Background Understanding human movement patterns and their association with risk factors for the acquisition and transmission of pathogens can inform guidance for disease control. In Vietnam, acute encephalitis syndrome (AES) has a wide-ranging etiology; however, it is hypothesized that many causes are due to vector-borne diseases. Methods We undertook a study in Ha Nam province, northern Vietnam, to determine the acceptability and feasibility of using i-gotU GT-120 GPS devices to understand the mobility patterns of healthy residents and evaluate the time spent in areas deemed to be at risk of bites from vectors. Focus group discussions (FGDs) were carried out to understand the knowledge and perceptions of GPS devices. Following this, 48 participants wore a GPS device for eight 72-hour periods over a year from which movement data and feedback were obtained. Results Concerns about the GPS included risks to privacy and health, and losing the device. However, compliance was good with 80,831 unique coordinates obtained and participants carrying the devices for 13,411 km over the study period. All groups of participants (adults and children, and those from urban and rural settings) travelled outside of Ha Nam province however, most spent the greatest proportion of time in areas with a low normalized difference vegetation index (NDVI) which was associated with a decreased risk of bites from vectors. Conclusions Our study demonstrates that the use of GPS devices in this setting was a feasible method for collecting data on movement patterns. However, for future studies, given the cost and logistics of using the GPS devices, we recommend exploring methods which allow for a larger sample size.

Sex differences in both innate and adaptive immunity are increasingly recognized as shaping responses to a range of pathogens. For antigenically variable pathogens that infect people many times over their lifetime, like influenza, sex differences may accumulate or be obscured by the interplay of immunity derived from each infection and future risk. However, sex-specific lifetime trajectories of influenza immunity are poorly characterized. Here, we analyzed hemagglutination inhibition antibody titers to multiple strains of influenza A/H3N2, measured in individuals spanning a wide age range to disentangle strain-specific and cross-reactive antibody responses by sex. To account for potential differences in exposure, we separately analyzed antibody titers to: (1) viruses circulating during an individual's lifetime, and (2) viruses isolated before birth (pre-birth) or after sampling, with responses to the latter interpreted as exclusively cross-reactive, given the absence of possible exposure to these strains. We found that females aged 15 to 40 generally have higher antibody titers than males against pre-birth and post-sampling strains, consistent with greater cross-reactivity. Conversely, older males have stronger responses to strains that they could have encountered during their lives, suggesting that they mount stronger responses upon infection.

Mobility data can help to reconstruct infectious disease dynamics and tailor control and elimination measures. We describe three challenges and opportunities to improve our understanding of human mobility for infectious disease research. We call for simulation and modelling, reporting guidelines and investment in data repositories.

Background: Human movement plays a critical role in the transmission of infectious diseases, especially those with environmental drivers like leptospirosis—a zoonotic bacterial infection linked to mud and water contact. Using GPS loggers, we collected detailed telemetry data to understand how fine-scale movements can be analysed in the context of an infectious disease. Methods: We recruited individuals living in urban slums in Salvador, Brazil, to analyse how they interact with environmental risk factors such as domestic rubbish piles, open sewers, and a local stream. We aimed to identify differences in movement patterns inside the study areas by gender, age, and leptospirosis serological status. Step selection functions, a spatio-temporal model used in animal movement ecology, estimated selection coefficients to represent the likelihood of movement toward specific environmental factors. Results: With 128 participants wearing GPS devices for 24–48 hr, recording locations every 35 s during active daytime hours, we segmented movements into morning, midday, afternoon, and evening. Our results suggested women moved closer to the central stream and farther from open sewers compared to men, while serologically positive individuals avoided open sewers. Conclusions: This study introduces a novel method for analysing human telemetry data in infectious disease research. Funding: Funding provided by Wellcome Trust, UK Medical Research Council, Brazilian National Research Council, Reckitt Global Hygiene Institute, and National Institute of Allergy and Infectious Diseases.

Background:We investigated endemic respiratory virus circulation patterns in Malawi, where no lockdown was imposed, during the COVID-19 pandemic. Methods:Within a prospective household cohort in urban and rural Malawi, adult participants provided upper respiratory tract (URT) samples at 4 time points between February 2021 and April 2022. Polymerase chain reaction (PCR) was performed for SARS-CoV-2, influenza, and other endemic respiratory viruses. Results:1626 URT samples from 945 participants in 542 households were included. Overall, 7.6% (n = 123) samples were PCR- positive for >1 respiratory virus; SARS-CoV-2 (4.4%) and rhinovirus (2.0%) were most common. No influenza A virus was detected. Influenza B and respiratory syncytial virus (RSV) were rare. Higher virus positivity were detected in the rural setting and at earlier time points. Coinfections were infrequent. Conclusions:Endemic respiratory viruses circulated in the community in Malawi during the pandemic, though influenza and RSV were rarely detected. Distinct differences in virus positivity and demographics were observed between urban and rural cohorts.

