Elegy of the coronavirus
March 18, 2021
(sections on vaccines in drop down menu)
Model of the coronavirus-19 particle
Hello dear friends,
As we all know, this new coronavirus, called SARS-Cov-2 (covid for short) has hit the world with a vengeance that is unknown to any of us living today. As of March 18, 2021, over 122 million people have been infected and over 2,7 million have died from it worldwide. In the US alone, the numbers are over 30 million infections and 552,000 deaths, in Canada ~920,000 cases with ~22,000 deaths. (For up to date numbers: https://www.worldometers.info/coronavirus/#countries).
Early in the morning of October 2, 2020 it was announced that the US President Trump and the first lady tested positive, together with several White House members, total of ~34 people.
We-breast cancer survivors know all too well that we have to be extra careful because our immune system may be compromised to different degrees, even after chemotherapy is over . Our bodies cannot fight infections from this covid (or other viruses) as well as before we got cancer. That’s why it is important to know how to deal with it differently.
Covid attacks the lungs and respiratory system primarily, but it also attacks the heart, digestive system, kidneys, skin and other organs too, while people may lose their sense of smell and taste, because of an attack to the brain. Actually, the virus can “hide” in the brain after you thought you have recovered, and reappear later. Covid can also cause severe anemia. It is worse if there are intestinal, heart or kidney problems already. Kidney disease is the leading risk factor for covid-related hospitalisation. In children and young adults it has been reported to cause an inflammation throughout the body (like the Kawasaki disease). It is worse in older people, because we have higher amounts of the receptor of the virus (called ACE2), ie the structures on the surface of the cell where the virus attaches to start an infection. Also, a study (November 2020) showed that children may have antibodies against other coronaviruses that cause common colds and these protect them to some degree. People with Parkinson’s disease have a 30% greater mortality rate. Worse in smokers and people that are even mildly obese, with a body mass index of >30%. Also, people with Chronic Lymphocytic Leukemia, either they received treatment or not, are at higher risk. Adults with blood cancers have a worse outcome, but children with blood cancers are apparently spared. In severe cases covid can be fatal. Even people who recover may have health issues, scars in the lungs, kidney damage, chronic fatigue, neurological problems and others.
According to statistics, 81% of covid-related deaths in Canada were in nursing homes, mostly residents but also workers that are exposed to the virus.
A study published in January 27, 2021 showed that symptoms and mortality are higher in covid-infected pregnant women than uninfected women of their age group https://www.ajog.org/article/S0002-9378(21)00033-8/pdf. Another study from Italy showed that covid can pass from the mother to the baby in the uterus, but the long term effects of this infection are not known yet.
Although overall a relatively small proportion of infected people die (~2%, depending on method of detection of the virus) compared to, for example, the SARS coronavirus that hit in 2003, covid spreads very effectively and is killing a larger number of people than SARS ever did, and all over the globe. This is for several reasons that are explained below, together with strategies to cope.
Testing for covid
Testing is key to fighting the virus, because only then you know what you are facing and what to avoid to protect yourself.
Testing for the presence of the virus itself, ie active and infectious and nasty, can be done by growing the virus in cultured cells but this is complicated, dangerous and slow. In practical terms, there are two main approaches used for testing: Since the virus appeared in earnest last December, scientists in China have isolated it and sequenced its RNA genome (January 11, 2020). A technique to detect the RNA of the virus in the nose or saliva, called RT-PCR was developed soon after. It usually takes a few hours, it is very sensitive, but the test shows the presence of viral RNA only, not infectious virus. A modification is called Loop-amplification (LAMP), gives faster results and the apparatus is much cheaper. Canada has bought ~2 million kits.
Another test detects viral proteins, instead of viral RNA. These types of tests are much faster, a bit like pregnancy tests, can be done at home by yourself, and they can be much cheaper. They are not as sensitive, but epidemiologists (interviewed by CBC) have calculated that if 50% of the population test themselves at home every 3 days and then quarantine if found positive, the virus would almost disappear in 4-6 weeks (!)*.
