Daily Archives: May 9, 2020

Three young children have died in New York of a mysterious, toxic-shock inflammation syndrome with links to the coronavirus, Gov. Andrew M. Cuomo said on Saturday.

The illness has taken the lives of three young New Yorkers, Mr. Cuomo said during his daily briefing in Manhattan. This is new. This is developing.

As of Saturday, more than 73 children in New York have been sickened by the rare illness, which has some similarities to Kawasaki disease. Governor Cuomo said many of these children did not show respiratory symptoms commonly associated with the coronavirus when they were brought to area hospitals, but all of them tested positive either for Covid-19 or for its antibodies.

So it is still very much a situation that is developing, but it is a serious situation, he added.

The state will be working with New York Genome Center and Rockefeller University to determine what is causing the illness that Governor Cuomo described on Saturday as truly disturbing.

When the coronavirus pandemic began ravaging the New York area two months ago, the state found solace in the initial evidence that children would be largely unaffected, Mr. Cuomo said. That sense of relief was shattered this week when a 5-year-old died in New York City of the newly discovered disease, which doctors described as a pediatric multisystem inflammatory syndrome.

Mr. Cuomo did not elaborate on the death of the two additional children.

We were laboring under the impression that young people were not affected by Covid-19, and that was actually good news, Mr. Cuomo said. We still have a lot to learn about this virus.

Mr. Cuomo has asked parents to be vigilant in looking for symptoms such as prolonged fever, severe abdominal pain, change in skin color, racing heart and chest pain.

Overall deaths from Covid-19 remained a stubborn problem in the state, Mr. Cuomo said Saturday. He announced 226 more deaths due to the disease, 10 more deaths than the number reported a day earlier.

That number has been infuriatingly constant, he said. We would like to see that number dropping at a faster rate that it is currently dropping.

Despite the setbacks, New York continued to make inroads in its fight against the coronavirus, Mr. Cuomo said.

New hospitalizations for Covid-19 patients had remained relatively flat, hovering in the 600s. On Saturday that trend held true, with 572 new patients being treated at city hospitals for the coronavirus. On Friday, 604 people were hospitalized.

Last weekend, a kind of split-screen photo montage of New York City circulated widely on social media.

One image showed a dense crowd of mostly white people sunbathing in Hudson River Park in Manhattan, apparently flouting social-distancing rules. Another showed a police officer beating a black man in a confrontation that began over an attempt to enforce those rules.

Many people pointed to the two images as evidence that the police were engaged in a racist double standard.

The notion gained further traction Thursday after the Brooklyn district attorney revealed that 35 of the 40 people arrested in the borough for social-distancing violations as of May 4 were black.

On Friday, Mayor Bill de Blasio said the city would address both concerns.

Mr. de Blasio said that the police would limit crowds at two piers at Hudson River Park and another popular park, Domino Park in Brooklyn, starting this weekend.

And concerning the lopsided race numbers in arrests, Mr. de Blasio wrote on Twitter that while summons and arrests were tools for saving lives, The disparity in the numbers does NOT reflect our values. We HAVE TO do better and we WILL.

The M.T.A., which operates the citys subway and bus system, began shutting down the subway system overnight on Wednesday, forcing those who otherwise would have ridden throughout the night to accept shelter offered by city employees or find their own.

The M.T.A. is providing 40 buses at 30 stations, and the vehicles will be controlled by the Police Department after they are dropped off, the transit agency said.

In a statement announcing the move, transit officials reiterated that the M.T.A. is not a social services agency and stressed that the buses were a short-term solution. They called on the city, which requested the buses, to to step up and take responsibility for providing safe shelter for those individuals experiencing homelessness.

To hop on the train, any train, earbuds intact, alone in the crowd on the way somewhere else. To walk out of the Metropolitan Museum of Art, exhausted as if from a march. The sweet-potato fries and a beer at Tubby Hook Tavern in Inwood; the coffee-cart guy on West 40th Street who remembers you take it black.

Sunday Mass and the bakery after. Seeing old friends in the synagogue. Play dates. The High Line. Hugs.

