'Coronavirus May Have Spread in U.S. for Weeks, Gene Sequencing Suggests' diff viewer (12/13)

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Coronavirus May Have Spread in U.S. for Weeks, Gene Sequencing Suggests	Coronavirus May Have Spread in U.S. for Weeks, Gene Sequencing Suggests
2020-06-10 00:01:07 UTC	2020-06-13 05:50:36 UTC (3 days later)
Researchers who have examined the genomes of two coronavirus infections in Washington State say the similarities between the cases suggest that the virus may have been spreading in the state for weeks.	Researchers who have examined the genomes of two coronavirus infections in Washington State say the similarities between the cases suggest that the virus may have been spreading in the state for weeks.
Washington had the United States’ first confirmed case of coronavirus, announced by the Centers for Disease Control and Prevention on Jan. 20. Based on an analysis of the virus’s genetic sequence, another case that surfaced in the state and was announced on Friday probably was descended from that first case.	Washington had the United States’ first confirmed case of coronavirus, announced by the Centers for Disease Control and Prevention on Jan. 20. Based on an analysis of the virus’s genetic sequence, another case that surfaced in the state and was announced on Friday probably was descended from that first case.
The two people live in the same county, but are not known to have had contact with one another, and the second case occurred well after the first would no longer be expected to be contagious. So the genetic findings suggest that the virus has been spreading through other people in the community for close to six weeks, according to one of the scientists who compared the sequences, Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington.	The two people live in the same county, but are not known to have had contact with one another, and the second case occurred well after the first would no longer be expected to be contagious. So the genetic findings suggest that the virus has been spreading through other people in the community for close to six weeks, according to one of the scientists who compared the sequences, Trevor Bedford, an associate professor at the Fred Hutchinson Cancer Research Center and the University of Washington.
Dr. Bedford said it was possible that the two cases could be unrelated, and had been introduced separately into the United States. But he said that was unlikely, however, because in both cases the virus contained a genetic variation that appears to be rare — it was found in only two of the 59 samples whose sequences have been shared from China, where the virus originated.	Dr. Bedford said it was possible that the two cases could be unrelated, and had been introduced separately into the United States. But he said that was unlikely, however, because in both cases the virus contained a genetic variation that appears to be rare — it was found in only two of the 59 samples whose sequences have been shared from China, where the virus originated.
A scientist who was not involved in the analysis said he agreed with the conclusion that the second case was connected to the original Washington case. “I think he’s right,” said Andrew Rambaut, professor of molecular evolution at the University of Edinburgh, referring to Dr. Bedford. “It’s extremely unlikely that two viruses coming from outside the U.S.A. independently would arrive in the same geographical area and be genetically related unless they were connected.”	A scientist who was not involved in the analysis said he agreed with the conclusion that the second case was connected to the original Washington case. “I think he’s right,” said Andrew Rambaut, professor of molecular evolution at the University of Edinburgh, referring to Dr. Bedford. “It’s extremely unlikely that two viruses coming from outside the U.S.A. independently would arrive in the same geographical area and be genetically related unless they were connected.”
State and local health officials have been hamstrung in their ability to test widely for the coronavirus. Until very recently, the C.D.C. had insisted that only its test could be used, and only on patients who met specific criteria — those who had traveled to China within 14 days of developing symptoms or had contact with a known coronavirus case.	State and local health officials have been hamstrung in their ability to test widely for the coronavirus. Until very recently, the C.D.C. had insisted that only its test could be used, and only on patients who met specific criteria — those who had traveled to China within 14 days of developing symptoms or had contact with a known coronavirus case.
If the virus has been spreading undetected in Washington since mid-January, that could mean that anywhere from 150 to 1,500 people may have it, with about 300 to 500 people the most likely range, said Dr. Mike Famulare, a principal research scientist at the Institute for Disease Modeling in Bellevue, Wa., who performed the analysis. These people “have either been infected and recovered, or currently are infected now,” he said.	If the virus has been spreading undetected in Washington since mid-January, that could mean that anywhere from 150 to 1,500 people may have it, with about 300 to 500 people the most likely range, said Dr. Mike Famulare, a principal research scientist at the Institute for Disease Modeling in Bellevue, Wa., who performed the analysis. These people “have either been infected and recovered, or currently are infected now,” he said.
