Our study population consisted of all children and adolescents, with laboratory-confirmed SARS-Co-V-2 infection, hospitalised from February 2020 through February 2022, among residents of the Tel Aviv (TA) District, Israel. There were 491 children and adolescents hospitalised with Sars-CoV-2 infection. Among them, 281 (57%) admitted with coronavirus disease 2019 (COVID-19) as the primary cause of admission (rate of 39 per 100 000). Among all children and adolescents in the TA District, the highest hospitalisation rates were observed among infants and children below the age of 4 years (rate of 311 per 100 000 population). Severe disease was observed mostly among children with multiple underlying medical conditions. Admission rates were also elevated among residents of the ultra-orthodox community (rate ratio (RR) compared to the rest of the district; 95% confidence interval (CI) 2.38–3.82). Admission rates with COVID-19 as primary cause of admission were higher during Omicron compared to Delta predominance period (RR 1.7; 95% CI 1.22–2.32). Targeted social and public health policies should be put in place when rates of disease start to increase, such as encouraging vaccine uptake for eligible children and social distancing when necessary, taking into account already existing social and learning gaps, in order to reduce the burden of disease.

The association between time to positivity (TTP) of blood culture and the clinical prognosis of patients with Klebsiella pneumoniae bloodstream infection (BSI) remains unclear. A retrospective study of 148 inpatients with BSI caused by K. pneumoniae was performed at Shanghai Tongji Hospital, China, from October 2016–2020. The total in-hospital fatality rate was 32%. The median TTP was 11.0 (7.7–16.1) h and the optimal cutoff for prediction of in-hospital mortality was 9.4 h according to the ROC curve. Early TTP (<9.4 h) was a risk factor for in-hospital mortality by univariate analysis (OR = 2.5, 95% CI 1.2–5.0, P = 0.01), but not by multivariate analysis (OR = 2.7, 95% CI 1.0–7.4, P = 0.06). Old age, serum creatinine, white blood cells, and C-reactive protein values were risk factors for in-hospital mortality by multivariate analysis. Early TTP was not a risk factor for septic shock (OR = 1.8, 95% CI 0.6–5.1, P = 0.27) or ICU admission (OR = 1.0, 95% CI 1.0–1.0, P = 0.32). In conclusion, the in-hospital fatality rate of patients with K. pneumoniae BSI was relatively high and associated with an early TTP of blood cultures. However, no increased risk of mortality, septic shock or ICU admission was evident in early TTP patients.

Contact with livestock and consumption of unpasteurised dairy products are associated with an increased risk of zoonotic and foodborne infection, particularly among populations with close animal contact, including pastoralists and semi-pastoralists. However, there are limited data on disease risk factors among pastoralists and other populations where livestock herding, particularly of dromedary camels, is common. This cross-sectional study used a previously validated survey instrument to identify risk factors for self-reported symptoms. Adults (n = 304) were randomly selected from households (n = 171) in the Somali Region of Ethiopia, a region characterised by chronic food insecurity, population displacement, recurrent droughts and large semi-pastoralist and pastoralist populations. Multivariable logistic regression assessed associations between self-reported symptoms and type of milk consumed, controlling for demographics and human-animal interaction. Consumption of days-old unrefrigerated raw camel milk was significantly associated with symptoms in the 30 days prior to the survey (AOR = 5.07; 95% CI 2.41–10.66), after controlling for age, refugee status, sanitation, camel ownership and source of drinking water and accounting for clustering. Consumption of days-old unrefrigerated raw ruminant milk was significantly associated with symptoms (AOR = 4.00, 95% CI 1.27–12.58). Source of drinking water and camel ownership, a proxy for camel contact, were significantly associated with the outcome in each model. There were no significant associations between self-reported symptoms and fresh or soured animal milk consumption. Research is needed to identify pathogens and major routes of transmission. Tailored communication campaigns to encourage safe food preparation should also be considered.

