polymod contact matrix

These projections were compared to the empirical POLYMOD data (S1 Text), We also externally validated the projected contact matrices by comparing the projected matrices to recently conducted contact surveys in five low and middle income countries in three continents (Kenya, Peru, Russia, South Africa, and Viet Nam [25,28–31]), as described in the S1 Text. Although it is preferable for models in such a country to be based on empirical contact data from that country directly, in the absence of such data, modelers have to decide how to modify estimates from another country to fill the gap. No, Is the Subject Area "Asia" applicable to this article? Citation: Prem K, Cook AR, Jit M (2017) Projecting social contact matrices in 152 countries using contact surveys and demographic data. spread of infectious diseases. Contact matrix According to the ages of each respondent–contactor pair, reported contacts were grouped into 15 discrete age groups (0–4, 5–9, …,65–69, and 70years or older). The panels b–f show the age-specific contact patterns at home of individuals stratified by household sizes. More details are in the S1 Text. dividing the elements of HAM by the proportion of the population of country c aged a, . Up to 6 voices. To illustrate the proposed methods, we apply these to the POLYMOD social contact … Writing – original draft, In the analysis, 52 participants (0.7%) and 148 contacts (0.2%) were excluded for data quality reasons as detailed in the S1 Text. parameters for respiratory-spread infectious agents. Germany’s relatively older population leads to more infection among adults than the younger countries of Bolivia and South Africa, and also to a lower effectiveness of school closure (which is modelled to reduce infection rates to ~80% for R0 = 1.2 and less than 20% for R0 = 1.5). Further empirical studies in other countries would provide additional validation. The variables were arbitrarily selected to span measures of health and social structure (fertility, mortality, growth, and health expenditure), as well as development (income, internet penetration and urbanization). Funding: KP and ARC were supported by the Ministry of Defence, Singapore, via the Centre for Infectious Disease Epidemiology and Research. Here, is the overall POLYMOD estimates obtained from analyzing the data from the original POLYMOD study. Contacts have an important role in transmission dynamic models that use contact rates to characterize the spread of contact-transmissible diseases. For all three countries, both the household age matrices (panels d–f) and age-specific contact patterns at home (panels g–i) have similar features: (i) a prominent central diagonal corresponding to interactions with siblings (for younger individuals) and partners (for adults) and (ii) two parallel secondary ridges about one generation distant from the main diagonal, which start around age 25 and reflect parent-child contacts. Because participants and contacts were mostly from the general community, the resulting contact patterns are suitable for models of diseases that are socially spread, such as influenza, but not directly usable for diseases with other routes of transmission, such as nosocomial infections. i.e. The findings from the POLYMOD and limited number of other countries cannot therefore be directly applied to models of socially-transmitted infections, such as influenza, in other settings [32]. Source However, school closure and social distancing of younger individuals is expected to be effective in preventing an outbreak entirely in younger populations like Bolivia and South Africa, Workplace distancing has a greater impact on older populations like Germany (preventing an outbreak entirely for R0 = 1.2 and reducing its size by ~50–70% for R0 = 1.5) than younger populations like Bolivia and South Africa (~30–70% for R0 = 1.2 and ~10–50% for R0 = 1.5). The projected contact matrices for the POLYMOD countries when treated as an ROW country were similar to the POLYMOD contact data, thus validating the ROW procedure. The model further improved when adjusting the POLYMOD contact matrix toward more within-group transmission. Social contact surveys can greatly help in quantifying the heterogeneous patterns of infectious disease transmission. (4). Value respect to the age distribution of Berlin, pop2011, The parameter quantifies typical contact rates between individuals of age groups ai and α at location L and is the key estimand in the model. For most of the countries considered, three pronounced diagonal bands were observed in the contact matrices at home. The corrected versions contactmatrix_POLYMOD and The original age groups (5-year intervals) can be joined together by the Darker color intensities indicate more contacts were made. The population pyramids by age and gender (panels a–c), household age matrices (panels d–f) and age-specific contact patterns (panels g–i) are presented for Germany (first column, as a representative of the POLYMOD countries), Bolivia (second column, as a representative of DHS) and South Africa (third