Many of those people would now be in the early stages of incubating the virus, and might not yet be contagious, Dr. Famulare said.	Many of those people would now be in the early stages of incubating the virus, and might not yet be contagious, Dr. Famulare said.
Dr. Famulare’s estimate was based on a simulation using what scientists have learned about the incubation period and transmissibility of the virus. He called his figures a “best guess, with broad uncertainty.” Another method, based on the size of the local population, the number of tests performed and the proportion of those that were positive, produced similar estimates of how widely the virus may have spread in the community.	Dr. Famulare’s estimate was based on a simulation using what scientists have learned about the incubation period and transmissibility of the virus. He called his figures a “best guess, with broad uncertainty.” Another method, based on the size of the local population, the number of tests performed and the proportion of those that were positive, produced similar estimates of how widely the virus may have spread in the community.
The scientists immediately reported the genomic sequence and their findings to state and federal health officials.	The scientists immediately reported the genomic sequence and their findings to state and federal health officials.
Dr. Scott Lindquist, the state epidemiologist for communicable diseases with the Washington State Department of Health, said on Sunday that though Dr. Bedford’s laboratory had “very limited” data to work with, “I would not be surprised if there was transmission and these two were related.”	Dr. Scott Lindquist, the state epidemiologist for communicable diseases with the Washington State Department of Health, said on Sunday that though Dr. Bedford’s laboratory had “very limited” data to work with, “I would not be surprised if there was transmission and these two were related.”
Dr. Lindquist said more would be known when genetic sequences from the state’s other cases have been similarly analyzed. “Seeing how they all relate to each other will be the real answer to the question of, has it been circulating,” he said. “I imagine within the week we should have some of these answers.”	Dr. Lindquist said more would be known when genetic sequences from the state’s other cases have been similarly analyzed. “Seeing how they all relate to each other will be the real answer to the question of, has it been circulating,” he said. “I imagine within the week we should have some of these answers.”
Heather Thomas, a spokeswoman for the Snohomish Health District, said in a statement that the district was aware of the preliminary findings suggesting that coronavirus had been spreading for close to six weeks.	Heather Thomas, a spokeswoman for the Snohomish Health District, said in a statement that the district was aware of the preliminary findings suggesting that coronavirus had been spreading for close to six weeks.
She said that it was important to remember that national testing capabilities have only been available for about six weeks, and in Washington, health personnel have only had the ability to test locally for a few days. “It is definitely possible that Covid-19 has been circulating, with people experiencing mild symptoms just like the flu,’’ she said.	She said that it was important to remember that national testing capabilities have only been available for about six weeks, and in Washington, health personnel have only had the ability to test locally for a few days. “It is definitely possible that Covid-19 has been circulating, with people experiencing mild symptoms just like the flu,’’ she said.
The C.D.C. did not respond to a request for comment.	The C.D.C. did not respond to a request for comment.
The first patient, a man in his 30s, has recovered after being treated in a hospital isolation unit. The later patient, a teenager, had a mild enough illness to recuperate at home.	The first patient, a man in his 30s, has recovered after being treated in a hospital isolation unit. The later patient, a teenager, had a mild enough illness to recuperate at home.
According to a statement by the Snohomish Health District, the teenager was unaware that he was being tested for the coronavirus. His case came to light on Friday because he went to a clinic on Feb. 24 to be tested for the flu, and his sample was shared with the Seattle Flu Study, which tested it for a variety of pathogens including the new coronavirus.	According to a statement by the Snohomish Health District, the teenager was unaware that he was being tested for the coronavirus. His case came to light on Friday because he went to a clinic on Feb. 24 to be tested for the flu, and his sample was shared with the Seattle Flu Study, which tested it for a variety of pathogens including the new coronavirus.
Tests have been performed on about 1,000 samples from the study, Dr. Lindquist said, with only one positive result thus far. “So it’s not like it’s super prevalent,” he said of the virus.	Tests have been performed on about 1,000 samples from the study, Dr. Lindquist said, with only one positive result thus far. “So it’s not like it’s super prevalent,” he said of the virus.
“I do think, as more community cases start popping up in the United States, this approach and technique could prove very useful to figuring out the extent of community transmission we currently are having,” Dr. Bedford said of the genetic analysis.	“I do think, as more community cases start popping up in the United States, this approach and technique could prove very useful to figuring out the extent of community transmission we currently are having,” Dr. Bedford said of the genetic analysis.
