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Category Archives: Genetic Medicine
Many people have been wondering about the relevance of intelligent design (ID) or evolution to the new coronavirus reported in Wuhan, China, in December 2019. What follows is my view as a molecular biologist.
The new virus goes by several names. It was initially called 2019-nCoV by the World Health Organization (with n standing for new). Since its DNA sequence is similar to that of the coronavirus that caused Severe Acute Respiratory Syndrome (SARS) in 2003, the International Committee on Taxonomy of Viruses renamed it SARS-CoV-2 in March 2020. The disease caused by the virus has been called COVID-19 (with d standing for disease).
There are other coronaviruses (including MERS-CoV, the virus that caused the 2012 epidemic of Middle East Respiratory Syndrome). To avoid confusion, I will refer to the latest coronavirus by its technical name, SARS-CoV-2.
Some people have maintained that SARS-CoV-2 is a product of human design. According to a February New York Post article, it may have escaped from a microbiology laboratory at the Wuhan Institute of Virology. But I have seen no scientific evidence to support this claim.
On March 17, 2020, an analysis of DNA from several different coronaviruses was published in Nature Medicine. The authors concluded, Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.
Jonathan Bartlett, who has studied the logic of design inferences in depth, subsequently argued that the scientists had ruled out only one design hypothesis, so design was still theoretically possible. But Bartlett did not maintain that SARS-CoV-2 is a product of human design.
Could SARS-CoV-2 have evolved from another coronavirus by mutation and natural selection? I dont see why not, though there is only indirect evidence (from DNA sequences) to support the idea. If it had happened, however, it would not provide support for Darwinian evolution.
First, viruses are not living organisms: They are just pieces of DNA or RNA enclosed in a protein coat. They do not carry out metabolism (the chemical processes that are essential for life), and they do not reproduce themselves (only living cells or skilled genetic engineers can make copies of them). Second, even if viruses were considered living things, the evolution of SARS-CoV-2 from another coronavirus would be akin to microevolution minor changes within existing biological species. (Species are not even defined the same way in viruses as they are in living organisms.)
But Darwin did not write a book titled How Existing Species Change Over Time. He wrote a book titled The Origin of Species. In other words, Darwin attempted to explain macroevolution the origin of new species, organs, and body plans.
What, then, is the relevance of ID or evolution to SARS-CoV-2? As we have seen, their relevance to the origin of the coronavirus is unclear. But what about their relevance to combating the disease, COVID-19? According to Darwinist Theodosius Dobzhansky (who distinguished between microevolution and macroevolution in the 1930s), nothing in biology makes sense except in the light of evolution. In 2003, Texas Tech University professor Michael Dini wrote:
The central, unifying principle of biology is the theory of evolution. How can someone who does not accept the most important theory in biology expect to properly practice in a field [medicine] that is so heavily based on biology?
Yet the measures being taken against the SARS-CoV-2 pandemic owe nothing to evolutionary theory. The use of quarantine to block the spread of disease began in the fourteenth century. In the 1790s, Edward Jenner vaccinated people to protect them from smallpox. In 1847, Hungarian obstetrician Ignc Semmelweis demonstrated that proper hand washing lowers mortality from infectious disease. The administration of oxygen to patients with labored breathing was first reported in the years just following the publication of The Origin of Species, but the practice was based on physiological and clinical considerations, not evolution. And if any treatments are found to cure COVID-19 or lessen its effects, they will come from the intelligently designed efforts of virologists, biochemists, and clinicians not evolutionary biologists.
Photo credit: Airman 1st Class Alexis Christian, via Peterson Air Force Base.
TAILOR-PCI: Using Genetic Testing to Guide Antiplatelet Therapy Post-PCI Misses Goal to Cut Rate of Cardiovascular Events in Half – Cath Lab Digest
WASHINGTON (Mar 28, 2020) - An international clinical trial that used genetic testing to guide which antiplatelet medication was given to patients following percutaneous coronary intervention (PCI) did not meet its stated goal for cutting in half the incidence of serious adverse cardiovascular events, such as heart attack and stroke, in the year following the procedure. However, researchers reported a 34% reduction in these adverse events at one year, as well as a significant reduction in the number of events per patient, according to study results presented at the American College of Cardiologys Annual Scientific Session Together with World Congress of Cardiology (ACC.20/WCC).
