Health Archives - Omics Help Desk

8Jan '21

COVID-19 vaccines are needed now more than ever. They arrive right on time as UK’s and South Africa’s problematic new strains emerge, B.1.1.7 and 501Y.V2, respectively. The strains have multiple mutations that appear to make the virus more transmissible. Both strains are different but share a mutation – called N501Y – which is in a crucial part of the virus that it uses to infect the body’s cells. The UK strain is now being discovered in many countries around the world.

Many people and also scientists ask themselves:

What happened? Why now?

COVID-19 mutates quickly during infection – What does it mean for us?

patyb

Health

26Mar '20

The image shows a transmission electron microscope image showing the new coronavirus emerging from the surface of human cells. (Image: © NIAID-RML)

A study by Shen et al. published on March 9th 2020, has shown by analyzing the lung microbiota (the microbes in the lung) of people infected with the coronavirus SARS-CoV-2, that the virus “evolves in vivo” after infection. “Evolves in vivo” means the virus evolves or mutates inside the body of an infected person during the infection. The virus undergoes a strong immunologic pressure in humans, and may thus accumulate mutations to outmaneuver the immune system. This observation implies that the evolution of the virus may affect its virulence or how it affects a person’s disease progression. This evolution may also affect its infectivity or how quickly the virus can replicate or reproduce itself inside the human body. And it may affect its transmissibility, or how easily the virus can be transmitted to other people.

It is not clear if or how this mutated virus is spread in the population, but the article recommends to strengthen the surveillance of the viral evolution in the population.

In conclusion, this small but significant study of 8 SARS-CoV-2 patients, makes many critical observations related to the quick evolution of the virus, but it suggests that more research is needed to understand what it means for us.

Coronavirus Web Site Visualizations with Stats

patyb

Health

23Mar '20

Figure shows a screenshot of the Genomic epidemiology of novel coronavirus. Maintained by the Nextstrain team. Enabled by data from GISAID. Showing 955 of 955 genomes sampled between Dec 2019 and Mar 2020.

Earlier we shared a Coronavirus vs Influenza Table listing the differences between the coronavirus and the flu. The numbers in the table are updated continuously as new data is reported by reputable organizations such as the World Health organization (WHO) and Center for Disease Control (CDC) of countries that are funding and managing them well. Here we offer a list of the most informative, most helpful, and best-designed online visualizations of the coronavirus pandemic.

Latest List Update: December 6 2020

These Coronavirus SARS-CoV-2 web sites offer different types of statistics and visualizations:

Comparison of Coronavirus and the Flu

patyb

Health

8Mar '20

Latest Table Update: August 8, 2020 (Table below text)

Some say the coronavirus is just like the flu. Is it? The answer is that while there are similarities, no, the coronavirus is not like the flu. It is different in many important ways. The main difference is the fact that when it spread in early 2020 in the Western world, people did not have immunity to the coronavirus because it was brand new and there is still no vaccine against it. No reason to panic but we should be cautious. The most similar virus based on the RNA sequence is SARS not influenza. The risk to children is moderate for coronavirus but is high for influenza. The mortality rate for coronavirus is much higher than influenza and varies between countries. The mortality rate in August 2020 was (5.3% in China) (14% in Italy) (2% in South Korea) (3.3% in USA), while for influenza it is 0.1% as measured in the 2018-2019 influenza season. The risk for the elderly is about 20% higher for coronavirus. The time that people who are infected with coronavirus remain infectious or contagious is 17-24 (middle 50%) while for influenza it is 8 days. Coronavirus survives on surfaces for up to 9 days while the flu virus only 2 days. On May 1 2020, the FDA issued an emergency use authorization (EUA) for the investigational antiviral drug remdesivir for the treatment of COVID-19. On June 15 2020, the FDA revoked the EUA for drug Hydroxychloroquine as a drug to treat coronavirus infections due to risk of heart rhythm problems.

The numbers in this table will be updated as new data is reported by reputable organizations such as the World Health organization (WHO) and Center for Disease Control (CDC) of countries that are funding and managing them well.

The Day You Test Your Viruses at Home

patyb

Health

3Mar '20

One day, people will be able to buy a ‘lab in a suitcase’, and use it to test their viruses at home or when travelling abroad or anywhere. It could be a great way to prevent the spread of viral epidemics. No, it is not available yet, but it might be for the next outbreak, if the Oxford Nanopore device manufacturers make the end-to-end testing workflow easy and the price affordable.