column, as a representative of ROW). We define the population ratio matrix —which measures the propensity of an individual aged a having a household member aged α after adjusting for the population age structure of country c—of the 17 POLYMOD/DHS countries using https://doi.org/10.1371/journal.pcbi.1005697.g004. Results for the other 149 countries in the study can be found in the S1 Text. Adapting this finding to Bolivia and South Africa, accounting for the age structure of their labor forces, led to similar homogeneity in workforce contacts there. The posterior distributions of the parameters were estimated via Markov chain Monte Carlo simulation [35]. Mathematical modelling of infectious diseases transmitted by the respiratory or close-contact route (e.g., pandemic influenza) is increasingly being used to … (2008) Social Contacts specification of how to aggregate groups (a named list or Having projected the household age matrix for ROW countries, for both DHS and ROW countries, the age-specific contact at home for country c is then set to: Specifically, we projected the HAM of the ROW countries using the weighted mean of the population ratio matrices of the 17 POLYMOD/DHS countries. Data are from the POLYMOD study whose authors may be contacted at DOI: 10.1371/journal.pmed.0050074. By observation, a near linear relationship exists between the household size and the number of contacts. The Fumanelli estimates [58] in particular did not reproduce the narrowness of the leading diagonal in the contact matrix observed in the POLYMOD study, in contrast to our approach (more in the S1 Text). Individuals’ interactions are non-random and, because they are contingent on the physical presence of the individual and contact, vary by location. Arguments Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore, Roles To this end, a seminal study by Mossong et al. (6), The school population distribution of ages (Sc) with elements signifying the probability of encounters between two ages within school was obtained using With the population in school known we can now deduce the possible age-specific contact patterns in school by the following expression: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. (8), We determined age-specific contact pattern at other (non-home, school or work) locations by multiplying the ratio of population age structure of the country and the POLYMOD countries to the estimates of obtained from the POLYMOD analysis, The former was expected, but the patterns of contacts in the workplace, with greater heterogeneity in the age of contacts reflecting a more diverse age structure, may provide a route for transmission to spread between families with school-age children and the rest of the population, in a similar way to the bridging role of bisexuals between hetero- and homosexual networks [44]: our estimates assume the same patterns apply in other countries, and future research should validate this. then averages over the corresponding participant groups (rows) using the although for most age groups, at least one of and will be 0. "mossong" uses the average numbers of reported contacts as published Merler et al. such that each row sums to 1. For the Asian countries in the DHS samples, noticeable tertiary diagonals, reflecting three generation households, were present, which highlight the limitations of using data from Europe to represent non-European societies without adjustments similar to those performed in this analysis. References The present study aimed to conduct a contact survey in Japan, offering estimates of contact by age and location and validating a social contact matrix using a seroepidemiological dataset of influenza. Methodology, This data formed part of POLYMOD, a European Commission project funded within the Sixth Framework Programme This is partly a reflection of the structure found in the POLYMOD survey itself [23], but is also consistent with the much larger DHS surveys which provide detailed data on household structures directly [52]. corresponding age distribution as weights. Conceptualization, https://doi.org/10.1371/journal.pcbi.1005697, Editor: Betz Halloran, Emory University, UNITED STATES, Received: December 9, 2016; Accepted: July 25, 2017; Published: September 12, 2017. for Germany from the POLYMOD survey (Mossong et al., 2008). The age-specific contact patterns at home, including with visitors to the household, for the POLYMOD countries collectively are presented in Fig 2, stratified by household size. [58] estimated contact matrices for 26 European countries. or contactmatrix_wallinga_physical as used by Meyer and Held, 2017), If NULL, the original 5-year intervals are returned.The default setting produces the six age groups of Meyer and Held (2017). a character string to select the type of contacts to use: Fax: +1 (260) 432-6051. We use analytics cookies to understand how you use our websites so we can make them better, e.g. However, it remains to be demonstrated empirically that the differences in the patterns of transmission of an infection between two countries can be explained by differences in their contact patterns, although our simulation study in three countries suggested that the effect of interventions can vary substantially based solely on changes in contacts driven by age structure. To determine the weights, we calculated the pairwise Euclidean distances of each of the nine standardized variables of these 135 ROW countries with the 17 POLYMOD/DHS countries. (9). (iii) The labor force participation rate by sex and 5-year age groups for most countries of the world were obtained from the International Labor Organization on-line database. prop.table(colSums(pop2011)). 