The primary endpoint of TAILOR-PCIthe largest cardiology trial to test the effectiveness of using genetic testing to guide treatment choicewas to demonstrate a 50% reduction at one year in the combined rate of death, heart attack, stroke, a blood clot in a stent (stent thrombosis) or a recurrent heart attack-like presentation. While the trial missed this mark, researchers observed a 34% drop in these events in the year following PCI. The trial also revealed a statistically significant 40% reduction in the total number of events per patient receiving genetically guided treatment compared with patients who received standard treatment.
Although these results fell short of the effect size that we predicted, they nevertheless provide a signal that offers support for the benefit of genetically guided therapy, with approximately one-third fewer adverse events in the patients who received genetically guided treatment compared with those who did not, said Naveen L. Pereira, MD, professor of medicine at the Mayo Clinic in Rochester, Minnesota, and co-principal investigator of the study.
Pereira added that a post hoc analysis, performed after the researchers knew the studys results, found a nearly 80% reduction in the rate of adverse events in the first three months of treatment among patients who received genetically guided therapy compared with those who did not. This period immediately after PCI is when patients are at the highest risk for adverse events, he said.
We now know from clinical practice and other studies that antiplatelet drug therapy is critical during the first three months after PCI, he said. This finding suggests that the lions share of the benefit of genetically guided therapy may occur during this high-risk period. Because this wasnt a pre-planned analysis, we cant draw firm conclusions from it, but it merits further study.
Patients with arterial blockages who undergo PCIthe insertion of a stent or stents to prop arteries openare commonly prescribed the antiplatelet medication clopidogrel, along with aspirin, for a year after the procedure to help prevent blood clots that can cause heart attack, stroke and other complications. However, studies have suggested that people who have a genetic variant in a liver enzyme known as CYP2C19 are unable to fully metabolize clopidogrel, reducing the effectiveness of the medication and leaving them at increased risk of developing blood clots and serious adverse cardiovascular events. Such patients may be good candidates to receive alternative antiplatelet medication.
In the U.S., about 30% of people carry the genetic variant that makes them less capable of metabolizing and, hence, activating clopidogrel, Pereira said. The proportion increases to 50% among people of Asian heritage. A simple-to-perform genetic test can identify whether a patient carries the abnormality, Pereira said. However, no prospective clinical trials have shown that outcomes are better for patients who have the abnormality when the test is used to guide their treatment. For this reason, guidelines published by the American College of Cardiology and the American Heart Association do not currently recommend that patients be tested for the abnormality before being prescribed clopidogrel, Pereira added.
The TAILOR-PCI trial was designed to fill this knowledge gap. The trial enrolled 5,302 patients who had been treated for an arterial blockage with one or more stents. Their median age was 62 years, and 75% were men. Patients were randomly assigned either to a group that was tested for the genetic variant affecting clopidogrel metabolism or to a group that received standard treatment without genetic testing. In the first group, 35% of patients were found to have the genetic variant and were prescribed another antiplatelet medication, ticagrelor, while those without it got clopidogrel. In the second group, everyone was prescribed clopidogrel. Patients were enrolled at 40 medical centers in the U.S., Canada, Mexico and South Korea and followed for one year.
Among patients who carried the genetic variant, the primary endpoint occurred in 35 (4%) in the group that received genetically guided treatment, compared with 54 (5.9%) in the conventionally treated group at one year.
Pereira said that the reduction in the number of adverse events per patient also has important clinical implications. Multiple adverse events represent a higher burden on the patient, so it is encouraging to see a significant reduction in cumulative events with genetically guided therapy, he said.
Among patients with the genetic variant, there were no differences in the safety endpoint of TIMI major bleeding (fatal bleeding, bleeding in the brain or any bleeding that requires medical assessment or treatment) or minor bleeding between those receiving genetically guided treatment (16 patients, 1.9%) and those in the conventional treatment arm (14 patients, 1.6%) at one year.
