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Covid Simulation


Viruses are by far the most abundant biological entities on Earth. Viruses have been described as "organisms at the edge of life",since they resemble organisms in that they possess genes, evolve by natural selection, and reproduce by creating multiple copies of themselves through self-assembly. Although they have genes, they do not have a cellular structure, which is often seen as the basic unit of life.
Viruses are found wherever there is life and have probably existed since living cells first evolved. The origin of viruses is unclear because they do not form fossils. Some viruses may have evolved from bits of DNA or RNA that "escaped" from the genes of a larger organism. Viruses may have evolved from complex molecules of protein and nucleic acid at the same time that cells first appeared on Earth and would have been dependent on cellular life for billions of years. There are millions of different types of viruses. As of September 2015, the NCBI Virus genome database has more than 75,000 complete genome sequences, but there are doubtlessly many more to be discovered.

COVID-19

COVID-19 is spreading rapidly across world. Main problem is that you may not know you’re infected but you have infected others. For those with underlying conditions, it can be especially lethal. Solving Covid19 is long term project.
As the novel coronavirus continues to spread, countries are putting their citizens on various forms lockdown. More than a third of the planet’s population is under some form of restriction. While “lockdown” isn’t a technical term used by public-health officials, it can refer to anything from mandatory geographic quarantines to non-mandatory recommendations to stay at home, closures of certain types of businesses, or bans on events and gatherings.

Model: Number of active cases any time under 4 conditions:
(1) No control or life as usual
(2) Arrival control varies from checking and isolating incoming visitors to stopping flight arrrivals
(3) Emergency/Control will also include control of oversea visitors. Crowd control and bubble sizes.
(4) Lockdown, extreme measure.

Note: Accuracy will be better, if done for a town or population size less than a million.
Dividing population into small bubbles, reduces no of contacts, but increase contact time or chance of spread. There should be optimum bubble size
Main error for this model is not identified infected cases.
Status as at 18 April 2020: Auckland 60 Active cases and Metro North and South reported 150 Active cases

Covid Simulation results

This simulation is approximate model to see the spread, with limited available information. Much information is missing and lot of data points will be required to validate. Model takes virus spread behavior during February/March, as reported by researchers from asia. Spread is dependent on unknown infected cases and discharged cases. Also depends on how well controls are implemented.

COVID Cases in Auckland

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COVID Cases in Metro North and South (Brisbane)

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Results:
1) Lockdown only has marginal advantage over crowd control. Though lock down is a good isolation strategy, it increase contact time or chance of spread.
2) Important thing is arrival control.
3) With control, stability can be achieved in 2 to 3 months time.
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Cells Microbes human

Number of cells in the human body is around 30-40 trillion.
Microbes - 300-400 trillion
Gastrointestinal tract alone comprise at least 10 trillion organisms of more than 1,000 species
Humans produce a new generation every 20 years
Bacteria do it every 20 to 30 minutes, and
Viruses even faster every 20 to 30 seconds.

There is a close connection between microbes and humans. Experts believe about half of all human DNA originated from viruses that infected and embedded their nucleic acid in our ancestors’ egg and sperm cells. Microbes occupy all of our body surfaces, including the skin, gut, and mucous membranes. Our bodies contain at least 10 times more bacterial cells than human ones. Microbes in the human gastrointestinal tract alone comprise at least 10 trillion organisms, representing more than 1,000 species, which are thought to prevent the gut from being colonized by disease-causing organisms. Among their other beneficial roles, microbes synthesize vitamins, break down food into absorbable nutrients, and stimulate our immune systems.

RNA is a molecule similar to DNA, and it is essentially a temporary copy of a short segment of DNA. DNA is transcribed into RNA. A rare Japanese flower named Paris japonica sports an astonishing 149 billion base pairs, making it 50 times the size of a human genome—and the largest genome ever found. Until now, the biggest genome belonged to the marbled lungfish, whose 130 billion base pairs weighed in at an impressive 132.83 picograms. (A picogram is one-trillionth of a gram). The smallest genome known among organisms with nuclei is that of a mammalian parasite known as Encephalitozoon intestinalis, with a relatively paltry 2.25 million base pairs
The diameter of the DNA helix is 2 nano metre and the vertical rise per base pair is 0.34 nano metre.

SARS-CoV-2

The coronavirus genome comprises around 26-32 thousand base pairs. Quite large for a virus, but small compared to the 3 billion base pairs that comprise the human genome.

