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2.
Sci Rep ; 11(1): 24171, 2021 12 17.
Article in English | MEDLINE | ID: covidwho-1593554

ABSTRACT

The transmission of COVID-19 is dependent on social mixing, the basic rate of which varies with sociodemographic, cultural, and geographic factors. Alterations in social mixing and subsequent changes in transmission dynamics eventually affect hospital admissions. We employ these observations to model and predict regional hospital admissions in Sweden during the COVID-19 pandemic. We use an SEIR-model for each region in Sweden in which the social mixing is assumed to depend on mobility data from public transport utilisation and locations for mobile phone usage. The results show that the model could capture the timing of the first and beginning of the second wave of the pandemic 3 weeks in advance without any additional assumptions about seasonality. Further, we show that for two major regions of Sweden, models with public transport data outperform models using mobile phone usage. We conclude that a model based on routinely collected mobility data makes it possible to predict future hospital admissions for COVID-19 3 weeks in advance.


Subject(s)
Algorithms , COVID-19/transmission , Cell Phone/statistics & numerical data , Hospitalization/statistics & numerical data , Models, Theoretical , Patient Admission/statistics & numerical data , COVID-19/epidemiology , COVID-19/virology , Disease Transmission, Infectious/statistics & numerical data , Forecasting/methods , Geography , Hospitalization/trends , Humans , Pandemics/prevention & control , Patient Admission/trends , Retrospective Studies , SARS-CoV-2/physiology , Sweden/epidemiology , Travel/statistics & numerical data
3.
Int J Environ Res Public Health ; 18(24)2021 12 20.
Article in English | MEDLINE | ID: covidwho-1599165

ABSTRACT

Increasing numbers of people living with dementia (PLWD), and a pressured health and social care system, will exacerbate inequalities in mortality for PLWD. There is a dearth of research examining multiple factors in mortality risk among PLWD, including application of large administrative datasets to investigate these issues. This study explored variation mortality risk variation among people diagnosed with dementia between 2002-2016, based on: age, sex, ethnicity, deprivation, geography and general practice (GP) contacts. Data were derived from electronic health records from a cohort of Clinical Practice Research Datalink GP patients in England (n = 142,340). Cox proportional hazards regression modelled mortality risk separately for people with early- and later- onset dementia. Few social inequalities were observed in early-onset dementia; men had greater risk of mortality. For early- and later-onset, higher rates of GP observations-and for later-onset only dementia medications-are associated with increased mortality risk. Social inequalities were evident in later-onset dementia. Accounting for other explanatory factors, Black and Mixed/Other ethnicity groups had lower mortality risk, more deprived areas had greater mortality risk, and higher mortality was observed in North East, South Central and South West GP regions. This study provides novel evidence of the extent of mortality risk inequalities among PLWD. Variance in mortality risk was observed by social, demographic and geographic factors, and frequency of GP contact. Findings illustrate need for greater person-centred care discussions, prioritising tackling inequalities among PLWD. Future research should explore more outcomes for PLWD, and more explanatory factors of health outcomes.


Subject(s)
Dementia , Cohort Studies , Demography , Geography , Humans , Male , Socioeconomic Factors
4.
PLoS One ; 16(12): e0260051, 2021.
Article in English | MEDLINE | ID: covidwho-1596447

ABSTRACT

OBJECTIVES: To model the risk of COVID-19 mortality in British care homes conditional on the community level risk. METHODS: A two stage modeling process ("doubly latent") which includes a Besag York Mollie model (BYM) and a Log Gaussian Cox Process. The BYM is adopted so as to estimate the community level risks. These are incorporated in the Log Gaussian Cox Process to estimate the impact of these risks on that in care homes. RESULTS: For an increase in the risk at the community level, the number of COVID-19 related deaths in the associated care home would be increased by exp (0.833), 2. This is based on a simulated dataset. In the context of COVID-19 related deaths, this study has illustrated the estimation of the risk to care homes in the presence of background community risk. This approach will be useful in facilitating the identification of the most vulnerable care homes and in predicting risk to new care homes. CONCLUSIONS: The modeling of two latent processes have been shown to be successfully facilitated by the use of the BYM and Log Gaussian Cox Process Models. Community COVID-19 risks impact on that of the care homes embedded in these communities.