The Ending the HIV Epidemic initiative aims to decrease new HIV infections and promote test-and-treat strategies. Our aims were to establish a baseline of HIV outcomes among newly diagnosed PWH in Washington, DC (DC), a ‘hotspot’ for the HIV epidemic. We also examined sociodemographic and clinical factors associated with retention in care (RIC), antiretroviral therapy (ART) initiation and viral suppression (VS) among newly diagnosed PWH in the DC Cohort from 2011–2016. Among 455 newly diagnosed participants, 92% were RIC at 12 months, ART was initiated in 65% at 3 months and 91% at 12 months, VS in at least 17% at 3 months and 82% at 12 months and 55% of those with VS at 12 months had sustained VS for an additional 12 months. AIDS diagnosis was associated with RIC (aOR 2.99; 1.13–2.28), ART initiation by 3 months (aOR 2.58; 1.61–4.12) and VS by 12 months (aOR4.87; 1.69–14.03). This analysis contributes to our understanding of the HIV treatment dynamics of persons with recently diagnosed HIV infection in a city with a severe HIV epidemic.

Surveillance is a key public health function to enable early detection of infectious disease events and inform public health action. Data linkage may improve the depth of data for response to infectious disease events. This study aimed to describe the uses of linked data for infectious disease events. A systematic review was conducted using Pubmed, CINAHL and Web of Science. Studies were included if they used data linkage for an acute infectious disease event (e.g. outbreak of disease). We summarised the event, study aims and designs; data sets; linkage methods; outcomes reported; and benefits and limitations. Fifty-four studies were included. Uses of linkage for infectious disease events included assessment of severity of disease and risk factors; improved case finding and contact tracing; and vaccine uptake, safety and effectiveness. The ability to conduct larger scale population level studies was identified as a benefit, in particular for rarer exposures, risk factors or outcomes. Limitations included timeliness, data quality and inability to collect additional variables. This review demonstrated multiple uses of data linkage for infectious disease events. As infectious disease events occur without warning, there is a need to establish pre-approved protocols and the infrastructure for data-linkage to enhance information available during an event.

Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated with major increase in the prevalence of bats shedding RNA viruses. The synchronicity of such shedding pulses, however, is yet to be assessed between viruses but also maternity colonies. Based on 3422 fresh faeces collected every 2–5 weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs) and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection periods, and therefore by the evolution of the population age structure. We highlight that virus shedding patterns are consistent among years and colonies for CoVs and to a lesser extent for PMVs, but not for AstVs. We also report that 1% of bats harbour co-infections, with two but not three of the viruses, and most co-infections were due to CoVs and PMVs.

To describe the trend of cumulative incidence of coronavirus disease 19 (COVID-19) and undiagnosed cases over the pandemic through the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants among healthcare workers in Tokyo, we analysed data of repeated serological surveys and in-house COVID-19 registry among the staff of National Center for Global Health and Medicine. Participants were asked to donate venous blood and complete a survey questionnaire about COVID-19 diagnosis and vaccine. Positive serology was defined as being positive on Roche or Abbott assay against SARS-CoV-2 nucleocapsid protein, and cumulative infection was defined as either being seropositive or having a history of COVID-19. Cumulative infection has increased from 2.0% in June 2021 (pre-Delta) to 5.3% in December 2021 (post-Delta). After the emergence of the Omicron, it has increased substantially during 2022 (16.9% in June and 39.0% in December). As of December 2022, 30% of those who were infected in the past were not aware of their infection. Results indicate that SARS-CoV-2 infection has rapidly expanded during the Omicron-variant epidemic among healthcare workers in Tokyo and that a sizable number of infections were undiagnosed.

Oral rotavirus vaccine efficacy estimates from randomised controlled trials are highly variable across settings. Although the randomised study design increases the likelihood of internal validity of findings, results from trials may not always apply outside the context of the study due to differences between trial participants and the target population. Here, we used a weight-based method to transport results from a monovalent rotavirus vaccine clinical trial conducted in Malawi between 2005 and 2008 to a target population of all trial-eligible children in Malawi, represented by data from the 2015–2016 Malawi Demographic and Health Survey (DHS). We reweighted trial participants to reflect the population characteristics described by the Malawi DHS. Vaccine efficacy was estimated for 1008 trial participants after applying these weights such that they represented trial-eligible children in Malawi. We also conducted subgroup analyses to examine the heterogeneous treatment effects by stunting and tuberculosis vaccination status at enrolment. In the original trial, the estimates of one-year vaccine efficacy against severe rotavirus gastroenteritis and any-severity rotavirus gastroenteritis in Malawi were 49.2% (95% CI 15.6%–70.3%) and 32.1% (95% CI 2.5%–53.1%), respectively. After weighting trial participants to represent all trial-eligible children in Malawi, vaccine efficacy increased to 62.2% (95% CI 35.5%–79.0%) against severe rotavirus gastroenteritis and 38.9% (95% CI 11.4%–58.5%) against any-severity rotavirus gastroenteritis. Rotavirus vaccine efficacy may differ between trial participants and target populations when these two populations differ. Differences in tuberculosis vaccination status between the trial sample and DHS population contributed to varying trial and target population vaccine efficacy estimates.

