This is a short report on various research findings by scientists and health professionals on the Coronvirus (aka COVID-19 and SARS-CoV-2). It is by no means comprehensive; it covers a number of topics that the average reader would find useful. Most of the info. is culled from writings by various scientists; hopefully, my summary of their work is reasonably accurate; please comment if something looks incorrect or misleading.
What we will not cover is the latest news about the spread of the virus or about the various actions (or non-actions) taken by organizations around the world.
The diary also tries to dispel some misunderstandings that have cropped up in popular media. Research on Coronavirus is happening at unprecedented speed. Studies are being conducted by medical experts, microbiologists, immunologists, public health experts and computational biologists; data and papers are being published are break-neck speed, there is little time to go through the traditional peer-review process before publishing. Occasionally, mistakes are occurring and incorrect conclusions are being drawn; but the nature of science is that it is not voodoo and it is not based on the pronouncements of some individual or organization; all data and studies get reviewed by professionals and mistakes are caught and corrected.
Did the Virus Mutate?
A recent paper from China drew a hasty conclusion that SARS-CoV-2 has mutated into two strains, one more aggressive than the other; the news has gone viral because it confirms people’s unscientific bias that viruses mutate and become more deadly, like they do in the movies.
Viruses mutate pretty much every time they reproduce; the DNA/RNA copying machinery makes mistakes. SARS-CoV-2 has a RNA sequence approximately 30,000 bases in length. But most mutations are non-consequential, some are harmful to the virus and some create new lineages with different properties. As we all know, the flu virus, over billions of reproductions, has evolved into multiple viable and harmful strains. SARS-CoV-2 may also evolve into multiple strains, but there is no evidence that it has done so yet.
This recent thread from this eminent scientist pretty much puts this misleading conclusion to rest —
This mutation appears to have happened very early on in the outbreak while the virus was still in Wuhan, China. Viruses with "L" and viruses with "S" have spread from Wuhan to the rest of the world. Visible at https://nextstrain.org/ncov?c=gt-ORF8_84&r=country…. 3/8
Generally, the expectation among virologists is that a random single amino acid change will have little impact on virus behavior. My "null" model would be that this mutation just happened to occur on an early branch on the tree and any "impact" is due solely to epidemiology. 4/8
Others scientists have also commented on this. E.g.,
Each branch in the tree above that is used to display virus lineages (phylogeny) has mutations relative its parent branch. Similar diagrams exist for SARS-CoV-2. The SL lineage in the diagram above is not a different strain or more aggressive than lineage A — it just hit a new heavily populated area and proliferated rapidly.
How Serious is Coronavirus Infection?
It is not the flu. Those who are elderly and have prior health problems have high fatality rate. Its contagiousness is also higher than that of flu.
Here are some of the scary findings of this study done on 52 critically ill adult patients in Wuhan during January. Most of these patients were elderly with prior health problems.
- For patients infected with the novel coronavirus who became critically ill with pneumonia and entered their ICU, the doctors recorded “high” numbers of fatalities. Of the 52 people included in the sample, 32 died in the 28-day span of the study, revealing a death rate of 61 percent. Most died within seven days of being admitted to the ICU.
- There are no targeted therapeutics or vaccines for the new virus — and so doctors and nurses in the ICUs are left to administer drugs and oxygen to keep patients alive long enough for their bodies to fight the infection and repair lungs ravaged by pneumonia.
- The Chinese doctors gave their patients antibiotics to fight secondary infections, and antivirals, including medicines considered experimental. They also tried antibodies and steroids.
- As the virus attacks the lungs, it becomes harder and harder for patients to get enough oxygen into their bloodstream to support their kidneys, liver and heart.
- For those who recovered, the recovery period was three to six weeks
Note that this provides some insights on how the virus affects the body and the severity of the symptoms; the fatality rate is much different for younger adults and children. Symptoms are also milder in younger adults and children, but data is still be analyzed on that front; we do not fully understand what damage the virus does to the body of healthy adults and children.