Subject(s)
COVID-19/epidemiology , Nursing Homes/statistics & numerical data , Residence Characteristics , Geography , Humans , Models, Statistical , Risk Factors
5.
Sci Rep ; 11(1): 23378, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1585808

ABSTRACT

Emissions of black carbon (BC) particles from anthropogenic and natural sources contribute to climate change and human health impacts. Therefore, they need to be accurately quantified to develop an effective mitigation strategy. Although the spread of the emission flux estimates for China have recently narrowed under the constraints of atmospheric observations, consensus has not been reached regarding the dominant emission sector. Here, we quantified the contribution of the residential sector, as 64% (44-82%) in 2019, using the response of the observed atmospheric concentration in the outflowing air during Feb-Mar 2020, with the prevalence of the COVID-19 pandemic and restricted human activities over China. In detail, the BC emission fluxes, estimated after removing effects from meteorological variability, dropped only slightly (- 18%) during Feb-Mar 2020 from the levels in the previous year for selected air masses of Chinese origin, suggesting the contributions from the transport and industry sectors (36%) were smaller than the rest from the residential sector (64%). Carbon monoxide (CO) behaved differently, with larger emission reductions (- 35%) in the period Feb-Mar 2020, suggesting dominance of non-residential (i.e., transport and industry) sectors, which contributed 70% (48-100%) emission during 2019. The estimated BC/CO emission ratio for these sectors will help to further constrain bottom-up emission inventories. We comprehensively provide a clear scientific evidence supporting mitigation policies targeting reduction in residential BC emissions from China by demonstrating the economic feasibility using marginal abatement cost curves.


Subject(s)
Air Pollutants/analysis , Air Pollution/analysis , COVID-19/prevention & control , Particulate Matter/analysis , SARS-CoV-2/isolation & purification , Soot/analysis , Algorithms , Atmosphere/analysis , COVID-19/epidemiology , COVID-19/virology , China , Climate Change , Environmental Monitoring/methods , Environmental Monitoring/statistics & numerical data , Geography , Human Activities , Humans , Models, Theoretical , Pandemics , Residence Characteristics , SARS-CoV-2/physiology , Seasons , Wind
6.
Sci Rep ; 11(1): 24124, 2021 12 16.
Article in English | MEDLINE | ID: covidwho-1585805

ABSTRACT

The quantification of spreading heterogeneity in the COVID-19 epidemic is crucial as it affects the choice of efficient mitigating strategies irrespective of whether its origin is biological or social. We present a method to deduce temporal and individual variations in the basic reproduction number directly from epidemic trajectories at a community level. Using epidemic data from the 98 districts in Denmark we estimate an overdispersion factor k for COVID-19 to be about 0.11 (95% confidence interval 0.08-0.18), implying that 10 % of the infected cause between 70 % and 87 % of all infections.


Subject(s)
Algorithms , Basic Reproduction Number/statistics & numerical data , COVID-19/transmission , Models, Theoretical , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/virology , Denmark/epidemiology , Epidemics/prevention & control , Geography , Humans , SARS-CoV-2/physiology
7.
Sci Rep ; 11(1): 24145, 2021 12 17.
Article in English | MEDLINE | ID: covidwho-1585802

ABSTRACT

Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46-7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.