SARS-CoV-2 virus appears to be mutating more slowly than the seasonal flu which may allow scientists to develop a vaccine. SARS-CoV-2 seems to have a mutation rate of less than 25 mutations per year, whereas the seasonal flu has a mutation rate of almost 50 mutations per year.

covid
Source:Photo by CDC on Unsplash

Coronaviruses are large pleomorphic spherical particles with average diameter of 120 nm (.12 μm). The diameter of the envelope is ~80 nm (.08 μm) and the spikes are ~20 nm (.02 μm) long. The viral envelope consists of a lipid bilayer where the membrane (M), envelope (E) and spike (S) structural proteins are anchored. Coronaviruses are named for the crown-like spikes on their surface. There are four main sub-groupings of coronaviruses, known as alpha, beta, gamma, and delta. Human coronaviruses were first identified in the mid-1960s. Coronaviruses that can infect people are:
229E (alpha coronavirus);
NL63 (alpha coronavirus);
OC43 (beta coronavirus);
HKU1 (beta coronavirus);
MERS-CoV (the beta coronavirus that causes Middle East Respiratory Syndrome, or MERS)
SARS-CoV (the beta coronavirus that causes severe acute respiratory syndrome, or SARS)
SARS-CoV-2 (the novel coronavirus that causes coronavirus disease 2019, or COVID-19)
Sometimes coronaviruses that infect animals can evolve and make people sick and become a new human coronavirus. Three recent examples of this are 2019-nCoV, SARS-CoV, and MERS-CoV.

Microbes and humans

The vast majority of microbes establish themselves as persistent "colonists" thriving in complex communities within and on our bodies. Some are harming us. From the moment we are born, microbes begin to colonize our bodies. Each of us has a unique set of microbial communities, which are believed to play an important role in digestion and in protection from disease. Lactobacillus bacteria, which produce lactic acid to help with digestion.

Though some microbes make us sick and even kill us, in the long run they have a shared interest in our survival. For these tiny invaders, a dead host is a dead end. The success of microorganisms is due to their remarkable adaptability. Humans produce a new generation every 20 years or so; bacteria do it every 20 to 30 minutes, and viruses even faster. Because they reproduce so quickly, microorganisms can assemble in enormous numbers with great variety in their communities.

There are five major categories of infectious agents: Viruses, bacteria, fungi, protozoa, and helminths.
Viruses are tiny, ranging in size from about 20 to 400 nanometers in diameter. Viruses are simply packets of nucleic acid, either DNA or RNA, surrounded by a protein shell and sometimes fatty materials called lipids. A virus is a dormant particle. Only when it enters a host cell does it go into action, hijacking the cell’s metabolic machinery to produce copies of itself.
Viruses are responsible for a wide range of diseases, including the common cold, measles, chicken pox, genital herpes, and influenza. Many of the emerging infectious diseases, such as AIDS and SARS, are caused by viruses.

Bacteria are 10 to 100 times larger than viruses and are more self-sufficient. These single-celled organisms, generally visible under a low-powered microscope, come in three shapes. Most bacteria carry a single circular molecule of DNA, which encodes (or programs) the essential genes for reproduction and other cellular functions. Sometimes they carry accessory small rings of DNA, known as plasmids, that encode for specialized functions like antibiotic resistance. Unlike more complex forms of life, bacteria carry only one set of chromosomes instead of two. They reproduce by dividing into two cells, a process called binary fission. Their offspring are identical, essentially clones with the exact same genetic material. When mistakes are made during replication and a mutation occurs, it creates variety within the population that could—under the right circumstances—lead to an enhanced ability to adapt to a changing environment. Bacteria can also acquire new genetic material from other bacteria, viruses, plants, and even yeasts. This ability means they can evolve suddenly and rapidly instead of slowly adapting.

Bacterial infections are associated with diseases such as strep throat, tuberculosis, staph skin infections, and urinary tract and bloodstream infections.

The other three major types of infectious agents include fungi (spore-forming organisms that range from bread mold to ringworm to deadly histoplasmosis), protozoa (such as the agents behind malaria and dysentery), and helminths (parasitic worms like those that cause trichinosis, hookworm, and schistosomiasis).

A newly recognized class of infectious agents—the prions, or proteinaceous infectious particles—consist only of protein. Prions are thought to cause variant Creutzfeldt-Jakob disease in humans and “mad cow disease” in cattle. These proteins are abnormally folded and, when they come in contact with similar normal proteins, turn them into prions like themselves, setting off a chain reaction that eventually riddles the brain with holes. Prions evoke no immune response and resist heat, ultraviolet light, radiation, and sterilization, making them difficult to control.