Ask New Yorkers what they miss most, nearly two months into isolation. To hear their answers is to witness a perfect version of the city built from the ground up, a place refracted through a lens of loss, where the best parts are huge and the annoyances become all but invisible.

The cheap seats in the outfield, the shouting to be heard at happy hour. Meeting cousins with a soccer ball in Brooklyn Bridge Park. The din of the theater as you scan the Playbill before the lights go down.

I miss my gym equipment, said Barbara James of Brooklyn.

The lamb over rice from the food cart by my office, at Seventh and 49th, said Chris Meredith of East Harlem.

Just everything, sighed a police officer sitting behind the wheel of his vehicle in Williamsburg, Brooklyn, last week. I miss everything.

As The New York Times follows the spread of the coronavirus across New York, New Jersey and Connecticut, we need your help. We want to talk to doctors, nurses, lab technicians, respiratory therapists, emergency services workers, nursing home managers anyone who can share whats happening in the regions hospitals and other health care centers.

A reporter or editor may contact you. Your information will not be published without your consent.

Reporting was contributed by Michael Gold, Andy Newman, Sarah Maslin Nir, Joel Petterson, Andrea Salcedo, Edgar Sandoval, Matt Stevens and Michael Wilson.

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Three Children Have Died in N.Y. of Illness Linked to Virus: Live Updates - The New York Times

That's not because the virus is particularly widespread in this community in north central New Mexico, nestled between a national forest and an Apache Nation reservation.

It's because in New Mexico, tests are free and plentiful. Some residents of Tierra Amarilla went to a one-day free testing event in town a few weeks ago, and if they missed that they can drive to a permanent testing center 45 minutes away. If residents don't have transportation, the Department of Health will come and test them in Tierra Amarilla.

So far, the state has performed 89,032 coronavirus tests. That's more than any other state with around the same population. New Mexico has conducted around the same number of tests or more than states such as Oklahoma, Nevada and South Carolina, which have considerably larger populations.

But not every state is like New Mexico. Months after federal officials said coronavirus testing would be plentiful, the tests are still hard to find in some parts of the country.

"We want to test for this the way we test for HIV, that you can do it without worrying. That's not the case in many parts of the country," said Dr. Amesh Adalja, a senior scholar at the Johns Hopkins Center for Health Security. "We have a patchwork of testing across the country."

Limited testing, despite promises

More than two months later, that's still not the case.

It's not just a matter of having the tests themselves, but also having supplies like swabs and chemical reagents that are needed to run the tests.

"We've never been able to get to full capacity because we are missing things in the supply chain," Michigan Gov. Gretchen Whitmer on CNN's State of the Union on May 3.

"We don't know how we're going to get that system in place," Davidson said.

Even labs associated with large academic medical centers are experiencing shortages.

"There are limited supplies and there are differences in which labs have been able to order which supplies and how much of the order shows up," said Heather Pierce, the senior director for science policy and regulatory counsel at the Association of American Medical Colleges.

It's a variable situation, she added.

"One lab that has everything that it needs for one week doesn't necessarily know what it's going to get the next week," she said.

Need for more tests

As recorded cases of coronavirus continue to rise in the United States by 20,000 to 30,000 per day, public health officials have emphasized that more testing will bring the numbers down and help the nation find a pathway out of the pandemic.

Once there is widespread testing, health experts say infected people can be identified and isolated, and close contacts can quarantine themselves at home.

Dr. Anthony Fauci, the nation's leading infectious disease expert, estimated on April 25 that the US is conducting approximately 1.5 to 2 million coronavirus tests per week.

"We probably should get up to twice that as we get into the next several weeks," Fauci said the same day during a Covid-19 briefing by the National Academy of Sciences.

Finding fixes

Last week, the White House released a testing blueprint that said the federal government should be the "supplier of last resort."

It's up to the states to come up with testing plans and "to identify and overcome barriers to efficient testing," including "misallocation of supplies" and "logistical failures," according to the blueprint.

Some states have had more success than others.

