key: cord-0777053-g1rvdxqm authors: Thindwa, D.; Jambo, K. C.; Ojal, J.; MacPherson, P.; Phiri, M. D.; Khundi, M.; Chiume, L.; Gallagher, K.; HEYDERMAN, R. S.; Corbett, E. L.; French, N.; Flasche, S. title: Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi. date: 2021-12-17 journal: nan DOI: 10.1101/2021.12.16.21267959 sha: 83bd7eddaaffc7f3e0e4e23919acd6d78027f382 doc_id: 777053 cord_uid: g1rvdxqm Introduction: Understanding human mixing patterns relevant to infectious diseases spread through close contact is vital for modelling transmission dynamics and optimisation of disease control strategies. Mixing patterns in low-income countries like Malawi are not well understood. Methodology: We conducted a social mixing survey in urban Blantyre, Malawi between April and July 2021 (between the 2nd and 3rd wave of COVID-19 infections). Participants living in densely-populated neighbourhoods were randomly sampled and, if they consented, reported their physical and non-physical contacts within and outside homes lasting at least 5 minutes during the previous day. Age-specific mixing rates were calculated, and a negative binomial mixed effects model was used to estimate determinants of contact behaviour. Results: Of 1,201 individuals enrolled, 702 (58.5%) were female, the median age was 15 years (interquartile range [IQR] 5-32) and 127 (10.6%) were HIV-positive. On average, participants reported 10.3 contacts per day (range: 1-25). Mixing patterns were highly age-assortative, particularly those within the community and with skin-to-skin contact. Adults aged 20-49y reported the most contacts (median:11, IQR: 8-15) of all age groups; 38% (95%CI: 16-63) more than infants (median: 8, IQR: 5-10), who had the least contacts. Household contact frequency increased by 3% (95%CI 2-5) per additional household member. Unemployed participants had 15% (95%CI: 9-21) fewer contacts than other adults. Among long range (>30 meters away from home) contacts, secondary school children had the largest median contact distance from home (257m, IQR 78-761). HIV-positive status in adults >18 years-old was not associated with increased contact patterns (1%, 95%CI -9-12). During this period of relatively low COVID-19 incidence in Malawi, 301 (25.1%) individuals stated that they had limited their contact with others due to COVID-19 precautions; however, their reported contacts were not fewer (8%, 95%CI 1-13). Conclusion: In urban Malawi, contact rates, are high and age-assortative, with little behavioural change due to either HIV-status or COVID-19 circulation. This highlights the limits of contact-restriction-based mitigation strategies in such settings and the need for pandemic preparedness to better understand how contact reductions can be enabled and motivated. Keywords: Social contacts, Transmission, Mixing data, Infectious disease, Malawi, Africa Social mixing studies in middle (MICs) and high (HICs) income countries have shown that 85 individuals in the same age groups tend to have higher contact rates than with other age 86 groups (age-assortative mixing) 7,8 , yet not much is known about contact patterns in LICs in 87 the era of fairly high urbanisation [12] [13] [14] . Intergenerational mixing between younger children 88 and adults was evident in Zimbabwe, reflecting parental or guardian roles played by adults 89 13 , though age-sex mixing patterns are not well knowm 12, 13 . Commonly, people tend to make 90 high number of contacts within a short distance of their homes, with this being most 91 pronounced for people living close to their usual place of work 9, 15 . Where commuting long 92 distances to work is common through mass transport, outbreak containment becomes more is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Age-stratified contact matrices were generated to investigate interactions between age 212 groups. Age-specific contact rates through contact matrices were constructed from the mean 213 number of daily contacts between participants and their contacts using the 'socialmixr' R 214 package 33 . Age-based contact matrices were estimated based on the ratio of the measured 215 probability of a contact event between individuals based on age group to a null model of the 216 probability of that contact event under an assumption of random mixing. Contact probabilities under the null model were determined by proportion of the population in each 218 given age category in Ndirande 24,30 . Our analyses were weighted by days of the week as 219 well as reciprocity in contact patterns such that the total number of contacts from age group 220 to were equal to the total number of contacts from age group to ( = ), where 221 . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint reported indoor cooking, and of which 23 (11.5%) were not well ventilated ( Figure S1 ). is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. ; is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint A total of 301 (25.1%) participants, almost exclusively adults, reported to have reduced their 297 social contacts due to COVID-19 pandemic, with home (n=225, 74.8%) and market (n=183, 298 60.8%) being the main localities where contact was reportedly reduced. Among all 299 participants, we estimated that preventive measures against the COVID-19 pandemic 300 contributed 9.1% (95%CI 0-13) to social contacts reduction e.g. from the median of 11 (IQR 301 7-18) daily contacts, actual and hypothesised (contacts that could have occured in absence 302 of COVID-19 pandemic), to 10 (IQR 7-13) actual contacts. However, actual contacts of those 303 affected by COVID-19 were 8% (95% CI: 1-13) higher than their counterparts who reported 304 no COVID-19 reduced social contacts (Table 1, Figure S2 , Figure S3 ). 