Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi. (preprint)

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

A prospective diagnostic evaluation of accuracy of self-taken and healthcare worker-taken swabs for rapid COVID-19 testing (preprint)

ObjectivesTo compare self-taken and healthcare worker (HCW)-taken throat/nasal swabs to perform rapid diagnostic tests (RDT) for SARS-CoV-2, and how these compare to RT-PCR. We hypothesised that self-taken samples are non-inferior for use with RDTs and in clinical and research settings could have substantial individual and public health benefit. DesignA prospective diagnostic accuracy evaluation as part of the Facilitating Accelerated Clinical Evaluation of Novel Diagnostic Tests for COVID -19 (FALCON C-19), workstream C (undifferentiated community testing). SettingNHS Test and Trace drive-through community PCR testing site (Liverpool, UK). Participants Eligible participants 18 years or older with symptoms of COVID-19. 250 participants recruited; one withdrew before analysis. SamplingSelf-administered throat/nasal swab for the Covios(R) RDT, a trained HCW taken throat/nasal sample for PCR and HCW comparison throat/nasal swab for RDT. Main outcome measuresSensitivity, specificity, and positive and negative predictive values (PPV, NPV) were calculated; comparisons between self-taken and HCW-taken samples used McNemars test. ResultsSeventy-five participants (75/249, 30.1%) were positive by RT-PCR. RDTs with self-taken swabs had a sensitivity of 90.5% (67/74, 95% CI: 83.9-97.2), compared to 78.4% (58/74, 95% CI: 69.0-87.8) for HCW-taken swabs (absolute difference 12.2%, 95% CI: 4.7-19.6, p=0.003). Specificity for self-taken swabs was 99.4% (173/174, 95% CI: 98.3-100.0), versus 98.9% (172/174, 95% CI: 97.3-100.0) for HCW-taken swabs (absolute difference 0.6%, 95% CI: 0.5-1.7, p=0.317). The PPV of self-taken RDTs (98.5%, 67/68, 95% CI: 95.7-100.0) and HCW-taken RDTs (96.7%, 58/60, 95% CI 92.1-100.0) were not significantly different (p=0.262). However, the NPV of self-taken swab RDTs was significantly higher (96.1%, 173/180, 95% CI: 93.2-98.9) than HCW-taken RDTs (91.5%, 172/188, 95% CI 87.5-95.5, p=0.003). ConclusionSelf-taken swabs for COVID-19 testing offer substantial individual benefits in terms of convenience, accuracy, and reduced risk of transmitting infection. Our results demonstrate that self-taken throat/nasal samples can be used by lay individuals as part of rapid testing programmes for symptomatic adults. Trial RegistrationIRAS ID:28422, clinical trial ID: NCT04408170 SummaryO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIRapid diagnostic tests (RDTs)for SARS-CoV-2 Ag are a cheaper point-of-care alternative to RT-PCR for diagnosing COVID-19 disease. C_LIO_LIThe accuracy of tests can vary dependent on sampling technique, test processing and reading of results. C_LI What this study adds?O_LISelf-taken throat-nasal swabs for RDTs can be used by symptomatic adults to give reliable results to diagnose SARS-CoV-2. C_LIO_LISelf-sampling can be implemented with little training and no assistance. C_LI

Impact of COVID-19 on tuberculosis notifications in Blantyre Malawi: an interrupted time series analysis and qualitative study with healthcare workers (preprint)

COVID-19 may impact on tuberculosis (TB) diagnosis and care. We analysed a city-wide electronic TB register in Blantyre, Malawi and interviewed TB officers. Malawi had no official "lockdown" but closed schools and borders on 23-March 2020. In interrupted time series analysis, there was an immediate 35.9% reduction in TB notifications (95% CI 22.0 to 47.3%) in April, which recovered to near pre-pandemic numbers by December 2020, but with 333 (95% CI 291 to 375) fewer cumulative notifications than anticipated. Women and girls were impacted (30.7% fewer cases, 95% CI 28.4 to 33.0%) more than men and boys (20.9% fewer, 95% CI 18.5 to 23.3). Fear of COVID-19 infection, temporary facility closure, inadequate protective equipment and COVID-19 stigma with similar presenting symptoms to TB were mentioned. Public health measures could benefit both TB and COVID-19, but only if diagnostic services remain accessible and are considered safe to attend.