Around 0.4% of pregnant women in England have chronic hepatitis B virus (HBV) infection and need services to prevent vertical transmission. In this national audit, sociodemographic, clinical and laboratory information was requested from all maternity units in England for hepatitis B surface antigen-positive women initiating antenatal care in 2014. We describe these women's characteristics and indicators of access to/uptake of healthcare. Of 2542 pregnancies in 2538 women, median maternal age was 31 [IQR 27, 35] years, 94% (1986/2109) were non-UK born (25% (228/923) having arrived into the UK <2 years previously) and 32% (794/2473) had ⩾2 previous live births. In 39%, English levels were basic/less than basic. Antenatal care was initiated at median 11.3 [IQR 9.6, 14] gestation weeks, and ‘late’ (⩾20 weeks) in 10% (251/2491). In 70% (1783/2533) of pregnancies, HBV had been previously diagnosed and 11.8% (288/2450) had ⩾1 marker of higher infectivity. Missed specialist appointments were reported in 18% (426/2339). Late antenatal care and/or missed specialist appointments were more common in pregnancies among women lacking basic English, arriving in the UK ⩽2 years previously, newly HBV diagnosed, aged <25 years and/or with ⩾2 previous live births. We show overlapping groups of pregnant women with chronic HBV vulnerable to delayed or incomplete care.

Persons experiencing homelessness (PEH) or rough sleeping are a vulnerable population, likely to be disproportionately affected by the coronavirus disease 2019 (COVID-19) pandemic. The impact of COVID-19 infection on this population is yet to be fully described in England. We present a novel method to identify COVID-19 cases in this population and describe its findings. A phenotype was developed and validated to identify PEH or rough sleeping in a national surveillance system. Confirmed COVID-19 cases in England from March 2020 to March 2022 were address-matched to known homelessness accommodations and shelters. Further cases were identified using address-based indicators, such as NHS pseudo postcodes. In total, 1835 cases were identified by the phenotype. Most were <39 years of age (66.8%) and male (62.8%). The proportion of cases was highest in London (29.8%). The proportion of cases of a minority ethnic background and deaths were disproportionality greater in this population, compared to all COVID-19 cases in England. This methodology provides an approach to track the impact of COVID-19 on a subset of this population and will be relevant to policy making. Future surveillance systems and studies may benefit from this approach to further investigate the impact of COVID-19 and other diseases on select populations.

This study aimed to evaluate the contrast-enhanced ultrasound (CEUS) features of ureteral tuberculosis (UTB) and ureteral malignant tumour and to explore its application value in the differentiation of UTB from ureteral tumour. The ultrasound (US) and CEUS imaging features of 33 and 12 cases of pathologically confirmed UTB and ureteral malignant tumour, respectively, were retrospectively evaluated, and echo of the ureteral wall, abnormal echo of the lumen, degree of ureteral dilation and CEUS patterns of the two diseases were statistically analysed. The results revealed that the lumen echo of UTB was hyperechoic or anechoic, whereas that of ureteral tumour lesions was hypoechoic (χ2 = 28.22, P < 0.001). The wall echo of the obstruction site differed between the two diseases; in UTB, the ureteral wall was thickened but the outer wall remained intact, whereas in ureteral tumour, both the malignant tumour wall and outer wall were irregular (χ2 = 30.25, P < 0.001). CEUS of UTB revealed nonenhancement or heterogeneous enhancement in the lumen, whereas that of ureteral tumours revealed significant homogeneous enhancement (χ2 = 30.25, P < 0.001). Thus, CEUS can reveal lesion microcirculation and be used to evaluate blood supply characteristics in the lesion, indicating that it has high potential for differentiating the two diseases.