Pereira said that recent improvements in the standard of care following PCI may have contributed to the trial not achieving its primary endpoint. When the TAILOR-PCI trial was designed in 2012, around 10% to 12% of patients who received a stent could be expected to have a major adverse event, such as a heart attack, stroke or stent thrombosis, within a year. Over the course of the trial, the standard of care evolved through greater use of drug-coated stents and other treatments, which reduced the expected rate of adverse events in a year to about 5%. This change in technology substantially improved care for patients, but at the same time may have made it more difficult for the trial to reach its goal of a 50% reduction in adverse events with the number of patients enrolled, Pereira said.
No special expertise in laboratory testing is required to perform the genetic test, Pereira said. In the trial, the tests were done by study coordinators who did not have a background in laboratory medicine and who were able to perform the tests in a consistent, reproducible fashion after receiving brief training.
The next step, he said, will be to analyze the cost effectiveness of genetically guided therapy. The National Heart, Lung, and Blood Institute has also funded an extended follow-up study to evaluate the effect of genotype guidance beyond the 12-month follow-up period of TAILOR PCI.
This study was funded by the Mayo Clinic in collaboration with the National Heart, Lung, and Blood Institute. Spartan Bioscience, Inc, supplied the genetic tests used.
ACC.20/WCC will take place March 28-30, bringing together cardiologists and cardiovascular specialists from around the world to share the newest discoveries in treatment and prevention. Follow @ACCinTouch, @ACCMediaCenter and #ACC20/#WCCardio for the latest news from the meeting.
The American College of Cardiology envisions a world where innovation and knowledge optimize cardiovascular care and outcomes. As the professional home for the entire cardiovascular care team, the mission of the College and its 54,000 members is to transform cardiovascular care and to improve heart health. The ACC bestows credentials upon cardiovascular professionals who meet stringent qualifications and leads in the formation of health policy, standards and guidelines. The College also provides professional medical education, disseminates cardiovascular research through its world-renowned JACC Journals, operates national registries to measure and improve care and offers cardiovascular accreditation to hospitals and institutions. For more, visit acc.org.
8 strains of the coronavirus are circling the globe. Here’s what clues they’re giving scientists. – USA TODAY
An epidemiologist answers the biggest questions she's getting about coronavirus. Wochit
SAN FRANCISCO At least eight strains of the coronavirus are making their way around the globe, creating a trail of death and disease that scientistsare tracking by their genetic footprints.
While much is unknown, hidden in the virus's unique microscopic fragments are clues to the origins of its original strain, how it behaves as it mutates and which strains are turning into conflagrations while others are dying out thanksto quarantine measures.
Huddled in once bustling and now almost empty labs, researchers who oversaw dozens of projects are instead focused on one goal:tracking the currentstrains of the SARS-CoV-2 virus that cause the illness COVID-19.
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Labs around the world are turning their sequencing machines, most about the size of a desktop printer, to the task ofrapidly sequencing the genomes of virus samples taken frompeople sick with COVID-19.The information is uploaded to a website called NextStrain.org that shows how the virus is migrating and splitting into similarbut new subtypes.
While researcherscaution they'reonly seeing the tip of the iceberg, the tiny differences between the virus strains suggest shelter-in-place orders are working in some areas and thatno one strain of the virus ismore deadly than another. They also say it does not appear the strains will grow more lethal as theyevolve.
The virus mutates so slowly that the virus strains are fundamentally very similar to each other, said Charles Chiu, a professor of medicine and infectious disease at the University of California, San Francisco School of Medicine.
A map of the main known genetic variants of the SARS-CoV-2 virus that causes COVID-19 disease. The map is being kept on the nextstrain.org website, which tracks pathogen evolution.(Photo: nextstrain.org)
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The SARS-CoV-2 virusfirst began causing illness in China sometimebetween mid-November and mid-December. Its genome is made up of about 30,000 base pairs. Humans, by comparison, have more than 3 billion. So fareven in the virus's most divergent strainsscientists have found only 11 base pair changes.
That makes iteasy to spot new lineages as they evolve, said Chiu.
The outbreaks are trackable. We have the ability to do genomic sequencing almost in real-time to see what strains or lineages are circulating, he said.
So far, mostcases on the U.S. West Coast are linked to a strainfirst identified in Washington state. It may have come from a man who had been in Wuhan, China, the virus epicenter, and returned home on Jan. 15. It is only three mutations away from the original Wuhan strain, according to work done early in the outbreakby Trevor Bedford, a computational biologist at Fred Hutch, a medical research center in Seattle.