Microbes have inhabited the earth for billions of years and may be the earliest life forms on the planet. They live in every conceivable ecological niche—soil, water, air, plants, rocks, and animals. They even live in extreme environments, such as hot springs, deep ocean thermal vents, and Antarctic ice. Grand Prismatic Spring, a geothermal hot spring in Yellowstone and home to microbes that have adapted to this extreme environment.Indeed microbes, by sheer mass, are the earth’s most abundant life form and are highly adaptable to external forces.

Spreading Diseases

Human travel and commerce have brought other risks. Almost 2 million passengers, each a potential carrier of infection, travel daily by aircraft to international destinations. International commerce, especially in foodstuffs, adds to the global traffic of disease-causing microbes. Because the transit times of people and goods are often shorter than the incubation periods of infection, carriers of disease can arrive at their destination before the infection they harbor is detectable.

Changes in human demographics and behavior are linked with the emergence of infections such as AIDS and hepatitis C, through sexual activity and intravenous drug use. More broad-scale changes that raise the risk of infectious disease include the breakdown of public health systems, poverty, war, and famine.

SARS-CoV-2 Virus Origin

The coronavirus was not engineered in a lab. Here's how we ...www.livescience.com › coronavirus-not-human-made-i...
Mar 21, 2020 - A persistent coronavirus myth that this virus, called SARS-CoV-2, was made by scientists and escaped from a lab in Wuhan is completely ... www.sciencealert.com › Scientists Are Tired of Explaining Why The COVID-19 Virus Was Not Made in a Lab JACINTA BOWLER 20 APRIL 2020
It's a rumour that just won't die. When asked whether the COVID-19 virus was genetically engineered in a lab, scientists have already said "no" rather firmly, but the matter of the new coronavirus' origin is unlikely to be put to rest so easily. Source: www.livescience.com (1) A group of researchers compared the genome of this novel coronavirus with the seven other coronaviruses known to infect humans: SARS, MERS and SARS-CoV-2, which can cause severe disease; along with HKU1, NL63, OC43 and 229E, which typically cause just mild symptoms.
Researchers looked at the genetic template for the spike proteins that protrude from the surface of the virus. The coronavirus uses these spikes to grab the outer walls of its host's cells and then enter those cells. They specifically looked at the gene sequences responsible for two key features of these spike proteins: the grabber, called the receptor-binding domain, that hooks onto host cells; and the so-called cleavage site that allows the virus to open and enter those cells.
That analysis showed that the "hook" part of the spike had evolved to target a receptor on the outside of human cells called ACE2, which is involved in blood pressure regulation. It is so effective at attaching to human cells that the researchers said the spike proteins were the result of natural selection and not genetic engineering.
SARS-CoV differs from SARS-CoV-2 — with several key letter changes in the genetic code. Yet in computer simulations, the mutations in SARS-CoV-2 don't seem to work very well at helping the virus bind to human cells. If scientists had deliberately engineered this virus, they wouldn't have chosen mutations that computer models suggest won't work. But it turns out, nature is smarter than scientists, and the novel coronavirus found a way to mutate that was better — and completely different— from anything scientists could have created.
The overall molecular structure of this virus is distinct from the known coronaviruses and instead most closely resembles viruses found in bats and pangolins that had been little studied and never known to cause humans any harm.
If someone were seeking to engineer a new coronavirus as a pathogen, they would have constructed it from the backbone of a virus known to cause illness.

(2) Where did the virus come from? No one knows yet.

Cures/Vaccine

(1)The Serum Institute of India, which produces 1.5 billion vaccine doses a year for an array of diseases, says it will start production before the targeted completion date of the Oxford trial. The Oxford Vaccine Group says it hopes to complete human trials on the hAdOx1 nCoV-19 vaccine in September 2020. The Serum Institute of India is not waiting for the trials, but will jump-start on manufacturing, to have enough doses available, if the clinical trials prove successful. The company expressed optimism of starting trials in India for this vaccine over the next 2-3 weeks. The Pune-based company has partnered with Oxford University as one of the seven global institutions manufacturing the vaccine.
https://www.livemint.com/news/india/pune-s-serum-institute-to-start-making-coronavirus-vaccine-that-is-under-trial-11587889621799.html

(2)Biocon is developing a customised non-replicating measles virus based vaccine for coronavirus, that can be commercialised quickly, along with two new generation repurposed drugs and an antibody diagnostic kit.
https://www.businesstoday.in/sectors/pharma/biocon-developing-vaccine-antibody-cure-and-repurposed-drugs-against-covid-19/story/402421.html