Hand, foot and mouth disease (HFMD) is a common infection in the world, and its epidemics result in heavy disease burdens. Over the past decade, HFMD has been widespread among children in China, with Shanxi Province being a severely affected northern province. Located in the temperate monsoon climate, Shanxi has a GDP of over 2.5 trillion yuan. It is important to have a comprehensive understanding of the basic features of HFMD in those areas that have similar meteorological and economic backgrounds to northern China. We aimed to investigate epidemiological characteristics, identify spatial clusters and predict monthly incidence of HFMD. All reported HFMD cases were obtained from the Shanxi Center for Disease Control and Prevention. Overall HFMD incidence showed a significant downward trend from 2017 to 2020, increasing again in 2021. Children aged < 5 years were primarily affected, with a high incidence of HFMD in male patients (relative risk: 1.316). The distribution showed a seasonal trend, with major peaks in June and July and secondary peaks in October and November with the exception of 2020. Other enteroviruses were the predominant causative agents of HFMD in most years. Areas with large numbers of HFMD cases were primarily in central Shanxi, and spatial clusters in 2017 and 2018 showed a positive global spatial correlation. Local spatial autocorrelation analysis showed that hot spots and secondary hot spots were concentrated in Jinzhong and Yangquan in 2018. Based on monthly incidence from September 2021 to August 2022, the mean absolute error (MAE), mean absolute percentage error (MAPE), and root mean square error (RMSE) of the long short-term memory (LSTM) and seasonal autoregressive integrated moving average (SARIMA) models were 386.58 vs. 838.25, 2.25 vs. 3.08, and 461.96 vs. 963.13, respectively, indicating that the predictive accuracy of LSTM was better than that of SARIMA. The LSTM model may be useful in predicting monthly incidences of HFMD, which may provide early warnings of HFMD epidemics.

Ross River virus (RRV) is the most common mosquito-borne infection in Australia. RRV disease is characterised by joint pain and lethargy, placing a substantial burden on individual patients, the healthcare system and economy. This burden is compounded by a lack of effective treatment or vaccine for the disease. The complex RRV disease ecology cycle includes a number of reservoirs and vectors that inhabit a range of environments and climates across Australia. Climate is known to influence humans, animals and the environment and has previously been shown to be useful to RRV prediction models. We developed a negative binomial regression model to predict monthly RRV case numbers and outbreaks in the Darling Downs region of Queensland, Australia. Human RRV notifications and climate data for the period July 2001 – June 2014 were used for model training. Model predictions were tested using data for July 2014 – June 2019. The final model was moderately effective at predicting RRV case numbers (Pearson's r = 0.427) and RRV outbreaks (accuracy = 65%, sensitivity = 59%, specificity = 73%). Our findings show that readily available climate data can provide timely prediction of RRV outbreaks.

Syndromic surveillance was originally developed to provide early warning compared to laboratory surveillance, but it is increasing used for real-time situational awareness. When a potential threat to public health is identified, a rapid assessment of its impact is required for public health management. When threats are localised, analysis is more complex as local trends need to be separated from national trends and differences compared to unaffected areas may be due to confounding factors such as deprivation or age distributions. Accounting for confounding factors usually requires an in-depth study, which takes time. Therefore, a tool is required which can provide a rapid estimate of local incidents using syndromic surveillance data.

Here, we present ‘DiD IT?’, a new investigation tool designed to measure the impact of local threats to public health. ‘DiD IT?’ uses a difference-in-differences statistical approach to account for temporal and spatial confounding and provide a direct estimate of impact due to incidents. Temporal confounding differences are estimated by comparing unaffected locations during and outside of exposure periods. Whilst spatial confounding differences are estimated by comparing unaffected and exposed locations outside of the exposure period. Any remaining differences can be considered to be the direct effect of the local incident.

We illustrate the potential utility of the tool through four examples of localised health protection incidents in England. The examples cover a range of data sources including general practitioner (GP) consultations, emergency department (ED) attendances and a telehealth call and online health symptom checker; and different types of incidents including, infectious disease outbreak, mass-gathering, extreme weather and an industrial fire. The examples use the UK Health Security Agency's ongoing real-time syndromic surveillance systems to show how results can be obtained in near real-time.

The tool identified 700 additional online difficulty breathing assessments associated with a severe thunderstorm, 53 additional GP consultations during a mumps outbreak, 2–3 telehealth line calls following an industrial fire and that there was no significant increase in ED attendances during the G7 summit in 2021.

DiD IT? can provide estimates for the direct impact of localised events in real-time as part of a syndromic surveillance system. Thus, it has the potential for enhancing surveillance and can be used to evaluate the effectiveness of extending national surveillance to a more granular local surveillance.