On the East Coast there are several strains, including the one from Washington and others that appear to have made their way from China to Europe and then to New York and beyond, Chiu said.
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Charles Chiu, MD, PhD, director of the UCSF-Abbott Viral Diagnostics and Discovery Center, inserts a tray of Universal Transport Medium (UTM) or vials for the collection, transport, maintenance and long term freeze storage of viruses into a Biomatrix sorter that the Chiu Lab will be using, starting Monday to study the genes of the Coronavirus.(Photo: Susan Merrell/UCSF)
This isnt the first time scientists have scrambled to do genetic analysis of a virus in the midst of an epidemic. They did it with Ebola, Zika and West Nile, but nobodyoutside the scientific community paid much attention.
This is the first time phylogenetic trees have been all over Twitter, said Kristian Andersen, a professor at Scripps Research, a nonprofit biomedical science research facility in La Jolla, California, speaking of the diagrams that show the evolutionary relationships between different strains of an organism.
The maps are available on NextStrain, an online resource for scientists that uses data from academic, independent and government laboratories all over the world to visually track the genomics of the SARS-CoV-2 virus. It currently represents genetic sequences of strains from 36 countries on six continents.
While the maps are fun, they can also be little dangerous said Andersen. The trees showing the evolution of the virus are complex and its difficult even for experts to draw conclusions from them.
Remember, were seeing a very small glimpse into the much larger pandemic. We have half a million described cases right now but maybe 1,000 genomes sequenced. So there are a lot of lineages were missing, hesaid.
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COVID-19 hitspeople differently, with some feeling only slightly under the weather for a day, others flat on their backs sick for two weeks and about 15% hospitalized. Currently, an estimated1% of those infected die. The rate varies greatly by country and experts say it is likely tied to testing rates rather than actual mortality.
Chiu says it appears unlikely the differences are related to people being infected withdifferent strains of the virus.
The current virus strains are still fundamentally very similar to each other, he said.
The COVID-19 virus does not mutate very fast. It does so eightto 10 times more slowly than the influenza virus, said Anderson, making its evolution rate similar to other coronaviruses such asSevere Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS).
Its also not expected tospontaneously evolve into a form more deadly than it already is to humans. The SARS-CoV-2 is so good at transmitting itself between human hosts,said Andersen,it is under no evolutionary pressure to evolve.
Chius analysis shows Californias strict shelter in place efforts appear to beworking.
Over half of the 50 SARS-CoV-2 virus genomes his San Francisco-based lab sequenced in the past two weeks are associated with travel from outside the state. Another 30% are associated with health care workers and families of people who have the virus.
Only 20% are coming from within the community. Its not circulating widely, he said.
Thats fantastic news, he said, indicating the virus has not been able to gain aserious foothold because of social distancing.
It's like a wildfire, Chiu said. A few sparks might fly off the fire and land in the grass and start new fires. But if the main fire is doused and itsembers stomped out, you can kill offan entire strain.In California, Chiu sees a lot of sparks hitting the ground, most coming from Washington,but they're quickly being put out.
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An example wasa small cluster of cases in Solano County, northeast of San Francisco. Chius team did a genetic analysis of the virus that infected patients there and found it was most closely related to a strain from China.
At the same time, his lab was sequencing a small cluster of cases in the city of Santa Clara in Silicon Valley. They discovered the patients there had the same strain as those in Solano County. Chiu believes someone in that cluster had contact with a traveler who recently returned from Asia.
This is probably an example of a spark that began in Santa Clara, may have gone to Solano County but then was halted, he said.
The virus, he said, can be stopped.
China is an unknown
So far researchers dont have a lot of information about the genomics of the virus inside China beyond the fact that it first appeared in the city of Wuhan sometime between mid-November and mid-December.
The viruss initial sequence was published on Jan. 10 by professor Yong-Zhen Zhang at the Shanghai Public Health Clinical Center. But Chiu says scientists dont know if there was justone strain circulating in China or more.
It may be that they havent sequenced many cases or it may be for political reasons they havent been made available, said Chiu. Its difficult to interpret the data because were missing all these early strains.
Researchers in the United Kingdom who sequenced the genomes of viruses found in travelers from Guangdong in south China found those patients strains spanned the gamut of strains circulating worldwide.