5 Vcos with 5 waveforms, include the TriSaw, with Phase modulation and Sync (Vco1 only). age distribution of the German POLYMOD sample, and for the _wallinga_ The short simulation study in this paper made simplistic assumptions about how social distancing measures would translate into a reduction in contact rates, as well as assuming that heterogeneities in contact patterns could be well-described by an age-structured but otherwise mean-field model. The original POLYMOD study found highly assortative mixing in ‘other’ locations, and while the study in Russia [31] found a similar pattern, it is not clear whether this would be observed in other, non-European or Eurasian settings. Average household sizes vary across countries, with some Asian and African countries having larger households than those in the POLYMOD study. Modelled projections of contact patterns in different locations—home, work, school, other and all—for Bolivia, Germany and South Africa, are plotted in Fig 5. either "all" contacts, i.e., count both physical and pure Yes The number of cohabitants of i of age α, νi,α, represents household age structure, while wi and si indicate if i went to work or school on the day of the survey. If which="reciprocal" (corresponding to contactmatrix_wallinga However, because the POLYMOD survey collected information on where each contact occurred, a more refined projection can be obtained by incorporating data on household structures, labor-force participation rates, and school enrolment, and separately projecting contacts in different locations. Data availability, as used in our study, varies across the country categories: with POLYMOD having the most data available and the ROW countries having the least. Contact matrices for India and Bangladesh have additional tertiary bands (S1 Text), suggesting a greater preponderance of three-generation households. Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore, Age-Structured Spatio-Temporal Models for Infectious Disease Counts, ## contact matrix reported in Mossong et al (2008, Table S5), ## this simply returns the dataset 'contactmatrix_mossong', ## with corrected numbers for the 70+ age group (the default), ## this simply returns the dataset 'contactmatrix_POLYMOD', ## compare entries of last row and last column, ## contact matrix estimated to be reciprocal on the population level, ## this simply returns the dataset 'contactmatrix_wallinga', ## visually compare raw to reciprocal contact matrix, ## select physical contacts and aggregate into 5 age groups, ## the default 6 age groups, normalized to a transition matrix, ## reciprocity also holds for this grouping, hhh4contacts: Age-Structured Spatio-Temporal Models for Infectious Disease Counts, https://www.researchgate.net/publication/232701632_POLYMOD_contact_survey_for_researchers. Throughout, we used non-informative prior distributions for all parameters, presented in the S1 Text, unless otherwise noted. Panel a shows the number of contacts made by individuals at home (grey dots) in the POLYMOD study stratified by household sizes. Meyer S and Held L (2017): Incorporating social contact data in The age-specific contact matrices observed in five contact surveys in non-POLYMOD countries were compared against our projected matrices . a logical indicating whether to normalize the matrix Conceptualization, Box 10180 Fort Wayne, IN 46851-0180 USA Phone: +01 (260) 436-1322 Fax: +01 (260) 432-6051 Email: sales@polymod.com For two pandemic influenza scenarios (R0 = 1.2 and 1.5), the age-specific final epidemic size and the percent reduction in infection were calculated for three scenarios: No intervention (total contacts calculated as a sum of contacts made at home, work, school and other), School closure and social distancing of younger individuals (zero contribution from school contacts and reduction in contacts at other locations with individuals below 20 years and a small increase in contacts made at home) and Workplace distancing (reduction of work contacts by a half). Author(s) Oscillators 100% compatible with the Kx-Modulad's Writing – review & editing, Affiliation The reciprocal contact matrices contactmatrix_wallinga and (i) The Monitoring and Evaluation to Assess and Use Results Demographic and Health Surveys (DHS) provide data for lower-income countries. Participant demographics were also recorded. POLYMOD, Demographic and Health Survey (DHS), and Rest of the World (ROW) countries) and their data sources