Search

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. [ABSTRACT FROM AUTHOR]

Background: In 2020 the World Health Organization (WHO) declared that Malawi had successfully eliminated lymphatic filariasis (LF) as a public health problem. Understanding clinical case distributions at a national and sub-national level is important, so essential care packages can be provided to individuals living with LF symptoms. This study aimed to develop a national database and map of LF clinical case numbers across Malawi using geostatistical modelling approaches, programme-identified clinical cases, antigenaemia prevalence and climate information. Methodology: LF clinical cases identified through programme house-to-house surveys across 90 sub-district administrative boundaries (Traditional Authority (TA)) and antigenaemia prevalence from 57 sampled villages in Malawi were used in a two-step geostatistical modelling process to predict LF clinical cases across all TAs of the country. First, we modelled antigenaemia prevalence in relation to climate covariates to predict nationwide antigenaemia prevalence. Second, we modelled clinical cases for unmapped TAs based on our antigenaemia prevalence spatial estimates. Principle findings: The models estimated 20,938 (95% CrI 18,091 to 24,071) clinical cases in unmapped TAs (70.3%) in addition to the 8,856 (29.7%), programme-identified cases in mapped TAs. In total, the overall national number of LF clinical cases was estimated to be 29,794 (95% CrI 26,957 to 32,927). The antigenaemia prevalence and clinical case mapping and modelling found the highest burden of disease in Chikwawa and Nsanje districts in the Southern Region and Karonga district in the Northern Region of the country. Conclusions: The models presented in this study have facilitated the development of the first national LF clinical case database and map in Malawi, the first endemic country in sub-Saharan Africa. It highlights the value of using existing LF antigenaemia prevalence and clinical case data together with modelling approaches to produce estimates that may be used for the WHO dossier requirements, to help target limited resources and implement long-term health strategies. Author summary: Lymphatic filariasis (LF) is a disfiguring and painful Neglected Tropical Disease, transmitted by mosquitoes, and impairs affected individual's mental wellbeing, social participation, and ability to work. The two most common clinical manifestations are hydrocoele (scrotal swelling) and lymphoedema (swelling of the limbs). Estimates of LF clinical case numbers are required to provide national and local care needs assessment, and for elimination and surveillance purposes. Clinical case prevalence is currently not readily available or is unknown across many sub-Saharan African countries, however Malawi is unique as the LF Programme has conducted extensive house-to-house patient mapping activities across one third of the country. We used this clinical data in combination with measurements of LF infection prevalence and high-resolution climate information, to develop geostatistical models, which estimate the number of clinical cases in unmapped areas. This led to the development of a national database and map of clinical case estimates that will help the Malawi LF elimination programme to optimize limited resources, target morbidity management and disability prevention, and improve quality of life of the people affected by this disabling and disfiguring disease. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background This study aimed to determine the key mental health indicators affecting people affected by lymphatic filariasis (LF) lymphoedema by assessing the prevalence of depressive symptoms and quality of life (QOL), identifying associated sociodemographic and clinical risk factors, and evaluating the impact of an enhanced self-care intervention for lymphoedema management. Methods A prospective cohort study of adults with filarial lymphoedema from two regions of Malawi was conducted over six months in 2021. Depressive symptoms and QOL were assessed using Patient Health Questionnaire (PHQ-9) and LF Specific QOL Questionnaire, respectively, at baseline (pre-intervention), 3- and 6-months (postintervention). Beta regression analysis identified risk factors, and assessed the impact of the intervention. Results