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1.
Epidemics ; 40: 100590, 2022 Jun 08.
Article in English | MEDLINE | ID: covidwho-1881988

ABSTRACT

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 known. 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 min 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 1201 individuals enroled, 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 20-49 y 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 m away from home) contacts, secondary school children had the largest median contact distance from home (257 m, IQR 78-761). HIV-positive status in adults >=18 years-old was not associated with changed contact patterns (rate ratio: 1.01, 95%CI: (0.91-1.12)). 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 8% (95%CI: 1-13) higher. CONCLUSION: In urban Malawi, contact rates, are high and age-assortative, with little reported 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.

2.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-296965

ABSTRACT

Objectives To 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. Design A 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)’. Setting NHS 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. Sampling Self-administered throat/nasal swab for the Covios® RDT, a trained HCW taken throat/nasal sample for PCR and HCW comparison throat/nasal swab for RDT. Main outcome measures Sensitivity, specificity, and positive and negative predictive values (PPV, NPV) were calculated;comparisons between self-taken and HCW-taken samples used McNemar’s test. Results Seventy-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). Conclusion Self-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 Registration IRAS ID:28422, clinical trial ID: NCT04408170 Summary What is already known on this topic? Rapid diagnostic tests (RDTs)for SARS-CoV-2 Ag are a cheaper point-of-care alternative to RT-PCR for diagnosing COVID-19 disease. The accuracy of tests can vary dependent on sampling technique, test processing and reading of results. What this study adds? Self-taken throat-nasal swabs for RDTs can be used by symptomatic adults to give reliable results to diagnose SARS-CoV-2. Self-sampling can be implemented with little training and no assistance.

3.
One Health ; 13: 100319, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1377426

ABSTRACT

BACKGROUND: Human-to-animal transmission of M. tuberculosis (Mtb) is reported in South Africa but there is a paucity of epidemiological data. The aim of this One Health manuscript is to describe zooanthroponotic exposure of domestic animals to TB patients, virtually all of whom had laboratory confirmed pulmonary Mtb disease. METHODS: This cross-sectional study was nested within two TB contact tracing studies and collected data from 2017 to 2019. TB index patients and their households in three provinces of South Africa were recruited. A questionnaire was administered to households, assessing type and number of animals owned, degree of exposure of animals to humans, and veterinary consultations. For this analysis, we compared descriptive variables by animal-keeping status (animal-keeping vs non-animal keeping households), calculated the chi square and respective p-values. RESULTS: We visited 1766 households with at least one confirmed case of TB, 33% (587/1766) had livestock or companion animals. Of non-animal-owning households, 2% (27/1161) cared for other community members' livestock. Few (16%, 92/587) households kept animals in their dwelling overnight, while 45% (266/587) kept animals outside the home, but within 10 m of where people slept and ate. Most (81%, 478/587) of people in animal-owning households were willing for their animal/s to have a TB skin test, but <1% (5/587) of animals had been skin-tested; 4% (24/587) of animal-owning households had a veterinary consultation in the past six months, and 5% (31/587) reported one of their animals dying from natural causes in the prior six months. CONCLUSION: Our survey suggests that a high proportion of patients with TB live in settings facilitating close contact with domestic animal species with known susceptibility to Mtb. There is a substantial exposure of household animals to patients with TB and therefore risk of both transmission to, and spillback from animals to humans.

4.
Emerg Infect Dis ; 27(7): 1831-1839, 2021 07.
Article in English | MEDLINE | ID: covidwho-1278364

ABSTRACT

The coronavirus disease (COVID-19) pandemic might affect tuberculosis (TB) diagnosis and patient care. We analyzed a citywide electronic TB register in Blantyre, Malawi and interviewed TB officers. Malawi did not have an official COVID-19 lockdown but closed schools and borders on March 23, 2020. In an interrupted time series analysis, we noted an immediate 35.9% reduction in TB notifications in April 2020; notifications recovered to near prepandemic numbers by December 2020. However, 333 fewer cumulative TB notifications were received than anticipated. Women and girls were affected more (30.7% fewer cases) than men and boys (20.9% fewer cases). Fear of COVID-19 infection, temporary facility closures, inadequate personal protective equipment, and COVID-19 stigma because of similar symptoms to TB were mentioned as reasons for fewer people being diagnosed with TB. Public health measures could benefit control of both TB and COVID-19, but only if TB diagnostic services remain accessible and are considered safe to attend.


Subject(s)
COVID-19 , Tuberculosis , Communicable Disease Control , Female , Humans , Malawi/epidemiology , Male , Pandemics , SARS-CoV-2 , Tuberculosis/diagnosis , Tuberculosis/epidemiology
6.
F1000Res ; 9: 671, 2020.
Article in English | MEDLINE | ID: covidwho-808823

ABSTRACT

Institutions such as hospitals and nursing or long-stay residential homes accommodate individuals at considerable risk of mortality should they acquire SARS-CoV-2 infection. In these settings, polymerase chain reaction tests play a central role in infection prevention and control. Here, we argue that both false negative and false positive tests are possible and that careful consideration of the prior probability of infection and of test characteristics are needed to prevent harm. We outline evidence suggesting that regular systematic testing of asymptomatic and pre-symptomatic individuals could play an important role in reducing transmission of SARS-CoV-2 within institutions. We discuss how such a programme might be organised, arguing that frequent testing and rapid reporting of results are particularly important. We highlight studies demonstrating that polymerase chain reaction testing of pooled samples can be undertaken with acceptable loss of sensitivity, and advocate such an approach where test capacity is limited. We provide an approach to calculating the most efficient pool size. Given the current limitations of tests for SARS-CoV-2 infection, physical distancing and meticulous infection prevention and control will remain essential in institutions caring for vulnerable people.


Subject(s)
Coronavirus Infections/diagnosis , Pneumonia, Viral/diagnosis , Polymerase Chain Reaction , Betacoronavirus , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques , False Negative Reactions , False Positive Reactions , Hospitals , Humans , Nursing Homes , Pandemics , SARS-CoV-2
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