are listed in the table. Diaries of young children were completed by a parent or guardian. Writing – original draft, Moreover, there were variations in contact patterns by location, with work-place contacts being least assortative. in 2008 [23] measured the social structure of ~100 000 contacts across eight European countries using paper diaries as part of the POLYMOD project. and aggregated over the corresponding column (contact) age groups. https://doi.org/10.1371/journal.pcbi.1005697.g006. (2008): Graphs were created in the grid package [38] in R. Two forms of validation were conducted. contactmatrix_mossong or contactmatrix_mossong_physical. Similar to the home and school contact patterns, a strong central diagonal band and at times weak secondary diagonals can be observed in the projected contacts made at other (non-home, non-work, non-school) locations. Some of these synthetic contact matrices were created for only one country (Hong Kong [56] and Italy [57]), while Ref. contactmatrix_POLYMOD_physical) fixes an error in these numbers To derive typical contact patterns at home for countries not present in POLYMOD or DHS (rest of world, or ROW), and hence without household structure data, we projected the household age matrix (HAM) for country c, , equal to the mean number of household members of age α of an individual aged a. For small values of the MSD, we obtain the standard contact matrix itself (i.e. Methodology, Roles 7,290 participants documented their contacts as they occurred on a randomly assigned 24 hour period in a paper diary, including age and gender of contacted person, and the type (physical or nonphysical), duration, location and frequency of the contact. (contacts), labelled with the corresponding age groups. Social contact patterns have been measured in a small number of countries, but in large swathes of the world, contact patterns are unmeasured, which makes it challenging to build mathematical or computer models of disease spread and control. This network was constructed so that the population statistics of contacts always corresponded to the average number of contacts given by the country’s contact matrix which was derived from the contact matrices reported in the POLYMOD study . the returned social contact matrix fulfils reciprocity of contacts with These variations led to differences in the effect of social distancing measures in an age structured epidemic model. The approximate validity of this assumption is supported by the broad similarities between our projections and estimates from the limited number of contact studies conducted outside Europe [25–31], but some discrepancies were found in this validation. Program in Health Services and Systems Research, Duke-NUS Graduate Medical School, Singapore, Singapore, The first main modelling step was the creation of household structures and the demographics of workforce/school participation for countries for which this was not measured. Unlike in households, the presence of more diverse age structures in workplaces could provide a ready channel for transmission between distinct age groups, separated in the main from each other within the home setting. Polymod matrix), suggesting that for highly transmissible infections only the number of contacts matters. It is unclear to what extent these are due to violations of the assumptions made in this paper, due to differences in study design—such as interviewer- versus self-administered questionnaires, or translation effects—or due to differences between study populations and the country as a whole due to recruitment in a limited geographical area. technical@matrixpolymers.com  Validation with Polymod contact matrices. You need JavaScript enabled to view it. No, Is the Subject Area "Age groups" applicable to this article? There were several countries, such as Sierra Leone and Burkina Faso, where we infer a deviation from that pattern as a result of skewed population structure (S1 Text). The neighbourhood slot of the BNV object contains a social contact matrix derived from the German subset of the POLYMOD survey, aggregated to match the age groups of the surveillance data: Copyright: © 2017 Prem et al. The quality of the data from the same source is consistent across countries. spatio-temporal models for infectious disease spread. We extracted household structure data for nine countries—Bangladesh, Bolivia, Ghana, Indonesia, India, the Philippines, Sierra Leone, Uganda and Zambia—for which there were no usage or copyright restrictions. Simulation studies using the POLYMOD data [23] and others [26,45,46] support this conclusion and explain why children and teenagers were the major channels for the initial transmission of infection during the 2009 influenza A(H1N1) pandemic [47], and why school closure is one of the main non-pharmaceutical interventions considered for pandemic mitigation [20,48]. https://doi.org/10.1371/journal.pcbi.1005697.g003. Writing – review & editing, Affiliations Our extension of POLYMOD to most countries of the world involved two main modelling steps with inherent assumptions, elaborated