(3)Israeli scientists: 'In a few weeks, we will have coronavirus vaccine' APRIL 13, 2020
MIGAL researchers examined it and found that the poultry coronavirus has high genetic similarity to the human one, and that it uses the same infection mechanism, which increases the likelihood of achieving an effective human vaccine in a very short period of time. Once the vaccine is developed, it will take at least 90 days to complete the regulatory process and potentially more to enter the marketplace. https://www.jpost.com/health-science/israeli-scientists-in-three-weeks-we-will-have-coronavirus-vaccine-619101

News Clips

Never Loose HOPE!: At age 102, Madam Yap is Singapore's oldest coronavirus survivor. She was discharged from Tan Tock Seng Hospital two days ago. It is the second time in her long life that a global pandemic has crossed her path. She was born in 1918 during the Spanish flu - the world's worst pandemic - which reportedly killed more than 50 million people worldwide, including 2,800 in Singapore.
https://www.straitstimes.com/singapore/health/at-102-she-fought-and-beat-covid-19

In its early stages, the infection wreaked havoc among the Iceland. But thanks to a rigorous regime of tracking and tracing, it has more or less been eliminated, giving the country confidence to reopen borders on June 15. There's no complacency though. Before entering Iceland, travelers must wear a mask on flights and within the arrival halls of Keflavik Airport. On landing, they join a new queue for nose and throat swabs to filter out anyone who might be carrying Covid-19. Visitors ushered into a cubicle, where two people dressed in full medical protective gear use long plastic sticks to prod much deeper than you might expect to take a sample. Ultimately, Iceland's screening and contact tracing system has been so efficient with one of the lowest virus death rates in the world: 30 per million people. https://edition.cnn.com/travel/article/iceland-reopens-coronavirus/index.html

Vietnam, the country of 97 million people has not reported a single coronavirus-related death and on Saturday had just 328 confirmed cases, despite its long border with China and the millions of Chinese visitors it receives each year. Vietnam is a low-middle income country. After a three-week nationwide lockdown, Vietnam lifted social distancing rules in late April. It hasn't reported any local infections for more than 40 days. Businesses and schools have reopened, and life is gradually returning to normal.

China's closest countries South Korea, Taiwan, Vietnam and Hong Kong are doing well. Singapore is ok, except for immigrants.

New Zealand Prime Minister ordered the military to oversee New Zealand's borders Wednesday after a quarantine bungle that allowed COVID-19 back into the country. A 24-day run with no new cases was broken, when it emerged two women who recently arrived from Britain were allowed out of quarantine early without being tested for the virus. The pair were proved to be infected. [18 June news]

Controversies:

(1) A doctor in China who sounded an early warning about the new coronavirus has now died of the illness. The doctor is being mourned in China as a hero. But when he first sounded the alarm in late December, he was detained by police for, quote, "disrupting social order." https://www.npr.org/2020/02/06/803520963/chinese-doctor-who-sounded-early-warning-about-coronavirus-dies-after-contractin

(2) When they heard about patients falling sick with a mysterious pneumonia in the Chinese city of Wuhan on Dec. 31, Taiwan’s health officials fired off an email to the World Health Organization asking for more information. WHO ignored an early warning that the coronavirus could likely be transmitted between people. Taiwan, in the critical early days of the pandemic, initiated a quick response that helped it keep its infection rate among the lowest in the world.

Taiwan was still “fifty percent trusting,” because released by WHO. WHO chief Tedros Adhanom Ghebreyesus accused Taiwan of backing a racist campaign against him. https://time.com/5826025/taiwan-who-trump-coronavirus-covid19/

The World Health Organisation reiterated on May 1 2020, that the new coronavirus was of natural origin. Scientists believe the killer virus jumped from animals to humans, emerging in China late last year, possibly from a market in Wuhan selling exotic animals for meat. WHO had sounded the highest level of alert by declaring that the Covid-19 outbreak constituted a “public health emergency of international concern” on Jan 30, when there were no deaths and only 82 cases registered outside China.

Financial Implication

COVID 19 has transferred 2 or 3 trillion USD from some one to some other one. One persons's loss is other persons's gain. All governments are trying to take savings of people who have saved and give it to people who have lost under COVID 19 program. Like any, these can be misused, and some more may become richer at other's costs.

New York (CNN Business)The past three months have been financially painful for many Americans -- but not for billionaires. https://edition.cnn.com/2020/06/04/business/billionaire-wealth-inequality-pandemic-jobs/index.html US billionaires have become $565 billion richer since March 18, according to a report published Thursday by the Institute for Policy Studies, a progressive think tank. Amazon (AMZN) boss Jeff Bezos alone is worth $36.2 billion more than he was on March 18.