Some Notes from the Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19)
A quick summary of the important report from Maria Van Kerkhove, who heads the World Health Organization’s emerging diseases and zoonoses unit. The study covered the period 16-24 February 2020.
- People are infectious really early in the course of their disease. Less so later.
- People can shed virus for weeks after they have recovered. But that doesn’t mean they are infectious.
- Truly asymptomatic Covid-19 infections are probably rare.
- People probably aren’t being re-infected after recovery.
- Transmission in China happened among family members and close contacts. True “community spread” was less common.
- China’s Covid-19 outbreak isn’t driven by spread in hospitals.
- China’s Covid-19 outbreak isn’t driven by spread in schools.
- In China, about 2.5% of children and teens who became infected developed severe disease and 0.2% developed critical disease. None of the infected children 9 and younger died; only one teenager succumbed to infection.
- They did not find a single example of a child bringing the infection into the household and transmitting to the parents. It was the other way around
Note that during the study period, Wuhan was in a lockdown state and hospitals and citizens were taking extreme precautions and preventative measures, so the lessons might not apply to newer situations as they arise in different countries. We should expect these “findings” to change a bit as we get more data from other locations around the world, so take them with a grain of salt.
The following study supports the finding that after recovery, our immunity to the virus builds up and prevents future infections.
Children and Coronavirus
It has been widely reported that the infection rate in children is low. It appears that children do get infected but the symptoms tend to be mild. May have something to do with healthier lungs, better immune system, no over-reaction by the immune system (the cytokine storm). Scientists are still trying to figure out why children are able to tolerate and fight the virus better than older men and women. Most health professionals believe that children can act as carriers of the virus although the study above found no evidence of children passing the virus to adults.
The tolerance of kids to the virus might provide some clues on how this virus works and how we can develop treatments for it. www.washingtonpost.com/...
However, here is a report of transmission from an infant to an adult.
Coronavirus Mortality Rate
Everyone has been discussing the average mortality rate being 3.4% or higher or lower. It is important to keep in mind that the mortality rate differs a lot across age groups, as shown below -
Fatality rate also depends a lot on the presence of pre-existing conditions. According to www.worldometers.info/… as of Feb 29, patients who reported no pre-existing ("comorbid") medical conditions had a case fatality rate of 0.9%. Pre-existing illnesses that put patients at higher risk of dying from a COVID-19 infection are shown below. Note that this data is not broken out by age groups.
|
PRE-EXISTING CONDITION
|
DEATH RATE
confirmed cases |
DEATH RATE
all cases |
|
Cardiovascular disease
|
13.2%
|
10.5%
|
|
Diabetes
|
9.2%
|
7.3%
|
|
Chronic respiratory disease
|
8.0%
|
6.3%
|
|
Hypertension
|
8.4%
|
6.0%
|
|
Cancer
|
7.6%
|
5.6%
|
|
no pre-existing conditions
|
|
0.9%
|
Some Simple Precautions
You have already heard about these simple guidelines many times. But they are worth repeating -
- Hand washing, 20-second hand-washing. Or hand sanitizers
- Avoid touching face
- Social-distancing, avoid hand-shakes
- Wipe cell-phones, glasses, other things we touch regularly
- Avoid nonessential travel, especially to high-risk areas
- Avoid large gatherings
- Stay healthy, exercise, eat well, take your vitamins, ...
- Don’t get too stressed out with Coronavirus news. Stress makes your system weak.
- If sick, call your doctor
- And as Dr. Greg Dworkin says — “I’m going to stop being 65 and try 50”
You want some scientific data on handshakes vs other forms of greeting, here it is. Namaste and hand-over-heart will become the new norm 😄
Take a look at this article for a good perspective on precautions and other discussion on the Coronavirus -
A quick bio-chemistry lesson on why soaps works on viruses. You don’t need hand sanitizers, although they can be helpful in many situations. Click on the tweet to read all 39-parts of the thread!