Subject(s)
Alphacoronavirus/genetics , Betacoronavirus/genetics , COVID-19/transmission , Chiroptera/growth & development , SARS-CoV-2/genetics , Alphacoronavirus/classification , Animals , Asia, Southeastern/epidemiology , Betacoronavirus/classification , COVID-19/epidemiology , COVID-19/virology , Cambodia/epidemiology , Chiroptera/classification , Chiroptera/virology , Epidemics/prevention & control , Evolution, Molecular , Genome, Viral/genetics , Geography , Humans , Longitudinal Studies , Male , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/physiology , Species Specificity
8.
BMC Res Notes ; 14(1): 468, 2021 Dec 24.
Article in English | MEDLINE | ID: covidwho-1582017

ABSTRACT

OBJECTIVE: The proliferation of false information on COVID-19 mostly through social media is adversely affecting control efforts. The objective of this study was to identify areas where targeted effective messaging can be useful in demystifying misinformation against COVID-19. RESULTS: The study showed high levels of misinformation on COVID-19 in the study area [mean score 2.71; standard deviation (SD) 1.5]. The highest levels of misinformation were observed in Dr. Ruth Segomotsi Mompati district, North West province (mean score: 3.84; SD: 2.1) and Sedibeng district, Gauteng province (mean score: 3.56; SD 1.7). Higher levels of misinformation were reported by those aged 18-24 years (mean score: 3.48; SD: 1.8), and men (mean score: 2.73; SD: 1.8). Across the two provinces, we identified geospatial hot and coldspots of misinformation highlighting the need to implement point of care strategies such as targeted messaging. Findings showed the need for targeted interventions to young people, students, those with low levels of education and the self-employed in the two districts more importantly, as South Africa expands its nationwide vaccination roll-out.


Subject(s)
COVID-19 , Adolescent , Communication , Geography , Humans , Male , SARS-CoV-2 , South Africa
9.
Elife ; 102021 10 15.
Article in English | MEDLINE | ID: covidwho-1518778

ABSTRACT

Simulating nationwide realistic individual movements with a detailed geographical structure can help optimise public health policies. However, existing tools have limited resolution or can only account for a limited number of agents. We introduce Epidemap, a new framework that can capture the daily movement of more than 60 million people in a country at a building-level resolution in a realistic and computationally efficient way. By applying it to the case of an infectious disease spreading in France, we uncover hitherto neglected effects, such as the emergence of two distinct peaks in the daily number of cases or the importance of local density in the timing of arrival of the epidemic. Finally, we show that the importance of super-spreading events strongly varies over time.


Subject(s)
COVID-19/epidemiology , Communicable Diseases/epidemiology , Epidemics/statistics & numerical data , Geography/methods , Public Health/methods , France/epidemiology , Humans , Public Health/instrumentation , Spatial Analysis
10.
PLoS One ; 16(11): e0259990, 2021.
Article in English | MEDLINE | ID: covidwho-1518365

ABSTRACT

BACKGROUND: COVID-19 vaccination in many countries, including England, has been prioritised primarily by age. However, people of the same age can have very different health statuses. Frailty is a commonly used metric of health and has been found to be more strongly associated with mortality than age among COVID-19 inpatients. METHODS: We compared the number of first vaccine doses administered across the 135 NHS Clinical Commissioning Groups (CCGs) of England to both the over 50 population and the estimated frail population in each area. Area-based frailty estimates were generated using the English Longitudinal Survey of Ageing (ELSA), a national survey of older people. We also compared the number of doses to the number of people with other risk factors associated with COVID-19: atrial fibrillation, chronic kidney disease, diabetes, learning disabilities, obesity and smoking status. RESULTS: We estimate that after 79 days of the vaccine program, across all Clinical Commissioning Group areas, the number of people who received a first vaccine per frail person ranged from 4.4 (95% CI 4.0-4.8) and 20.1 (95% CI 18.3-21.9). The prevalences of other risk factors were also poorly associated with the prevalence of vaccination across England. CONCLUSIONS: Vaccination with age-based priority created area-based inequities in the number of doses administered relative to the number of people who are frail or have other risk factors associated with COVID-19. As frailty has previously been found to be more strongly associated with mortality than age for COVID-19 inpatients, an age-based priority system may increase the risk of mortality in some areas during the vaccine roll-out period. Authorities planning COVID-19 vaccination programmes should consider the disadvantages of an age-based priority system.