A group of scientists from the ARTIC group are working with Oxford Nanopore to sequence the coronavirus COVID-19 in real-time, contributing to a rapid 8-hour end-to-end workflow. Currently, once a sample is received by a laboratory, and that may also take time, it takes 24 hours to get a result, 24-48 hours in some locations.

In January, Oxford Nanopore noted that it had sent 200 of their portable MinION devices to China, to enable the rapid, local sequencing of the coronavirus COVID-19 .

The scientists from universities of Edinburgh, Birmingham, Cambridge, Oxford, KU Leuven, UCLA and the Fred Hutchinson Cancer Centre, had previously developed and delivered ‘lab in a suitcase’ sequencing resources/solutions and collaborative local training in multiple outbreaks including Ebola, Zika virus and Yellow Fever.

What if people could test their coronavirus COVID-19 at home? How would it have changed the current outbreak and epidemic pattern?

Can you transform yourself from a couch potato to an elite athlete? Maybe with omics.

patyb

Health

21Jan '20

Studies have found that certain bacteria make mice run longer on the treadmill. They have found the same bacteria in the human gut of athletes right after exercise. Does it mean that if we had those strains of bacteria in our system, we could improve our endurance when doing sports? Science seems to point to a yes answer. Other studies have looked at epigenetic markers in people who exercise, and have seen marked changes in some cells, because epigenetics change the activity of our genes, usually by “silencing” some genes. Many of us know or can guess that our athletic potential is linked to our genes, but what if those genes are silenced, and what if our bacteria can bring their own genes into play?

There are many genes that are associated with athletic performance, the most well-known ones are ACTN3 and ACE. Studies have found that most elite power athletes have a specific genetic variant of the ACTN3 gene, the fast twitch muscle gene, and gene ACE, which is associated with human physical performance. What is now being studied is how our genes are modified sometimes on a daily basis through epigenetics, especially through a process called methylation. A study by Schenk et al 2019 studied epigenetic changes in five healthy women who performed an incremental step test. Blood samples were taken before and after exercise to study 33 methylation markers in their natural killer cells (NKC). NKC have an important role in controlling immune responses and inflammation, and it is known that inflammation increases after strenuous exercise. The study found that after acute exercise, DNA-methylation was changed, with 25 genes showing increased and some decreased methylation. It was surprising for them to observe that DNA-methylation which was thought to be a more stable epigenetic modification could be so dynamic.

Sleep problems? Your microbiome may have some answers!

patyb

Health

13Jan '20

We have known for a while that the population of bacteria in our gut, our gut microbiome, affects the digestive, metabolic, and immune functions in our bodies, but science is showing that it also regulates our sleep and mental states through the microbiome-gut-brain axis. A scientific review study by Rijo-Ferreira and Takahashi published December 2019, discusses how our sleep and wake cycles, also called circadian rhythms, are affected by our genes, by our metabolism, by time-restricted feeding protocols, and by our microbiome.

An earlier review study by Li et al 2018, listed several gut bacteria that affect sleep. For example, some spore-forming bacteria, primarily from the Clostridium genus, modulate the amount of serotonin in the blood. Serotonin is known to promote REM sleep and low levels of serotonin are linked to the development of depression. In addition, Escherichia coli and Enterococcus, which are common in the intestinal tract, also produce small amounts of serotonin. The bacteria Lactobacillus and Bifidobacterium can secrete the neurotransmitter GABA, and abnormal expression of GABA mRNA is often observed in patients with depression and insomnia.

Discussing Yang’s Claim in the Context of a Healthcare Human-in-the-Loop AI Model

patyb

Health

7Jan '20

Democratic Presidential Candidate Andrew Yang foresees a future where artificial intelligence (AI) and the automation of jobs will lead to the disintegration of our society with human workers being replaced by machines, which is one of his main campaign messages.

As stated in a November 2019 article by Martin Ford in The Hill: “AI and automation will disrupt our world — but only Andrew Yang is warning about it”. The article also includes these statistics:

A recent report from the consulting firm Deloitte found that, among more than a thousand surveyed American executives, 63 percent agreed with the statement that “to cut costs, my company wants to automate as many jobs as possible using AI,” and 36 percent already believe that job losses from AI-enabled automation should be viewed as an ethical issue.

The statements are usually attributed to manufacturing jobs and low-paid jobs, definitely not highly educated professionals, like lawyers, doctors, or scientists. Yet lawyers and doctors will also see a decline in demand when AI takes over decision making in their fields. But for those decisions to be made, the machines will have to learn correctly. So, what kind of humans will still be needed to perform any work that machines cannot do?