In any test of this kind, how “good” the test is depends on (1): how sensitive the test is, ie how many particles of virus have to be present for the test to “see” them (e.g. at least ~50 particles per milliliter of blood in the case of AIDS virus detection) but also, on (2): how specific it is, ie whether or not it gives false alarms, ie shows a positive result when there is something else, not covid that the test is picking up (e.g. a different, harmless coronavirus). Both of these can vary enormously with different test kits, sold by different companies. Also, with how well the virus was picked up by the little brush up the nose, or how concentrated the saliva sample was. Some people with no symptoms, ie that do not cough or sneeze, may not have much mucous in their nose to be able to test, but of course it is possible to test most people.
Testing for the presence of viral RNA, even fragments of it, is very useful to get an idea of where a virus has been and if levels are going down or up. As the virus exists in the gut in many infected people, it is also found in sewage, like other viruses growing in the intestines, like eg the poliomyelitis virus. Even if covid does not live long in sewage, its RNA lingers for quite some time and scientists can follow viral spread and progression from one place to another.
Another way is to look for the presence of antibodies to the virus in a person’s blood. This is much faster but it only shows that there are antibodies, ie that the person has been infected. It cannot differentiate whether this happened recently or months before ie whether the person is shedding virus or not. Actually, if there are enough antibodies, then not only the person is not spreading virus but they may also be immune to the virus. In the case of Ebola virus infections, blood from people who recovered was used to treat people in the throes of the infection. However, since we do not know yet how well these antibodies protect, issuing “immunity passports” to people that recovered from covid at this time is not wise.
The Kingston public health labs announced recently that there will be more testing centers in Kingston; Pharmacies, a building at Queen’s etc. Nice news, but we need the quicker tests too. Also, we need to invest in testing more people. Unfortunately, this lasted for a couple of months only. People were waiting in line for many hours at the few centers and results took several days.
How to kill the virus
Many viruses die once they are found outside a human body. Unlike viruses like influenza or AIDS, covid is quite stable in the environment, that is it can survive for several days after being shed through coughing or sneezing. Then it waits to attack somebody who will become its new “customer” and knowing how stable it is on different surfaces is key to getting rid of it.
In early papers only viral RNA was examined, but more recently a paper came out where they looked for live and active virus on different surfaces .
The researchers spotted solutions containing known amounts of infectious virus on different surfaces. After a number of hours to days they eluted the virus and examined how infectious it was. The results showed that liquid soap does not kill the virus very effectively, it just washes it off. Washing with soap is useful but not enough. Besides, you can’t wash your hands for 20 seconds when e.g. you are out shopping, when you need protection the most.
covid is not flimsy like other viruses, but it does die by itself in the environment. It is infectious on the following surfaces, at 20oC for the following lengths of time:
paper: 3 hrs (I wonder if it is because it gets absorbed into the fiber and hard to elute, not really killed?)
wood, cloth: 2 days (same question as paper)
glass: 4 days
steel, plastic, eg cell phones: 7 days (or even more in some cases)
That is, if you leave groceries outside on the porch or in the car for ~4-7 days that should be enough to inactivate the covid, but be careful: If the temperature is low, less than 4 oC, then the virus is still alive. In the freezer (-20 oC) the virus is alive for a very long time.
However, in a new study from Australia they tested for virus that is alive ie infectious and can be cultured and under similar conditions as in the natural situation. They found that the virus can be alive on glass, plastic or metal for up to 28 days (!). Eg banknotes can have infectious virus, touch-screens, cell phones and all sorts of handles. What did they do different? They kept the surfaces in the dark because Ultraviolet light is known to inactivate the virus, which means that the 28 days may be an overestimate, unless the virus is in the dark, eg a wallet.