Subject(s)
COVID-19 Vaccines/immunology , Vaccination , COVID-19/epidemiology , COVID-19/immunology , Dose-Response Relationship, Immunologic , England/epidemiology , Geography , Humans , Prevalence , Risk Factors
11.
Soc Sci Med ; 288: 114370, 2021 11.
Article in English | MEDLINE | ID: covidwho-1517472

Subject(s)
Rivers , Geography , Humans
12.
Sci Rep ; 11(1): 21783, 2021 11 08.
Article in English | MEDLINE | ID: covidwho-1506845

ABSTRACT

To reduce the spread and the effect of the COVID-19 global pandemic, non-pharmaceutical interventions have been adopted on multiple occasions by governments. In particular lockdown policies, i.e., generalized mobility restrictions, have been employed to fight the first wave of the pandemic. We analyze data reflecting mobility levels over time in Italy before, during and after the national lockdown, in order to assess some direct and indirect effects. By applying methodologies based on percolation and network science approaches, we find that the typical network characteristics, while very revealing, do not tell the whole story. In particular, the Italian mobility network during lockdown has been damaged much more than node- and edge-level metrics indicate. Additionally, many of the main Provinces of Italy are affected by the lockdown in a surprisingly similar fashion, despite their geographical and economic dissimilarity. Based on our findings we offer an approach to estimate unavailable high-resolution economic dimensions, such as real time Province-level GDP, based on easily measurable mobility information.


Subject(s)
COVID-19/epidemiology , Communicable Disease Control/legislation & jurisprudence , Physical Distancing , Algorithms , COVID-19/therapy , Geography , Humans , Italy/epidemiology , Models, Economic , Public Health Informatics , Travel
13.
PLoS One ; 16(11): e0257548, 2021.
Article in English | MEDLINE | ID: covidwho-1506154

ABSTRACT

BACKGROUND: The transmission dynamics of SARS-CoV-2 varies depending on social distancing measures, circulating SARS-CoV-2 variants, host factors and other environmental factors. We sought to investigate the clinical and epidemiological characteristics of a SARS-CoV-2 outbreak that occurred in a highly dense population area in Colombo, Sri Lanka from April to May 2020. METHODOLOGY/PRINCIPAL FINDINGS: We carried out RT-qPCR for SARS-CoV2, assessed the SARS-CoV-2 specific total and neutralizing antibodies (Nabs) in a densely packed, underserved settlement (n = 2722) after identification of the index case on 15th April 2020. 89/2722 individuals were detected as infected by RT-qPCR with a secondary attack rate among close contacts being 0.077 (95% CI 0.063-0.095). Another 30 asymptomatic individuals were found to have had COVID-19 based on the presence of SARS-CoV-2 specific antibodies. However, only 61.5% of those who were initially seropositive for SARS-CoV-2 had detectable total antibodies at 120 to 160 days, while only 40.6% had detectable Nabs. 74/89 (83.1%) of RT-qPCR positive individuals were completely asymptomatic and all 15 (16.9%) who experienced symptoms were classified as having a mild illness. 18 (20.2%) were between the ages of 61 to 80. 11/89 (12.4%) had diabetes, 8/89 (9%) had cardiovascular disease and 4 (4.5%) had asthma. Of the two viruses that were sequenced and were of the B.1 and B.4 lineages with one carrying the D614G mutation. DISCUSSION/CONCLUSION: Almost all infected individuals developed mild or asymptomatic illness despite the presence of comorbid illnesses. Since the majority of those who were in this underserved settlement were not infected despite circulation of the D614G variant, it would be important to further study environmental and host factors that lead to disease severity and transmission.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Population Surveillance , Adolescent , Adult , Aged , Aged, 80 and over , Antibodies, Neutralizing , Antibodies, Viral , Child , Child, Preschool , Disease Outbreaks , Female , Geography , Humans , Infant , Male , Middle Aged , Prospective Studies , RNA, Viral , SARS-CoV-2 , Sri Lanka/epidemiology , Young Adult
14.
PLoS One ; 16(11): e0259257, 2021.
Article in English | MEDLINE | ID: covidwho-1504723