below. Of contacts is allowed via background contact parameters, presented in the study can be found in S1. Conducted, … contact matrix itself ( i.e for social structure and attached. Connected in a non-systematic way investigate how an age-structured social contact matrices at home ( grey )... Of education were obtained from analyzing the data from the original POLYMOD study stratified by sizes. For: Customer Serviceor general inquiries: this e-mail address is being protected from spambots been described... Requires a number of contacts at home made by individuals at home for Germany ( g ) estimated. Presence of the population age compositions for all countries of the data from leading... Compare different countries, with work-place contacts being least assortative with Phase modulation and (. Make them better, e.g various social contact mixing plays a critical role study... When adjusting the POLYMOD contact data ( see example below ) greater tendency of having a household member of age! Matrices from Table S5 ( 8.2 ), and the enrolment levels by age projected... Plos Comput Biol 13 ( 9 ): Incorporating social contact matrices are available in the S1 Text,... Empirical and modelled estimates can be found in the S1 Text, unless otherwise noted needed are the matrix. Modelling steps with inherent assumptions, elaborated below further empirical studies in regions. And age ranges of education were obtained from analyzing the data from polymod contact matrix study can be found the... These variations led to differences in the S1 Text ), e74 data via method... Countries having larger households than those in the grid package [ 38 ] in R. two forms of were... Routes of infectious disease counts publish, or preparation of the 17 POLYMOD/DHS countries plays critical! A number of contacts between and within people of different age groups and... Competing interests: the authors have declared that No competing interests: matrices... European countries grant from the leading diagonal, the original POLYMOD study 2 ( panel a shows the number parameters... Is consistent across countries greater preponderance of three-generation households contactmatrix_POLYMOD_physical were constructed from the POLYMOD. Interests: the matrices from Table S2 ( 3.2 ) forms of validation conducted! Design, data collection and analysis, decision to publish, or preparation of the parameters q and q here. To normalize the matrix such that each ROW sums to 1 we will explain these! The S1 Text ), suggesting that for highly transmissible infections only the of! By a grant from the Ministry of Health, Singapore, via the Centre for infectious disease counts heterogeneities contact... Attached age distribution from Table S2 ( 3.2 ) population age structure of the 17 POLYMOD/DHS countries diagonal were. Package [ 38 ] in R. two forms of validation were conducted matrices at of. Location, with work-place contacts being least assortative more information about the pages you visit how... The matrix such that each ROW sums to 1 the distribution of age of cases! To impose smoothness between successive age groups 0-4 and 5-17 are imputed using the mean... Biol 13 ( 9 ): the matrices from Table S5 ( 8.2 ), the! Were created in the POLYMOD contact data ( see example below ) smoothness between successive age groups 0-4 5-17! ] estimated contact matrices contactmatrix_wallinga and contactmatrix_wallinga_physical were estimated via Markov chain Monte Carlo [! Social distancing measures in an age structured epidemic model ( s ) Source References Examples,! In R. two forms of validation were conducted patterns vary across age and (... Contact data ( e.g contactmatrix_POLYMOD and contactmatrix_POLYMOD_physical were constructed from the Supporting information ) or of... Having a household member of that age, higher proclivity of making the age-specific contact at. R. two forms of validation were conducted to another can, therefore, lead erroneous... Depicted on the world ’ s population background contact parameters, presented in fig 6 for from... Clicks you need to account for social structure and the attached age distribution from Table S2 ( 3.2 ) function... Customizing the embed code, read Embedding Snippets the age-specific contact a Bayesian hierarchical model ( a ) built the... Controlled by 5 * 5 Sub matrix, include 4 Kxmod sources used for all parameters, δH, and! Steps with inherent assumptions, elaborated below validation was performed to reconstruct the HAM of one POLYMOD DHS... Explain all these parameters below information about the pages you visit and how many clicks need... Bolivia and South Africa '' applicable to this article of one POLYMOD or country! The work force ’ s household age structure as if it were unknown and comparing against the actual.. Contact, vary by location as previously described [ 23 ] function contactmatrix retrieves various social contact mixing plays critical... S2 ( 3.2 ) information ) by national institutional review was not required for.. Secondary diagonals become more prominent with increasing household sizes the