bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID–19 Disease Dynamics in Germany: First Models and Parameter
Identification
Authors: Götz Thomas , Heidrich Peter
Published: April 2020

Since the end of 2019 an outbreak of a new strain of coronavirus, called
SARS– CoV–2, is reported from China and later other parts of the world. Since
January 21, WHO reports daily data on confirmed cases and deaths from both China
and other countries [1]. The Johns Hopkins University [5] collects those data
from various sources worldwide on a daily basis. For Germany, the
Robert–Koch–Institute (RKI) also issues daily reports on the current number of
infections and infection related fatal cases [2]. However, due to delays in the
data collection, the data from RKI always lags behind those reported by Johns
Hopkins. In this work we present an extended SEIR–model to describe the disease
dynamics in Germany. The parameter values are identified by matching the model
output to the officially reported cases. An additional parameter to capture the
influence of unidentified cases is also included in the model.

There’s an evil virus that’s

threatening mankind […]

A menace to society

Iron Maiden, Virus, 1996.
Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios
Authors: Mukandavire Z. , Nyabadza F. , Malunguza N. J. , Cuadros D. F. , Shiri T. , Musuka G.
Published: April 2020

Background

COVID-19 has emerged and spread at great speed globally and has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the spectrum of disease severity is not yet clear.

Methods

We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverages to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented.

Results

Early model estimates show that COVID-19 outbreak in South Africa had a basic re-productive number of 2.95 (95% credible interval [CrI] 2.83-3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44-99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72-69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76-80.85%).

Conclusions

Findings suggest a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
TESTING, TRACING AND SOCIAL DISTANCING: ASSESSING OPTIONS FOR THE CONTROL OF COVID_19
Authors: Humphrey Lia , Thommes Edward W. , Fields Roie , Coudeville Laurent , Hakim Naseem , Chit Ayman , Cojocaru Monica G.
Published: April 2020

In this work we present an analysis of non-pharmaceutical interventions implemented around the world in the fight against COVID-19: Social distancing, shelter-in-place, mask wearing, etc measures to protect the susceptible, together with, in various degrees, testing & contact-tracing to identify, isolate and treat the infected. The majority of countries have relied on the former, while ramping up their testing and tracing capabilities. We consider the examples of South Korea, Italy, Canada and the United States. By fitting a disease transmission model to daily case report data, we show that in each of the four countries their combination of social-distancing and testing/tracing to date have had a significant impact on the evolution of their pandemic curves. In this work we estimate the average isolation rates of infected individuals needing to occur in each country as a result of large-scale testing and contact tracing as a mean of lifting social distancing measures, without a resurgence of COVID-19. We find that an average isolation rate of an infected individual every 4.5 days (South Korea), 5.7 days (Canada) and to 6 days (Italy) would be sufficient. We also find that a rate of under 3.5 days will help in the United States, although it would not completely mitigate the second wave the country is currently under.
A new design of an adaptive model of infectious diseases based on artificial intelligence approach: monitoring and forecasting of COVID-19 epidemic cases
Authors: Nail Bachir , Rabehi Abdelaziz , Bekhiti Belkacem , Arbaoui Taha
Published: April 2020

Background

Mathematical infectious disease models available in literature, mostly take in their design that the parameters of basic reproduction number R0 and interval serial SI as constant values during tracking the outbreak cases. In this report a new intelligent model called HH-COVID-19 is proposed, with simple design and adaptive parameters.

Methods

The parameters R0 and SI are adapted by adding three new weighting factors α, β and γ and two free parameters σ1 and σ2 in function of time t, thus the HH-COVID-19 become time-variant model. The parameters R0, SI, α, β, γ, σ1 and σ2 are estimated optimally based on a recent algorithm of artificial intelligence (AI), inspired from nature called Harris Hawks Optimizer (HHO), using the data of the confirmed infected cases in Algeria country in the first t = 55 days.

Results

Parameters estimated optimally: R0 = 1.341, SI = 5.991, α = 2.987, β = 1.566, γ = 4.998, σ1 = −0.133 and σ2 = 0.0324. R0 starts on 1.341 and ends to 2.677, and SI starts on 5.991 and ends to 6.692. The estimated results are identically to the actual infected incidence in Algeria, HH-COVID-19 proved its superiority in comparison study. HH-COVID-19 predicts that in 1 May, the infected cases exceed 50 000, during May, to reach quickly the herd immunity stage at beginning of July.

