bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using viral genomics to estimate undetected infections and extent of superspreading events for COVID-19
Authors: Li Lucy M. , Ayscue Patrick 
Published: May 2020

AbstractAsymptomatic infections and limited testing capacity have led to under-reporting of SARS-CoV-2 cases. This has hampered the ability to ascertain true infection numbers, evaluate the effectiveness of surveillance strategies, determine transmission dynamics, and estimate reproductive numbers. Leveraging both viral genomic and time series case data offers methods to estimate these parameters.Using a Bayesian inference framework to fit a branching process model to viral phylogeny and time series case data, we estimated time-varying reproductive numbers and their variance, the total numbers of infected individuals, the probability of case detection over time, and the estimated time to detection of an outbreak for 12 locations in Europe, China, and the United States.The median percentage of undetected infections ranged from 13% in New York to 92% in Shanghai, China, with the length of local transmission prior to two cases being detected ranging from 11 days (95% CI: 4-21) in California to 37 days (9-100) in Minnesota. The probability of detection was as low as 1% at the start of local epidemics, increasing as the number of reported cases increased exponentially. The precision of estimates increased with the number of full-length viral genomes in a location. The viral phylogeny was informative of the variance in the reproductive number with the 32% most infectious individuals contributing 80% of total transmission events.This is the first study that incorporates both the viral genomes and time series case data in the estimation of undetected COVID-19 infections. Our findings suggest the presence of undetected infections broadly and that superspreading events are contributing less to observed dynamics than during the SARS epidemic in 2003. This genomics-informed modeling approach could estimate in near real-time critical surveillance metrics to inform ongoing COVID-19 response efforts.FundingAWS provided computational credit via the Diagnostic Development Initiative.
Impact of small-area lockdowns for the control of the COVID-19 pandemic
Authors: Cuadrado Cristóbal , Monsalves María José , Gajardo Jean , Bertoglia María Paz , Nájera Manuel , Alfaro Tania , Canals Mauricio , Kaufman Jay S. , Peña Sebastián 
Published: May 2020

AbstractBackgroundCountries confronting the COVID-19 pandemic are implementing different social distancing strategies. We evaluated the impact of small-area lockdowns in Chile, aimed to reduce viral transmission while minimizing the population disrupted. The effectiveness of this intervention on the outbreak control is unknown.MethodsA natural experiment assessing the impact of small-area lockdowns between February 15th and April 25th, 2020. We used mobility data and official governmental reports to compare regions with small-area lockdowns versus regions without. The primary outcome was the mean difference in the effective reproductive number (Re) of COVID-19. Secondary outcomes were changes in mobility indicators. We used quasi-experimental methods for the analysis and examined the impact of other concurrent public health interventions to disentangle their effects.ResultsSmall-area lockdown produced a sizable reduction in human mobility, equivalent to an 11.4% reduction (95%CI −14.4% to −8.38%) in public transport and similar effects in other mobility indicators. Ten days after implementation, the small-area lockdown produced a reduction of the effective reproductive number (Re) of 0.86 (95%CI −1.70 to −0.02). School and university closures, implemented earlier, led to a 40% reduction in urban mobility. Closure of educational institutions resulted in an even greater Re reduction compared with small-area lockdowns.ConclusionsSmall-area lockdowns produced a reduction in mobility and viral transmission, but the effects were smaller than the early closures of schools and universities. Small-area lockdowns may have a relevant supporting role in reducing SARS-CoV-2 transmission and could be useful for countries considering scaling-down stricter social distancing interventions.
Phasic containment of COVID-19 in substantially affected states of India
Authors: Mandal Manisha , Mandal Shyamapada 
Published: May 2020

AbstractThe spread of COVID-19 epidemic in some highly-impacted Indian states displayed a characteristic sub-exponential growth projected up to 3 May 2020, as a consequence of lockdown strategies, in addition to improvement of reproduction number (R), serial interval, and daily growth rate, but not case fatality rate (CFR). The effect of COVID-19 containment was more prominent in second phase of lockdown with declining R, which was still >1, suggesting the requirement of sustained interventions for effective containment of COVID-19 pandemic in Indian context.
A Divide and Conquer Strategy against the Covid-19 Pandemic?!
Authors: Mangat Patrick 
Published: May 2020