ABSTRACT

Protective behaviors such as mask wearing and physical distancing are critical to slow the spread of COVID-19, even in the context of vaccine scale-up. Understanding the variation in self-reported COVID-19 protective behaviors is critical to developing public health messaging. The purpose of the study is to provide nationally representative estimates of five self-reported COVID-19 protective behaviors and correlates of such behaviors. In this cross-sectional survey study of US adults, surveys were administered via internet and telephone. Adults were surveyed from April 30-May 4, 2020, a time of peaking COVID-19 incidence within the US. Participants were recruited from the probability-based AmeriSpeak® national panel. Brief surveys were completed by 994 adults, with 73.0% of respondents reported mask wearing, 82.7% reported physical distancing, 75.1% reported crowd avoidance, 89.8% reported increased hand-washing, and 7.7% reported having prior COVID-19 testing. Multivariate analysis (p critical value .05) indicates that women were more likely to report protective behaviors than men, as were those over age 60. Respondents who self-identified as having low incomes, histories of criminal justice involvement, and Republican Party affiliation, were less likely to report four protective behaviors, though Republicans and individuals with criminal justice histories were more likely to report having received COVID-19 testing. The majority of Americans engaged in COVID-19 protective behaviors, with low-income Americans, those with histories of criminal justice involvement, and self-identified Republicans less likely to engage in these preventive behaviors. Culturally competent public health messaging and interventions might focus on these latter groups to prevent future infections. These findings will remain highly relevant even with vaccines widely available, given the complementarities between vaccines and protective behaviors, as well as the many challenges in delivering vaccines.


Subject(s)
COVID-19 Testing , COVID-19 Vaccines , COVID-19/epidemiology , COVID-19/prevention & control , Hand Disinfection , Masks , Adolescent , Adult , Aged , Communicable Disease Control , Cross-Sectional Studies , Female , Geography , Health Behavior , Humans , Infectious Disease Medicine/methods , Internet , Male , Middle Aged , Multivariate Analysis , Poverty , Probability , SARS-CoV-2 , Surveys and Questionnaires , United States/epidemiology , Young Adult
15.
Sci Rep ; 11(1): 21715, 2021 11 05.
Article in English | MEDLINE | ID: covidwho-1504467

ABSTRACT

Prediction of complex epidemiological systems such as COVID-19 is challenging on many grounds. Commonly used compartmental models struggle to handle an epidemiological process that evolves rapidly and is spatially heterogeneous. On the other hand, machine learning methods are limited at the beginning of the pandemics due to small data size for training. We propose a deep learning approach to predict future COVID-19 infection cases and deaths 1 to 4 weeks ahead at the fine granularity of US counties. The multi-variate Long Short-term Memory (LSTM) recurrent neural network is trained on multiple time series samples at the same time, including a mobility series. Results show that adding mobility as a variable and using multiple samples to train the network improve predictive performance both in terms of bias and of variance of the forecasts. We also show that the predicted results have similar accuracy and spatial patterns with a standard ensemble model used as benchmark. The model is attractive in many respects, including the fine geographic granularity of predictions and great predictive performance several weeks ahead. Furthermore, data requirement and computational intensity are reduced by substituting a single model to multiple models folded in an ensemble model.


Subject(s)
COVID-19/epidemiology , Deep Learning , Neural Networks, Computer , Algorithms , Geography , Humans , Machine Learning , Memory, Short-Term , Models, Statistical , Monte Carlo Method , Population Dynamics , Public Health Informatics , Reproducibility of Results , SARS-CoV-2 , Time Factors , United States/epidemiology
16.
BMJ Glob Health ; 6(5)2021 05.
Article in English | MEDLINE | ID: covidwho-1504398