Background The aim of this study was to characterize the epidemiology of human seasonal coronaviruses (HCoVs) in southern Malawi.Methods We tested for HCoVs 229E, OC43, NL63, and HKU1 using real-time polymerase chain reaction (PCR) on upper respiratory specimens from asymptomatic controls and individuals of all ages recruited through severe acute respiratory illness (SARI) surveillance at Queen Elizabeth Central Hospital, Blantyre, and a prospective influenza-like illness (ILI) observational study between 2011 and 2017. We modeled the probability of having a positive PCR for each HCoV using negative binomial models, and calculated pathogen-attributable fractions (PAFs).Results Overall, 8.8% (539/6107) of specimens were positive for >= 1 HCoV. OC43 was the most frequently detected HCoV (3.1% [191/6107]). NL63 was more frequently detected in ILI patients (adjusted incidence rate ratio [aIRR], 9.60 [95% confidence interval {CI}, 3.25-28.30]), while 229E (aIRR, 8.99 [95% CI, 1.81-44.70]) was more frequent in SARI patients than asymptomatic controls. In adults, 229E and OC43 were associated with SARI (PAF, 86.5% and 89.4%, respectively), while NL63 was associated with ILI (PAF, 85.1%). The prevalence of HCoVs was similar between children with SARI and controls. All HCoVs had bimodal peaks but distinct seasonality.Conclusions OC43 was the most prevalent HCoV in acute respiratory illness of all ages. Individual HCoVs had distinct seasonality that differed from temperate settings. Human seasonal coronaviruses (HCoVs) were prevalent among children and adults with mild and severe acute respiratory illness (SARI) in Malawi between 2011 and 2017. 229E and OC43 were associated with SARI, and NL63 with influenza-like illness. Individual HCoVs had distinct seasonality.

Humans experience many influenza infections over their lives, resulting in complex and varied immunological histories. Although experimental and quantitative analyses have improved our understanding of the immunological processes defining an individual’s antibody repertoire, how these within-host processes are linked to population-level influenza epidemiology in humans remains unclear. Here, we used a multilevel mathematical model to jointly infer antibody dynamics and individual-level lifetime influenza A/H3N2 infection histories for 1,130 individuals in Guangzhou, China, using 67,683 haemagglutination inhibition (HI) assay measurements against 20 A/H3N2 strains from repeat serum samples collected between 2009 and 2015. These estimated infection histories allowed us to reconstruct historical seasonal influenza patterns in humans and to investigate how influenza incidence varies over time, space, and age in this population. We estimated median annual influenza infection rates to be approximately 19% from 1968 to 2015, but with substantial variation between years; 88% of individuals were estimated to have been infected at least once during the study period (2009 to 2015), and 20% were estimated to have 3 or more infections in that time. We inferred decreasing infection rates with increasing age, and found that annual attack rates were highly correlated across all locations, regardless of their distance, suggesting that age has a stronger impact than fine-scale spatial effects in determining an individual’s antibody profile. Finally, we reconstructed each individual’s expected antibody profile over their lifetime and inferred an age-stratified relationship between probability of infection and HI titre. Our analyses show how multi-strain serological panels provide rich information on long-term epidemiological trends, within-host processes, and immunity when analysed using appropriate inference methods, and adds to our understanding of the life course epidemiology of influenza A/H3N2.

The emergence of SARS-CoV-2 into a highly susceptible global population was primarily driven by human mobility-induced introduction events. Especially in the early stages, understanding mobility was vital to mitigating the pandemic prior to widespread vaccine availability. We conducted a systematic review of studies published from January 1, 2020, to May 9, 2021, that used population-level human mobility data to understand SARS-CoV-2 transmission. Of the 5505 papers with abstracts screened, 232 were included in the analysis. These papers focused on a range of specific questions but were dominated by analyses focusing on the USA and China. The majority included mobile phone data, followed by Google Community Mobility Reports, and few included any adjustments to account for potential biases in population sampling processes. There was no clear relationship between methods used to integrate mobility and SARS-CoV-2 data and goals of analysis. When considering papers focused only on the estimation of the effective reproductive number within the US, there was no clear relationship identified between this measure and changes in mobility patterns. Our findings underscore the need for standardized, systematic ways to identify the source of mobility data, select an appropriate approach to using it in analysis, and reporting.

