There are concerns that pneumococcal conjugate vaccines (PCVs) in sub-Saharan Africa sub-optimally interrupt Streptococcus pneumoniae vaccine-serotype (VT) carriage and transmission. Here we assess PCV carriage using rolling, prospective nasopharyngeal carriage surveys between 2015 and 2018, 3.6-7.1 years after Malawi's 2011 PCV13 introduction. Carriage decay rate is analysed using non-linear regression. Despite evidence of reduction in VT carriage over the study period, there is high persistent residual carriage. This includes among PCV-vaccinated children 3-5-year-old (16.1% relative reduction from 19.9% to 16.7%); PCV-unvaccinated children 6-8-year-old (40.5% reduction from 26.4% to 15.7%); HIV-infected adults 18-40-years-old on antiretroviral therapy (41.4% reduction from 15.2% to 8.9%). VT carriage prevalence half-life is similar among PCV-vaccinated and PCV-unvaccinated children (3.26 and 3.34 years, respectively). Compared with highincome settings, there is high residual VT carriage 3.6-7.1 years after PCV introduction. Rigorous evaluation of strategies to augment vaccine-induced control of carriage, including alternative schedules and catch-up campaigns, is required.

Vaccination and disease The United Kingdom has high rates of vaccination for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exceeding 80% of adults. As immunity wanes and social distancing is relaxed, how are rates of illness and severe disease affected by more infectious variants? Elliott et al . used reverse transcription PCR data from the REACT-1 study, which showed exponential transmission as the Alpha variant (B.1.1.7) was replaced by the Delta variant (B.1.617.2). After adjusting for age and other variables, vaccine effectiveness for the new variant averaged 55% in June and July of 2020. Despite the slower growth of the pandemic in the summer, it looks as if increased indoor mixing in the autumn will sustain transmission of the Delta variant despite high levels of adult vaccination. —CA

Surveillance of the SARS-CoV-2 epidemic has mainly relied on case reporting which is biased by health service performance, test availability and test-seeking behaviors. We report a community-wide national representative surveillance program in England involving self-administered swab results from 594,000 individuals tested for SARS-CoV-2, regardless of symptoms, from May to beginning of September 2020. The epidemic declined between May and July 2020 but then increased gradually from mid-August, accelerating into early September 2020 at the start of the second wave. When compared to cases detected through routine surveillance, we report here a longer period of decline and a younger age distribution. Representative community sampling for SARS-CoV-2 can substantially improve situational awareness and feed into the public health response even at low prevalence.

Due to the COVID-19 pandemic, many key neglected tropical disease (NTD) activities have been postponed. This hindrance comes at a time when the NTDs are progressing towards their ambitious goals for 2030. Mathematical modelling on several NTDs, namely gambiense sleeping sickness, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiases (STH), trachoma, and visceral leishmaniasis, shows that the impact of this disruption will vary across the diseases. Programs face a risk of resurgence, which will be fastest in high-transmission areas. Furthermore, of the mass drug administration diseases, schistosomiasis, STH, and trachoma are likely to encounter faster resurgence. The case-finding diseases (gambiense sleeping sickness and visceral leishmaniasis) are likely to have fewer cases being detected but may face an increasing underlying rate of new infections. However, once programs are able to resume, there are ways to mitigate the impact and accelerate progress towards the 2030 goals.

As neglected tropical diseases approach elimination status, there is a need to develop efficient sampling strategies for confirmation (or not) that elimination criteria have been met. This is an inherently difficult task because the relative precision of a prevalence estimate deteriorates as prevalence decreases, and classic survey sampling strategies based on random sampling therefore require increasingly large sample sizes. More efficient strategies for survey design and analysis can be obtained by exploiting any spatial correlation in prevalence within a model-based geostatistics framework. This framework can be used for constructing predictive probability maps that can inform in-country decision makers of the likelihood that their elimination target has been met, and where to invest in additional sampling. We evaluated our methodology using a case study of lymphatic filariasis in Ghana, demonstrating that a geostatistical approach outperforms approaches currently used to determine an evaluation unit’s elimination status.

Key Points Question What are the pooled prevalence of congenital cytomegalovirus infection and factors associated with the rates in high-income and low- and middle-income countries? Findings In this systematic review and meta-analysis including 77 studies from 36 countries comprising 515 646 infants younger than 3 weeks, the pooled overall prevalence of congenital cytomegalovirus was 0.67%. The infection burden was 3-fold greater in low- and middle-income countries than in high-income countries. Lower rates were reported in screening methods using blood compared with urine or saliva. Meaning The findings of this study suggest that low- and middle-income countries incur the greatest infection burden of congenital cytomegalovirus; a global effort to address congenital cytomegalovirus in regions with the greatest prevalence is needed to reduce disease incidence and morbidity.