Epidemics in History

Plagues and epidemics have ravaged humanity throughout its existence, often changing the course of history. Throughout the course of history, disease outbreaks have ravaged humanity, sometimes changing the course of history and, at times, signaling the end of an entire civilization. Empires decline and even disappear, not only due to military power. But due to calamities including epidemics and economy.

Not properly documented on Dravidian kingdoms:
(1) Gastro intestinal plaque during Appar or Thirunavukkarasar times (seventh-century), affected Jain monasteries and were spreading. Samanas (Jains, but also include buddhists) were the dominant political force at that time. Thirunavukkarasar left Jains and his sister Thilagavathiar at Atikai treated him with some herbs (burnt or mixed with ash) as medicine. Food habits of saivites are different from jains, with use of underground vegetables and spices including garlic. This seems to have worked to cure illness. Ash or carbon is used in many systems of medicine. Many turned to saivites for cure. Pallava Kings and other prominent people who are affected, might have adopted saivam after this epidemic. Still earth/ash medicine is popular in vaidheswaran kovil.

(2) Spread of stoamch related plaque or presense of deadly worms in stomach, during the rule of Kuloththunga Chola II or Kirumi kantha cholan during Ramanuja times. King (saivite extremist) wanted to harm/punish Ramanuja acharya. Epidemic was considered as a curse from vaishnavites. This led to popularity of vaishnava cult by his successors. Srirangam has been gifted to Vaishnavas (Ramanuja) and whole island belongs to Lord Renganatha. Tirupathi also became a popular Vaishnava temple

(3) Cholas were masters of sea trade and known for its powerful navy. Suddenly, there was epidemic spread from oversea territories (kadaram or some Indonesian islands affected by epidemic from natural calamity, may be eartyhquake or volcanic eruption). All trade and travel links to south east asia are stopped. Sick People were isolated and oversea travel was discouraged. (Some communities still retained the custom of isolating people who travelled overseas). From then on, Cholas influence over overseas territories declined. Southeast asian trade went to Gujarathi muslims, whose beliefs influenced Malaysia annd Indonesia. Here are some of the worst epidemics and pandemics documented, dating from prehistoric to modern times. This is not exhaustive or complete list.

  1. Prehistoric epidemic: Circa 3000 B.C. The archaeological site is now called "Hamin Mangha"
  2. Plague of Athens: 430 B.C.
  3. Antonine Plague: A.D. 165-180 may have killed over 5 million people in the Roman empire. Christianity became increasingly popular after the plague occurred.
  4. Plague of Cyprian: A.D. 250-271 is estimated to have killed 5,000 people a day in Rome alone.
  5. Plague of Justinian: A.D. 541-542 led to the start of decline of byzonites.
  6. The Black Death: 1346-1353 spread by fleas on infected rodents.
  7. Cocoliztli epidemic: 1545-1548 that killed 15 million inhabitants of Mexico and Central America.
  8. American Plagues: 16th century brought to the Americas by European explorers. These illnesses, including smallpox, contributed to the collapse of the Inca and Aztec civilizations.
  9. Great Plague of London: 1665-1666
  10. Great Plague of Marseille: 1720-1723
  11. Russian plague: 1770-1772
  12. Flu pandemic: 1889-1890
  13. American polio epidemic: 1916
  14. Spanish Flu: 1918-1920
  15. Avian Flu: 1957-1958
  16. AIDS pandemic and epidemic: 1981-present day has claimed an estimated 35 million lives.
  17. Severe Acute Respiratory Syndrome (SARS) - 2003
  18. H1N1 Swine Flu pandemic: 2009-2010
  19. West African Ebola epidemic: 2014-2016
  20. Zika Virus epidemic: 2015-present day

Closing Note

The world of biology is dynamic and there is always a chance that deadly viruses like this would jump from animals to humans. Harmful microbes/viruses are unaffected by human created borders, politics or morality. But naturally occurring viruses might pale in comparison to the viruses that could potentially be created by the powerful new tools of synthetic biology, agents precision-engineered to cause harm. There may be future human created pandemics or accidents.

All countries need to maintain essential capabilities by investing the necessary time and money to prepare for rare but inevitable events. We must develop new sensor systems that can identify new infectious agents in real time and act before a major outbreak emerges. Build emergency response capabilities for pandemics, with trained emergency response teams, both national and international level. Create medicines/vaccines platforms that can rapidly counter novel threats.

Ref. Sources

  1. https://www.livescience.com/
  2. www.sciencealert.com
  3. www.health.nsw.gov.au
  4. https://en.wikipedia.org/wiki/Coronavirus
  5. microbewiki.kenyon.edu
  6. Nextstrain, an open-source project that provides users real-time reports of the spread of seasonal influenza, Ebola and many other infectious diseases.