Here are some tips from NYT on how to avoid touching your face -
- Keep a box of tissues handy.
- Identify triggers. Pause throughout the day to notice compulsive behavior. Once you’re more aware of when and why you’re touching your face, addressing the root cause can be an effective solution.
- Keep your hands busy.
- Chill. Stress impacts your immune system, and the more you’re stressed, the more you’re reducing your body’s ability to fight off infections
Can the Virus survive on surfaces?
The answer is yes, but I have not found specific information on the viability of COVID-19 on external surfaces.
Coronaviruses in general, and SARS-CoV in particular have been studied for viability on surfaces. From www.hindawi.com/… - “The dried (SARS-CoV) virus on smooth surfaces retained its viability for over 5 days at temperatures of 22–25°C and relative humidity of 40–50%, that is, typical air-conditioned environments.”
Viability outside these conditions is lower. Higher temperatures damage the virus faster and high humidity tends to reduce the “hang-time” of the aerosol particles that carry the virus.
Here is another paper that analyzed 22 different studies of SARS and MERS viruses (which are coronaviruses). Viability is typically 4-5 days but can be up to 9 days depending on surface type, temperature and humidity.
The analysis of 22 studies reveals that human coronaviruses such as Severe Acute Respiratory Syndrome (SARS) coronavirus, Middle East Respiratory Syndrome (MERS) coronavirus or endemic human coronaviruses (HCoV) can persist on inanimate surfaces like metal, glass or plastic for up to 9 days, but can be efficiently inactivated by surface disinfection procedures with 62–71% ethanol, 0.5% hydrogen peroxide or 0.1% sodium hypochlorite within 1 minute. Other biocidal agents such as 0.05–0.2% benzalkonium chloride or 0.02% chlorhexidine digluconate are less effective.
So the lesson here is that after touching surfaces (door knobs, elevator buttons, gas dispensers, touch screens, ...), avoid touching your face and wash your hands as soon as possible. In addition, use paper napkins and tissue paper when touching objects that could potentially be infected. Also, wipe/disinfect surfaces at home and work.
Will the Virus Subside in Summer?
It is well known that the flu virus slows down in summer and hence is referred to as seasonal flu. The precise reason is not known but various studies have pointed to multiple reasons. From en.wikipedia.org/… -
- People are outdoors more often during summer, they are in close contact less often, and this reduces person to person transmission.
- Vitamin D production in the skin from sunlight increases in summer and strengthens the immune system.
- Ultraviolet radiation damages the virus that resides on surfaces and there is more of it during summer
- Cold temperatures lead to drier air, which dries out mucous membranes, which is less effective in defending against the virus.
- Viruses survive longer in cooler temperatures and hence linger longer on exposed surfaces (doorknobs, countertops, etc.). Note that in our air-conditioned environments, viruses live longer, even in summer.
- Humidity decreases the distance viruses can travel. The aerosol particles that harbor the virus pick up moisture, get heavier and fall. Similarly, in dry air, the moisture in the droplets evaporates making the droplets lighter and helping them travel farther,
- In nations where children do not go to school in the summer, there is a more pronounced beginning to flu season, coinciding with the start of public school. It is thought that the day care environment is perfect for the spread of illness.
But this analysis is for the flu virus and COVID-19 is not related to the flu virus. Studies of the SARS and MERS virus, which are closer to COVID-19, found less of an effect of warm weather on the virus (www.nationalgeographic.com/...). So, it is likely that some of the factors cited above will slow down COVID-19 somewhat in summer, but given its contagiousness, we should expect it to be dangerous over summer. Besides, it won’t be summer all across the globe and this virus travels fast.
Slowing the Spread of the Virus
Many folks have wondered what the big deal is about washing hands, social distancing, quarantines and city lock-downs. Can it really stop the spread of the virus? Won’t everyone get infected eventually anyways?