Similar analyses have helped public health officials trace cases and fight outbreaks of Ebola in West Africa and the Democratic Republic of Congo.	Similar analyses have helped public health officials trace cases and fight outbreaks of Ebola in West Africa and the Democratic Republic of Congo.
~~Updated June 5, 2020~~	Updated June 12, 2020
	Touching contaminated objects and then infecting ourselves with the germs is not typically how the virus spreads. But it can happen. A number of studies of flu, rhinovirus, coronavirus and other microbes have shown that respiratory illnesses, including the new coronavirus, can spread by touching contaminated surfaces, particularly in places like day care centers, offices and hospitals. But a long chain of events has to happen for the disease to spread that way. The best way to protect yourself from coronavirus — whether it’s surface transmission or close human contact — is still social distancing, washing your hands, not touching your face and wearing masks.
So far, the evidence seems to show it does. A widely cited paper published in April suggests that people are most infectious about two days before the onset of coronavirus symptoms and estimated that 44 percent of new infections were a result of transmission from people who were not yet showing symptoms. Recently, a top expert at the World Health Organization stated that transmission of the coronavirus by people who did not have symptoms was “very rare,” but she later walked back that statement.	So far, the evidence seems to show it does. A widely cited paper published in April suggests that people are most infectious about two days before the onset of coronavirus symptoms and estimated that 44 percent of new infections were a result of transmission from people who were not yet showing symptoms. Recently, a top expert at the World Health Organization stated that transmission of the coronavirus by people who did not have symptoms was “very rare,” but she later walked back that statement.
A study by European scientists is the first to document a strong statistical link between genetic variations and Covid-19, the illness caused by the coronavirus. Having Type A blood was linked to a 50 percent increase in the likelihood that a patient would need to get oxygen or to go on a ventilator, according to the new study.	A study by European scientists is the first to document a strong statistical link between genetic variations and Covid-19, the illness caused by the coronavirus. Having Type A blood was linked to a 50 percent increase in the likelihood that a patient would need to get oxygen or to go on a ventilator, according to the new study.
The unemployment rate fell to 13.3 percent in May, the Labor Department said on June 5, an unexpected improvement in the nation’s job market as hiring rebounded faster than economists expected. Economists had forecast the unemployment rate to increase to as much as 20 percent, after it hit 14.7 percent in April, which was the highest since the government began keeping official statistics after World War II. But the unemployment rate dipped instead, with employers adding 2.5 million jobs, after more than 20 million jobs were lost in April.	The unemployment rate fell to 13.3 percent in May, the Labor Department said on June 5, an unexpected improvement in the nation’s job market as hiring rebounded faster than economists expected. Economists had forecast the unemployment rate to increase to as much as 20 percent, after it hit 14.7 percent in April, which was the highest since the government began keeping official statistics after World War II. But the unemployment rate dipped instead, with employers adding 2.5 million jobs, after more than 20 million jobs were lost in April.
Mass protests against police brutality that have brought thousands of people onto the streets in cities across America are raising the specter of new coronavirus outbreaks, prompting political leaders, physicians and public health experts to warn that the crowds could cause a surge in cases. While many political leaders affirmed the right of protesters to express themselves, they urged the demonstrators to wear face masks and maintain social distancing, both to protect themselves and to prevent further community spread of the virus. Some infectious disease experts were reassured by the fact that the protests were held outdoors, saying the open air settings could mitigate the risk of transmission.	Mass protests against police brutality that have brought thousands of people onto the streets in cities across America are raising the specter of new coronavirus outbreaks, prompting political leaders, physicians and public health experts to warn that the crowds could cause a surge in cases. While many political leaders affirmed the right of protesters to express themselves, they urged the demonstrators to wear face masks and maintain social distancing, both to protect themselves and to prevent further community spread of the virus. Some infectious disease experts were reassured by the fact that the protests were held outdoors, saying the open air settings could mitigate the risk of transmission.