I always have a squirt bottle with 70% alcohol with me whenever I go out and I use it a lot, even on my lymphedema-compression glove. I like it better than hand sanitizer because ethanol does not leave residues that get caked on the glove fabric.
The virus can be killed by:
Bleach 1:100, ethanol 70%, rubbing alcohol (isopropanol) 70%, Benzalconium chloride (BAC)-containing disinfectants. With any of these solutions in 5 min it’s gone.
Soap is only partly effective at killing covid, although it does wash the virus off.
Stable at 4oC for >14 days, killed at 70oC in 30 minutes.
A good question is: Why use 70% alcohol, not 100%? 100% will kill the virus and many other viruses and bacteria. However 70%, even 60% is as effective as 100%. 70% offers security, in case your hands or other surfaces have some humidity that would dilute the alcohol. Another consideration is the cost, also 70% does not dry the hands as much as 100%.
Covid is spread by asymptomatics, and through the air
Another issue is, how do you catch it? Of course, if someone is infected, they usually cough and have a fever. Then a test can show the presence of the virus high up in the nostrils, or more recently in saliva . The problem is that lots of people do not show symptoms right away, but after several (1-14) days. During this time the virus is replicating in them slowly and they can spread it by simply breathing or talking, even if they are not yet coughing. Some people have very light symptoms or even none at all. In Korea, after a two-hour performance of a choir 40 people were infected, although nobody was coughing… As a result of transmission by apparently “healthy” people, up to 90% of transmission is from asymptomatics … Of course, if a test is to be able to detect virus in people that do not have symptoms, which is the vast majority of positives that transmit the virus to others, then the test has to be especially sensitive, because these people do not have as much virus in them. In a study from Boston, they tested random people walking in the street, with no symptoms at all, and almost a third were positive! In another study with women about to give birth in New York city, out of 215 women 4 had symptoms and were positive, but another 29 had no symptoms and were positive too. That is, 87.7% of infectious women were asymptomatic!
In July 2, 2020 a paper was published in the Journal Cell, showing that a new covid mutant has been taking over the original one of Wuhan. At a critical position (called 614) of the “spike” of the virus (that is, a projection on the outside of the virus that the virus uses to attach to and enter the cell), the original virus has an aminoacid called “D”, while the new one has a different one called “G”. The new virus grows much better in a person and produces more progeny, but it does not cause worse disease. That is, the “G”-covid spreads more easily because (1) more virus grows in the nose of each infected person, and (2) because it lets infected people walk around without any worse symptoms, to spread virus to others… Other viruses like the Ebola or SARS make the person very sick and unable to walk around shedding and spreading virus, but the covid is sneaky!
Besides the asymptomatic transmissions, and the stability of virus on different surfaces, another important question is, is it transmitted through the air and how effectively? A paper came out in Nature from Wuhan, and showed that covid RNA can be found in tiny droplets (aerosols) that remain aloft in the air and can be inhaled by others for at least two hours! That is, despite earlier findings, that covid is transmitted through larger droplets that fall to the ground and do not stay in the air for long (ie it can travel for 2 meters at the most, then falls to the ground), or through touching contaminated surfaces, covid is transmitted through the air also, and carried around in air currents. In hospitals, in areas where the ventilation was good, very little viral RNA was detected, but it was found again in areas where staff members were taking off their protective equipment, indicating that it settles on clothing and it is knocked off back into the air. Luckily, the amounts of covid RNA found were greatly reduced when hospitals implemented more rigorous cleaning procedures . Virus can also attach to dust particles, and is lifted in the air by walking on the floor. How much dust hovers in the air would greatly depend upon humidity, the drier the air the more dust (and virus) there is in the air . (This study examined RNA only, they did not try to culture the virus to see if it was active when recovered from the air, or not, but the presence of RNA showed that covid can be in the air).