AbstractThe concern about (socio-)economic consequences of collective lockdowns in the Covid-19 pandemic calls for alternative strategies. We consider adivide and conquer strategyin which a high risk group (HRG) is put on strict isolation, whereas the remainder of the population is exposed to the virus, building up immunity against Covid-19. The question is whether this strategy may suppress the effective reproduction number below the critical value ofwithout further lockdown once the HRG is released from isolation. While this proposal appears already rather academic, we show thatcan only be obtained provided that the HRG is less than ~ 20 − 30% of the total population. Hence, this strategy is likely to fail in countries with a HRG larger than the given upper bound. In addition, we argue that the maximum infection rate occurring in this strategy is likely to exceed realistic capacities of most health care systems. While the conclusion is rather negative in this regard, we emphasise that the strategy ofstopping the curveat an early stage of the Covid-19 pandemic has a chance to work out. The required duration of the lockdown is estimated to be τ ~ 14 days/(up to some order one factor) for, provided a systematic tracing strategy of new infections exists for the subsequent relaxation phase. In this context we also argue whyremains the crucial parameter which needs to be accurately monitored and controlled.
Containing Covid-19 outbreaks with spatially targeted short-term lockdowns and mass-testing
Authors: Alsing Justin , Usher Naïri , Crowley Philip JD 
Published: May 2020

ABSTRACTWe assess the efficacy of spatially targeted lockdown or mass-testing and case-isolation in individual communities, as a complement to contact-tracing and social-distancing, for containing SARS-CoV-2 outbreaks. Using the UK as a case study, we construct a stochastic branching process model for the virus transmission, embedded on a network interaction model encoding mobility patterns in the UK. The network model is based on commuter data from the 2011 census, a catchment area model for schools, and a phenomenological model for mobility and interactions outside of work, school, and the home. We show that for outbreak scenarios where contact-tracing and moderate social distancing alone provide suppression but do not contain the spread, targeted lockdowns or mass-testing interventions at the level of individual communities (with just a few thousand inhabitants) can be effective at containing outbreaks. For spatially targeted mass-testing, a moderate increase in testing capacity would be required (typically < 40000 additional tests per day), while for local lockdowns we find that only a small fraction (typically < 0.1%) of the population needs to be locked down at any one time (assuming that one third of transmission occurs in the home, at work or school, and out in the wider community respectively). The efficacy of spatially targeted interventions is contingent on an appreciable fraction of transmission events occurring within (relative to across) communities. Confirming the efficacy of community-level interventions therefore calls for detailed investigation of spatial transmission patterns for SARS-CoV-2, accounting for sub-community-scale transmission dynamics, and changes in mobility patterns due to the presence of other containment measures (such as social distancing and travel restrictions).
Awareness, knowledge, attitude and practice towards measures for prevention of the spread of COVID-19 in the Ugandans: A nationwide online cross-sectional Survey
Authors: Ssebuufu Robinson , Sikakulya Franck Katembo , Binezero Simon Mambo , Wasingya Lucien , Nganza Sifa K. , Ibrahim Bwaga , Kyamanywa Patrick 
Published: May 2020

AbstractBackgroundThe world is facing the Coronavirus pandemic which is highly infectious. A number of measures have been put in place to prevent its spread among the population. However, for these preventive measures to be effective, the population requires an appropriate and sufficient knowledge. Thus, a survey was conducted with the aim of assessing the awareness, knowledge, attitude and practices towards measures for prevention of the spread of Covid-19 amongst Ugandans.MethodsThis was a cross-sectional study conducted during the lockdown in Uganda. An online questionnaire and a snowballing approach was used for participant recruitment of 18 years above literate Ugandans. Data collection was done from 6thto 15thApril 2020 during which 1763 people participated. We analyzed all data using STATA 14.2, applying appropriate statistical tests.ResultsOut of 1763 participants, 97.6% were aware of the current pandemic. 83.9% of participants had a good knowledge score (21.8/27), 72.4% had a good attitude and 85.3% were practicing measures to prevent the spread of the Coronavirus disease. The ordered logistic regression showed that being a Health worker was significantly associated with a high knowledge (aOR:6 (3.32-10.93); a good attitude (aOR:2.5(1.68-3.8)]) and good practice (aOR:2.9 (1.95-4.2). On contrary, being a driver, business entrepreneur and a security personnel were found to have less rate in awareness, knowledge, attitude and practice.ConclusionsUgandans had a good overall awareness, knowledge, attitude and practice. However, there is still a gap of knowledge, attitude and practice among drivers, business entrepreneur and security personnel. There is a need to mobilize the population in the country to have the same degree of awareness and knowledge which will have an impact on attitude and practice to prevent spread of COVID-19.
Impact of essential workers in the context of social distancing for epidemic control
Authors: Milligan William R. , Fuller Zachary L. , Agarwal Ipsita , Eisen Michael B. , Przeworski Molly , Sella Guy 
Published: May 2020

