Using mortuary and burial data to place COVID-19 in Lusaka, Zambia within a global context.

Reported COVID-19 cases and associated mortality remain low in many sub-Saharan countries relative to global averages, but true impact is difficult to estimate given limitations around surveillance and mortality registration. In Lusaka, Zambia, burial registration and SARS-CoV-2 prevalence data during 2020 allow estimation of excess mortality and transmission. Relative to pre-pandemic patterns, we estimate age-dependent mortality increases, totalling 3212 excess deaths (95% CrI: 2104-4591), representing an 18.5% (95% CrI: 13.0-25.2%) increase relative to pre-pandemic levels. Using a dynamical model-based inferential framework, we find that these mortality patterns and SARS-CoV-2 prevalence data are in agreement with established COVID-19 severity estimates. Our results support hypotheses that COVID-19 impact in Lusaka during 2020 was consistent with COVID-19 epidemics elsewhere, without requiring exceptional explanations for low reported figures. For more equitable decision-making during future pandemics, barriers to ascertaining attributable mortality in low-income settings must be addressed and factored into discourse around reported impact differences.

Individual's daily behaviour and intergenerational mixing in different social contexts of Kenya.

We investigated contact patterns in diverse social contexts in Kenya and the daily behaviours that may play a pivotal role in infection transmission to the most vulnerable leveraging novel data from a 2-day survey on social contacts and time use (TU) from a sample of 1407 individuals (for a total of 2705 person days) from rural, urban formal, and informal settings. We used TU data to build six profiles of daily behaviour based on the main reported activities, i.e., Homestayers (71.1% of person days), Workers (9.3%), Schoolers (7.8%), or locations at increasing distance from home, i.e., Walkers (6.6%), Commuters (4.6%), Travelers (0.6%). In the rural setting, we observed higher daily contact numbers (11.56, SD 0.23) and percentages of intergenerational mixing with older adults (7.5% of contacts reported by those younger than 60 years vs. less than 4% in the urban settings). Overall, intergenerational mixing with older adults was higher for Walkers (7.3% of their reported contacts), Commuters (8.7%), and Homestayers (5.1%) than for Workers (1.5%) or Schoolers (3.6%). These results could be instrumental in defining effective interventions that acknowledge the heterogeneity in social contexts and daily routines, either in Kenya or other demographically and culturally similar sub-Saharan African settings.

Differential impact of physical distancing strategies on social contacts relevant for the spread of SARS-CoV-2: evidence from a cross-national online survey, March-April 2020.

OBJECTIVES: We investigate changes in social contact patterns following the gradual introduction of non-pharmaceutical interventions and their implications for infection transmission in the early phase of the pandemic. DESIGN, SETTING AND PARTICIPANTS: We conducted an online survey based on targeted Facebook advertising campaigns across eight countries (Belgium, France, Germany, Italy, the Netherlands, Spain, UK and USA), achieving a sample of 51 233 questionnaires in the period 13 March-12 April 2020. Poststratification weights based on census information were produced to correct for selection bias. OUTCOME MEASURES: Participants provided data on social contact numbers, adoption of protective behaviours and perceived level of threat. These data were combined to derive a weekly index of infection transmission, the net reproduction number [Formula: see text] . RESULTS: Evidence from the USA and UK showed that the number of daily contacts mainly decreased after governments issued the first physical distancing guidelines. In mid-April, daily social contact numbers had decreased between 61% in Germany and 87% in Italy with respect to pre-COVID-19 levels, mostly due to a contraction in contacts outside the home. Such reductions, which were uniform across age groups, were compatible with an [Formula: see text] equal or smaller than one in all countries, except Germany. This indicates lower levels of infection transmission, especially in a period of gradual increase in the adoption rate of the face mask outside the home. CONCLUSIONS: We provided a comparable set of statistics on social contact patterns during the COVID-19 pandemic for eight high-income countries, disaggregated by week and other demographic factors, which could be leveraged by the scientific community for developing more realistic epidemic models of COVID-19.

Rapid Review of Social Contact Patterns During the COVID-19 Pandemic.