What proportion of new infections is due to these aerosols has been a matter of debate, but the consensus is that infectious covid does spread through the air, and can be inhaled. Aerosols do travel to distances beyond 6 feet and remain suspended in the air for hours. There is nothing more to do to avoid catching it through aerosols, other than increasing ventilation. Also, a UV lamp setup is sold commercially and it kills the virus in the air. Of course, the beam cannot reach any corner that is not exposed, ie it is not to use as a sanitizer. Also, UV light can be harmful, especially to the eyes, and is a carcinogen, but a UV lamp adapted to the air intakes can sterilize the incoming air. We heard in the CBC News that St. Michael’s school in Toronto has adopted this system.
That is, clean and clean and clean and mask and ventilate and decontaminate with alcohol or BAC-containing disinfectants…
A study that came out in July showed that covid is not transmitted by mosquitoes.
How to deal with the virus. Testing vs quarantine
When a virus starts to spread, at first few people are infected but as you don’t know who is shedding virus, and as viruses like covid can even spread through the air, the number of cases goes up fast. The only way to know is by testing, since 90% of spreaders have no symptoms. Then you know where the danger is and positive people only are quarantined. Negatives go back to work.
However, testing is expensive and so far woefully inadequate. Only people with symptoms, or who traveled or came in contact with someone positive were tested because of the cost, that is, the vast majority of asymptomatic transmitters was not. As you do not know who is shedding virus, we have to treat everybody as if they are infectious, that is we stay home to avoid getting sick and infecting others… However, in this way we are over fifty to a hundred times more careful than we need to be, based on the best estimates of total infected people, and productivity grinds to a halt! Even if we get paid by the government while under quarantine, we cannot eat money, someone has to produce food. And people involved in all stages of food production, farmers, factory workers, grocery store workers, cooks, etc must be tested and be negative, because otherwise lots of people will get sick.
Testing is expensive, but paying people to stay home is far more so.
This massive loss of productivity is not necessary, as shown from Korea, New Zealand and Taiwan. Back in March in Korea, by extensive testing and tracing all contacts and quarantining the positives they reduced the new infections from 900 to 10-20 cases a day in two weeks, without closing down schools or stores! In Germany (population 83 million) they have been doing over 100,000 tests a day and tracing contacts, and the number increased to a million a week when the lockdown was eased gradually. Unfortunately, once summer came, people started travelling and the covid became hard to control.
Routine testing of asymptomatic people is something that is not being done extensively in Canada. Massive testing of asymptomatic people started in Los Angeles and in Boston since ~May. Also in parts of China. When we do this, negative people can go back to work. With masks perhaps and keeping distances but they can work.
Testing is now performed in public health labs mostly, but hospital labs or University research labs could pitch in too. This happened very extensively in Greece and other places, and at a fraction of the cost of commercial labs. Research labs do not have the capacity to do hundreds of tests a day but they have the knowledge in spades.
Tracking Apps vs privacy
The pandemic has exposed society’s vulnerabilities. In cases of crisis there is a need for a central government to coordinate efforts. Eg testing, hospitals, closing down businesses to inhibit spread, and helping financially people who are affected. No matter what, it is expected that a large number of people will get sick, or even will test positive without many symptoms. Private, for profit insurance companies would want to increase premiums to positive people, regardless of their state of health. The tracking apps that warn you of someone positive being nearby can help with the control of the disease, but they raise ethical issues, especially in the US. Security of the data is scant, so insurance companies may get hold of them and increase premiums even if the chances of long term effects are slim or unknown.
Luckily, in Canada there is basic healthcare for free, so being tracked is less important. Still, the apps where your data are collected by the lab doing the testing (where they may stay for who knows how long), make the use of these personal tests for the viral proteins, that you can do yourself at home in minutes, so important.
Wear a mask!
The covid virus enters through the nose, mouth or eyes. By covering your mouth and nose you avoid a good part of the infection. There are many masks that are quite effective. The best ones are called N95 and they fit tightly around the mouth and nose. Less effective are the “surgical masks”, made of layers of neoprene material. However, since the advent of covid, both are very hard to find. Even nurses working at Intensive Care Units at hospitals do not have enough N95’s.