305 306 Table 1 . Characteristics of participants and their reported daily in Blantyre, Malawi, April-July 2021. The relative numbers of daily contacts (contacts rate ratio, CRR) were obtained from a negative binomial mixed model. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. ; https://doi.org/10.1101/2021.12.16.21267959 doi: medRxiv preprint More than 95% (12,136/12,540) of all contacts happened within than outside the 316 community ( Figure 2) . 317 318 Data on spatial distances between participant house and place of mixing was available for is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint Figure S4 , Figure S5 ). . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. ; https://doi.org/10.1101/2021.12.16.21267959 doi: medRxiv preprint mobility and trading activities on social contacts 16 , which in part has motivated lockdowns in 421 some MICs and HICs during the COVID-19 pandemic 39 . Increasing number of contacts with 422 house size has also been reported in some MICs and HICs 7 , with household density 423 suggested to be a driving factor particularly in this setting where extended families sharing a 424 compound is common. We also report higher proportion of home contacts similar to other 425 LICs and MICs than those reported in HICs, and by contrast, the proportion of school and 426 work contacts were substantially lower than those in HICs 7 . This implies that household may 427 be a key site of transmission for respiratory diseases 40 , and public preventive measures 428 may only be efficacious at reducing the speed for spatial spread outside homes. However, 429 the relevance of contact location on transmission will also depend on, among other things, 430 specific pathogen and transmission routes e.g. droplet, fomite or aerosol 7 . The strong age-assortative contacts in this study are consistent with widespread evidence is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint In conclusion, high rates of physical, age-assortative and localised contacts were observed, is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. The daily average rate of mixing between different age groups comparing participants who reported their social contact behaviour being affected and not affected by COVID-19 pandemic for all the contact events (A); physical contact events (B); and non-physical contact events (C). The number in each cell represents the daily mean number of contact events between two given age groups, corrected for mixing reciprocity between participants and contacts and weighted by day of the week. The assortativity index Q quantifies the weight of mixing between individuals of the same age groups. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint The copyright holder for this this version posted December 17, 2021. ; https://doi.org/10.1101/2021.12.16.21267959 doi: medRxiv preprint Social Mixing Patterns Within a South African Township 573 Community: Implications for Respiratory Disease Transmission and Control Characteristics of human encounters and social mixing 576 patterns relevant to infectious diseases spread by close contact: a survey in Southwest 577 Associations between ethnicity, social contact, and pneumococcal 579 carriage three years post-PCV10 in Fiji Age-and Sex-Specific Social Contact Patterns and Incidence of 581 Mycobacterium tuberculosis Infection Social Contact Structures and Time Use Patterns in the Manicaland 583 Province of Zimbabwe Social contacts and other risk factors for respiratory infections 585 among internally displaced people in Somaliland Close encounters of 589 the infectious kind: methods to measure social mixing behaviour Travel Patterns in China The impact of COVID-19 control measures on social contacts and 593 transmission in Kenyan informal settlements Rapid review of social contact patterns during the COVID-19 pandemic CoMix: Changes in social contacts as measured by the contact survey 599 during the COVID-19 pandemic in England between A model and predictions for COVID-19 604 considering population behavior and vaccination Disparities in COVID-19 Vaccination among Low The Mediating Role of Vaccination Policy. 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Malawi Population and Housing Census I will finally ask you to recall who you were in contact with between now and yesterday? I will ask this for each of places you listed previously. Now I am only interested in your direct contacts. These are individuals with who you spent 5 mins, and with whom you spoke 3 words. For each of contact. I would like to know their age in years, sex, your relationship to him/her, where the contact happened, how often you contact this person in general, and the total time spent with this person in that place. I would also like to know whether contact was physical or nonphysical. Nonphysical contact happens when you haven't touched the person. Physical contact includes hand shaking, embracing, kissing, and sharing a bike, and also sharing a glass or other utensils passed directly from mouth to mouth. I only ask for contact initials to help remember the contact, but will delete the information at the end of the interview. If you had contact with same person in multiple settings, I will record these multiple times, once for each setting. If