Exercise researchers and physicians have some blunt advice for those of us aiming to return to regular exercise now: Start slowly and then rev up your workouts, also slowly. American adults tended to be about 12 percent less active after the stay-at-home mandates began in March than they were in January. But there are steps you can take to ease your way back into regular exercise safely. First, “start at no more than 50 percent of the exercise you were doing before Covid,” says Dr. Monica Rho, the chief of musculoskeletal medicine at the Shirley Ryan AbilityLab in Chicago. Thread in some preparatory squats, too, she advises. “When you haven’t been exercising, you lose muscle mass.” Expect some muscle twinges after these preliminary, post-lockdown sessions, especially a day or two later. But sudden or increasing pain during exercise is a clarion call to stop and return home.	Exercise researchers and physicians have some blunt advice for those of us aiming to return to regular exercise now: Start slowly and then rev up your workouts, also slowly. American adults tended to be about 12 percent less active after the stay-at-home mandates began in March than they were in January. But there are steps you can take to ease your way back into regular exercise safely. First, “start at no more than 50 percent of the exercise you were doing before Covid,” says Dr. Monica Rho, the chief of musculoskeletal medicine at the Shirley Ryan AbilityLab in Chicago. Thread in some preparatory squats, too, she advises. “When you haven’t been exercising, you lose muscle mass.” Expect some muscle twinges after these preliminary, post-lockdown sessions, especially a day or two later. But sudden or increasing pain during exercise is a clarion call to stop and return home.
States are reopening bit by bit. This means that more public spaces are available for use and more and more businesses are being allowed to open again. The federal government is largely leaving the decision up to states, and some state leaders are leaving the decision up to local authorities. Even if you aren’t being told to stay at home, it’s still a good idea to limit trips outside and your interaction with other people.	States are reopening bit by bit. This means that more public spaces are available for use and more and more businesses are being allowed to open again. The federal government is largely leaving the decision up to states, and some state leaders are leaving the decision up to local authorities. Even if you aren’t being told to stay at home, it’s still a good idea to limit trips outside and your interaction with other people.
Touching contaminated objects and then infecting ourselves with the germs is not typically how the virus spreads. But it can happen. A number of studies of flu, rhinovirus, coronavirus and other microbes have shown that respiratory illnesses, including the new coronavirus, can spread by touching contaminated surfaces, particularly in places like day care centers, offices and hospitals. But a long chain of events has to happen for the disease to spread that way. The best way to protect yourself from coronavirus — whether it’s surface transmission or close human contact — is still social distancing, washing your hands, not touching your face and wearing masks.
Common symptoms include fever, a dry cough, fatigue and difficulty breathing or shortness of breath. Some of these symptoms overlap with those of the flu, making detection difficult, but runny noses and stuffy sinuses are less common. The C.D.C. has also added chills, muscle pain, sore throat, headache and a new loss of the sense of taste or smell as symptoms to look out for. Most people fall ill five to seven days after exposure, but symptoms may appear in as few as two days or as many as 14 days.	Common symptoms include fever, a dry cough, fatigue and difficulty breathing or shortness of breath. Some of these symptoms overlap with those of the flu, making detection difficult, but runny noses and stuffy sinuses are less common. The C.D.C. has also added chills, muscle pain, sore throat, headache and a new loss of the sense of taste or smell as symptoms to look out for. Most people fall ill five to seven days after exposure, but symptoms may appear in as few as two days or as many as 14 days.
If air travel is unavoidable, there are some steps you can take to protect yourself. Most important: Wash your hands often, and stop touching your face. If possible, choose a window seat. A study from Emory University found that during flu season, the safest place to sit on a plane is by a window, as people sitting in window seats had less contact with potentially sick people. Disinfect hard surfaces. When you get to your seat and your hands are clean, use disinfecting wipes to clean the hard surfaces at your seat like the head and arm rest, the seatbelt buckle, the remote, screen, seat back pocket and the tray table. If the seat is hard and nonporous or leather or pleather, you can wipe that down, too. (Using wipes on upholstered seats could lead to a wet seat and spreading of germs rather than killing them.)	If air travel is unavoidable, there are some steps you can take to protect yourself. Most important: Wash your hands often, and stop touching your face. If possible, choose a window seat. A study from Emory University found that during flu season, the safest place to sit on a plane is by a window, as people sitting in window seats had less contact with potentially sick people. Disinfect hard surfaces. When you get to your seat and your hands are clean, use disinfecting wipes to clean the hard surfaces at your seat like the head and arm rest, the seatbelt buckle, the remote, screen, seat back pocket and the tray table. If the seat is hard and nonporous or leather or pleather, you can wipe that down, too. (Using wipes on upholstered seats could lead to a wet seat and spreading of germs rather than killing them.)