Nosocomial infections threaten patient safety, and were widely reported during the COVID-19 pandemic. Effective hospital infection control requires a detailed understanding of the role of different transmission pathways, yet these are poorly quantified. Using patient and staff data from a large UK hospital, we demonstrate a method to infer unobserved epidemiological event times efficiently and disentangle the infectious pressure dynamics by ward. A stochastic individual-level, continuous-time state-transition model was constructed to model transmission of SARS-CoV-2, incorporating a dynamic staff-patient contact network as time-varying parameters. A Metropolis-Hastings Markov chain Monte Carlo (MCMC) algorithm was used to estimate transmission rate parameters associated with each possible source of infection, and the unobserved infection and recovery times. We found that the total infectious pressure exerted on an individual in a ward varied over time, as did the primary source of transmission. There was marked heterogeneity between wards; each ward experienced unique infectious pressure over time. Hospital infection control should consider the role of between-ward movement of staff as a key infectious source of nosocomial infection for SARS-CoV-2. With further development, this method could be implemented routinely for real-time monitoring of nosocomial transmission and to evaluate interventions.

Objective To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations.Design A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data).Setting All UK medical schools, foundations and specialty training organisation.Participants All UK medical students from 2002 to 2015, for a total of 97 932 participants.Outcome measures Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training.Methods Leslie matrix, principal components analysis, Gini coefficient, χ2 test, generalised linear models and variable selection methods were employed to explore the different facets of students’ and junior doctors’ movements from the family home to medical school and for the full pathway (from family home to specialty training).Results The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50 km; although the proportion of movements changed from year-to-year, with longer movements during 2007–2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties.Conclusion Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK.

Longitudinal, community-based sampling is important for understanding prevalence and transmission of respiratory pathogens. Using a minimally invasive sampling method, the FAMILY Micro study monitored the oral, nasal and hand microbiota of families for 6 months. Here, we explore participant experiences and opinions. A mixed methods approach was utilised. A quantitative questionnaire was completed after every sampling timepoint to report levels of discomfort and pain, as well as time taken to collect samples. Participants were also invited to discuss their experiences in a qualitative structured exit interview. We received questionnaires from 36 families. Most adults and children >5y experienced no pain (94% and 70%) and little discomfort (73% and 47% no discomfort) regardless of sample type, whereas children ≤5y experienced variable levels of pain and discomfort (48% no pain but 14% hurts even more, whole lot or worst; 38% no discomfort but 33% moderate, severe, or extreme discomfort). The time taken for saliva and hand sampling decreased over the study. We conducted interviews with 24 families. Families found the sampling method straightforward, and adults and children >5y preferred nasal sampling using a synthetic absorptive matrix over nasopharyngeal swabs. It remained challenging for families to fit sampling into their busy schedules. Adequate fridge/freezer space and regular sample pick-ups were found to be important factors for feasibility. Messaging apps proved extremely effective for engaging with participants. Our findings provide key information to inform the design of future studies, specifically that self-sampling at home using minimally invasive procedures is feasible in a family context.

Introduction Since the outbreak of coronavirus disease 2019 (COVID-19), non-pharmaceutical interventions (NPIs) have been the primary preventative measure to mitigate the COVID-19 burden. However, these NPIs have also altered the pattern and incidence of other respiratory pathogens. This review aims to explore the effects of NPIs used against COVID-19, on influenza incidence.Methods A systematic literature search was conducted in selected databases (PubMed, Medline, Embase). Documents that highlighted a change in influenza epidemiology during the COVID-19 pandemic and were linked to NPIs were included. The search covered articles from 1 January 2020 to 7 December 2022.Results This review included 13 studies reporting data from three different continents. A 14-100% decrease of influenza activity was observed since the enforcement of NPIs in early 2020.Conclusion This study suggests that the NPIs implemented during the COVID-19 pandemic have also significantly reduced influenza incidence. This is most likely because both coronavirus and influenza are transmitted through a similar route and the NPIs prevent this. The use of NPIs is suggested to overcome some burden of future influenza epidemics.

BACKGROUND:Household transmission studies inform how viruses spread among close contacts, but few characterize household transmission of endemic coronaviruses. METHODS:We used data collected from 223 households with school-age children participating in weekly disease surveillance over 2 respiratory virus seasons (December 2015 to May 2017), to describe clinical characteristics of endemic human coronaviruses (HCoV-229E, HcoV-HKU1, HcoV-NL63, HcoV-OC43) infections, and community and household transmission probabilities using a chain-binomial model correcting for missing data from untested households. RESULTS:Among 947 participants in 223 households, we observed 121 infections during the study, most commonly subtype HCoV-OC43. Higher proportions of infected children (<19 years) displayed influenza-like illness symptoms than infected adults (relative risk, 3.0; 95% credible interval [CrI], 1.5-6.9). The estimated weekly household transmission probability was 9% (95% CrI, 6-13) and weekly community acquisition probability was 7% (95% CrI, 5-10). We found no evidence for differences in community or household transmission probabilities by age or symptom status. Simulations suggest that our study was underpowered to detect such differences. CONCLUSIONS:Our study highlights the need for large household studies to inform household transmission, the challenges in estimating household transmission probabilities from asymptomatic individuals, and implications for controlling endemic CoVs.