New Mexico has more than 80 testing sites in all 33 counties. Not all operate at the same time -- some are permanent, others are drive-through or open for a few hours a day.

The state offers free testing to anyone with symptoms of coronavirus, anyone who's been in close contact with someone who's had the virus, or anyone at high risk for contracting the virus, such as an essential worker or a nursing home resident.

"We believe testing is critical. We always have, and so it's a priority," said Kathy Kunkel, New Mexico's secretary of health.

Some other states have also made it relatively easy for people to get tested.

On April 2, Utah launched a website where residents can find out if they qualify for free testing at a drive-through. So far, nearly 20,000 tests have been administered by the "TestUtah" initiative.

Despite the federal blueprint, Michigan hopes to receive some relief from the federal government. On May 3, a senior Trump administration official told CNN that the administration is sending the state 450,000 additional swabs and other supplies to help it meet its goal to perform 450,000 tests in May, which is more than three times the number of tests performed there from the beginning of the outbreak through the end of April.

Others also see reason for optimism.

"Over the last several weeks it's become easier for me to order tests for people," said Adalja, the Hopkins physician. "But the point is doctors and people have to be comfortable ordering tests and not worrying about supply chain issues."

Ryan Nobles and Sara Murray contributed to this story.

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US falls short in coronavirus testing in some areas of the country - CNN

This image made by a scanning electron micrograph shows SARS-COV-2 virus particles (colorized pink) from a patient sample. There are various studies looking at changes to the virus genome and the possible impact on how the virus affects humans. NIAID/NIH hide caption

This image made by a scanning electron micrograph shows SARS-COV-2 virus particles (colorized pink) from a patient sample. There are various studies looking at changes to the virus genome and the possible impact on how the virus affects humans.

This week, the question of mutation has been front and center in coverage of the coronavirus from controversial claims about changes that make the virus more contagious to reassurances that any mutations are not yet consequential.

Here are some of the questions being raised and what the specialists can (and can't yet) say to answer them.

Is the coronavirus mutating?

Researchers say the coronavirus is making small changes to itself as they would expect it to at a relatively predictable and steady rate of around one to two changes per month.

"Viruses mutate naturally as part of their life cycle," says Ewan Harrison, scientific project manager for the COVID-19 Genomics UK Consortium. The coronavirus is no different.

When a virus infects a person, it enters their cells and makes copies of itself, which then circulate through the body or are transmitted respiratory droplets is one method to other humans.

Inevitably, viruses "make mistakes in their genomes" as they copy themselves, Harrison says. Those changes can accumulate and carry over to future copies of the virus. Mutations are akin to typos in text most typos are nonevents, but some can change the meaning of a word or sentence. Likewise, many mutations will be dead ends with no effect on people who are infected. But some of these mutations in a virus may change how quickly it infects people and replicates, or what kind of damage it does to cells.

These small, cumulative changes are useful to researchers, because they act as identification cards that help trace the pathway of the virus through groups of people over time. For instance, in a surveillance study on the Arizona State University campus, researchers found that the people who were showing up sick in mid-March with the coronavirus had different versions of the virus from each other. Comparing the virus genomes helped them figure out that the spike in mid-March cases probably didn't signify an outbreak on campus; the cases had had likely caught this version of the virus elsewhere, perhaps when they traveled for spring break, and brought it back. So tracking virus genomes is valuable in tracing how and where the virus is spreading.

Is the coronavirus becoming more transmissible?

Twitter lit up this week when a draft research paper posted to the preprint server bioRxiv got picked up by the media. The paper suggests in the title that their analysis of coronavirus mutations "reveals the emergence of a more transmissible form of SARS-CoV-2."

The study was conducted by researchers at Los Alamos National Laboratory, The University of Sheffield and Duke. They analyzed publicly available genome sequences from around the world posted on GISAID, a global research platform that has amassed over 16,000 coronavirus sequences to date.

The researchers found that a version of the virus, which was first detected in Europe in early February, appears to have become the most common strain in the U.S., Australia, parts of Africa basically, anywhere it spread. The study authors hypothesize that a mutation in this virus strain, which changes one amino acid in the part of the coronavirus that finds and binds to cells, could cause the virus to spread more easily.