The only other solution is, to sew one yourself if you have a sewing machine, or just use any piece of cloth like a bandana. Look at the cloth against the light, do you see little holes of the fabric? If not, then the filtering of the droplets with the virus is OK.
Just to clarify: Virus particles themselves are too tiny to be retained by any filter that retains eg bacteria, but many viruses are found in clumps with mucous or other respiratory secretions that are much bigger and are held back by the fabric.
In any event, you have to be careful how you use a mask. Put it on with the elastics around the ears and take it off carefully by holding it from the elastics, not the middle. If you come across a positive person, the outside of your mask will be contaminated. If you take it off and put it back on backwards, then you will breathe in all the virus the mask caught, and concentrated too…
Masks are now compulsory in Ontario, at least in closed spaces eg stores and buses. Don’t just keep a mask in your pocket to whip it out when the corona-mask-police shows up, then put it back in your pocket together with the virus… Put it on, make sure it covers mouth and nose, and keep it on till you need to take it off. Take it out from the ear-elastics and throw it in the wash, or soak it in 70% alcohol. When you launder it, make sure all traces of soap are rinsed well, because otherwise it may smell nice but as you keep breathing through the cloth, the soap may irritate your lungs and you will start coughing and sneezing and touching your face to blow your nose, which exposes you to virus. I have made many masks for myself and family so that I wash them all in one go. I run them through a second cycle with no soap to make sure traces of soap are gone. If I use it for just an hour or so, then I just dip the mask in 70% Ethanol or isopropanol (rubbing alcohol) to kill any viruses. Ethanol kills the nasty covid but also influenza viruses, other (benign) coronaviruses, common cold viruses (rhinoviruses), bacteria and other microorganisms too.
I do not like putting a mask back on after I use it even for a few minutes, because avoiding contaminated surfaces of the mask is almost impossible; as you breathe in, you suck viruses that stay on the outside of the mask, then if you put it down, even in a paper bag, how do you avoid getting any virus onto the inside, when you can’t NOT shake the mask or the paper at all? So, once in the car in the parking lot back from shopping I squirt alcohol on it to kill viruses, then I throw it in the laundry once I get home. If I go to another store, I get out a fresh mask. I have made cloth masks, I got lots.
It has been estimated that if two people are talking without masks for 15 min and one is positive, the chances of infection are ~95%. If both have masks on, the chances are ~2%.
Touching your face has always been a big no-no, because it allows the virus to infect. But, how do you blow your nose? Perhaps we should wear one of those “cones” around our necks that dogs have to wear to prevent them from scratching their faces or pulling out stitches…
Wearing a mask outside in the cold protects your nose from the wind too, so that you do not need to blow your nose and risk infection as much.