Conclusion

HH-COVID-19 can be used for tracking any COVID-19 outbreak cases around the world, just should updating its new parameters to fitting the area to be studied, especially when the population is directly vulnerable to COVID-19 infection.
The Epidemic Severity Index: Estimating Relative Local Severity of Novel Disease Outbreaks
Authors: Davies Gareth
Published: April 2020

Determining the severity of a novel pathogen in the early stages is difficult in the absence of reliable data. The pattern of outbreaks for COVID-19 across the globe have differed markedly above and below 30°N latitudes, suggesting very different levels of severity, but countries worldwide have implemented the same lockdown strategies. Existing methods for estimating severity appear not to have been useful in informing strategic decisions, possibly due to mismatches between the data required and those available, overly sophisticated methods with undesirable biases, or perhaps confusion and uncertainly generated by the wide range of estimates these methods produced early on.

The Epidemic Severity Index (ESI) is a simple, robust method for estimating the local severity of novel epidemic outbreaks using early and widely-available data and that does not depend on any estimated values. ESI allows rapid, meaningful comparisons across territories that can be tracked as the outbreaks unfold. The ESI quantifies severity relative to a parameterised baseline rather than attempting to estimate values for infection fatality rates, case fatality rates or transmission rates. The relative nature of the ESI sidesteps any problems of confidence associated with absolute rate estimation methods and offers immediate practical strategic value.
Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing
Authors: Ghosh Sabyasachi , Rajwade Ajit , Krishna Srikar , Gopalkrishnan Nikhil , Schaus Thomas E. , Chakravarthy Anirudh , Varahan Sriram , Appu Vidhya , Ramakrishnan Raunak , Ch Shashank , Jindal Mohit , Bhupathi Vadhir , Gupta Aditya , Jain Abhinav , Agarwal Rishi , Pathak Shreya , Rehan Mohammed Ali , Consul Sarthak , Gupta Yash , Gupta Nimay , Agarwal Pratyush , Goyal Ritika , Sagar Vinay , Ramakrishnan Uma , Krishna Sandeep , Yin Peng , Palakodeti Dasaradhi , Gopalkrishnan Manoj
Published: April 2020

The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We presentTapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android applicationBYOM Smart Testingwhich guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample.

NOTE: This protocol has been validated with in vitro experiments that used synthetic RNA and DNA fragments and additionally, its expected behavior has been confirmed using computer simulations. Validation with clinical samples is ongoing. We are looking for clinical collaborators with access to patient samples. Please contact the corresponding author if you wish to validate this protocol on clinical samples.
Ecological processes underlying the emergence of novel enzootic cycles—arboviruses in the neotropics as a case study
Authors: Guth Sarah , Hanley Kathryn , Althouse Benjamin M. , Boots Mike
Published: April 2020

Pathogens originating from wildlife (zoonoses) pose a significant public health burden, comprising the majority of emerging infectious diseases. Efforts to control and prevent zoonotic disease have traditionally focused on animal-to-human transmission, or “spillover”. However, in the modern era, increasing international mobility and commerce facilitate the spread of infected humans, non-human animals (hereafter animals), and their products worldwide, thereby increasing the risk that zoonoses will be introduced to new geographic areas. Imported zoonoses can potentially ‘spill back’ to infect local wildlife—a danger magnified by urbanization and other anthropogenic pressures that increase contacts between human and wildlife populations. In this way, humans can function as vectors, dispersing zoonoses from their ancestral enzootic systems to establish reservoirs elsewhere in novel animal host populations. Once established, these enzootic cycles are largely unassailable by standard control measures and have the potential to feed human epidemics. Understanding when and why translocated zoonoses establish novel enzootic cycles requires disentangling ecologically complex and stochastic interactions between the zoonosis, the human population, and the natural ecosystem. We address this challenge by delineating potential ecological mechanisms affecting each stage of enzootic establishment—wildlife exposure, enzootic infection, and persistence—applying existing ecological concepts from epidemiology, invasion biology, and population ecology. We ground our study in the neotropics, where four arthropod-borne viruses (arboviruses) of zoonotic origin—yellow fever, dengue, chikungunya, and Zika viruses—have separately been introduced into the human population. This paper is a step towards developing a framework for predicting and preventing novel enzootic cycles in the face of zoonotic translocations.
Comprehensive Investigation and Isolation have Effectively Suppressed the Spread of COVID-19
Authors: Huang Yubo , Zhang Weidong
Published: April 2020

The outbreak of COVID-19 since Dec. 2019 has caused severe life and economic damage worldwide, many countries are trapped by medical resource constraints or absence of targeted therapeutics, and therefore the implement of systemic policies to block this pandemic should be prioritized. Based on the transmission mechanisms and physicochemical properties of betacoron-aviruses, we construct a fine-grained transmission dynamics model (ICRD) to forecast the crucial information of public concern, therein using dynamical coefficients to quantify the impact of the implement time and intensity of containment policies on the spread of epidemic. We find that the comprehensive investigation policy for susceptible population and the quarantine for suspected cases eminently contribute to reduce casualties during the phase of the dramatic increase of diagnosed cases. Statistic evidences strongly suggest that society should take such forceful public health interventions to cut the infection channels in the initial stage until the pandemic is interrupted.
Modelling the impact of control measures against the COVID-19 pandemic in Viet Nam
Authors: Nguyen Thu-Anh , Cuong Quoc Nguyen , Kim Anh Le Thi , Nguyen Huyen Nguyen , Huong Thao Nguyen Thi
Published: April 2020