Background REACT-1 measures prevalence of SARS-CoV-2 infection in representative samples of the population in England using PCR testing from self-administered nose and throat swabs. Here we report interim results for round 6 of observations for swabs collected from the 16th to 25th October 2020 inclusive. Methods REACT-1 round 6 aims to collect data and swab results from 160,000 people aged 5 and above. Here we report results from the first 86,000 individuals. We estimate prevalence of PCR-confirmed SARS-CoV-2 infection, reproduction numbers (R) and temporal trends using exponential growth or decay models. Prevalence estimates are presented both unweighted and weighted to be representative of the population of England, accounting for response rate, region, deprivation and ethnicity. We compare these interim results with data from round 5, based on swabs collected from 18th September to 5th October 2020 inclusive. Results Overall prevalence of infection in the community in England was 1.28% or 128 people per 10,000, up from 60 per 10,000 in the previous round. Infections were doubling every 9.0 (6.1, 18) days with a national reproduction number (R) estimated at 1.56 (1.27, 1.88) compared to 1.16 (1.05, 1.27) in the previous round. Prevalence of infection was highest in Yorkshire and The Humber at 2.72% (2.12%, 3.50%), up from 0.84% (0.60%, 1.17%), and the North West at 2.27% (1.90%, 2.72%), up from 1.21% (1.01%, 1.46%), and lowest in South East at 0.55% (0.45%, 0.68%), up from 0.29% (0.23%, 0.37%). Clustering of cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands. Interim estimates of R were above 2 in the South East, East of England, London and South West, but with wide confidence intervals. Nationally, prevalence increased across all age groups with the greatest increase in those aged 55-64 at 1.20% (0.99%, 1.46%), up 3-fold from 0.37% (0.30%, 0.46%). In those aged over 65, prevalence was 0.81% (0.58%, 0.96%) up 2-fold from 0.35% (0.28%, 0.43%). Prevalence remained highest in 18 to 24-year olds at 2.25% (1.47%, 3.42%). Conclusion The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage. Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from COVID-19 are to be avoided.

ObjectiveCancer incidence and mortality rates in Africa are increasing, yet their geographic distribution and determinants are incompletely characterized. The present study aims to establish the spatial epidemiology of cancer burden in Africa and delineate the association between cancer burden and the country-level socioeconomic status. The study also examines the forecasts of the cancer burden for 2040 and evaluates infrastructure availability across all African countries.MethodsThe estimates of age, sex, and country-specific incidence and mortality of 34 neoplasms in 54 African countries, were procured from GLOBOCAN 2020. Mortality-to-incidence ratio (MIR) was employed as a proxy indicator of 5-year survival rates, and the socioeconomic development of each country was measured using its human development index (HDI). We regressed age-standardized incidence rate (ASIR), age-standardized mortality rate (ASMR), and MIR on HDI using linear regression model to determine the relationship between cancer burden and HDI. Maps were generated for each cancer group for each country in Africa. The data about the cancer infrastructure of African countries were extracted from the WHO Cancer Country Profiles.ResultsIn Africa, an estimated 1.1 million new cases [95% uncertainty intervals (UIs) 1.0 – 1.3 million] and 711,429 [611,604 – 827,547] deaths occurred due to neoplasms in 2020. The ASIR was estimated to be 132.1/100,000, varying from 78.4/100,000 (Niger) to 212.5/100,000 (La Réunion) in 2020. The ASMR was 88.8/100,000 in Africa, ranging from 56.6/100,000 in the Republic of the Congo to 139.4/100,000 in Zimbabwe. The MIR of all cancer combined was 0.64 in Africa, varying from 0.49 in Mauritius to 0.78 in The Gambia. HDI had a significant negative correlation with MIR of all cancer groups combined and main cancer groups (prostate, breast, cervical and colorectal). HDI explained 75% of the variation in overall 5-year cancer survival (MIR). By 2040, the burden of all neoplasms combined is forecasted to increase to 2.1 million new cases and 1.4 million deaths in Africa.ConclusionHigh cancer mortality rates in Africa demand a holistic approach toward cancer control and management, including, but not limited to, boosting cancer awareness, adopting primary and secondary prevention, mitigating risk factors, improving cancer infrastructure and timely treatment.