Taking one’s temperature to look for signs of fever is not as easy as it sounds, as “normal” temperature numbers can vary, but generally, keep an eye out for a temperature of 100.5 degrees Fahrenheit or higher. If you don’t have a thermometer (they can be pricey these days), there are other ways to figure out if you have a fever, or are at risk of Covid-19 complications.	Taking one’s temperature to look for signs of fever is not as easy as it sounds, as “normal” temperature numbers can vary, but generally, keep an eye out for a temperature of 100.5 degrees Fahrenheit or higher. If you don’t have a thermometer (they can be pricey these days), there are other ways to figure out if you have a fever, or are at risk of Covid-19 complications.
The C.D.C. has recommended that all Americans wear cloth masks if they go out in public. This is a shift in federal guidance reflecting new concerns that the coronavirus is being spread by infected people who have no symptoms. Until now, the C.D.C., like the W.H.O., has advised that ordinary people don’t need to wear masks unless they are sick and coughing. Part of the reason was to preserve medical-grade masks for health care workers who desperately need them at a time when they are in continuously short supply. Masks don’t replace hand washing and social distancing.	The C.D.C. has recommended that all Americans wear cloth masks if they go out in public. This is a shift in federal guidance reflecting new concerns that the coronavirus is being spread by infected people who have no symptoms. Until now, the C.D.C., like the W.H.O., has advised that ordinary people don’t need to wear masks unless they are sick and coughing. Part of the reason was to preserve medical-grade masks for health care workers who desperately need them at a time when they are in continuously short supply. Masks don’t replace hand washing and social distancing.
If you’ve been exposed to the coronavirus or think you have, and have a fever or symptoms like a cough or difficulty breathing, call a doctor. They should give you advice on whether you should be tested, how to get tested, and how to seek medical treatment without potentially infecting or exposing others.	If you’ve been exposed to the coronavirus or think you have, and have a fever or symptoms like a cough or difficulty breathing, call a doctor. They should give you advice on whether you should be tested, how to get tested, and how to seek medical treatment without potentially infecting or exposing others.
If you’re sick and you think you’ve been exposed to the new coronavirus, the C.D.C. recommends that you call your healthcare provider and explain your symptoms and fears. They will decide if you need to be tested. Keep in mind that there’s a chance — because of a lack of testing kits or because you’re asymptomatic, for instance — you won’t be able to get tested.	If you’re sick and you think you’ve been exposed to the new coronavirus, the C.D.C. recommends that you call your healthcare provider and explain your symptoms and fears. They will decide if you need to be tested. Keep in mind that there’s a chance — because of a lack of testing kits or because you’re asymptomatic, for instance — you won’t be able to get tested.
On Saturday, local health officials in Seattle said that delays in being able to test for the virus had slowed identification of community cases, meaning those who did not travel to places with major outbreaks or have contact with known patients. “If we had the ability to test earlier, I’m sure we would have been able to identify patients earlier,” said Dr. Jeffrey Duchin, health officer for Seattle and King County.	On Saturday, local health officials in Seattle said that delays in being able to test for the virus had slowed identification of community cases, meaning those who did not travel to places with major outbreaks or have contact with known patients. “If we had the ability to test earlier, I’m sure we would have been able to identify patients earlier,” said Dr. Jeffrey Duchin, health officer for Seattle and King County.
Two more confirmed cases in the state were announced on Sunday.	Two more confirmed cases in the state were announced on Sunday.
The genomic technique used to compare the viruses is akin to constructing a family tree. “As a virus passes from person to person, there will be errors that occur” as copies of the virus are made, Dr. Bedford said. To explain, he compared the tiny mutations in the genetic sequence to mistakes made during a game of telephone. “Those can link up,” he said.	The genomic technique used to compare the viruses is akin to constructing a family tree. “As a virus passes from person to person, there will be errors that occur” as copies of the virus are made, Dr. Bedford said. To explain, he compared the tiny mutations in the genetic sequence to mistakes made during a game of telephone. “Those can link up,” he said.