Objectives

Health care system of many countries are facing a surging burden of COVID-19. Although Vietnam has successfully controlled the COVID-19 pandemic to date, there is a sign of initial community transmission. An estimate of possible scenarios to prepare health resources in the future is needed. We used modelling methods to estimate impacts of mitigation measures on the COVID-19 pandemic in Vietnam.

Methods

SEIR model built in the COVIDSIM1.1 tool was adopted using available data for estimation. The herd immunization scenario was with no intervention implemented. Other scenarios consisted of isolation and social distancing at different levels (25%, 50%, 75% and 10%, 20%, 30%, respectively). Outcomes include epidemic apex, daily new and cumulative cases, deaths, hospitalized patients and ICU beds needed.

Results

By April 8, 2020, there would be 465 infected cases with COVID-19 in Viet Nam, of those 50% were detected. Cumulatively, there would be 1,400 cases and 30 deaths by end of 2020, if 75% of cases was detected and isolated, and 30% of social distancing could be maintained.

The most effective intervention scenario is the detection and isolation of 75% infected cases and reduction of 10% social contacts. This will require an expansion of testing capacity at health facilities and in the community, posing a challenge to identify high-risk groups to prioritized testing.

Conclusions

In a localized epidemic setting, the expansion of testing should be the key measure to control the epidemic. Social distancing plays a significant role to prevent further transmission to the community.
Predicting COVID-19 peaks around the world
Authors: Tsallis Constantino , Tirnakli Ugur
Published: April 2020

The official data for the time evolution of active cases of COVID-19 pandemics around the world are available online. For all countries, a peak has been either observed (China and South Korea) or is expected in near future. The approximate dates and heights of those peaks imply in important epidemiological issues. Inspired by similar complex behaviour of volumes of transactions of stocks at NYSE and NASDAQ, we propose a q-statistical functional form which appears to describe satisfactorily the available data of all countries. Consistently, predictions become possible of the dates and heights of those peaks in severely affected countries unless efficient treatments or vaccines, or sensible modifications of the adopted epidemiological strategies, emerge.
Reconstructed diagnostic sensitivity and specificity of the RT-PCR test for COVID-19
Authors: Padhye N. S.
Published: April 2020

Real-time reverse transcription polymerase chain reaction (RT-PCR) targeting select genes of the SARS-CoV-2 RNA has been the main diagnostic tool in the global response to the COVID-19 pandemic. This study was aimed at the estimation of diagnostic sensitivity and specificity of the first RT-PCR test developed by China CDC in January 2020. The study design is a secondary analysis of published findings on 1014 patients in Wuhan, China, of whom 59.3% tested positive for COVID-19 in RT-PCR tests and 87.6% tested positive in chest CT exams. We utilized previously ignored expert opinions in the form of verbal probability classifications of patients with conflicting test results to estimate the informative prior distribution of the infected proportion. It was then used in a Bayesian version of a previously developed model to reconstruct the sensitivity and specificity of the diagnostic tests without the need for specifying an inaccurate test as the gold standard. The sensitivity of the RT-PCR diagnostic test was estimated to be 0.707 (95% CI: 0.668, 0.749), while the specificity was 0.851 (95% CI: 0.774, 0.941). Caution is advised in generalizing these findings to other versions of the RT-PCR test that are being used in diverse geographic regions.
Evaluating a Widely Implemented Proprietary Deterioration Index Model Among Hospitalized COVID-19 Patients
Authors: Singh Karandeep , Valley Thomas S. , Tang Shengpu , Li Benjamin Y. , Kamran Fahad , Sjoding Michael W. , Wiens Jenna , Otles Erkin , Donnelly John P. , Wei Melissa Y. , McBride Jonathon P. , Cao Jie , Penoza Carleen , Ayanian John Z. , Nallamothu Brahmajee K.
Published: April 2020

Introduction

The Epic Deterioration Index (EDI) is a proprietary prediction model implemented in over 100 U.S. hospitals that was widely used to support medical decision-making during the COVID-19 pandemic. The EDI has not been independently evaluated, and other proprietary models have been shown to be biased against vulnerable populations.

Methods

We studied adult patients admitted with COVID-19 to non-ICU care at a large academic medical center from March 9 through May 20, 2020. We used the EDI, calculated at 15-minute intervals, to predict a composite outcome of ICU-level care, mechanical ventilation, or in-hospital death. In a subset of patients hospitalized for at least 48 hours, we also evaluated the ability of the EDI to identify patients at low risk of experiencing this composite outcome during their remaining hospitalization.

Results

Among 392 COVID-19 hospitalizations meeting inclusion criteria, 103 (26%) met the composite outcome. Median age of the cohort was 64 (IQR 53-75) with 168 (43%) African Americans and 169 (43%) women. Area under the receiver-operating-characteristic curve (AUC) of the EDI was 0.79 (95% CI 0.74-0.84). EDI predictions did not differ by race or sex. When exploring clinically-relevant thresholds of the EDI, we found patients who met or exceeded an EDI of 68.8 made up 14% of the study cohort and had a 74% probability of experiencing the composite outcome during their hospitalization with a median lead time of 24 hours from when this threshold was first exceeded. Among the 286 patients hospitalized for at least 48 hours who had not experienced the composite outcome, 14 (13%) never exceeded an EDI of 37.9, with a negative predictive value of 90% and a sensitivity above this threshold of 91%.

Conclusion

We found the EDI identifies small subsets of high- and low-risk COVID-19 patients with fair discrimination. We did not find evidence of bias by race or sex. These findings highlight the importance of independent evaluation of proprietary models before widespread operational use among COVID-19 patients.
Gender-Based Disparities in COVID-19 Patient Outcomes: A Propensity-matched Analysis
Authors: Singh Shailendra , Chowdhry Monica , Chatterjee Arka , Khan Ahmad
Published: April 2020

COVID-19 epidemiological data show higher mortality among males as compared to females. However, it remains unclear if this disparity is due to gender differences in high-risk characteristics. Our study, including a large cohort of male and female patients, showed that males have a higher risk for mortality, hospitalization and mechanical ventilation even when compared to a matched cohort of females with similar age, high-risk behavior, and comorbidities. This gender-based risk of poor outcomes among COVID-19 patients is especially more pronounced in advanced age. High-risk characteristics only partially explain the gender disparity, and further research is needed to understand the causes of this disparity.
The values of coagulation function in COVID-19 patients
Authors: Jin Xin , Duan Yongwei , Bao Tengfei , Gu Junjuan , Chen Yawen , Li Yuanyuan , Mao Shi , Chen Yongfeng , Xie Wen
Published: April 2020

Objective

To investigate the blood coagulation function in COVID-19 patients, and the correlation between coagulopathy and disease severity.

Methods

We retrospectively collected 147 clinically diagnosed COVID-19 patients at Wuhan Leishenshan Hospital of Hubei, China. We analyzed the coagulation function in COVID-19 patients through the data including thrombin-antithrombin complex (TAT), α2-plasmininhibitor-plasmin Complex (PIC), thrombomodulin (TM), t-PA/PAI-1 Complex (t-PAIC), prothrombin time (PT), international normalized ratio (INR), activated partial thromboplastin time (APTT), fibrinogen (FIB), thrombin time (TT), D-Dimer (DD), and platelet (PLT).

Result

The levels of TAT, PIC, TM, t-PAIC, PT, INR, FIB, and DD in COVID-19 patients were higher than health controls (p<0.05), and also higher in the patients with thrombotic disease than without thrombotic disease (p<0.05). What’s more, the patients with thrombotic disease had a higher case-fatality (p<0.05). TAT, PIC, TM, t-PAIC, PT, INR, APTT, FIB, DD, and PLT were also found correlated with disease severity. Meanwhile, we found that there were significant difference in TAT, TM, t-PAIC, PT, INR, APTT, DD, and PLT in the death and survival group. Further using univariate and multivariate logistic regression analysis also found that t-PAIC and DD were independent risk factors for death in patients and are excellent predicting the mortality risk of COVID-19.

Conclusion

The coagulation systems in COVID-19 patients are inordinate, and dynamic monitoring of them, might be a key in the control of COVID-19 death.
Gut microbiota features on nursing home admission are associated with subsequent acquisition of antibiotic resistant organism colonization
Authors: Wang Joyce , Cassone Marco , Gibson Kristen , Lansing Bonnie , Mody Lona , Snitkin Evan , Rao Krishna
Published: April 2020

Nursing home (NH) patients often acquire colonization with antibiotic-resistant organisms (AROs). We show that patients exposed to broad-spectrum antibiotics during previous hospitalizations have elevated enterococcal relative abundances on NH admission and higher risk of subsequent ARO acquisition. Our findings suggest that interventions preventing ARO spread should extend beyond NH doors.
Unraveling the Myths of R0 in Controlling the Dynamics of COVID-19 Outbreak: a Modelling Perspective
Authors: Mohd Mohd Hafiz , Sulayman Fatima
Published: April 2020

COVID-19 is an emerging and rapidly evolving pandemic around the world, which causes severe acute respiratory syndrome and results in substantial morbidity and mortality. To examine the transmission dynamics of COVID19 and its interactions with some exogenous factors such as limited medical resources and false detection problems, we employ a simple epidemiological model and analyse this system using modelling and dynamical systems techniques. We discover some contrasting findings with respect to the observations of basic reproduction number, and we investigate how the issues of limited medical resources and false detection problems affect the COVID-19 pandemic outbreak.
Predicting the COVID-19 epidemic in Algeria using the SIR model
Authors: Boudrioua Mohamed Samir , Boudrioua Abderrahmane
Published: April 2020

The aim of this study is to predict the daily infected cases with Coronavirus (COVID-19) in Algeria. We apply the SIR model on data from 25 February 2020 to 24 April 2020 for the prediction. Following Huang et al (12), we develop two SIR models, an optimal model and a model in a worst-case scenario COVID-19. We estimate the parameters of our models by minimizing the negative log likelihood function using the Nelder-Mead method. Based on the simulation of the two models, the epidemic peak of COVID-19 is predicted to attain 24 July 2020 in a worst-case scenario, and the COVID-19 disease is expected to disappear in the period between September 2020 and November 2020 at the latest. We suggest that Algerian authorities need to implement a strict containment strategy over a long period to successfully decrease the epidemic size, as soon as possible.
Pregnancy and breastfeeding during COVID-19 pandemic: A systematic review of published pregnancy cases
Authors: Rodrigues Carina , Baía Inês , Domingues Rosa , Barros Henrique
Published: April 2020

Background

The COVID-19 pandemic is an emerging concern regarding the potential adverse effects during pregnancy. This study reviews knowledge on the impact of COVID-19 on pregnancy and describes the outcome of published cases of pregnant women diagnosed with COVID-19.

Methods

Searches were conducted in PubMed® up to 8 April 2020, using PRISMA standards, to identify original published studies describing pregnant women at any gestational age diagnosed COVID-19. There were no date or language restrictions on the search. All identified studies were included irrespective of assumptions on study quality.

Results

We identified 30 original studies reporting 212 cases of pregnant women with COVID-19 (30 discharged while pregnant), 200 from China and 12 from other countries. The 182 published deliveries resulted in one stillbirth and 185 live births. Four women with severe COVID-19 required admission to an intensive care unit but no cases of maternal death were reported. There was one neonatal death. Preterm births occurred in 28.7% of cases, but it is unclear whether this was iatrogenic. All cases with amniotic fluid, placenta, and/or cord blood analyzed for the SARS-CoV-2 virus were negative. Four newborns were positive for SARS-CoV-2 and three newborns had high levels of IgM antibodies. Breast milk samples from 13 mothers and described in seven studies showed no evidence of SARS-CoV-2.

Conclusion

The evidence related to the effect of COVID-19 on pregnant women is still limited. Pregnant women and newborns should be considered particularly vulnerable populations regarding COVID-19 prevention and management strategies.
COVID-19 Outcomes in Saudi Arabia and the UK: A Tale of Two Kingdoms
Authors: Komies Saleh , Aldhahir Abdulelah M. , Almehmadi Mater , Alghamdi Saeed M. , Alqarni Ali , Oyelade Tope , Alqahtani Jaber S.
Published: April 2020

Background

While the number of COVID-19 cases and deaths around the world is starting to peak, it is essential to point out how different countries manage the outbreak and how different measures and experience resulted in different outcomes. This study aimed to compare the effect of the measures taken by Saudi Arabia and the United Kingdom (UK) governments on the outcome of the COVID-19 pandemic as predicted by a mathematical model.

Method

Data on the numbers of cases, deaths and government measures were collected from Saudi’s Ministry of Health and Public Health England. A prediction of the trend of cases, deaths and days to peak was then modelled using the mathematical technique, Exponential Logistic Growth and Susceptible Infectious Recovered (SIR) model. The measures taken by the governments and the predicted outcomes were compared to assess effectiveness.

Result

We found over three months that 22 fast and extreme measures had been taken in Saudi Arabia compared to eight slow and late measures in the UK. This resulted in a decline in numbers of current infected cases per day and mortality in Saudi Arabia compared to the UK. Based on the SIR model, the predicted number of COVID-19 cases in Saudi as of 31st of March was 2,064, while the predicted number of cases was 63012 in the UK. In addition, the pandemic is predicted to peak earlier on the 27th of March in Saudi Arabia compared to the 2nd of May 2020 in the UK. The end of transition phases for Saudi and UK according to the model, were predicted to be on 18th of April and 24th of May, respectively. These numbers relate to early and decisive measures adopted by the Saudi government.

Conclusion

We show that early extreme measures, informed by science and guided by experience, helped reduce the spread and related deaths from COVID-19 in Saudi. Actions were taken by Saudi under the national slogan “We are all responsible” resulted in the observed reduced number of current and predicted cases and deaths compared to the UK approach “keep calm and carry on”.
Who is at the highest risk from COVID-19 in India? Analysis of health, healthcare access, and socioeconomic indicators at the district level
Authors: Nandi Arindam , Balasubramanian Ruchita , Laxminarayan Ramanan
Published: April 2020

Introduction

Despite measures such as travel restrictions and lockdowns, the novel coronavirus (SARS-COV-2) is projected to spread across India. Considering that a vaccine for COVID-19 is will not be available soon, it is important to identify populations with high risk from COVID-19 and take measures to prevent outbreaks and build healthcare infrastructure at the local level.

Methods

We used data from two large nationally representative household surveys, administrative sources, and published studies to estimate the risk of COVID-19 at the district level in India. We employed principal component analysis to create an index of the health risk of COVID-19 from demographic and comorbidity indicators such as the proportions of elderly population and rates of diabetes, hypertension, and respiratory illnesses. Another principal component index examined the socioeconomic and healthcare access risk from COVID-19, based on the standard of living, proportion of caste groups, and per capita access to public healthcare in each district.

Results

Districts in northern, southern and western Indian states such as Punjab, Tamil Nadu, Kerala, and Maharashtra were at the highest health risk from COVID-19. Many of these districts have been designated as COVID-19 hotspots by the Indian government because of emergent outbreaks. Districts in eastern and central states such as Uttar Pradesh, Bihar, and Madhya Pradesh have higher socioeconomic and healthcare access risk as compared with other areas.

Conclusion

Districts at high risk of COVID-19 should prioritize policy measures for preventing outbreaks, and improving critical care infrastructure and socioeconomic safety nets.
Taxonomic, temporal, and spatial variation in the dynamics of High-Arctic arthropod populations
Authors: Høye Toke T. , Loboda Sarah , Koltz Amanda M. , Gillespie Mark A. K. , Bowden Joseph J. , Schmidt Niels M.
Published: April 2020

Time-series data on arthropod populations are critical for understanding the magnitude, direction, and drivers of abundance changes. However, most arthropod monitoring programs are short-lived and limited in taxonomic resolution and spatial extent. Consequently, variation in population dynamics among taxa and habitats remains poorly understood. Monitoring data from the Arctic are particularly underrepresented, yet important to assessments of species abundance changes because many anthropogenic drivers of change that are present in other regions are absent in polar regions. Here, we utilise 24 years of abundance data from Zackenberg in High-Arctic Greenland, which is the longest running Arctic arthropod monitoring program, to study temporal trends in abundance. Despite a strong warming signal in air temperature, we only find evidence of weak temporal trends in arthropod abundances across most taxa. These trends are more pronounced in the most recent decade, with change point analyses suggesting distinct non-linear dynamics within some functional groups such as predators and detritivores. Although the abundances of many taxa were correlated, we detected both positive and negative correlations, suggesting that multiple processes are affecting arthropod populations even in this relatively simple Arctic food web. Finally, we found clear differences among species within single families of arthropods, indicating that an apparent lack of change in abundance at broader taxonomic or functional levels could mask substantial species-specific trends. Our results reiterate the need for more basic research into the life-history, ecology, and adaptation of arthropod species to better understand their sensitivity to global changes.

Significance statement

Terrestrial arthropods, including insects and spiders, serve critical ecosystem functions and are excellent indicators of environmental change due to their physiology, short generation time, and abundance. The Arctic, with its rapid climate change and limited direct anthropogenic impact, is ideal for examining arthropod population dynamics. We use the most comprehensive, standardized dataset available on Arctic arthropods to evaluate the variability in population dynamics for the most common arthropod groups at various taxonomic levels across 24 years. Our results highlight that temporal trends of arthropod populations seem less directional in the Arctic than in temperate regions. Although abundances of some arthropod taxa are declining, particularly in recent decades, population trends still display high variation among time periods, taxa, and habitats.
The qBED track: a novel genome browser visualization for point processes
Authors: Moudgil Arnav , Li Daofeng , Hsu Silas , Purushotham Deepak , Wang Ting , Mitra Robi D.
Published: April 2020

Transposon calling cards is a genomic assay for identifying transcription factor binding sites in both bulk and single cell experiments. Here we describe the qBED format, an open, text-based standard for encoding and analyzing calling card data. In parallel, we introduce the qBED track on the WashU Epigenome Browser, a novel visualization that enables researchers to inspect calling card data in their genomic context. Finally, through examples, we demonstrate that qBED files can be used to visualize non-calling card datasets, such as CADD scores and GWAS/eQTL hits, and may have broad utility to the genomics community.