BACKGROUND: Physical distancing measures aim to reduce person-to-person contact, a key driver of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. In response to unprecedented restrictions on human contact during the coronavirus disease 2019 (COVID-19) pandemic, studies measured social contact patterns under the implementation of physical distancing measures. This rapid review synthesizes empirical data on the changing social contact patterns during the COVID-19 pandemic. METHOD: We conducted a systematic review using PubMed, Medline, Embase, and Google Scholar following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We descriptively compared the distribution of contacts observed during the pandemic to pre-COVID data across countries to explore changes in contact patterns during physical distancing measures. RESULTS: We identified 12 studies reporting social contact patterns during the COVID-19 pandemic. Eight studies were conducted in European countries and eleven collected data during the initial mitigation period in the spring of 2020 marked by government-declared lockdowns. Some studies collected additional data after relaxation of initial mitigation. Most study settings reported a mean of between 2 and 5 contacts per person per day, a substantial reduction compared to pre-COVID rates, which ranged from 7 to 26 contacts per day. This reduction was pronounced for contacts outside of the home. Consequently, levels of assortative mixing by age substantially declined. After relaxation of initial mitigation, mean contact rates increased but did not return to pre-COVID levels. Increases in contacts post-relaxation were driven by working-age adults. CONCLUSION: Information on changes in contact patterns during physical distancing measures can guide more realistic representations of contact patterns in mathematical models for SARS-CoV-2 transmission.

Linking excess mortality to mobility data during the first wave of COVID-19 in England and Wales.

Non-pharmaceutical interventions have been implemented worldwide to curb the spread of COVID-19. However, the effectiveness of such governmental measures in reducing the mortality burden remains a key question of scientific interest and public debate. In this study, we leverage digital mobility data to assess the effects of reduced human mobility on excess mortality, focusing on regional data in England and Wales between February and August 2020. We estimate a robust association between mobility reductions and lower excess mortality, after adjusting for time trends and regional differences in a mixed-effects regression framework and considering a five-week lag between the two measures. We predict that, in the absence of mobility reductions, the number of excess deaths could have more than doubled in England and Wales during this period, especially in the London area. The study is one of the first attempts to quantify the effects of mobility reductions on excess mortality during the COVID-19 pandemic.

Behaviours and attitudes in response to the COVID-19 pandemic: insights from a cross-national Facebook survey.

BACKGROUND: In the absence of medical treatment and vaccination, individual behaviours are key to curbing the spread of COVID-19. Here we describe efforts to collect attitudinal and behavioural data and disseminate insights to increase situational awareness and inform interventions. METHODS: We developed a rapid data collection and monitoring system based on a cross-national online survey, the "COVID-19 Health Behavior Survey". Respondent recruitment occurred via targeted Facebook advertisements in Belgium, France, Germany, Italy, the Netherlands, Spain, the United Kingdom, and the United States. We investigated how the threat perceptions of COVID-19, the confidence in the preparedness of organisations to deal with the pandemic, and the adoption of preventive and social distancing behaviours are associated with respondents' demographic characteristics. RESULTS: We analysed 71,612 questionnaires collected between March 13-April 19, 2020. We found substantial spatio-temporal heterogeneity across countries at different stages of the pandemic and with different control strategies in place. Respondents rapidly adopted the use of face masks when they were not yet mandatory. We observed a clear pattern in threat perceptions, sharply increasing from a personal level to national and global levels. Although personal threat perceptions were comparatively low, all respondents significantly increased hand hygiene. We found gender-specific patterns: women showed higher threat perceptions, lower confidence in the healthcare system, and were more likely to adopt preventive behaviours. Finally, we also found that older people perceived higher threat to themselves, while all respondents were strongly concerned about their family. CONCLUSIONS: Rapid population surveys conducted via Facebook allow us to monitor behavioural changes, adoption of protective measures, and compliance with recommended practices. As the pandemic progresses and new waves of infections are a threatening reality, timely insights from behavioural and attitudinal data are crucial to guide the decision-making process. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1140/epjds/s13688-021-00270-1.