That could mean several of the strains were seeing outside of China first evolved there from the original strain, or that there are multiple lines of infection. Its very hard to know, said Chiu.
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While there remain many questions about the trajectory of the COVID-19 disease outbreak, one thing is broadly accepted in the scientific community: Thevirus was not created in a lab but naturally evolved in an animal host.
SARS-CoV-2s genomic molecular structure thinkthe backbone of the virus is closest to a coronavirus found in bats. Parts of its structure also resemble a virus found in scaly anteaters, according to a paper published earlier this month in the journal Nature Medicine.
Someone manufacturing a virus targetingpeople would have started with one that attacked humans, wrote National Institutes of Health Director Francis Collinsin an editorial that accompanied the paper.
Andersen was lead author on the paper. He said it could have been a one-time occurrence.
Its possible it was a single event, from a single animal to a single human, and spread from there.
By Michael Le Page
ED JONES/AFP via Getty Images
The UK has ordered 3.5 million antibody tests designed to reveal whether people have been infected with the new coronavirus. The UKs prime minister, Boris Johnson, who today announced he himself has tested positive for the virus, has said these tests will be a game changer, but the reality is they might not have that much of an impact in the short term.
Almost all testing for the virus around the world is based on looking for its genetic sequence. But such tests require nose or throat swabs to be taken by trained personnel and sent to a specialised lab for analysis, and there is a global shortage of equipment. Genetic tests also detect only active infections.
Antibody tests, by contrast, detect the antibodies our bodies produce to kill the virus, which we keep producing even after the virus is eliminated. These tests can reveal who has been infected even after they have recovered. Handheld tests that require only a drop of blood can give results in 10 minutes, and can be mass produced quickly and cheaply.
If we know someone has had the virus, they can potentially leave their home without risk of being re-infected, which would help countries get moving again. However, the accuracy of the tests has yet to be established. The one thing thats worse than no test is an inaccurate test, Chris Whitty, the UKs chief medical adviser, said on 25 March. Someone wrongly told they have already had covid-19 could go out and get infected.
How accurate do the tests need to be? Its very difficult to say, says Emily Adams at the Liverpool School of Tropical Medicine in the UK, who is helping assess the tests developed by Mologic, one of the companies supplying the UK. Part of that process will be working out what accuracy is required for different uses, says Adams.
Ideally, we want to find out whether the thousands of health workers who are currently self-isolating because they or someone else in their home have symptoms that might be covid-19 can get back to work. Unfortunately, the antibody test may not help with this.
The antibody response to the coronavirus may be delayed compared with other infections. The tests can be used only 14 days or more after people develop symptoms, says Adams.
This also means antibody testing will be of limited use for tracing the contacts of infected people which many think is crucial for controlling the outbreak because health authorities will be weeks behind.
Widespread antibody testing will also reveal whether large numbers of mild infections have gone unnoticed. It would be great news if this is the case, allowing many to return to work and meaning that the infection fatality rate is lower than thought. Unfortunately, places like South Korea that have been doing lots of genetic testing havent found vast numbers of mild cases.
On the plus side, many groups are working on faster genetic tests and on antigen tests that can detect the virus in, say, saliva. Testing widely for both active infections and past infections should be a highly effective combination.
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As of Friday afternoon, Thomass county was up to 110 confirmed cases. Winter is coming, as he put it. But Thomas maintains hope that a blanket DNR policy will not be necessary. Assess, make decisions, reassess, make another decision. Repeat is how he described the coronavirus-treatment playbook to me. We can do this as long as we have PPE and vents.
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Although explicit, widespread rationing by health-care providers is unprecedented in the modern history of the United States, it is constantly happening around the world. Our doctors face moral dilemmas and impossible choices every day, said Doctors Without Borders Avril Benoit. Even while COVID-19 is requiring reallocation of resources, we still have women who need emergency C-sections and children with malnutrition. We are converting trauma and burn clinics to care for the disease. You do the best you can with what you have. And many of our locations will not be able to do more than isolate people and provide palliative care.