AbstractMany governments have responded to the ongoing COVID-19 pandemic by imposing social policies that restrict interactions outside of the home, resulting in a large fraction of the workforce either working from home or not working. However, to maintain essential services, a substantial number of workers are not subject to these limitations, and maintain many of their pre-intervention interactions. To explore how interactions among such “essential” workers, and between essential workers and the rest of the population, impact disease risk and the effectiveness of pandemic control, we evaluated several models of essential worker interactions within a standard epidemiology framework. The models were designed to correspond to key characteristics of, respectively, cashiers, factory employees, and healthcare workers. We find in all three models that essential workers are at substantially elevated risk of infection compared to the rest of the population, and that increasing the numbers of essential workers necessitates the imposition of more stringent interaction controls on the rest of the population in order to manage the pandemic. However, different archetypes of essential workers differ in both their individual probability of infection and impact on the broader pandemic, highlighting the need to understand and target for intervention the specific risks faced by different groups of essential workers.
Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing
Authors: Thi Viet Loan Dao , Herbst Konrad , Boerner Kathleen , Meurer Matthias , Kremer Lukas PM , Kirrmaier Daniel , Freistaedter Andrew , Papagiannidis Dimitrios , Galmozzi Carla , Klein Steffen , Chlanda Petr , Khalid Dina , Miranda Isabel Barreto , Schnitzler Paul , Kräusslich Hans-Georg , Knop Michael , Anders Simon 
Published: May 2020

AbstractThe COVID-19 pandemic caused by the novel SARS-CoV-2 virus poses a significant public-health problem. In order to control the pandemic, rapid tests for detecting existing infections and assessing virus spread are critical.Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) hold outstanding promise towards greatly simplified and broadly applicable testing methods. RT-LAMP assays appear more robust than qPCR-based methods and only require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation.Here, we tested a two-color RT-LAMP protocol using clinical SARS-CoV-2 samples and also established a protocol that does not require prior RNA isolation (“swab-to-RT-LAMP”). Our study is based on several hundred clinical patient samples with a wide range of viral loads, thus allowing, for the first time, to accurately determine the sensitivity and specificity of the RT-LAMP assay for the detection of SARS-CoV-2 in patients. We found that RT-LAMP can reliably detect SARS-CoV-2 samples with a qPCR threshold cycle number (CT value) of up to 30 in the standard RT-qPCR assay. We used both, either purified RNA or direct pharyngeal swab specimens and showed that RT-LAMP assays have, despite a decreased sensitivity compared to RT-qPCR, excellent specificity. We also developed a multiplexed LAMP-sequencing protocol as a diagnostic and validation procedure to detect and record the outcome of RT-LAMP assays. LAMP-sequencing is fully scalable and can assess the results of thousands of LAMP reactions in parallel. Finally, we propose applications of RT-LAMP based assays for SARS-CoV-2 detection.
Ethnicity and risk of death in patients hospitalised for COVID-19 infection in the UK: an observational cohort study in an urban catchment area
Authors: Sapey E , Gallier S , Mainey C , Nightingale P , McNulty D , Crothers H , Evison F , Reeves K , Pagano D , Denniston A.K , Nirantharakumar K. , Diggle P , Ball S 
Published: May 2020

AbstractBackgroundStudies suggest that certain Black and Asian Minority Ethnic groups experience poorer outcomes from COVID-19 but these studies have not provided insight into potential reasons for this. We hypothesised that outcomes would be poorer for those of South Asian ethnicity hospitalised from a confirmed SARS-CoV-2 infection, once confounding factors, health seeking behaviours and community demographics were considered and that this might reflect a more aggressive disease course in these patients.MethodsPatients with confirmed SARS-CoV-2 infection requiring admission to University Hospitals Birmingham NHS Foundation Trust(UHB) in Birmingham UK between 10thMarch 2020-17thApril 2020 were included. Standardised Admission Ratio(SAR) and Standardised Mortality Ratio(SMR) were calculated using observed COVID-19 admissions/deaths and 2011 census data. Hazard Ratio (aHR) for mortality was estimated using Cox proportional hazard model adjusting and propensity score matching.ResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2–1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)).ConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.
IKONOS: An intelligent tool to support diagnosis of Covid-19 by texture analysis of x-ray images
Authors: Gomes Juliana C. , de F. Barbosa Valter A. , Santana Maira A. , Bandeira Jonathan , Valença Mêuser Jorge Silva , de Souza Ricardo Emmanuel , Ismael Aras Masood , dos Santos Wellington P. 
Published: May 2020