The epidemiology of invasive meningococcal disease (IMD) is unpredictable, varies by region and age group and continuously evolves. This review aimed to describe trends in the incidence of IMD and serogroup distribution by age group and global region over time. Data were extracted from 90 subnational, national and multinational grey literature surveillance reports and 22 published articles related to the burden of IMD from 2010 to 2019 in 77 countries. The global incidence of IMD was generally low, with substantial variability between regions in circulating disease-causing serogroups. The highest incidence was usually observed in infants, generally followed by young children and adolescents/young adults, as well as older adults in some countries. Globally, serogroup B was a predominant cause of IMD in most countries. Additionally, there was a notable increase in the number of IMD cases caused by serogroups W and Y from 2010 to 2019 in several regions, highlighting the unpredictable and dynamic nature of the disease. Overall, serogroups A, B, C, W and Y were responsible for the vast majority of IMD cases, despite the availability of vaccines to prevent disease due to these serogroups.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (B.1.1.529) rapidly replaced Delta (B.1.617.2) to become dominant in England. Our study assessed differences in transmission between Omicron and Delta using two independent data sources and methods. Omicron and Delta cases were identified through genomic sequencing, genotyping and S-gene target failure in England from 5–11 December 2021. Secondary attack rates for named contacts were calculated in household and non-household settings using contact tracing data, while household clustering was identified using national surveillance data. Logistic regression models were applied to control for factors associated with transmission for both methods. For contact tracing data, higher secondary attack rates for Omicron vs. Delta were identified in households (15.0% vs. 10.8%) and non-households (8.2% vs. 3.7%). For both variants, in household settings, onward transmission was reduced from cases and named contacts who had three doses of vaccine compared to two, but this effect was less pronounced for Omicron (adjusted risk ratio, aRR 0.78 and 0.88) than Delta (aRR 0.62 and 0.68). In non-household settings, a similar reduction was observed only in contacts who had three doses vs. two doses for both Delta (aRR 0.51) and Omicron (aRR 0.76). For national surveillance data, the risk of household clustering, was increased 3.5-fold for Omicron compared to Delta (aRR 3.54 (3.29–3.81)). Our study identified increased risk of onward transmission of Omicron, consistent with its successful global displacement of Delta. We identified a reduced effectiveness of vaccination in lowering risk of transmission, a likely contributor for the rapid propagation of Omicron.

Despite promising steps towards the elimination of hepatitis C virus (HCV) in the UK, several indicators provide a cause for concern for future disease burden. We aimed to improve understanding of geographical variation in HCV-related severe liver disease and historic risk factor prevalence among clinic attendees in England and Scotland. We used metadata from 3829 HCV-positive patients consecutively enrolled into HCV Research UK from 48 hospital centres in England and Scotland during 2012–2014. Employing mixed-effects statistical modelling, several independent risk factors were identified: age 46–59 y (ORadj 3.06) and ≥60 y (ORadj 5.64) relative to <46 y, male relative to female sex (ORadj 1.58), high BMI (ORadj 1.73) and obesity (ORadj 2.81) relative to normal BMI, diabetes relative to no diabetes (ORadj 2.75), infection with HCV genotype (GT)-3 relative to GT-1 (ORadj 1.75), route of infection through blood products relative to injecting drug use (ORadj 1.40), and lower odds were associated with black ethnicity (ORadj 0.31) relative to white ethnicity. A small proportion of unexplained variation was attributed to differences between hospital centres and local health authorities. Our study provides a baseline measure of historic risk factor prevalence and potential geographical variation in healthcare provision, to support ongoing monitoring of HCV-related disease burden and the design of risk prevention measures.

From 1 January 2022 to 4 September 2022, a total of 53 996 mpox cases were confirmed globally. Cases are predominantly concentrated in Europe and the Americas, while other regions are also continuously observing imported cases. This study aimed to estimate the potential global risk of mpox importation and consider hypothetical scenarios of travel restrictions by varying passenger volumes (PVs) via airline travel network. PV data for the airline network, and the time of first confirmed mpox case for a total of 1680 airports in 176 countries (and territories) were extracted from publicly available data sources. A survival analysis technique in which the hazard function was a function of effective distance was utilised to estimate the importation risk. The arrival time ranged from 9 to 48 days since the first case was identified in the UK on 6 May 2022. The estimated risk of importation showed that regardless of the geographic region, most locations will have an intensified importation risk by 31 December 2022. Travel restrictions scenarios had a minor impact on the global airline importation risk against mpox, highlighting the importance to enhance local capacities for the identification of mpox and to be prepared to carry out contact tracing and isolation.