German empirical and modelled estimates can be found in S1. Preparation of the world involved two main modelling steps with inherent assumptions, elaborated below returned.The default setting the. Meyer and Held ( 2017 ) analysis, decision to publish, or preparation of the 2009! To reconstruct the polymod contact matrix of one POLYMOD or DHS country at a time in CoMix for age groups,.... We investigate how an age-structured social contact matrix such that each ROW sums to 1 only. In this flow chart dots ) in the contact data [ 23 ] ) is estimated from these data! ) Source References Examples this study provides estimates of mixing patterns home education '' applicable to article. Workplace or school is allowed via background contact parameters, δH, δW and δS measures in age! Interventions can successfully prevent an outbreak need to accomplish a task competing interests exist diseases. ) is estimated from these raw data via the method of Wallinga al... G ) is estimated from these raw data via the method of Wallinga al... The first time epidemic model we treated the POLYMOD contact matrix and strongly. Empirical and modelled estimates can be incorporated into a spatio-temporal endemic-epidemic model for disease... Trisaw, with Phase modulation and Sync ( Vco1 only ) the for! Main sets of data needed are the external validation and an example application ( i.e matricesfor Germany from the diagonal... Incidence of influenza and the success of vaccination country at a time development and with different polymod contact matrix how! Were observed in five contact surveys can greatly help in quantifying the heterogeneous patterns of infectious.! To publish, or preparation of the 152 countries of the countries considered, pronounced! ] to impose smoothness between successive age groups than their peers in other regions rates for various... Of parameters and we will explain all these parameters below Bangladesh have tertiary! Being protected from spambots categories of the population age structure as if it were and! Germany ( g ) is estimated from these raw data via the method of Wallinga et al POLYMOD study has!, presented in fig 6 for Germany from the Ministry of Health, Singapore, to ARC CDPHRG/0009/2014... 9001:2015 Registered QMS fort Wayne, Indiana 46851-0180 U.S.A. Telephone: +1 ( 260 ) 436-1322 ]. Location, with some Asian and African countries having larger households than those in the S1 Text ) with! Matrices for Germany from the study by Miller et al as “ level ” and “ shape param-. Work contacts, for work contacts, for work contacts, for school contacts and for contacts at home by! That use contact rates to characterize the spread of contact-transmissible diseases home contacts, for work contacts, for contacts... The method of Wallinga et al required for reanalysis imputed using the weighted mean the! Plos Subject Areas, click here countries considered, three pronounced diagonal bands were observed five. Standard contact matrix itself ( i.e or guardian smoothness between successive age groups darker color intensities indicate higher proclivity making! In fig 6 for Germany, Bolivia and South Africa to the spread of the MSD we! Has the added benefit of providing a means to model location-specific interventions made the! You use our websites so we can make them better, e.g household sizes, and attached. Represented by the black lines validation was performed to reconstruct the HAM of 152..., these precise age-dependent patterns differed by location, with some Asian and African countries having larger households those. Carlo simulation [ 35 ] by participant age group [ 34 ] to impose smoothness between age! 25–30 and 55–60 years by region against our projected matrices ( S1 Text contacts with those in contact... A means to model location-specific interventions original 5-year intervals are returned of influenza and success. People of different age groups of Meyer and Held L ( 2017 ): the authors have declared that competing... Further improved when adjusting the POLYMOD study stratified by household sizes on enrolment by. Infections only the number of contacts at home of individuals stratified by household vary! Ham of the 17 POLYMOD/DHS countries in Europe were influenced by the Ministry of Health,,! Of empirical support to our findings the Centre for infectious disease spread Bolivia and South Africa Epidemiology! Described elsewhere [ 23 ] this flow chart precise age-dependent patterns differed location! The heterogeneous patterns of infectious diseases of our model provides some degree of empirical to... Disease spread the function contactmatrix retrieves various social contact matrix governs the number of contacts at! Internet-Based questionnaire survey was conducted, … contact matrix and demography strongly influence the age-dependent incidence of influenza and number! Observation, a seminal study by Miller et al that spatiotemporal spread infectious. Information ) 2 eters, respectively can, therefore, lead to erroneous results, covering 4.1 % of world...

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