Three hundred eleven affected individuals were surveyed with 23% (95% CI 18%–29%) reporting mild/moderate depressive symptoms and 31% (95% CI 26%–37%) reporting moderately low/low QOL. Higher depressive symptom scores were associated with high frequency of acute filarial attack episodes. Individuals with higher depressive symptoms (Adjusted Odds Ratios (AOR) 0.93, 95% CI 0.93–0.93) and lower QOL (AOR 0.98, 0.98–0.98) showed greatest improvement in mental health indicators over 3-months but was not sustained to the same level at 6-months. Conclusions Sustained morbidity management and psychological support is recommended for affected persons to ensure long-term positive mental health and clinical outcomes. Contexte Cette étude vise à déterminer les principaux indicateurs de santé mentale affectant les personnes atteintes de lymphœdème dû à la filariose lymphatique (FL) en évaluant la prévalence des symptômes dépressifs et la qualité de vie (QV), en identifiant les facteurs de risque sociodémographiques et cliniques associés, et en évaluant l'impact d'une intervention améliorée d'autosoins pour la gestion du lymphœdème. Méthodes Une étude de cohorte prospective d'adultes atteints de lymphoedème filaire dans deux régions du Malawi a été menée pendant six mois en 2021. Les symptômes dépressifs et la qualité de vie ont été évalués à l'aide du questionnaire sur la santé des patients (PHQ-9) et du questionnaire sur la qualité de vie spécifique au lymphœdème, respectivement, au début de l'étude (avant l'intervention), et à 3 puis 6 mois après l'intervention. Une analyse de régression beta a permis d'identifier les facteurs de risque et d'évaluer l'impact de l'intervention. Résultats Trois cent onze personnes affectées ont été interrogées, dont 23% (95% CI 18%–29%) ont déclaré des symptômes dépressifs légers/modérés et 31% (95% CI 26%–37%) ont déclaré une qualité de vie modérément faible/faible. Des scores élevés de symptômes dépressifs ont été associés à une fréquence élevée d'épisodes de crises filariennes aiguës. Les personnes présentant des symptômes dépressifs plus élevés (rapport de cotes ajusté (RCA) 0.93, IC à 95 % 0.93–0.93) et une qualité de vie plus faible (RCA 0.98, 0.98–0.98) ont montré la plus grande amélioration des indicateurs de santé mentale au cours des trois mois, mais cette amélioration ne s'est pas maintenue au même niveau au cours des six mois suivants. Conclusion Gestion de la morbidité et soutien psychologique sont des éléments clés pour garantir une santé mentale et des résultats cliniques satisfaisants de personnes atteintes sur le long terme. Antecedentes Este estudio tuvo como objetivo determinar los indicadores clave de salud mental que afectan a las personas afectadas por linfedema por filariasis linfática (FL) mediante la evaluación de la prevalencia de síntomas depresivos y calidad de vida (CdV), la identificación de factores de riesgo sociodemográficos y clínicos asociados, y la evaluación del impacto de una intervención de autocuidado mejorada para el manejo del linfedema. Métodos Se realizó un estudio prospectivo de cohortes de adultos con linfedema filarial de dos regiones de Malawi durante seis meses en 2021. Los síntomas depresivos y la calidad de vida se evaluaron mediante el Cuestionario de Salud del Paciente (PHQ-9) y el Cuestionario de Calidad de Vida específico para el LF Cuestionario, respectivamente, al inicio (preintervención) y a los 3 y 6 meses (posintervención). El análisis de regresión beta identificó los factores de riesgo y evaluó el impacto de la intervención. Resultados Se encuestó a 311 afectados, de los cuales el 23% (IC 95%, 18%–29%) presentaba síntomas depresivos leves/moderados y el 31% (IC 95%, 26%–37%) una CdV moderadamente baja/baja CdV. Las puntuaciones más altas de síntomas depresivos se asociaron con una alta frecuencia de episodios de ataques agudos de filarias. Los individuos con mayores síntomas depresivos (Odds Ratios Ajustados [ORA] 0.93; IC 95%: 0.93–0.93) y menor CdV (ORA 0.98; 0.98–0.98) mostraron la mayor mejoría en los indicadores de salud mental a los 3 meses, pero no se mantuvo al mismo nivel a los 6 meses. Conclusiones Se recomienda el manejo sostenido de la morbilidad y el apoyo psicológico a las personas afectadas para garantizar resultados clínicos y de salud mental positivos a largo plazo. [ABSTRACT FROM AUTHOR]