AbstractIn late 2019, the SARS-Cov-2 spread worldwide. The virus has high rates of proliferation and causes severe respiratory symptoms, such as pneumonia. There is still no specific treatment and diagnosis for the disease. The standard diagnostic method for pneumonia is chest X-ray image. There are many advantages to using Covid-19 diagnostic X-rays: low cost, fast and widely available. We propose an intelligent system to support diagnosis by X-ray images. We tested Haralick and Zernike moments for feature extraction. Experiments with classic classifiers were done. Support vector machines stood out, reaching an average accuracy of 89.78%, average recall and sensitivity of 0.8979, and average precision and specificity of 0.8985 and 0.9963 respectively. The system is able to differentiate Covid-19 from viral and bacterial pneumonia, with low computational cost.
A preliminary study on analytical performance of serological assay for SARS-CoV-2 IgM/IgG and application in clinical practice
Authors: Zhou Quan , Zhu Danping , Yan Huacheng , Quan Jingwen , Kuang Zhenzhan , Zhang Weiyun , Huang Ling , Lei Ting , Liu Jiahui , Xiao Bin , Luo Aiwu , Sun Zhaohui , Li Linhai 
Published: May 2020

AbstractObjectiveTo investigate the performance of serological test and dynamics of serum antibody with the progress of SARS-CoV-2 infections.MethodsA total of 419 patients were enrolled including 19 confirmed cases and 400 patients from fever clinics. Their serial serum samples collected during the hospitalization were menstruated for IgM and IgG against SARS-CoV-2 using gold immunochromatographic assay and chemiluminescence immunoassay. We investigated whether thermal inactivation could affect the results of antibody detection. The dynamics of antibodies with the disease progress and false positive factors for antibody testing were also analyzed.ResultsThe positive rate of IgG detection was 91.67% and 83.33% using two CLIA, respectively. However, the IgM positive rate was dramatically declined might due to the lack of blood samples at early stages of the disease. The chemiluminescence immunoassay had a favorable but narrow linear range. Our work showed increased IgG values in serums from virus-negative patients and four negative samples were IgG weak-positive after thermal incubation. Our data showed the specificity of viral N+S proteins was higher than single antigen. Unlike generally thought that IgM appeared earlier than IgG, there is no certain chronological order of IgM and IgG seroconversion in COVID-19 patients. It was difficult to detect antibodies in asymptomatic patients suggesting that their low viral loads were not enough to cause immune response. Analysis of common interferent in three IgG false-positive patients, such as rheumatoid factor, proved that false positives were not caused by these interfering substances and antigenic cross-reaction.ConclusionsViral serological test is an effective means for SARS-CoV-2 infect detection using both chemiluminescence immunoassay and gold immunochromatographic assay. Chemiluminescence immunoassay against multi-antigens has obvious advantages but still need improve in reducing false positives.
Epidemiological Transition of Covid-19 in India from Higher to Lower HDI States and Territories: Implications for Prevention and Control
Authors: Gupta Rajeev , Dhamija Rajinder K , Gaur Kiran 
Published: May 2020

ABSTRACTBackground & ObjectiveSocial determinants of evolving covid-19 pandemic have not been well studied. To determine trends in transition of this epidemic in India we performed a study in states at various levels of human development index (HDI).MethodsWe used publicly available data sources to track progress of covid-19 epidemic in India in different states and territories where it was reported in significant numbers. The states (n=20) were classified into tertiles of HDI and weekly trends in cases and deaths plotted from 15 March to 2 May 2020. To assess association of HDI with state-level covid-19 burden we performed Pearson’s correlation. Logarithmic trends were evaluated for calculation of projections. A microlevel study was performed in select urban agglomerations for identification of socioeconomic status (SES) differentials.ResultsThere is wide regional variation in covid-19 cases and deaths in India from mid-March to early-May 2020. High absolute numbers have been reported from states of Maharashtra, Gujarat, Delhi, Madhya Pradesh, Rajasthan and Tamilnadu. Growth rate in cases and deaths is slow in high HDI states while it has increased rapidly in middle and lower HDI states. In mid-March 2020 there was a strong positive correlation of state-level HDI with weekly covid-19 cases (r= 0.37, 0.40) as well as deaths (r= 0.31, 0.42). This declined by early-May for cases (r= 0.04, 0.06) as well as deaths (r= - 0.005, 0.001) with significant negative logarithmic trend (cases R squared= 0.92; deaths R squared= 0. 84). These trends indicate increasing cases and deaths in low HDI states. Projection reveals that this trend is likely to continue to early-June 2020. Microlevel evaluation shows that urban agglomerations are major focus of the disease in India and it has transited from middle SES to low SES locations.ConclusionThere is wide variability in burden of covid-19 in India. Slow growth and flattening of curve is observed in high-HDI states while disease is increasing in mid and lower HDI states. Projections reveal that lower HDI states would achieve parity with high HDI states by early-June 2020. Covid-19 is mostly present in urban agglomerations where it has transited from upper-middle to low SES locations. Public health strategies focusing on urban low SES locations and low HDI states are crucial to decrease covid-19 burden in India.