Addressing Public Health Emergencies via Facebook Surveys: Advantages, Challenges, and Practical Considerations.

Surveys of the general population can provide crucial information for designing effective nonpharmaceutical interventions to tackle public health emergencies, such as the COVID-19 pandemic. Yet, conducting such surveys can be difficult, especially when timely data collection is required. In this viewpoint paper, we discuss our experiences with using targeted Facebook advertising campaigns to address these difficulties in relation to the COVID-19 pandemic. We describe central advantages, challenges, and practical considerations. This includes a discussion of potential sources of bias and how they can be addressed.

The impact of demographic changes, exogenous boosting and new vaccination policies on varicella and herpes zoster in Italy: a modelling and cost-effectiveness study.

BACKGROUND: The present study aims to evaluate the cost-effectiveness of the newly introduced varicella and herpes zoster (HZ) vaccination programmes in Italy. The appropriateness of the introduction of the varicella vaccine is highly debated because of concerns about the consequences on HZ epidemiology and the expected increase in the number of severe cases in case of suboptimal coverage levels. METHODS: We performed a cost-utility analysis based on a stochastic individual-based model that considers realistic demographic processes and two different underlying mechanisms of exogenous boosting (temporary and progressive immunity). Routine varicella vaccination is given with a two-dose schedule (15 months, 5-6 years). The HZ vaccine is offered to the elderly (65 years), either alone or in combination with an initial catch-up campaign (66-75 years). The main outcome measures are averted cases and deaths, costs per quality-adjusted life years gained, incremental cost-effectiveness ratios, and net monetary benefits associated with the different vaccination policies. RESULTS: Demographic processes have contributed to shaping varicella and HZ epidemiology over the years, decreasing varicella circulation and increasing the incidence of HZ. The recent introduction of varicella vaccination in Italy is expected to produce an enduring reduction in varicella incidence and, indirectly, a further increase of HZ incidence in the first decades, followed by a significant reduction in the long term. However, the concurrent introduction of routine HZ vaccination at 65 years of age is expected to mitigate this increase and, in the longer run, to reduce HZ burden to its minimum. From an economic perspective, all the considered policies are cost-effective, with the exception of varicella vaccination alone when considering a time horizon of 50 years. These results are robust to parameter uncertainties, to the two different hypotheses on the mechanism driving exogenous boosting, and to different demographic projection scenarios. CONCLUSIONS: The recent introduction of a combined varicella and HZ vaccination programme in Italy will produce significant reductions in the burden of both diseases and is found to be a cost-effective policy. This programme will counterbalance the increasing trend of zoster incidence purely due to demographic processes.

Cost-benefit analysis of controlling the spotted wing drosophila (Drosophila suzukii (Matsumura)) spread and infestation of soft fruits in Trentino, Northern Italy.

BACKGROUND: We assessed the economic impact of the invasive pest Drosophila suzukii (Matsumura) on the soft fruit industry (strawberries, raspberries, blackberries and blueberries) in Trentino, Northern Italy, using cost-benefit analysis. A conventional integrated pest management (IPM) based on insecticide, mass trapping and cultural measures is compared with an upgraded IPM strategy based on exclusion netting. Costs and benefits associated with the change between the two are estimated to evaluate the most profitable strategy from a societal point of view. The robustness of the results to uncertainty in parameter values is assessed through probabilistic sensitivity analysis. RESULTS: In a period of low pest pressure, the conventional IPM strategy would likely be more profitable than no management. However, with higher pest pressure levels, the upgraded IPM strategy would increasingly be more profitable than conventional IPM as pest damage levels increase. CONCLUSION: For the problem considered in this study, insecticide-based management is expected to prove less and less profitable as rising pest pressure levels lead to an intensification of the insecticide applications. Conversely, exclusion netting, despite being more expensive, is expected to be much more profitable, in terms of both its effectiveness in reducing pest pressure and its lower societal impact. © 2017 Society of Chemical Industry.

Social Contact Structures and Time Use Patterns in the Manicaland Province of Zimbabwe.