Patients, too, make rationing decisions. Every time we weigh whether or not to go to the doctor or to take medication, were balancing costs and benefits. Many peoplean estimated third of U.S. adultsalso make decisions about what they want should they become very ill. In the form of advance directives, they give instructions about when medical professionals should extend their lives with so-called extraordinary measures, and when they shouldnt.
The directives can be elaborate or spare, but generally land on a spectrum between prioritizing comfort and prolonging life, should the two become mutually exclusive. The most common designations are full code and DNR, but directives can also get very specific. The options are not binary, care or none. A person who voluntarily designates as DNR wouldnt be abandonedhe or she would still get IV fluids, oxygen, and medication, especially for pain.
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After determining advance directives, you should share them with family members or friends who might be communicating with medical professionals on your behalf. Have nuanced conversations with people close to you about what you do or dont want in various dire scenarios. This eases the burden on them.
It eases the burden on medical providers as well. Too often, Lindsey said, a person is found unconscious by paramedics, then shocked back to life and brought to the hospital, or put on a ventilator, and only hours later a family member shows up with an advance directive that indicates that this was not what the patient wanted. This was a tragic and challenging scenario pre-COVID, particularly if an individuals directives werent followed during that period of resuscitation, he said. But in the midst of this pandemic, the delay puts all the providers in the chain of care at unnecessary risk of exposure. And it takes a ventilator out of use for someone who might have wanted it.
As straightforward as it is to establish an advance directive and talk through what kind of care you want with your family, many of us avoid doing precisely that. Who wants to talk about the possibility of getting sick and dying? Thomas does. Im still a relatively young person, and my wife and I have that discussion relatively often, he told me. It should be had frequently, but especially now.
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The Curve Is Not Flat Enough - The Atlantic
Iceland has done a first-class job of rolling out a large-scale COVID-19 testing strategy across its population. Although it's is only a small nation, their approach is already providing somefascinatinginsights into the COVID-19 and the current pandemic.
Iceland health authorities, together with private biopharmaceutical company deCode Genetics, have so far administered 12,615 tests across the country, accounting for almost 3.5 percent of the total population. For context, the US has tested around 540,252 people, around 0.16 of the population.
Unlike most other countries, Iceland has been offering free screening among the general population even if they dont have any symptoms. This testing has identified up to 802 confirmed COVID-19 infections, at least 253 of which were obtained by a foreign traveler.
You can see all of the testing results on the health ministrys COVID-19 live data page.
What can we learn from this data? Well, first things first: these are preliminary results, for the time being, so we can't take them as gospel. Equally, every country has a unique infrastructure, culture, and social structure, so each countrys outbreak may not necessarily behave like Icelands.
The most interesting revelation is that Icelands data suggests around half of people who tested positive for COVID-19 in the country did not display any symptoms.
Early results from deCode Genetics indicate that a low proportion of the general population has contracted the virus and that about half of those who tested positive are non-symptomatic. The other half displays very moderate cold-like symptoms, Thorolfur Gunason, Icelands chief epidemiologist, told Buzzfeed News.
The work has also allowed researchers to understand how the novel coronavirus SARS-CoV-2 has mutated within the country. In one unique situation, it even appears that one Icelandic person was infected with two different variants of SARS-CoV-2 with subtlydifferent genetic material.
We have found 40 island-specific virus mutations. We found someone who had a mixture of viruses," explains Kri Stefnsson, director of deCode Genetics speaking to Danish newspaper Information. "They had viruses from before and after the mutation, and the only infections traceable to that person are the mutated virus.
While this number of mutations is slightly higher than other estimates, its nothing to worry about. According to Nathan Grubaugh, an epidemiologist at the Yale School of Public Health, mutations are a natural part of the virus lifecycle and we shouldnt worry when a virus mutates during disease outbreaks. By and large, preliminary data suggests SARS-CoV-2 has a relatively stable genome.
Iceland's small population means it's in aunique situation to carry out this kind of testing strategy, but every country would be doing this in an ideal world.The World Health Organization (WHO) has maintained that all countries need to start widespread testing for COVID-19, even among people who don't have symptoms. If we don't have the data, they say, the pandemic cannot be fought effectively.
You cannot fight a fire blindfolded and we cannot stop this pandemic if we don't know who is infected. We have a simple message for all countries; test, test, test,"Dr Tedros Adhanom Ghebreyesus, director-general of the WHO, said on March 16.