Stochastic epidemic models which incorporate interactions between space and human mobility are a key tool to inform prioritisation of outbreak control to appropriate locations. However, methods for fitting such models to national-level population data are currently unfit for purpose due to the difficulty of marginalising over high-dimensional, highly-correlated censored epidemiological event data. Here we propose a new Bayesian MCMC approach to inference on a spatially-explicit stochastic SEIR meta-population model, using a suite of novel model-informed Metropolis-Hastings samplers. We apply this method to UK COVID-19 case data, showing real-time spatial results that were used to inform UK policy during the pandemic.

ObjectivesTo quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic. MethodsWe conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021. ResultsDelivery drivers had a mean number of 71.6 (95% CI 61.0 to 84.1) customer contacts per shift and 15.0 (95% CI 11.2 to 19.2) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 min) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. In addition, 5.3% (95% CI 2.3% to 10.2%) of participants reported having worked while ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19. ConclusionDelivery drivers had a large number of face-to-face customer and depot contacts per shift compared with other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitiser was widespread.

Background There is an urgent global call for health systems to strengthen access to quality sexual, reproductive, maternal, newborn and adolescent health, particularly for the most vulnerable. Professional midwives with enabling environments are identified as an important solution. However, a multitude of barriers prevent midwives from fully realizing their potential. Effective interventions to address known barriers and enable midwives and quality sexual, reproductive, maternal, newborn and adolescent health are less well known. This review intends to evaluate the literature on (1) introducing midwives in low- and middle-income countries, and (2) on mentoring as a facilitator to enable midwives and those in midwifery roles to improve sexual, reproductive, maternal, newborn and adolescent health service quality within health systems. Methods An integrative systematic literature review was conducted, guided by the Population, Intervention, Comparison, Outcome framework. Articles were reviewed for quality and relevance using the Gough weight-of-evidence framework and themes were identified. A master table categorized articles by Gough score, methodology, country of focus, topic areas, themes, classification of midwives, and mentorship model. The World Health Organization health systems building block framework was applied for data extraction and analysis. Results Fifty-three articles were included: 13 were rated as high, 36 as medium, and four as low according to the Gough criteria. Studies that focused on midwives primarily highlighted human resources, governance, and service delivery while those focused on mentoring were more likely to highlight quality services, lifesaving commodities, and health information systems. Midwives whose pre-service education met global standards were found to have more efficacy. The most effective mentoring packages were comprehensive, integrated into existing systems, and involved managers. Conclusions Effectively changing sexual, reproductive, maternal, newborn and adolescent health systems is complex. Globally standard midwives and a comprehensive mentoring package show effectiveness in improving service quality and utilization. Trial registration The protocol is registered in PROSPERO (CRD42022367657).

Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics1,2, but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens.

Objectives: This study aimed to investigate the changing SARS-CoV-2 seroprevalence and associated health and sociodemographic factors in Malawi between February 2021 and April 2022.Methods: In total, four 3-monthly serosurveys were conducted within a longitudinal population-based cohort in rural Karonga District and urban Lilongwe, testing for SARS-CoV-2 S1 immunoglobulin (Ig)G antibodies using an enzyme-linked immunosorbent assay. Population seroprevalence was estimated in all and unvaccinated participants. Bayesian mixed-effects logistic models estimated the odds of seropositivity in the first survey, and of seroconversion between surveys, adjusting for age, sex, occupation, location, and assay sensitivity/specificity.Results: Of the 2005 participants (Karonga, n = 1005; Lilongwe, n = 1000), 55.8% were female and me-dian age was 22.7 years. Between Surveys (SVY) 1 and 4, population-weighted SARS-CoV-2 seroprevalence increased from 26.3% to 89.2% and 46.4% to 93.9% in Karonga and Lilongwe, respectively. At SVY4, sero-prevalence did not differ by COVID-19 vaccination status in adults, except for those aged 30 + years in Karonga (unvaccinated: 87.4%, 95% credible interval 79.3-93.0%; two doses: 98.1%, 94.8-99.5%). Location and age were associated with seroconversion risk. Individuals with hybrid immunity had higher SARS-CoV-2 seropositivity and antibody titers, than those infected.Conclusion: High SARS-CoV-2 seroprevalence combined with low morbidity and mortality indicate that universal vaccination is unnecessary at this stage of the pandemic, supporting change in national policy to target at-risk groups.(c) 2023 The Author(s). Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )