China's control measures may have prevented 700,000 COVID-19 cases
March 31, 2020
Science Daily/Penn State
China's control measures during the first 50 days of the COVID-19 epidemic may have delayed the spread of the virus to cities outside of Wuhan by several days and, by interrupting transmission nationwide, prevented more than 700,000 infections across the country, according to an international team of researchers. The findings, published March 31 in the journal Science, could be useful to countries that are still in early phases of the COVID-19 outbreak.
"The number of confirmed cases in China by day 50 (February 19) of the epidemic, was around 30,000," said Christopher Dye, visiting professor of zoology and visiting fellow at the Oxford Martin School, University of Oxford. "Our analysis suggests that without the Wuhan travel ban and the national emergency response there would have been more than 700,000 confirmed COVID-19 cases outside of Wuhan by that date. China's control measures appear to have worked by successfully breaking the chain of transmission -- preventing contact between infectious and susceptible people."
The researchers used a unique combination of case reports, human movement data and public health intervention information to investigate the spread and control of COVID-19. They examined the movements of 4.3 million people out of Wuhan before the travel ban, the types and timing of control measures implemented across the cities of China and the numbers of COVID-19 cases reported each day in every city.
"One fascinating aspect of our work is that it shows the power of novel data streams such as cell phone mobility data," said Ottar Bjornstad, distinguished professor of entomology and biology, Penn State. "Since the time period we studied included the Spring Festival holiday and Chinese Lunar New Year, we were able to compare patterns of travel into and out of Wuhan during the outbreak with cell phone data from two previous spring festivals. The analysis revealed an extraordinary reduction in movement following the travel ban of January 23, 2020. Based on this data, we could also calculate the likely reduction in Wuhan-associated cases in other cities across China."
The team's model also analyzed the specific effects of the Wuhan shutdown and found that it delayed the arrival of COVID-19 in other cities by several days. "This delay provided extra time to prepare for the arrival of COVID-19 in more than 130 cities," said Huaiyu Tian, associate professor of epidemiology, Beijing Normal University.
These cities banned public gatherings, closed entertainment venues and suspended public transport, among other actions. As a result, they reported 33% fewer confirmed cases during the first week of their outbreaks than cities that did not implement a Level 1 Response.
While the control measures taken thus far have reduced the number of COVID-19 infections to very low levels, China, is by no means out of the woods.
"Given the small fraction of the Chinese population that has been infected, a much larger number of people remains at risk of COVID-19," said Tian. "We are acutely aware that resident or imported infections could lead to a resurgence of transmission."
Bjornstad noted that SARS-CoV-2 may establish as a human endemic globally in the years to come.
"It is critical to keep in mind that this virgin epidemic likely will affect people of different ages and susceptibilities, and therefore have different fatality levels, than possible subsequent seasonal epidemics," he said.
https://www.sciencedaily.com/releases/2020/03/200331130012.htm
Wastewater test could provide early warning of COVID-19
March 31, 2020
Science Daily/Cranfield University
Researchers at Cranfield University are working on a new test to detect SARS-CoV-2 in the wastewater of communities infected with the virus.
The wastewater-based epidemiology (WBE) approach could provide an effective and rapid way to predict the potential spread of novel coronavirus pneumonia (COVID-19) by picking up on biomarkers in faeces and urine from disease carriers that enter the sewer system.
Rapid testing kits using paper-based devices could be used on-site at wastewater treatment plants to trace sources and determine whether there are potential COVID-19 carriers in local areas.
Dr Zhugen Yang, Lecturer in Sensor Technology at Cranfield Water Science Institute, said: "In the case of asymptomatic infections in the community or when people are not sure whether they are infected or not, real-time community sewage detection through paper analytical devices could determine whether there are COVID-19 carriers in an area to enable rapid screening, quarantine and prevention.
"If COVID-19 can be monitored in a community at an early stage through WBE, effective intervention can be taken as early as possible to restrict the movements of that local population, working to minimise the pathogen spread and threat to public health."
Recent studies have shown that live SARS-CoV-2 can be isolated from the faeces and urine of infected people and the virus can typically survive for up to several days in an appropriate environment after exiting the human body.
The paper device is folded and unfolded in steps to filter the nucleic acids of pathogens from wastewater samples, then a biochemical reaction with preloaded reagents detects whether the nucleic acid of SARS-CoV-2 infection is present. Results are visible to the naked eye: a green circle indicating positive and a blue circle negative.
"We have already developed a paper device for testing genetic material in wastewater for proof-of-concept, and this provides clear potential to test for infection with adaption," added Dr Yang. "This device is cheap (costing less than £1) and will be easy to use for non-experts after further improvement.
"We foresee that the device will be able to offer a complete and immediate picture of population health once this sensor can be deployed in the near future."
WBE is already recognised as an effective way to trace illicit drugs and obtain information on health, disease, and pathogens. Dr Yang has developed a similar paper-based device to successfully conduct tests for rapid veterinary diagnosis in India and for malaria in blood among rural populations in Uganda.
Paper analytical devices are easy to stack, store and transport because they are thin and lightweight, and can also be incinerated after use, reducing the risk of further contamination.
https://www.sciencedaily.com/releases/2020/03/200331092713.htm
Study helps to identify medications which are safe to use in treatment of COVID-19
March 30, 2020
Science Daily/King's College London
A recent study has found that there is no evidence for or against the use of non-steroidal anti-inflammatory drugs such as ibuprofen for patients with COVID-19.
The study, led by researchers at King's College London, also found other types of drugs, such as TNF blockers and JAK inhibitors safe to use.
89 existing studies on other coronavirus strains such as MERS and SARS, as well as the limited literature on COVID-19, were analysed to find out if certain pain medications, steroids, and other drugs used in people already suffering from diseases should be avoided if they catch COVID-19.
Some patients, for example those with cancer, are already given immunosuppressive drugs -- therapies that can lower the body's immune system -- or immunostimulant drugs -- therapies that boost it. If these patients then catch COVID-19, doctors need to know what medication to stop.
Dr Mieke Van Hemelrijck, a cancer epidemiologist and an author on the paper, said "This pandemic has led to challenging decision-making about the treatment of COVID-19 patients who were already critically unwell. In parallel, doctors across multiple specialties are making clinical decisions about the appropriate continuation of treatments for patients with chronic illnesses requiring immune suppressive medication."
The article has been published in ecancermedicalscience, an open access oncology journal, and is authored by researchers from King's College London and Guy's and St. Thomas NHS Foundation Trust, London.
There had been some speculation that non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen might make things worse for some COVID-19 patients, but the researchers did not find evidence to support this statement.
Other types of drugs such as TNF blockers and JAK inhibitors, used to treat arthritis or other forms of inflammation, were also found to be safe to use. Another class of drug known as anti-interleukin-6 agents is being investigated for helping to fight COVID-19, although there is no conclusive proof yet.
The researchers found that low amounts of prednisolone or tacrolimus therapy may be helpful in treating COVID-19. Co- author, Dr Sophie Papa, a medical oncologist and immunologist said: "Current evidence suggests that low dose prednisolone (a steroid used to treat allergies) and tacrolimus therapy (an immunosuppressive drug given to patients who have had an organ transplant) may have beneficial impact on the course of coronavirus infections. However further investigation is needed."
As more people catch the disease, researchers will continue to investigate how it interacts with commonly used medications and make further guidance recommendations.
https://www.sciencedaily.com/releases/2020/03/200330152143.htm
Experimental AI tool predicts which COVID-19 patients develop respiratory disease
March 30, 2020
Science Daily/NYU Langone Health / NYU School of Medicine
An artificial intelligence tool accurately predicted which patients newly infected with the COVID-19 virus would go on to develop severe respiratory disease, a new study found.
The work was led by NYU Grossman School of Medicine and the Courant Institute of Mathematical Sciences at New York University, in partnership with Wenzhou Central Hospital and Cangnan People's Hospital, both in Wenzhou, China.
Named "SARS-CoV-2," the new virus causes the disease called "coronavirus disease 2019" or "COVID-19." As of March 30, the virus had infected 735,560 patients worldwide. According to the World Health Organization, the illness has caused more than 34,830 deaths to date, more often among older patients with underlying health conditions. The New York State Department of Health has reported more than 33,700 cases to date in New York City.
Published online March 30 in the journal Computers, Materials & Continua, the study also revealed the best indicators of future severity, and found that they were not as expected.
"While work remains to further validate our model, it holds promise as another tool to predict the patients most vulnerable to the virus, but only in support of physicians' hard-won clinical experience in treating viral infections," says corresponding study author Megan Coffee, MD, PhD, clinical assistant professor in the Division of Infectious Disease & Immunology within the Department of Medicine at NYU Grossman School of Medicine.
"Our goal was to design and deploy a decision-support tool using AI capabilities -- mostly predictive analytics -- to flag future clinical coronavirus severity," says co-author Anasse Bari, PhD, a clinical assistant professor in Computer Science at the Courant institute. "We hope that the tool, when fully developed, will be useful to physicians as they assess which moderately ill patients really need beds, and who can safely go home, with hospital resources stretched thin."
Surprise Predictors
For the study, demographic, laboratory, and radiological findings were collected from 53 patients as each tested positive in January 2020 for the SARS-CoV2 virus at the two Chinese hospitals. Symptoms were typically mild to begin with, including cough, fever, and stomach upset. In a minority of patients, however, severe symptoms developed with a week, including pneumonia.
The goal of the new study was to determine whether AI techniques could help to accurately predict which patients with the virus would go on to develop Acute Respiratory Distress Syndrome or ARDS, the fluid build-up in the lungs that can be fatal in the elderly.
For the new study, the researchers designed computer models that make decisions based on the data fed into them, with programs getting "smarter" the more data they consider. Specifically, the current study used decision trees that track series of decisions between options, and that model the potential consequences of choices at each step in a pathway.
The researchers were surprised to find that characteristics considered to be hallmarks of COVID-19, like certain patterns seen in lung images (e.g. ground glass opacities), fever, and strong immune responses, were not useful in predicting which of the many patients with initial, mild symptoms would go to develop severe lung disease. Neither were age and gender helpful in predicting serious disease, although past studies had found men over 60 to be at higher risk.
Instead, the new AI tool found that changes in three features -- levels of the liver enzyme alanine aminotransferase (ALT), reported myalgia, and hemoglobin levels -- were most accurately predictive of subsequent, severe disease. Together with other factors, the team reported being able to predict risk of ARDS with up to 80 percent accuracy.
ALT levels -- which rise dramatically as diseases like hepatitis damage the liver -- were only a bit higher in patients with COVID-19, researchers say, but still featured prominently in prediction of severity. In addition, deep muscle aches (myalgia) were also more commonplace, and have been linked by past research to higher general inflammation in the body.
Lastly, higher levels of hemoglobin, the iron-containing protein that enables blood cells to carry oxygen to bodily tissues, were also linked to later respiratory distress. Could this explained by other factors, like unreported smoking of tobacco, which has long been linked to increased hemoglobin levels? Of the 33 patients at Wenzhou Central Hospital interviewed on smoking status, the two who reported having smoked, also reported that they had quit.
Limitations of the study, say the authors, included the relatively small data set and the limited clinical severity of disease in the population studied. The latter may be due in part to an as yet unexplained dearth of elderly patients admitted into the hospitals during the study period. The average patient age was 43.
"I will be paying more attention in my clinical practice to our data points, watching patients closer if they for instance complain of severe myalgia," adds Coffee. "It's exciting to be able to share data with the field in real time when it can be useful. In all past epidemics, journal papers only published well after the infections had waned."
https://www.sciencedaily.com/releases/2020/03/200330152135.htm
Lessons from the Spanish flu: Early restrictions lowered disease, mortality rates
March 30, 2020
Science Daily/Loyola University Health System
A review of published data and analysis on the Spanish flu, found that cities that adopted early and broad isolation and prevention measures had disease and mortality rates that were 30% to 50% lower than other cities.
Large events are cancelled, restaurants and non-essential businesses are closed, and in many states, residents have been asked to shelter in place, all to limit the spread and impact of the COVID-19 virus. But are strict and early isolation and other preventative mandates really effective in minimizing the spread and impact of a disease outbreak?
Stefan E. Pambuccian, MD, a Loyola Medicine cytologist, surgical pathologist and professor and vice chair of the Department of Pathology and Laboratory Medicine at Loyola University Chicago Stritch School of Medicine, has reviewed published data and research from three papers dating back to the 1918-19 Spanish flu pandemic, which infected one-fifth to one-third of the world's population and killed 50 million people.
According to the data and analysis, cities that adopted early, broad isolation and prevention measures -- closing of schools and churches, banning of mass gatherings, mandated mask wearing, case isolation and disinfection/hygiene measures -- had lower disease and mortality rates. These cities included San Francisco, St. Louis, Milwaukee and Kansas City, which collectively had 30% to 50% lower disease and mortality rates than cities that enacted fewer and later restrictions. One analysis showed that these cities also had greater delays in reaching peak mortality, and the duration of these measures correlated with a reduced total mortality burden.
"The stricter the isolation policies, the lower the mortality rate," says Dr. Pambuccian. He studied the Spanish flu, including prevention measures and outcomes, to help develop standards for staffing and safety in the cytology lab, where infectious diseases like the COVID-19 virus are diagnosed and studied at the cellular level. His broader article appeared online this week in the Journal of the American Society of Cytopathology.
Like today, not everyone in 1918 and 1919 thought the strict measures were appropriate or effective at the time.
An estimated 675,000 people died in the U.S. from the Spanish flu, "and there was skepticism that these policies were actually working," says Dr. Pambuccian. "But they obviously did make a difference."
In 1918, the world was still at war "with overcrowded barracks," and much of the U.S. lived with "poverty, poor nutrition, poor hygiene, household/community-level crowding, and a lack of preparation of the population and decision makers due to cognitive inertia and poor medical and insufficient nursing care," says Dr. Pambuccian.
"Although the world is a much different place than it was 100 years ago, the efficacy of the measures instituted during the 1918-19 pandemic gives us hope that the current measures will also limit the impact of the COVID-19 pandemic."
https://www.sciencedaily.com/releases/2020/03/200330110344.htm
Some COVID-19 patients still have coronavirus after symptoms disappear
March 27, 2020
Science Daily/American Thoracic Society
Researchers found that half of the patients they treated for mild COVID-19 infection still had coronavirus for up to eight days after symptoms disappeared.
In a new study, researchers found that half of the patients they treated for mild COVID-19 infection still had coronavirus for up to eight days after symptoms disappeared. The research letter was published online in the American Thoracic Society's American Journal of Respiratory and Critical Care Medicine.
In "Time Kinetics of Viral Clearance and Resolution of Symptoms in Novel Coronavirus Infection," Lixin Xie, MD, Lokesh Sharma, PhD, and co-authors report on a study of 16 patients with COVID-19, who were treated and released from the Treatment Center of PLA General Hospital in Beijing between January 28 and Feb. 9, 2020. Patients studied had a median age of 35.5 years.
Researchers collected samples from throat swabs taken from all patients on alternate days and analyzed. Patients were discharged after their recovery and confirmation of negative viral status by at least two consecutive polymerase chain reaction (PCR) tests.
"The most significant finding from our study is that half of the patients kept shedding the virus even after resolution of their symptoms," said co-lead author Dr. Sharma, instructor of medicine, Section of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, Yale School of Medicine. "More severe infections may have even longer shedding times."
The primary symptoms in these patients included fever, cough, pain in the pharynx (pharyngalgia) and difficult or labored breathing (dyspnea). Patients were treated with a range of medications.
The time from infection to onset of symptoms (incubation period) was five days among all but one patient. The average duration of symptoms was eight days, while the length of time patients remained contagious after the end of their symptoms ranged from one to eight days. Two patients had diabetes and one had tuberculosis, neither of which affected the timing of the course of COVID-19 infection.
"If you had mild respiratory symptoms from COVID-19 and were staying at home so as not to infect people, extend your quarantine for another two weeks after recovery to ensure that you don't infect other people," recommended corresponding author Lixin Xie, MD, professor, College of Pulmonary and Critical Care Medicine, Chinese PLA General Hospital, Beijing.
The authors had a special message for the medical community: "COVID-19 patients can be infectious even after their symptomatic recovery, so treat the asymptomatic/recently recovered patients as carefully as symptomatic patients."
The researchers emphasized that all of these patients had milder infections and recovered from the disease, and that the study looked at a small number of patients. They noted that it is unclear whether similar results would hold true for more vulnerable patients such as the elderly, those with suppressed immune systems and patients on immunosuppressive therapies.
"Further studies are needed to investigate if the real-time PCR-detected virus is capable of transmission in the later stages of COVID-19 infection," Dr. Xie added.
https://www.sciencedaily.com/releases/2020/03/200327091234.htm
'Feeling obligated' can impact relationships during social distancing
March 19, 2020
Science Daily/Michigan State University
In a time where many are practicing "social distancing" from the outside world, people are relying on their immediate social circles more than usual. Does a sense of obligation -- from checking on parents to running an errand for an elderly neighbor -- benefit or harm a relationship? A Michigan State University study found the sweet spot between keeping people together and dooming a relationship.
"We were looking to find whether obligation is all good or all bad," said William Chopik, assistant professor of psychology at MSU and co-author of the study. "When we started, we found that people were responding to types of obligations in different ways. People distinguished between requests that were massive obligations and requests that were simple. There's this point that obligation crosses over and starts to be harmful for relationships."
According to Jeewon Oh, MSU doctoral student and co-author of the study, obligation is sometimes the "glue that holds relationships together," but it often carries negative connotations.
"We found that some obligations were linked with greater depressive symptoms and slower increases in support from friends over time," Oh said. "However, other obligations were linked with both greater support and less strain from family and friends initially."
Chopik and Oh's findings suggest that there's a distinct point at which obligation pushes individuals to the brink of feeling burdened, which can start to harm their relationships.
"The line in our study is when it crosses over and starts to be either a massive financial burden or something that disrupts your day-to-day life," Chopik said. "While engaging in substantive obligation can benefit others and make someone feel helpful, it is still costly to a person's time, energy and money."
Until now, similar research showed inconsistencies in how obligation impacts relationships, which Chopik attributes to the spectrum of obligation. This spectrum ranges from light obligation, like keeping in touch with a friend, to substantive obligation, like lending that friend a considerable amount of money.
"In a way, major obligations violate the norms of friendships," Chopik said. "Interestingly, you don't see that violation as much in relationships with parents or spouses."
Chopik explained that friendships are viewed as low-investment, fun relationships that make people feel good.
"Our longest lasting friendships continue because we enjoy them. But if obligations pile up, it might compromise how close we feel to our friends," Chopik said. "Because friendships are a relationship of choice, people can distance themselves from friends more easily than other types of relationships when faced with burdensome obligations."
Additionally, substantive obligations may create strain in a friendship as we try to encourage our friends to do the same even when they might not be able to do so, Oh said.
"Although we may feel good when we do things for our friends, and our friends are grateful to us, we may start to feel like we are investing too much in that relationship," Oh said.
On the other end of the spectrum, light obligation creates what Chopik calls a "norm of reciprocity."
"Those light obligations make us feel better, make us happier and make our relationships stronger," Chopik said. "There's a sense that 'we're both in this together and that we've both invested something in the relationship.'"
That's why, among the best relationships, low-level acts of obligation don't feel like obligations at all. Small acts of kindness, which strengthen the bonds of our relationships, are done without any fuss or burden.
Still, some types of relationships can make even minor obligations seem daunting. If someone doesn't have a great relationship with a parent, a quick phone call to check in isn't enjoyable, it's an encumbrance.
"Even for things we would expect family members to do, some in the study did them begrudgingly," Chopik said.
Chopik and Oh's findings reveal a spectrum of obligations as diverse as the relationships one has in life.
"It's the little things you do that can really enhance a friendship, but asking too much of a friend can damage your relationship," Chopik said.
https://www.sciencedaily.com/releases/2020/03/200319125132.htm
How to boost immune response to vaccines in older people
Apply immune expertise and some genital wart cream!
March 27, 2020
Science Daily/Babraham Institute
Identifying interventions that improve vaccine efficacy in older persons is vital to deliver healthy aging for an aging population. Immunologists have identified a route for counteracting the age-related loss of two key immune cell types by using genital wart cream to boost immune response to vaccination in aged mice. After this validation in mice, the findings offer an attractive intervention to tailor the make-up of vaccines for older people.
Research just published by the Linterman lab shows that the immune system of older mice can be given a helping hand by applying immunology expertise and some genital wart treatment (don't try this at home just yet)!
Mice and humans show similar age-dependent changes in their immune system so this finding offers hope for easily increasing the robustness of vaccination response in the older population.
As we age, the function of our immune system declines, rendering us more susceptible to infections, and making us less able to generate protective immunity after vaccination. By understanding the cellular and molecular mechanisms that underpin this poor response in older individuals, researchers in the Linterman lab were able to repurpose an existing treatment for genital warts, and demonstrate that this was effective in overcoming the age-related effects on two of the many cell types making up our immune system. The research is published online in the journal eLife.
Dr Michelle Linterman, a group leader in the Institute's Immunology research programme, said: "The current coronavirus pandemic highlights that older members of our families and communities are more susceptible to the morbidity and mortality associated with infectious diseases. Therefore, it is imperative that we understand how the immune system in older people works, and to explore how we might be able to boost their immune responses to vaccines to ensure they work well in this vulnerable part of our society."
Vaccines work by generating antibodies that are able to block the ability of pathogens to infect us. Antibody secreting cells are produced in the germinal centre, immune reaction hubs that forms after infection or vaccination. With age, the magnitude and quality of the germinal centre reaction declines.
Immune cells called T follicular helper cells are essential to the germinal centre response. In this study the team used mice and humans to investigate why T follicular helper cell numbers decline with age, and if there is a way to boost them upon vaccination.
"The germinal centre response is a highly collaborative process that requires multiple cell types to interact at the right place and the right time. Therefore, it made sense to us that defects in one or more of these cell types could explain the poor germinal centre response observed in older individuals after vaccination," explains Dr Linterman.
The researchers found that older mice and humans form fewer T follicular helper cells after vaccination, which is linked with a poor germinal centre response and antibody response. By developing our understanding of the cellular and molecular events occurring in the germinal centre after vaccination, the researchers identified that T follicular helper cells in older mice and people received less stimulatory interactions from their immune system co-workers. By using a cream (imiquimod, currently used to treat genital warts in humans) on the site of immunisation to boost the number of stimulatory cells, they were able to restore the formation of T follicular helper cells in older mice and also rescue the age-dependent defects in another immune cell type (dendritic cells). Encouragingly, this demonstrates that the age-related defects in T follicular helper cell formation in ageing are not irreversible, and can be overcome therapeutically.
The full picture and evaluation of whether this approach will work as an intervention in humans requires more research into why the germinal centre response changes with age, and what can be done to overcome this. Once achieved, it could be that clinical trials are established to incorporate this knowledge into new vaccine formulations for older people.
https://www.sciencedaily.com/releases/2020/03/200327113752.htm
Standardizing COVID-19 data analysis to aid international research efforts
March 27, 2020
Science Daily/Center for Genomic Regulation
Researchers from the Centre for Genomic Regulation (CRG) have launched a new database to advance the international research efforts studying COVID-19.
The publicly-available, free-to-use resource (https://covid.crg.eu) can be used by researchers from around the world to study how different variations of the virus grow, mutate and make proteins.
"Scientists are working round the clock to understand SARS-CoV-2, the virus causing COVID-19, so that we can find its weak spots and beat it. A huge amount of scientific data is being published around the world," says Eva Novoa, a researcher at the CRG in Barcelona.
"However, some of the technologies we use to study SARS-CoV-2, such as nanopore RNA sequencing, are so new that the results of one paper aren't comparable to another due to the patchwork of different standards and methodologies used. We are taking all this data and analyzing it so that it meets a more universally comparable standard. This will help researchers more quickly and accurately spot the strengths and weaknesses of the coronavirus."
To understand how the coronavirus grows, mutates and replicates, scientists have to sequence the RNA of COVID-19. The RNA sequence reveals crucial information about the proteins the virus makes to invade human cells and replicate, which in turn informs governments on the infectiousness and severity of the pandemic.
Traditional sequencing tools can take a long time to provide results. In recent years, sequencing data in real time has become a reality thanks to the use of nanopore sequencing technologies, revolutionizing genomics research and disease outbreak monitoring. Nanopore sequencing provides scientists and clinicians with immediate access to the DNA and RNA sequence information of any living cell in real-time, enabling a rapid response against the threat of a pandemic.
However, the raw data produced by nanopore sequencing is highly complex. Scientists and clinicians currently lack systematic guidelines for the reproducible analysis of the data, limiting the vast potential of the nascent technology.
To standardize the analysis of publicly available SARS-CoV-2 nanopore sequencing data, researchers at the Centre for Genomic Regulation (CRG) in Barcelona are using MasterOfPores, a computer program developed by the group of Eva Novoa and CRG Bioinformatics Unit. The software was first described last week in Frontiers in Genetics.
"The internet and an increasing culture of open science, data sharing and preprints have transformed the research landscape. Infrastructure that would take months to set up to research an emerging virus can now be done in just a few days owing to novel scientific computing approaches," says Julia Ponomarenko, Head of the Bioinformatics Unit at the CRG.
MasterOfPores can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies, and is freely available in Github. The publicly-available, free-to-use resource has currently analysed 3TB of SARS-CoV-2 nanopore RNA sequencing data. The CRG researchers will continue to update the resource with new data as soon as it becomes available.
https://www.sciencedaily.com/releases/2020/03/200327122315.htm
COVID-19 linked to cardiac injury, worse outcomes for patients with heart conditions
March 27, 2020
Science Daily/University of Texas Health Science Center at Houston
COVID-19 can have fatal consequences for people with underlying cardiovascular disease and cause cardiac injury even in patients without underlying heart conditions, according to a review published today in JAMA Cardiology by experts at The University of Texas Health Science Center at Houston (UTHealth).
Experts have known that viral illnesses such as COVID-19 can cause respiratory infections that may lead to lung damage and even death in severe cases. Less is known about the effects on the cardiovascular system.
"It is likely that even in the absence of previous heart disease, the heart muscle can be affected by coronavirus disease," said Mohammad Madjid, MD, MS, the study's lead author and an assistant professor of cardiology at McGovern Medical School at UTHealth. "Overall, injury to heart muscle can happen in any patient with or without heart disease, but the risk is higher in those who already have heart disease."
The study authors explained that research from previous coronavirus and influenza epidemics suggest that viral infections can cause acute coronary syndromes, arrhythmias, and the development of, or exacerbation of, heart failure.
In a clinical bulletin issued by the American College of Cardiology, it was revealed that the case fatality rate of COVID-19 for patients with cardiovascular disease was 10.5%. Data also points to a greater likelihood that individuals over the age of 65 with coronary heart disease or hypertension can contract the illness, as well experience more severe symptoms that will require critical care.
According to the study authors, critical cases are those that reported respiratory failure, septic shock, and/or multiple organ dysfunction or failure that resulted in death. "It is reasonable to expect that significant cardiovascular complications linked to COVID-19 will occur in severe symptomatic patients because of the high inflammatory response associated with this illness," said Madjid, who also sees patients at the UT Physicians Multispecialty -- Bayshore clinic.
The novel virus that causes COVID-19 was first identified in January 2020. This novel virus originated in Wuhan, China, and by March 11, 2020, the World Health Organization had declared it a global pandemic. The three most common symptoms of COVID-19 include fever, cough, and shortness of breath. Other less common symptoms are muscle pain, sore throat, nasal congestion, and headache. Symptoms can appear as soon as two days after exposure to the virus to up to14 days after. There is a high viral load in both symptomatic and asymptomatic patients, meaning asymptomatic spread between person to person is likely.
Previously identified coronaviruses known to cause severe illness in humans include Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrome (MERS-CoV). SARS-CoV was first identified in southern China in 2002, and by 2003 it had killed over 8,000 individuals in 29 countries. Data suggests that SARS-CoV may have resulted in cardiovascular complications, such as acute coronary syndrome and myocardial infarction. MERS-CoV was first discovered in 2012 in Saudi Arabia. As of 2019, 2,494 cases have been confirmed along with 858 deaths in 26 countries.
Current COVID-19 treatment options are being researched, and there is a large effort to develop vaccines for prevention and to test antivirals for the treatment of the disease. In the meantime, the study authors encourage all individuals to consult with their health care providers about being vaccinated against influenza and that at-risk patients seek advice on receiving a pneumonia vaccine from their primary care physician. While these vaccines will not provide specific protection against COVID-19, they can help prevent superimposed infections alongside COVID-19.
https://www.sciencedaily.com/releases/2020/03/200327113743.htm