BACKGROUND: Patterns of person-to-person contacts relevant for infectious diseases transmission are still poorly quantified in Sub-Saharan Africa (SSA), where socio-demographic structures and behavioral attitudes are expected to be different from those of more developed countries. METHODS AND FINDINGS: We conducted a diary-based survey on daily contacts and time-use of individuals of different ages in one rural and one peri-urban site of Manicaland, Zimbabwe. A total of 2,490 diaries were collected and used to derive age-structured contact matrices, to analyze time spent by individuals in different settings, and to identify the key determinants of individuals' mixing patterns. Overall 10.8 contacts per person/day were reported, with a significant difference between the peri-urban and the rural site (11.6 versus 10.2). A strong age-assortativeness characterized contacts of school-aged children, whereas the high proportion of extended families and the young population age-structure led to a significant intergenerational mixing at older ages. Individuals spent on average 67% of daytime at home, 2% at work, and 9% at school. Active participation in school and work resulted the key drivers of the number of contacts and, similarly, household size, class size, and time spent at work influenced the number of home, school, and work contacts, respectively. We found that the heterogeneous nature of home contacts is critical for an epidemic transmission chain. In particular, our results suggest that, during the initial phase of an epidemic, about 50% of infections are expected to occur among individuals younger than 12 years and less than 20% among individuals older than 35 years. CONCLUSIONS: With the current work, we have gathered data and information on the ways through which individuals in SSA interact, and on the factors that mostly facilitate this interaction. Monitoring these processes is critical to realistically predict the effects of interventions on infectious diseases dynamics.

Estimating Age-Specific Immunity and Force of Infection of Varicella Zoster Virus in Norway Using Mixture Models.

This study applies mixture modelling to examine age-specific immunity to varicella zoster virus (VZV) infection in Norway based on the first large-scale serological study in the general population. We estimated the seropositive proportions at different ages and calculated the underlying force of infection by using a sample of 2103 residual sera obtained from patients seeking primary and hospital care. A rapid increase in the VZV-associated immunity is observed in the first years of life with 63% of children being immune by age 5. The increase in the immunity levels slows down thereafter, with a large proportion of adults still susceptible by age 20 (around 14.5%), thus at risk of serious sequelae of varicella infection. The corresponding force of infection peaks during the preschool period, subsequently declines to a minimum between ages 10 and 20 years, and afterwards moderately increases to reach a plateau lasting throughout the childbearing period. In comparison with the traditional cut-off approach, mixture modelling used the whole data without producing any inconclusive cases, led to an unbiased classification of individuals between susceptible and immune, and provided a smoother immune profile by age. These findings represent an important step towards any decision about the introduction of varicella vaccination in Norway, as they are a primary input for mathematical transmission models aimed at evaluating potential vaccination scenarios.

Transition to Parenthood and HIV Infection in Rural Zimbabwe.

BACKGROUND: The relationship between the risk of acquiring human immunodeficiency virus (HIV) infection and people's choices about life course events describing the transition to parenthood-sexual debut, union (in the form of marriage, cohabitation, or long-term relationship), and parenthood-is still unclear. A crucial role in shaping this relationship may be played by the sequence of these events and by their timing. This suggests the opportunity to focus on the life courses in their entirety rather than on the specific events, thus adopting a holistic approach that regards each individual's life course trajectory as a whole. METHODS: We summarise the individual life courses describing the transition to parenthood using ordered sequences of the three considered events. We aim to (i) investigate the association between the sequences and HIV infection, and (ii) understand how these sequences interact with known mechanisms for HIV transmission, such as the length of sexual exposure and the experience of non-regular sexual partnerships. For this purpose, we use data from a general population cohort study run in Manicaland (Zimbabwe), a Sub-Saharan African area characterised by high HIV prevalence. RESULTS: For both genders, individuals who experienced either premarital or delayed childbearing have higher HIV risk compared to individuals following more standard transitions. This can be explained by the interplay of the sequences with known HIV proximate determinants, e.g., a longer exposure to sexual activity and higher rates of premarital sex. Moreover, we found that people in the younger birth cohorts experience more normative and safer sequences. CONCLUSIONS: The shift of younger generations towards more normative transitions to parenthood is a sign of behaviour change that might have contributed to the observed reduction in HIV prevalence in the area. On the other hand, for people with less normative transitions, targeted strategies are essential for HIV prevention.

