes compound this, altering both true dynamics and reporting patterns, particularly for diseases with nonspecific symptoms, such as influenza. We disentangle these effects to unravel the hidden dynamics of the 2009 influenza A/H1N1pdm pandemic in London, where surveillance suggests an unusual dominant peak in the summer. We embed an age-structured model into a bayesian synthesis of multiple evidence sources to reveal substantial changes in contact patterns and health-seeking behavior throughout the epidemic, uncovering two similar infection waves, despite large differences in the reported levels of disease. We show how this approach, which allows for real-time learning about model parameters as the epidemic progresses, is also able to provide a sequence of nested projections that are capable of accurately reflecting the epidemic evolution.

Changes in hepatitis C virus (HCV) prevalence from 1992 to 2006 were examined by using 24,311 records from unlinked anonymous surveillance of injecting drug users in England and Wales. Bayesian logistic regression was used to estimate annual prevalence, accounting for changing recruitment patterns (age, gender, injecting duration, geographic region, interactions) and the sensitivity and specificity of different oral fluid testing devices. After controlling for these differences, the authors found that the adjusted HCV prevalence decreased from 70% (95% credible interval: 62, 78) in 1992 to 47% (95% credible interval: 43, 51) in 1998 before rising again to 53% (95% credible interval: 48, 58) in 2006. Women injecting drug users had a higher HCV risk than did men (odds ratio = 1.50, 95% credible interval: 1.31, 1.73). Two regions (London and North West) had a markedly higher HCV prevalence than did the rest of England and Wales. Among individuals who had injected for less than 1 year, the adjusted HCV prevalence in 2006 was higher than that in 1992 (28% vs. 19%, respectively). HCV infection can be prevented. The public health challenge in England and Wales is to increase action in order to regain a downward trend in HCV risk and the benefit that has been lost since 1998.

Objective: To describe the impact of HIV on mortality in men and women aged 15-54 in London., Design: Combination of routine mortality statistics with reports of AIDS deaths adjusted for underreporting and change in address from time of report to time of death. Calculation of standardised mortality ratios (SMRs) for males including and excluding HIV comparing inner London and outer London with the rest of England and Wales., Methods: Comparison of trends in all cause mortality and SMRs in males over time. Comparison of trends in HIV related deaths with other main causes of deaths in males and females in London., Results: Age standardised rates for the rest of England and Wales showed a continual decline from 1979 to 1996 but rates in inner London males (ages 15-54) stopped declining around 1984-5 leading to a considerable increase in the SMR for inner London from 127 for 1985-7 to 171 for 1994-6. SMRs excluding HIV related deaths for inner London, however, showed no significant change over this time. There was a fall in HIV related mortality in 1996, though HIV was still the leading cause of death in males and second leading cause of death in females in inner London, and the fourth commonest cause of death in males in outer London., Conclusion: These data are the first to indicate the impact of HIV on mortality within a significant population in England and Wales. They show that public health priorities in London are different from the rest of the country. Analyses of trends of all cause mortality in people under 65 may mislead unless they take account of HIV.