"I think that it is an important observation," says Angela Rasmussen, a virologist at Columbia Mailman School of Public Health, "We have seen in other virus epidemics, such as the Ebola epidemic, that there are these mutations that seem to persist and become the dominant form of the virus."

However, Rasmussen says, there's no clear evidence that the mutation referenced in the paper does anything to change how the virus spreads.

Other factors could also account for why the virus from Europe is dominant, says Justin Bahl, a computational biologist at University of Georgia. It could possibly be explained by the so-called "founder effect," where the European version spread rapidly across international borders and established itself as the dominant strain because countries were slow to lock down.

To prove whether the mutation identified in the paper causes the virus to spread more easily, researchers want to see experimental evidence: for instance, a study where both strains are tested in live cells, to see if the mutated virus replicates faster. If those results show such signs, they'll want to see if one virus spreads more readily in lab animals.

Is the coronavirus mutating to become less harmful?

Another study, published in Journal of Virology, identified one patient in Arizona who was carrying a version of the virus with a chunk of it missing. The deletion was sizable 81 nucleotides long, out of the 30,000 or so that make up the coronavirus' genome sequence (in case you're wondering, a nucleotide is a molecule that forms the building block of a DNA or RNA strand and is too tiny to be seen under most microscopes). It was also found in a location on the genome which, on the classic SARS virus, helped the virus fight the immune system, according to study co-author Efrem Lim, a virologist at Arizona State University.

The researchers hypothesize that the deletion "may potentially reduce virus fitness" a claim Lim says they're now testing in labs.

The paper is based on just one virus genome, out of the 16,000 that have been sequenced and shared, which makes it difficult to generalize to the larger group of circulating versions of the novel coronavirus. "We actually have no idea whether [a virus with this deletion] is transmissible or not," Bahl says. "We don't know whether it was just a one-off event or whether these variants are transmitting and becoming more frequent in the population [of people getting coronavirus]."

More evidence is needed to see if Lim's hypothesis holds and it will emerge as research continues.

Do the mutations we're seeing affect the development of treatments and vaccines?

Not yet. "We're getting the mutations that we're kind of expecting here," says Vineet Menachery, a virologist at the University of Texas Medical Branch, so the research process already accounts for these changes.

Menachery says the European mutation tracked in the Los Alamos paper is adjacent to, but not directly on, the receptor binding domain, which is a specific part area on the virus' protein shell that initiates first contact in attaching to human cells. "If these mutations were there, there'd be a little bit more worry about antibody-based approaches and vaccine approaches," he says, because the shifts might make it harder for antibodies to recognize the virus. But the mutations are not directly on the receptor binding domain, so researchers aren't too worried about those specific changes.

Vaccines are also developed to target multiple sites on a virus, so it's unlikely that a few random mutations to the virus can knock out their power completely, Rasmussen says.

Versions of the virus that are drug- or vaccine-resistant may crop up once therapies are in use, says Lim. If a particular strain is obliterated by drugs or vaccines, then any viruses that survive will be the ones not affected by those treatments and could go on to infect others. But for now, there's no pressure on the virus to change in a way that would help it evade measures that haven't been introduced.

Why are scientists sharing unproven theories?

The main scientific purpose of sharing these papers early and often is to alert other researchers to interesting theories and call attention to potentially meaningful mutations, Lim says.

"It helps us prioritize what mutations should be studied in the lab, because there are so many mutations out there," Lim says. By sharing leads and data-backed theories, scientists are highlighting specific mutations that may be affecting the behavior of the virus, in a sea of all the small changes the virus makes.

So it helps researchers to know that scientists at Los Alamos Lab think that a particular change in the genome is worth additional study, or that a deletion in the virus has been found once and could be found again. The answers may not be definitive, but it feeds the global brain trust of researchers who are all working to understand the coronavirus better and help defeat it.

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What We Know About Coronavirus Mutations : Goats and Soda - NPR