Identification of pharmacogenomic markers of clinical efficacy in a dose-dense therapy regimen (R-CHOP14) in diffuse large B-cell lymphoma.

About 60% of patients with diffuse large B-cell lymphoma (DLBCL) may be cured by primary chemotherapy with an R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone) regimen. Most of the rest will die of the disease, mainly due to the occurrence of tumor drug resistance. Many efforts have been made to explain the molecular mechanisms of drug resistance in patients with cancer, including those with DLBCL. This exploratory study was designed to correlate the mRNA expression levels of candidate genes mainly involved in the doxorubicin pathway (ABCB1, GSTP1, TOPO2α, BCL2, PKCßII) with the outcome of 54 patients with DLBCL undergoing a dose-dense R-CHOP regimen. After multivariate analysis, high GSTP1 (p = 0.003) and TOPO2α (p = 0.02) gene expressions were associated with shorter overall survival and progression-free survival, respectively, suggesting that these genes may represent an unfavorable prognostic factor in the case of R-CHOP treatment. These biomarkers may be useful for selecting patients eligible for personalized chemotherapy after validation in an independent set.

Perspectives on the impact of varicella immunization on herpes zoster. A model-based evaluation from three European countries.

The introduction of mass vaccination against Varicella-Zoster-Virus (VZV) is being delayed in many European countries because of, among other factors, the possibility of a large increase in Herpes Zoster (HZ) incidence in the first decades after the initiation of vaccination, due to the expected decline of the boosting of Cell Mediated Immunity caused by the reduced varicella circulation. A multi-country model of VZV transmission and reactivation, is used to evaluate the possible impact of varicella vaccination on HZ epidemiology in Italy, Finland and the UK. Despite the large uncertainty surrounding HZ and vaccine-related parameters, surprisingly robust medium-term predictions are provided, indicating that an increase in HZ incidence is likely to occur in countries where the incidence rate is lower in absence of immunization, possibly due to a higher force of boosting (e.g. Finland), whereas increases in HZ incidence might be minor where the force of boosting is milder (e.g. the UK). Moreover, a convergence of HZ post vaccination incidence levels in the examined countries is predicted despite different initial degrees of success of immunization policies. Unlike previous model-based evaluations, our investigation shows that after varicella immunization an increase of HZ incidence is not a certain fact, rather depends on the presence or absence of factors promoting a strong boosting intensity and which might or not be heavily affected by changes in varicella circulation due to mass immunization. These findings might explain the opposed empirical evidences observed about the increases of HZ in sites where mass varicella vaccination is ongoing.

Hope-Simpson's progressive immunity hypothesis as a possible explanation for herpes zoster incidence data.

Varicella-zoster virus (VZV) is the causative agent of both varicella (chickenpox) and herpes zoster (HZ) (shingles). After varicella infection, the virus remains dormant in the host's dorsal ganglia and can reactivate due to waning cell-mediated immunity, causing HZ. Exposure of varicella-immune persons to VZV may boost the host's immune response, resulting in a protective effect against HZ. In this study, we used mathematical models of VZV transmission and HZ development to test the biological hypothesis of "progressive immunity," originally proposed by Hope-Simpson (Proc R Soc Med. 1965;58:9-20), that cell-mediated protection against HZ increases after each episode of exposure to VZV. Predictions from a model incorporating such a hypothesis were compared with those of other concurrent models proposed for explaining HZ epidemiology. The progressive immunity model fits significantly better the age profile of HZ incidence for Finland (years 2000-2006), Italy (2003-2005), Spain (1997-2004), and the United Kingdom (1991-1992), suggesting that this mechanism may be critical in shaping HZ patterns. The model thus validated is an alternative to VZV models currently used to evaluate the impact of mass immunization programs for varicella and therefore extends the range of tools available to assist policy-makers with the present decision paralysis on the introduction of vaccination.