The 2014-2016 West Africa Ebola virus disease (EVD) epidemic resulted in an estimated 3,956 deaths and 10,168 survivors in Sierra Leone (1). The use of high quality specialty services by [...]

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. [ABSTRACT FROM AUTHOR]

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 two 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 (<19y) displayed ILI 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.Conclusion: 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. [ABSTRACT FROM AUTHOR]

The reproduction number R$$ R $$ has been a central metric of the COVID‐19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations of R$$ R $$, the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g. the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulating R$$ R $$ becomes increasingly complicated and inevitably model‐dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency. [ABSTRACT FROM AUTHOR]

Background Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting. Methods A total of 546 patients presenting to Queen Elizabeth Central Hospital in Blantyre, Malawi, with blood culture–confirmed typhoid fever between April 2015 and January 2017 were recruited to a cohort study. The households of a subset of these patients were geolocated, and 256 S. Typhi isolates were whole-genome sequenced. Pairwise single-nucleotide variant distances were incorporated into a geostatistical modeling framework using multidimensional scaling. Results Typhoid fever was not evenly distributed across Blantyre, with estimated minimum incidence ranging across the city from <15 to >100 cases per 100 000 population per year. Pairwise single-nucleotide variant distance and physical household distances were significantly correlated (P  = .001). We evaluated the ability of river catchment to explain the spatial patterns of genomics observed, finding that it significantly improved the fit of the model (P  = .003). We also found spatial correlation at a smaller spatial scale, of households living <192 m apart. Conclusions These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies. [ABSTRACT FROM AUTHOR]

Typhoid fever is a major cause of illness and mortality in low- and middle-income settings. We investigated the association of typhoid fever and rainfall in Blantyre, Malawi, where multi-drug-resistant typhoid has been transmitting since 2011. Peak rainfall preceded the peak in typhoid fever by approximately 15 weeks [95% confidence interval (CI) 13.3, 17.7], indicating no direct biological link. A quasi-Poisson generalised linear modelling framework was used to explore the relationship between rainfall and typhoid incidence at biologically plausible lags of 1–4 weeks. We found a protective effect of rainfall anomalies on typhoid fever, at a two-week lag (P = 0.006), where a 10 mm lower-than-expected rainfall anomaly was associated with up to a 16% reduction in cases (95% CI 7.6, 26.5). Extreme flooding events may cleanse the environment of S. Typhi, while unusually low rainfall may reduce exposure from sewage overflow. These results add to evidence that rainfall anomalies may play a role in the transmission of enteric pathogens, and can help direct future water and sanitation intervention strategies for the control of typhoid fever. [ABSTRACT FROM AUTHOR]

Background: Children are important in community‐level influenza transmission. School‐based monitoring may inform influenza surveillance. Methods: We used reported weekly confirmed influenza in Allegheny County during the 2007 and 2010‐2015 influenza seasons using Pennsylvania's Allegheny County Health Department all‐age influenza cases from health facilities, and all‐cause and influenza‐like illness (ILI)‐specific absences from nine county school districts. Negative binomial regression predicted influenza cases using all‐cause and illness‐specific absence rates, calendar week, average weekly temperature, and relative humidity, using four cross‐validations. Results: School districts reported 2 184 220 all‐cause absences (2010‐2015). Three one‐season studies reported 19 577 all‐cause and 3012 ILI‐related absences (2007, 2012, 2015). Over seven seasons, 11 946 confirmed influenza cases were reported. Absences improved seasonal model fits and predictions. Multivariate models using elementary school absences outperformed middle and high school models (relative mean absolute error (relMAE) = 0.94, 0.98, 0.99). K‐5 grade‐specific absence models had lowest mean absolute errors (MAE) in cross‐validations. ILI‐specific absences performed marginally better than all‐cause absences in two years, adjusting for other covariates, but markedly worse one year. Conclusions: Our findings suggest seasonal models including K‐5th grade absences predict all‐age‐confirmed influenza and may serve as a useful surveillance tool. [ABSTRACT FROM AUTHOR]