ABSTRACT

INTRODUCTION: Diverse gender and geographical representation matters in research. We aimed to review medical and global health journals' sex/gender reporting, and the gender and geography of authorship. METHODS: 542 research and non-research articles from 14 selected journals were reviewed using a retrospective survey design. Paper screening and systematic data extraction was conducted with descriptive statistics and regression analyses calculated from the coded data. Outcome measures were journal characteristics, the extent to which published articles met sex/gender reporting guidelines, plus author gender and location of their affiliated institution. RESULTS: Five of the fourteen journals explicitly encourage sex/gender analysis in their author instructions, but this did not lead to increased sex/gender reporting beyond the gender of study participants (OR=3.69; p=0.000 (CI 1.79 to 7.60)). Just over half of research articles presented some level of sex/gender analysis, while 40% mentioned sex/gender in their discussion. Articles with women first and last authors were 2.4 times more likely to discuss sex/gender than articles with men in those positions (p=0.035 (CI 1.062 to 5.348)). First and last authors from high-income countries (HICs) were 19 times as prevalent as authors from low-income countries; and women from low-income and middle-income countries were at a disadvantage in terms of the impact factor of the journals they published in. CONCLUSION: Global health and medical research fails to consistently apply a sex/gender lens and remains largely the preserve of authors in HIC. Collaborative partnerships and funding support are needed to promote gender-sensitive research and dismantle historical power dynamics in authorship.


Subject(s)
Global Health , Periodicals as Topic , Female , Geography , Humans , Male , Publishing , Retrospective Studies
17.
PLoS One ; 16(11): e0258738, 2021.
Article in English | MEDLINE | ID: covidwho-1502067

ABSTRACT

BACKGROUND: Epidemics of COVID-19 in student populations at universities were a key concern for the 2020-2021 school year. The University of California (UC) System developed a set of recommendations to reduce campus infection rates. SARS-CoV-2 test results are summarized for the ten UC campuses during the Fall 2020 term. METHODS: UC mitigation efforts included protocols for the arrival of students living on-campus students, non-pharmaceutical interventions, daily symptom monitoring, symptomatic testing, asymptomatic surveillance testing, isolation and quarantine protocols, student ambassador programs for health education, campus health and safety pledges, and lowered density of on-campus student housing. We used data from UC campuses, the UC Health-California Department of Public Health Data Modeling Consortium, and the U.S. Census to estimate the proportion of each campus' student populations that tested positive for SARS-CoV-2 and compared it to the fraction individuals aged 20-29 years who tested positive in their respective counties. RESULTS: SARS-CoV-2 cases in campus populations were generally low in September and October 2020, but increased in November and especially December, and were highest in early to mid-January 2021, mirroring case trajectories in their respective counties. Many students were infected during the Thanksgiving and winter holiday recesses and were detected as cases upon returning to campus. The proportion of students who tested positive for SARS-CoV-2 during Fall 2020 ranged from 1.2% to 5.2% for students living on campus and was similar to students living off campus. For most UC campuses the proportion of students testing positive was lower than that for the 20-29-year-old population in which campuses were located. CONCLUSIONS: The layered mitigation approach used on UC campuses, informed by public health science and augmented perhaps by a more compliant population, likely minimized campus transmission and outbreaks and limited transmission to surrounding communities. University policies that include these mitigation efforts in Fall 2020 along with SARS-CoV-2 vaccination, may alleviate some local concerns about college students returning to communities and facilitate resumption of normal campus operations and in-person instruction.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , SARS-CoV-2 , Universities , Adult , COVID-19 Testing , COVID-19 Vaccines , California/epidemiology , Communicable Disease Control , Disease Outbreaks , Educational Status , Epidemics , Female , Geography , Humans , Male , Mass Screening , Quarantine , Students , Young Adult
18.
Sci Rep ; 11(1): 21054, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1493209

ABSTRACT

During the COVID-19 pandemic, evidence has accumulated that movement restrictions enacted to combat virus spread produce disparate consequences along socioeconomic lines. We investigate the hypothesis that people engaged in financially secure employment are better able to adhere to mobility restrictions, due to occupational factors that link the capacity for flexible work arrangements to income security. We use high-resolution spatial data on household internet traffic as a surrogate for adaptation to home-based work, together with the geographical clustering of occupation types, to investigate the relationship between occupational factors and increased internet traffic during work hours under lockdown in two Australian cities. By testing our hypothesis based on the observed trends, and exploring demographic factors associated with divergences from our hypothesis, we are left with a picture of unequal impact dominated by two major influences: the types of occupations in which people are engaged, and the composition of households and families. During lockdown, increased internet traffic was correlated with income security and, when school activity was conducted remotely, to the proportion of families with children. Our findings suggest that response planning and provision of social and economic support for residents within lockdown areas should explicitly account for income security and household structure. Overall, the results we present contribute to the emerging picture of the impacts of COVID-19 on human behaviour, and will help policy makers to understand the balance between public health and social impact in making decisions about mitigation policies.


Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Internet , Quarantine , Socioeconomic Factors , Australia , Communicable Disease Control , Employment , Environment , Family Characteristics , Geography , Humans , Income , Occupations , Policy , Risk Factors , SARS-CoV-2
19.
Sci Rep ; 11(1): 21108, 2021 10 26.
Article in English | MEDLINE | ID: covidwho-1493205

ABSTRACT

SARS-CoV-2, the virus causing the COVID-19 pandemic emerged in December 2019 in China and raised fears it could overwhelm healthcare systems worldwide. Mutations of the virus are monitored by the GISAID database from which we downloaded sequences from four West African countries Ghana, Gambia, Senegal and Nigeria from February 2020 to April 2020. We subjected the sequences to phylogenetic analysis employing the nextstrain pipeline. We found country-specific patterns of viral variants and supplemented that with data on novel variants from June 2021. Until April 2020, variants carrying the crucial Europe-associated D614G amino acid change were predominantly found in Senegal and Gambia, and combinations of late variants with and early variants without D614G in Ghana and Nigeria. In June 2021 all variants carried the D614G amino acid substitution. Senegal and Gambia exhibited again variants transmitted from Europe (alpha or delta), Ghana a combination of several variants and in Nigeria the original Eta variant. Detailed analysis of distinct samples revealed that some might have circulated latently and some reflect migration routes. The distinct patterns of variants within the West African countries point at their global transmission via air traffic predominantly from Europe and only limited transmission between the West African countries.


Subject(s)
COVID-19/transmission , COVID-19/virology , Computational Biology/methods , Mutation , SARS-CoV-2 , Africa, Western , Biodiversity , China , Europe , Gambia , Genetic Variation , Genome, Viral , Geography , Ghana , Humans , Nigeria , Phylogeny , Senegal , Time Factors
20.
Sci Rep ; 11(1): 20987, 2021 10 25.
Article in English | MEDLINE | ID: covidwho-1483149

ABSTRACT

Acid suppressants are widely-used classes of medications linked to increased risks of aerodigestive infections. Prior studies of these medications as potentially reversible risk factors for COVID-19 have been conflicting. We aimed to determine the impact of chronic acid suppression use on COVID-19 infection risk while simultaneously evaluating the influence of social determinants of health to validate known and discover novel risk factors. We assessed the association of chronic acid suppression with incident COVID-19 in a 1:1 case-control study of 900 patients tested across three academic medical centers in California, USA. Medical comorbidities and history of chronic acid suppression use were manually extracted from health records by physicians following a pre-specified protocol. Socio-behavioral factors by geomapping publicly-available data to patient zip codes were incorporated. We identified no evidence to support an association between chronic acid suppression and COVID-19 (adjusted odds ratio 1.04, 95% CI 0.92-1.17, P = 0.515). However, several medical and social features were positive (Latinx ethnicity, BMI ≥ 30, dementia, public transportation use, month of the pandemic) and negative (female sex, concurrent solid tumor, alcohol use disorder) predictors of new infection. These findings demonstrate the value of integrating publicly-available databases with medical data to identify critical features of communicable diseases.


Subject(s)
COVID-19/epidemiology , COVID-19/therapy , Gastroesophageal Reflux/complications , Social Determinants of Health , Aged , Behavior , COVID-19/psychology , California , Case-Control Studies , Computational Biology/methods , Databases, Factual , Female , Gastroenterology , Gastroesophageal Reflux/drug therapy , Geography , Histamine H2 Antagonists/pharmacology , Humans , Incidence , Male , Middle Aged , Odds Ratio , Proton Pump Inhibitors/pharmacology , Risk Factors , Social Class
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