Towards measles elimination in Italy: monitoring herd immunity by Bayesian mixture modelling of serological data.

The analysis of post-vaccination serological data poses nontrivial issues to the epidemiologists and policy makers who want to assess the effects of immunisation programmes. This is especially true for infections on the path to elimination as is the case for measles. We address these problems by using Bayesian Normal mixture models fitted to antibody counts data. This methodology allows us to estimate the seroprevalence of measles by age and, in contrast to conventional methods based on fixed cut-off points, to also distinguish between groups of individuals with different degrees of immunisation. We applied our methodology to two serological samples collected in Tuscany (Italy) in 2003 and in 2005-2006 respectively, i.e., before and after a large vaccination campaign targeted to school-age children. Besides showing the impact of the campaign, we were able to accurately identify a large pocket of susceptible individuals aged about 13-14 in 2005-2006, and a larger group of weakly immune individuals aged about 20 in 2005-2006. These cohorts therefore represent possible targets for further interventions towards measles elimination.

High prevalence of F4+ and F18+ Escherichia coli in Cuban piggeries as determined by serological survey.

Little information is available on the prevalence of swine enteropathogens in Cuba where diarrheic diseases are responsible for 31% and 37% of the total mortality during the neonatal and postweaning periods. F4+ and F18+ enterotoxigenic Escherichia coli and F18+ verotoxigenic E. coli induce diarrhea and edematous disease in pigs, but their distribution has never been thoroughly studied in the Cuban swine population. Therefore, the present study estimated the prevalence of F4- and F18-specific antibodies in sera of 1,044 6-month-old gilts distributed in 34 piggeries spread over the Cuban territory. For the data analysis, which included the optical density of individual samples tested by ELISA, random-effects models and a mixture model in R (package "mixAK"; Komárek, Computational Statistics and Data Analysis 53:3932-3947, 2009) were fitted. Low, moderate, and high levels of F4-specific antibodies were found in 67.6%, 26.8%, and 5.6% of the gilts, while 66.4% and 33.6% of gilts showed low and high levels of F18-specific antibodies. Hereby, we show that F4+ and F18+ E. coli are highly prevalent as potential enteropathogens in Cuban piggeries.

Little Italy: an agent-based approach to the estimation of contact patterns- fitting predicted matrices to serological data.

Knowledge of social contact patterns still represents the most critical step for understanding the spread of directly transmitted infections. Data on social contact patterns are, however, expensive to obtain. A major issue is then whether the simulation of synthetic societies might be helpful to reliably reconstruct such data. In this paper, we compute a variety of synthetic age-specific contact matrices through simulation of a simple individual-based model (IBM). The model is informed by Italian Time Use data and routine socio-demographic data (e.g., school and workplace attendance, household structure, etc.). The model is named "Little Italy" because each artificial agent is a clone of a real person. In other words, each agent's daily diary is the one observed in a corresponding real individual sampled in the Italian Time Use Survey. We also generated contact matrices from the socio-demographic model underlying the Italian IBM for pandemic prediction. These synthetic matrices are then validated against recently collected Italian serological data for Varicella (VZV) and ParvoVirus (B19). Their performance in fitting sero-profiles are compared with other matrices available for Italy, such as the Polymod matrix. Synthetic matrices show the same qualitative features of the ones estimated from sample surveys: for example, strong assortativeness and the presence of super- and sub-diagonal stripes related to contacts between parents and children. Once validated against serological data, Little Italy matrices fit worse than the Polymod one for VZV, but better than concurrent matrices for B19. This is the first occasion where synthetic contact matrices are systematically compared with real ones, and validated against epidemiological data. The results suggest that simple, carefully designed, synthetic matrices can provide a fruitful complementary approach to questionnaire-based matrices. The paper also supports the idea that, depending on the transmissibility level of the infection, either the number of different contacts, or repeated exposure, may be the key factor for transmission.