Apart form certain service industry jobs where humans prefer human touch or human communication such as nurses, masseuses, waiters, the only other jobs that will not only be available but highly requested besides computer and robot programmers, are data scientists. Data scientists clean and prepare the data and configure the machine learning models to learn from the data.

An IBM survey by a different Wang (Dakuo Wang et al 2019) looked at “Human-AI Collaboration in Data Science: Exploring Data Scientists’ Perceptions of Automated AI”. The goal of the study was to understand data scientists current work practices and how these practices might change with Automated AI (AutoAI). Reactions were reported to be mixed with some expressing concern about the trend of automating their jobs which they also strongly felt was inevitable while others remained optimistic about their future job security due to a view that the future of data science work will be a collaboration between humans and AI systems.

The portable MinION sequences a microbiome in 1-5 hours – Can we use it at home?

patyb

Health

30Dec '19

A study by Leggett et al 2019, published in December, presents results from using the portable MinION to sequence the microbiome of preterm newborns admitted to the neonatal intensive care unit of a university hospital. The bacterial DNA sequence analysis pipeline developed by the authors of the study obtained a majority of the results (or 70% of reads) after 1 hour with no more differences found after 6 hours. In this short time, the pipeline identified pathogenic bacteria and their corresponding antimicrobial resistance gene profiles, which for patients in the ICU can provide a lifesaving diagnosis when deciding on the right antibiotic.

Some of the remarkable features of the MinION, which is produced by Oxford Nanopore Technologies (ONT) are the small size of the DNA sequencing device, the long read length of the DNA sequences, and the sequencing speed. 1 to 6 hours is very quick compared to current rapid clinical microbiology tests, which include determination of antibiotic susceptibility, and take between 36 and 48 hours. More widely-used and larger DNA sequencers like Illumina MiSeq take between 4 and 55 hours for a run according to the Illumina web site. This new research presents a promising life-saving diagnostic tool in the clinical setting, but one wonders, if it is so small and portable and so quick to sequence DNA, can we use it at home to sequence our own microbiome?

The answer would be yes if we disregard for a moment the “wet lab” hurdles required to operate the MinION. Having a little home DNA sequencer would allow us not only to monitor an infection by sequencing our microbiome early on, when we feel we are coming down with something, but also monitor our overall health and moods now that we have so much evidence of how the gut-brain axis affects our well-being and how our diet, our fitness, and our moods affect our microbiome.

Insomnia – When your genes and emotions cause havoc at nighttime

patyb

Health

20Dec '19

It is said that someone “suffers” from insomnia, but we do not say someone suffers from a cold, or a flue, or even cancer. New studies are showing that suffering is the correct verb to use in this context. Two studies published in 2019 found that insomnia is linked to emotional disorders. One study by (Wassing et al. 2019) found that people with insomnia have a hard time forgetting painful or shameful past experiences compared to normal sleepers who settle those emotions during sleep. By now we know that sleep helps consolidate experiences in memory, which is essential for learning new information, but sleep also helps clear away emotional distress triggered during those experiences. The study looked at MRI images of people with insomnia and found a neurobiological link between long-lasting emotional distress and hyperarousal or inability to sleep.

The second study by (Jansen et al. 2019) looked at the genes that are linked to insomnia in a large study of over one million people with insomnia from 23andMe research participants. It discovered many insomnia-risk genes which are expressed in limbic circuits and are involved in disturbed emotion processing and more specifically in depression, anxiety, attention deficit hyperactivity disorder (ADHD), and neuroticism. Among the prominent insomnia-risk genes are MEIS1, LRGUK, and BTBD9 and several genes that are expressed in the brain. MEIS1 is associated with insomnia complaints and restless legs syndrome (RLS). Although RLS is a physical disorder, a study by (Tully et al. 2019) found an association between RLS and anxiety-depression comorbidity. LRGUK was also found to be associated with type 2 diabetes and autism spectrum disorder. BTBD9 is part of a pathway that regulates circadian rhythms, it is expressed in the brain and has been associated with RLS and Tourette syndrome.

Whether insomnia has a genetic cause or an emotional cause, the evidence is clear that emotions only exacerbate the problem. People with insomnia might ask what they can do with the new information? Understanding the problem is a first step, getting a genetic analysis done can help too, and then sharing the information with their physicians about how to modify existing treatments using that knowledge. And in this case, they may be able to do so without waiting for a new drug or without drugs.