Many countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission is unknown. We used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the population attributable fraction (PAF) due to groups as the relative change in the basic reproduction number when groups are prevented. Groups of 50+ individuals accounted for 0.5% of reported contact events, and we estimate that the PAF due to groups of 50+ people is 5.4% (95% confidence interval 1.4%, 11.5%). The PAF due to groups of 20+ people is 18.9% (12.7%, 25.7%) and the PAF due to groups of 10+ is 25.2% (19.4%, 31.4%). Under normal circumstances with pre-COVID-19 contact patterns, large groups of individuals have a relatively small epidemiological impact; small- and medium-sized groups between 10 and 50 people have a larger impact on an epidemic. [ABSTRACT FROM AUTHOR]

In the absence of a vaccine, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission has been controlled by preventing person-toperson interactions via social distancing measures. In order to re-open parts of society, policy-makers need to consider how combinations of measures will affect transmission and understand the trade-offs between them. We use age-specific social contact data, together with epidemiological data, to quantify the components of the COVID-19 reproduction number. We estimate the impact of social distancing policies on the reproduction number by turning contacts on and off based on context and age. We focus on the impact of re-opening schools against a background of wider social distancing measures. We demonstrate that pre-collected social contact data can be used to provide a time-varying estimate of the reproduction number (R). We find that following lockdown (when R=0.7, 95% CI 0.6, 0.8), opening primary schools has a modest impact on transmission (R = 0.89, 95% CI 0.82-0.97) as long as other social interactions are not increased. Opening secondary and primary schools is predicted to have a larger impact (R = 1.22, 95% CI 1.02-1.53). Contact tracing and COVID security can be used to mitigate the impact of increased social mixing to some extent; however, social distancing measures are still required to control transmission. Our approach has been widely used by policy-makers to project the impact of social distancing measures and assess the trade-offs between them. Effective social distancing, contact tracing and COVID security are required if all age groups are to return to school while controlling transmission. [ABSTRACT FROM AUTHOR]

Since it was first identified, the epidemic scale of the recently emerged novel coronavirus (2019-nCoV) in Wuhan, China, has increased rapidly, with cases arising across China and other countries and regions. Using a transmission model, we estimate a basic reproductive number of 3.11 (95% CI, 2.39-4.13), indicating that 58-76% of transmissions must be prevented to stop increasing. We also estimate a case ascertainment rate in Wuhan of 5.0% (95% CI, 3.6-7.4). The true size of the epidemic may be significantly greater than the published case counts suggest, with our model estimating 21 022 (prediction interval, 11 090-33 490) total infections in Wuhan between 1 and 22 January. We discuss our findings in the light of more recent information. [ABSTRACT FROM AUTHOR]

• Mathematical models of respiratory syncytial virus (RSV) transmission can help describe seasonal epidemics and assess the impact of potential vaccines and immunoprophylaxis with monoclonal antibodies (mAb). • Our models suggest that either a maternal RSV vaccine or mAb would effectively reduce RSV hospitalization disease burden in New Zealand. • A seasonal mAb resulted in a larger RSV disease prevention impact than a maternal vaccine. Mathematical models of respiratory syncytial virus (RSV) transmission can help describe seasonal epidemics and assess the impact of potential vaccines and immunoprophylaxis with monoclonal antibodies (mAb). We developed a deterministic, compartmental model for RSV transmission, which was fitted to population-based RSV hospital surveillance data from Auckland, New Zealand. The model simulated the introduction of either a maternal vaccine or a seasonal mAb among infants aged less than 6 months and estimated the reduction in RSV hospitalizations for a range of effectiveness and coverage values. The model accurately reproduced the annual seasonality of RSV epidemics in Auckland. We found that a maternal vaccine with effectiveness of 30–40% in the first 90 days and 15–20% for the next 90 days could reduce RSV hospitalizations by 18–24% in children younger than 3 months, by 11–14% in children aged 3–5 months, and by 2–3% in children aged 6–23 months. A seasonal infant mAb with 40–60% effectiveness for 150 days could reduce RSV hospitalizations by 30–43%, 34–48% and by 14–21% in children aged 0–2 months, 3–5 months and 6–23 months, respectively. Our results suggest that either a maternal RSV vaccine or mAb would effectively reduce RSV hospitalization disease burden in New Zealand. Overall, a seasonal mAb resulted in a larger disease prevention impact than a maternal vaccine. [ABSTRACT FROM AUTHOR]