Availability and Implementation

The qBED track is available on the WashU Epigenome Browser (http://epigenomegateway.wustl.edu/browser), beginning with version 46. Source code for the WashU Epigenome Browser with qBED support is available on GitHub (http://github.com/arnavm/eg-reactandhttp://github.com/lidaof/eg-react). We have also released a tutorial on how to upload qBED data to the browser (dx.doi.org/10.17504/protocols.io.bca8ishw).
HiTea: a computational pipeline to identify non-reference transposable element insertions in Hi-C data
Authors: Jain Dhawal , Chu Chong , Alver Burak Han , Lee Soohyun , Lee Eunjung Alice , Park Peter J.
Published: April 2020

Hi-C is a common technique for assessing three-dimensional chromatin conformation. Recent studies have shown that long-range interaction information in Hi-C data can be used to generate chromosome-length genome assemblies and identify large-scale structural variations. Here, we demonstrate the use of Hi-C data in detecting mobile transposable element (TE) insertions genome-wide. Our pipeline HiTea (Hi-C basedTransposableelementanalyzer) capitalizes on clipped Hi-C reads and is aided by a high proportion of discordant read pairs in Hi-C data to detect insertions of three major families of active human TEs. Despite the uneven genome coverage in Hi-C data, HiTea is competitive with the existing callers based on whole genome sequencing (WGS) data and can supplement the WGS-based characterization of the TE insertion landscape. We employ the pipeline to identify TE insertions from human cell-line Hi-C samples. HiTea is available athttps://github.com/parklab/HiTeaand as a Docker image.
Age-dependent VDR peak DNA methylation as a mechanism for latitude-dependent MS risk
Authors: Ong Lawrence T C , Schibeci Stephen D , Fewings Nicole L , Booth David R , Parnell Grant P
Published: April 2020

Background

The mechanisms linking UV radiation and vitamin D exposure to the risk of acquiring the latitude and critical period dependent autoimmune disease, multiple sclerosis, is unclear. We examined the effect of vitamin D on DNA methylation as well as DNA methylation at vitamin D receptor binding sites in adult and paediatric myeloid cells.

Results

Very few DNA methylation changes occurred in adult and paediatric cells treated with calcitriol. However, several VDR binding sites across the genome demonstrated increased DNA methylation in cells of adult origin. Genes associated with these VDR binding sites were enriched for intracellular signalling and cell activation pathways, suggesting that age-dependent potential for myeloid cell differentiation and adaptive immune system regulation may be encoded for by DNA methylation.

Conclusions

These results suggest vitamin D exposure at critical periods in immune system development may contribute to the well characterised latitude related differences in autoimmune disease incidence.
Evolutionary Genetic Species Detected in Prokaryotes by Applying the K/θ Ratio to DNA Sequences
Authors: Birky C. William , Maughan Heather
Published: April 2020

Previous papers in this series described the “evolutionary genetic species concept” which is based on population genetic theory and should be applicable to any organism. Also described was a species criterion, the K/θ ratio, that delimits independently evolving evolutionary species based on single-gene sequences, and its application to sexual and asexual eukaryotes was illustrated. Here, we show how the evolutionary genetic species concept and the K/θ ratio can be applied to bacteria, using the sequences from some genes of the core genome that are rarely, if ever, transferred horizontally between different species. This completes the demonstration that K/θ is a general method for species delimitation, applicable to all organisms. Also, it adds to the evidence that bacteria have species in the most general sense, even though they have the ability to exchange genes across species boundaries. Finally, we show that a published critique of the use of K/θ ≥ 4 as a criterion for independently evolving species rests on two errors in the application of population/evolutionary genetic theory.
Overexpressed Nup88 stabilized through interaction with Nup62 promotes NFκB dependent pathways in cancer
Authors: Singh Usha , Samaiya Atul , Mishra Ram Kumar
Published: April 2020

Nuclear pores control nucleo-cytoplasmic trafficking and directly or indirectly regulate vital cellular processes. Nup88, important for Crm1 mediated nuclear export process, is overexpressed in many cancers. A positive correlation exists between progressive stages of cancer and Nup88 expression. However, links between Nup88 overexpression and head and neck cancer are insignificant, and mechanistic details are non-existent. Here, we report that Nup88 exhibits positive correlation in head and neck cancer in addition to elevated Nup62 levels. We demonstrate that Nup88 interacts with Nup62 in a cell-cycle and glycosylation independent manner. The overexpression of Nup88 or Nup62 imparts proliferation and migration advantages to cells. We further report that the interaction with Nup62 stabilizes Nup88 by inhibiting proteasome-mediated degradation of overexpressed Nup88. Overexpressed Nup88 is stabile and partly inside the nucleus and can interact with NFκB (p65). Nup88 overexpression induces proliferative and inflammatory responses downstream of p65. Altogether, we suggest that simultaneous overexpression of Nup62 and Nup88 in head and neck cancer stabilizes overexpressed Nup88. Stable Nup88 interacts with p65 and induces inflammatory, proliferative, and migratory advantages to cells, which perhaps is the underlying mechanism driving tumorigenic transformations.
Transient high glucose causes delayed wound healing by the DNMT1-mediated Ang-1/NF-κB pathway
Authors: Zhao Jingling , Yang Shuai , Chen Lei , Yang Ronghua , Xu Yingbin , Xie Julin , Liu Xusheng , Shu Bin , Qi Shaohai
Published: April 2020