The advent of covid made the monster of politics wake up, and this is not good. We are all looking up to officers of health for advice and guidance, not for confusion. Back in March, all governments were caught by surprise, not prepared for a pandemic. So, at first we were told to not wear masks, just keep at 2 meters distance and not touch our face, and that masks are bad because you may touch it etc. The size of the droplets is > 20 microns we were told, ie big enough to fall to the ground within 2 meters. Droplets of <5 microns can hover in the air for hours, like smoke (aerosols) but the covid spreads with >20 micron droplets, for whatever reason. Ie, no need for a mask. But, a bit later, as production of masks picked up, Dr. Fauci and others admitted that the reason for the edict was that there were not enough masks for health care providers, and they could not trust the public to show understanding. However, papers came out of China in April where they took samples of the air around markets, hospital rooms, bathrooms etc and covid RNA was definitely present… Still, no masks we were told. Till in June, masks were not only “useful” but became mandatory everywhere inside in Ontario at least, and in some places outside too… Still, cloth masks were considered good enough, no N95’s needed. Then, in October 14, I read in the news that yes, covid is transmitted with aerosols too after all, ie just by breathing, no need to sneeze to give the present to someone, and N95 masks are useful – if you can find them…
Just keep that in mind. Try to find the original, scientific papers that have been written by scientists working on the problems and read those, don’t rely on government officials alone. This is why I cite a few original papers at the bottom. I don’t blame government officials, still I would like to know the facts, same as all of us, since we – the public are going to be paying for whatever is needed, either masks, or research for drugs and vaccines…
It seems that covid is here to stay. You would think that wearing a mask cannot be fashionable, but you would be wrong. Famous fashion designers like Yves St. Laurent, Ralph Lauren and Balenciaga are making masks to match sweaters, blouses and suits… What is left is makeup and lipstick to wear under a mask, but there is still hope…
Other covid transmitters
Bats are the only mammals that fly (apart from pigs..). For several reasons bats can be infected by several viruses for a long time without showing symptoms, ie they are good “reservoirs” of viruses such as rabies, SARS, Ebola and now covid. All indications point to a bat or perhaps a pangolin (anteater) coronavirus mutating enough as to infect humans too, and very effectively. These animals can multiply the virus and keep it for ever, so that getting rid of the virus completely as was done for the smallpox virus, is not possible. Luckily, we do not keep bats as pets.
Many of us love cats. But, cats can be infected with covid by their human owners, according to a recent paper. Then the cats can infect other cats and amplify the virus, but whether an infected cat can pass on the virus to people is not yet clear, because we don’t screen cats to know. In any case, in the Bronx zoo tigers and lions started coughing and sneezing after coming into contact with an asymptomatic keeper that tested positive (no, they did not eat him…). Zoo vets anesthetised one tiger named Nadia to stick a thin brush up her nose to get a sample to test, and lo and behold she was infected! This means that the virus does grow in felines. Most of us do not keep tigers at home, but I do not let my cat out since I found out that he could catch the virus. He loved being outside and when I told him he can’t, he was most upset! He is bored and I don’t blame him but I tried catnip, cat-treats to chase or playing with strings and a laser pointer to get him to exercise a bit but he would rather be outside. Finally, he got demoted to an outside-cat for the summer at least, and he is happy.
In June it was shown that animals in mink farms in Holland and Denmark infected handlers. They had to destroy ~1.7 million animals to stop the transmission! We can certainly live without mink coats, but knowing that animals can transmit covid shows that it will be hard to get rid of it, unlike viruses like eg smallpox that can infect humans only. As it turned out, many other animals can get infected with this virus but to different degrees .
Here is President Trump’s corona-anthem:
Number of cases and deaths: https://www.worldometers.info/coronavirus/country/us/
*CBC news, The National, October 11, 2020.
1]. Coronavirus: Cancer patients nearly three times more likely to die of Covid-19, study says. The Independent, April 28, 2020. https://www.independent.co.uk/news/health/coronavirus-cancer-patient-death-rate-study-china-hubei-us-a9488481.html
2]. Stability of SARS-CoV-2 in different environmental conditions. Alex Chin et al.
Lancet Microbe 2020 Published Online April 2, 2020 https://doi.org/10.1016/ S2666-5247(20)30003-3
4]. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2). R. Li et al., Science 10.1126/science.abb3221 (2020). https://science.sciencemag.org/content/early/2020/03/24/science.abb3221
5]. Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals. Liu et al. Nature, April 27, 2020.
6]. Reducing transmission of SARS-CoV-2. Prather et al, Science, May 27, 2020
8]. SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals. Lam, SD, Orengo CA et al, Scientific Reports, volume 10, article number: 16471 (2020) October 5.
9]. The effect of temperature on persistence of SARS-CoV-2 on common surfaces. Riddel S, Goldie S. Hill A, Eagles D, Drew TW. Virology Journal, volume 17, Article number 145. October 7, 2020.