Study after study has shown that these steps slow down the spread of the virus. By now, everyone is familiar with the concept that the number of cases doubles every 5-7 days, people even proudly mention the parameter R0 as being two point something. But these numbers generally apply to situations where the virus spreads unconstrained. Throw in some containment and prevention measures and the rate can decrease substantially. That buys more time for health professional to treat patients and develop treatments. It also prevents hospitals from getting overwhelmed with a surge of patients. Note that not everyone dies; most patients recover with proper treatment; the recovery rate will improve with new drugs.
Presciently, BBC Four conducted a citizen science experiment in 2018, where they simulated the effects of the spread of highly infectious flu-like virus in the UK and estimated the reduction in the rate of spread as a function of various preventative methods. It was found that the simple act of washing hands meticulously slowed down (not stopped) the spread considerably. This data was presented in a BBC documentary in 2018 called Contagion: The BBC Four Pandemic. Mathematician Dr. Hannah Fry co-presented documentary. This paper has some of the mathematics behind the model.
China’s travel bans also helped slow down and delay the spread of the virus.
Vaccines and Treatments
In spite of all this madness and the frightening prospects of the impending pandemic, there are some silver linings —
- There are over 18 companies and organizations actively developing vaccines for COVID-19
- Over 18 companies are developing treatments and drugs
- One vaccine has entered phase 1 trials (but still probably 18 months away from approval)
- Few anti-viral treatments (many developed for Ebola and HIV) are being tested in China, one in the U.S.
Check out diary “Coronovirus Vaccines and Treatments under Development” for more info.
Here are some hot off-the-press announcements on treatments and vaccines —
The Prognosis
So far, given the bungled response by the U.S. government, things look bad. Most experts are warning of huge surge in infections, the kind seen in China and Italy. Those two countries have taken drastic measures to contain the virus, the U.S. does not have the will or the infrastructure to take similar measures. The administration is trying to downplay the whole affair while alarm bells are going off everywhere.
Projections of infections in the coming days and weeks look scary. This analysis is just for the Washington state cluster. Note that the infection growth factor will reduce as mitigation steps are deployed, so the graphs will not keep following the projected trajectory for too long.
Epilogue
Much is being learnt about the Coronavirus, much else remains to be learnt. Scientists and health professionals will figure out ways to stop it. Meanwhile, we have to do all we can to slow down the spread of the diseases and prevent ourselves and our loved ones from getting infected. Of course it would help if our government was more competent, but that’s another story.
Let’s focus our comments on science, the nature of the virus and any information that can help others. Let’s avoid venting about trump and the criminal administration in this diary; there will be plenty of other diaries that will cover that topic.
Stay healthy, stay prepared, stay informed, stay vigilant, and stay positive. And let’s all work to flatten that epidemic graph.
By the same token, stay away from misinformation, exaggerations and non-expert opinion. On social media, anyone who can multiply by 2 is supposedly an expert. Follow scientists and reputable organizations, do not search for #Coronavirus on twitter. Do not post info. about “stuff” you read on the Internet, disinformation spreads faster than this virus on social media!
Further Reading
- Report of the WHO-China Joint Mission on Coronavirus Disease 2019 (COVID-19) — www.who.int/…
- Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study —
- Severe acute respiratory syndrome coronavirus 2 — en.wikipedia.org/...
- coronavirus.1point3acres.com/… — a good site to follow the numbers for the U.S., including state-by-state counts
- Implications of the Coronavirus infections in Washington State — www.dailykos.com/…
- Coronovirus Vaccines and Treatments under Development — www.dailykos.com/...
- Coronavirus Control - Novel High Tech. Solutions or Mass Surveillance? — www.dailykos.com/…
- Coronavirus - Music and Culture to improve Preparedness and to Help Victims and Caregivers — www.dailykos.com/…
- Wuhan Coronavirus - An Update, Prognosis and Projections — www.dailykos.com/...
P.S.
For some practical info from a health expert and lots of good Q&As, check out diary “ER Doc 411: Report from the front lines on COVID19 and some practical thoughts” at www.dailykos.com/...