The progression of diabetic complications does not halt despite termination of hyperglycemia, suggesting a “metabolic memory” phenomenon. However, whether metabolic memory exists in and affects the healing of diabetic wounds, as well as the underlying molecular mechanisms, remain unclear. In this study, we found that wound healing was delayed and angiogenesis was decreased in diabetic mice, despite normalization of glycemic control. Thus, we hypothesized that transient hyperglycemic spikes may be a risk factor for diabetic wound healing. We showed that transient hyperglycemia caused persistent damage to the vascular endothelium. Transient hyperglycemia directly upregulated DNMT1 expression, leading to the hypermethylation of Ang-1 and reduced Ang-1 expression, which, in turn, induced long-lasting activation of nuclear factor (NF)-κB and subsequent endothelial dysfunction. An in vivo study further showed that inhibition of DNMT1 promoted angiogenesis and accelerated diabetic wound healing by regulating the Ang-1/NF-κB signaling pathway. These results highlight the dramatic and long-lasting effects of transient hyperglycemic spikes on wound healing and suggest that DNMT1 is a novel target for diabetic vascular complications.
Genomic and immunogenic changes over the history of the Viral Hemorrhagic Septicemia (VHS-IVb) fish virus (=Piscine novirhabdovirus) in the Laurentian Great Lakes
Authors: Niner Megan D. , Stepien Carol A. , Gorgoglione Bartolomeo , Leaman Douglas W.
Published: April 2020

Viral Hemorrhagic Septicemia Virus (VHSV) (=Piscine novirhabdovirus) appeared in the Laurentian Great Lakes in 2005, constituting a unique and highly virulent genogroup (IVb), which killed >32 fish species in large 2005 and 2006. Periods of apparent dormancy punctuated smaller outbreaks in 2007, 2008, and 2017. We conducted the first whole genome analysis of IVb, evaluating its evolutionary changes using 46 isolates, in reference to immunogenicity in cell culture, and the genomes of other VHS genogroups (I–IVa) and other Novirhabdoviruses. IVb isolates had 253 genomic nucleotide substitutions (2.3% of the total 11,158 nucleotides), with 85 (16.6%) being non-synonymous. The greatest number of substitutions occurred in the non-coding region (NCDS; 4.3%) followed by theNv-(3.8%), andM-(2.8%) genes. TheM-gene possessed the greatest proportions of amino acid changes (52.9%), followed by theNv-(50.0%),G-(48.6%),N-(35.7%) andL-(23.1%) genes. Among VHS genogroups, IVa from the northeastern Pacific exhibited the fastest substitution rate (2.01×10-3), followed by Ivb (6.64×10−5), and I/III from Europe (4.09×10−5). A 2016 gizzard shad isolate from Lake Erie was the most divergent IVb isolate (38 NT, 15.0%, 15 AA), yet exhibited reduced virulence within vitroimmunogenicity analyses, as did other 2016 isolates, in comparison to the first IVb isolate (2003). The 2016 isolates exhibited lower impact on innate antiviral responses, suggesting phenotypic effects. Results suggest continued sequence change and lower virulence over the history of IVb, which may facilitate its long-term persistence in fish host populations.
A validation scale to determine the readiness of environmental DNA assays for routine species monitoring
Authors: Thalinger Bettina , Deiner Kristy , Harper Lynsey R. , Rees Helen C. , Blackman Rosetta C. , Sint Daniela , Traugott Michael , Goldberg Caren S. , Bruce Kat
Published: April 2020

The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. “in silicoanalysis”), and arranged on a 5-level validation scale from “incomplete” to “operational” with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimalin silicoandin vitrotesting, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.
Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation
Authors: Ren Wendan , Fan Huitao , Grimm Sara A , Guo Yiran , Kim Jae Jin , Li Linhui , Petell Christopher James , Tan Xiao-Feng , Zhang Zhi-Min , Coan John P. , Yin Jiekai , Gao Linfeng , Cai Ling , Detrick Brittany , Çetin Burak , Wang Yinsheng , Cui Qiang , Strahl Brian D. , Gozani Or , Miller Kyle M. , O’Leary Seán E. , Wade Paul A. , Patel Dinshaw J. , Wang Gang Greg , Song Jikui
Published: April 2020

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.