{"id":1837,"date":"2021-02-01T11:06:00","date_gmt":"2021-02-01T03:06:00","guid":{"rendered":"https:\/\/opentrons.com.cn\/news\/\/"},"modified":"2024-04-17T17:02:47","modified_gmt":"2024-04-17T09:02:47","slug":"new-york-city-barely-tests-for-virus-variants-can-that-change","status":"publish","type":"post","link":"https:\/\/opentrons.com.cn\/en\/news\/new-york-city-barely-tests-for-virus-variants-can-that-change\/","title":{"rendered":"New York City has barely tested for virus variants. Can this change?"},"content":{"rendered":"\n

January's growth rate was well below the 10% suggested by some experts. Now, officials are aiming to implement a more robust plan.<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

New York City has been averaging more than 5,000 new coronavirus cases per day in recent weeks. Photo credit: James Estrin\/The New York Times<\/p>\n\n\n\n

In New York City, only about 55 coronavirus cases a day were sequenced and screened for more contagious variants last month, on average, despite the presence of many large hospitals and research facilities.<\/p>\n\n\n\n

That accounts for just 1% of new cases in the city, a rate far lower than the 10% some experts have said as more contagious variants emerge, including some that could weaken existing virus variants. case, it is necessary to understand the epidemic dynamics in New York. Vaccines have led to surges in cases in the UK, Brazil and South Africa.<\/p>\n\n\n\n

By the end of February, New York City health officials hope to have a more robust surveillance plan that includes genomic sequencing, which checks the genetic material for mutations, on about 10% of new virus cases, Dr. Jay Varma, senior public health adviser at City Hall.<\/p>\n\n\n\n

Dr. Varma said the average number of new cases per day in recent weeks is more than 5,000, which gives a good idea of \u200b\u200bwhich variants are present in New York and how widespread they are.<\/p>\n\n\n\n

But the effort to reach that benchmark highlights how local, state and federal officials have often been slow to mobilize resources to meet public health needs a year into the pandemic.<\/p>\n\n\n\n

\"Trying to get labs that have primarily focused on things like human genome sequencing specifically for cancer or other diseases to shift their interest toward pathogen research sometimes takes effort,\" he said.<\/p>\n\n\n\n

The ability to sequence the genomes of as many viral samples as possible already exists, distributed across cities, although it is largely untapped.<\/p>\n\n\n\n

\"Each institution is doing its own thing,\" said Professor Adriana Heggie of NYU Grossman School of Medicine, whose team sequenced about 96 samples a week and last year's study helped identify New York's outbreak. It spread through Europe, not China.<\/p>\n\n\n\n

Over the past few weeks, City Hall aides have reportedly been asking a number of research scientists and lab directors across the city to commit to sequencing more coronavirus samples than they have so far and uploading the results to an online database. Go for an interview. On Monday, a single laboratory sequenced more than 90 cases, a significant increase.<\/p>\n\n\n\n

\"The scientific community can't really be organized without an overarching structure,\" Professor Heggie said. \u201cThe city is really trying to organize this event right now and it\u2019s the right thing to do.\u201d<\/p>\n\n\n\n

Until recently, coronavirus cases were expected to decline as vaccinations progressed. But public health experts and a modeling team at New York University say that if one of the more contagious variants begins to spread widely in New York City, it could trigger a new wave of cases that could mask the second wave of cases that New York is still battling. .<\/p>\n\n\n\n

It's unclear which track New York is on, or heading toward, in large part because of a lack of genomic surveillance. The new variant may start to take hold in New York, or it may not: discovering this will only require regular sequencing of enough cases of the new virus.<\/p>\n\n\n\n

One of the variants, first identified in the United Kingdom and known as B.1.1.7, was detected in 13 cases in New York City in January, according to data provided by the city's health department. The samples were identified from 1,703 samples in the city that were sequenced in January, according to the department.<\/p>\n\n\n\n

What percentage of virus cases should be sequenced remains a controversial issue. The UK is currently sequencing up to 10% of new cases, compared with well below 1% in the US a few weeks ago.<\/p>\n\n\n\n

\"I think we should get to 10 to 15 percent,\" Professor Heguy said.<\/p>\n\n\n\n

Dr Varma said the city's 10% target came from the UK's success in quickly identifying the variant and tracking its spread.<\/p>\n\n\n\n

With its major academic medical centers and research institutions, New York has far more sequencing machines than would be needed to examine the coronavirus genome of every positive case, if anyone cared to do so.<\/p>\n\n\n\n

\"Our machines can process thousands or hundreds of thousands of data,\" said Dr. Neville Sanjana, a scientist at the New York Genome Center Laboratory in lower Manhattan. \"So capacity is not an issue.\"<\/p>\n\n\n\n

Oddly, in the midst of a pandemic that may have infected more than a quarter of New Yorkers, research labs face the problem of getting samples. In New York, there are no large numbers of positive virus samples coming from hospitals or testing sites to research labs for genetic monitoring.<\/p>\n\n\n\n

\"It's really just tissue sample collection, and I think that's what's missing,\" said Dr. Sanjana, whose research involves finding which drugs can block infection by inhibiting the human genes hijacked by the coronavirus.<\/p>\n\n\n\n

What cities or other entities need is to fundamentally separate the current coronavirus testing process, scientists said in interviews. Every day, tens of thousands of New Yorkers provide swab samples, which are typically sent to several large labs for testing. If these labs can set aside a portion of the sample, that portion can later be used for genome sequencing if the results are positive.<\/p>\n\n\n\n

\"This is solvable, but it will require coordination of resources and people,\" said Professor Heggie, who listed the necessary steps: A portion of the original sample needs to be retained; RNA needs to be isolated from it; someone needs to transport the RNA sample to be sequenced 's laboratory.<\/p>\n\n\n\n

The city's goal of expanding sequencing coverage by at least tenfold will require recruiting an array of outside labs and research projects, large and small. The city expects the largest portion of genome sequencing to be performed at a lab in Long Island City, Queens, run by a small robotics company.<\/p>\n\n\n\n

Opentrons also operates a facility in Manhattan called the Epidemic Response Laboratory. The lab was built last year to help the city address a testing crisis that emerged over the summer, when large commercial labs struggled to cope with surging caseloads. People have to wait days, sometimes even a week or two, for coronavirus test results. The lab is now testing 20,000 samples per day.<\/p>\n\n\n\n

Opentrons co-founder Will Canine said couriers regularly transport RNA samples prepared by the Epidemic Response Laboratory to the company's facility in Queens, where the samples are sequenced.<\/p>\n\n\n\n

Company officials said the lab aims to sequence up to 2,000 positive samples per week by mid-February at a cost of less than $75 per sequenced sample to the city.<\/p>\n\n\n\n

In addition, the city is encouraging a range of other institutions, including some hospitals, medical schools and research institutions, to sequence more samples.<\/p>\n\n\n\n

Few places have as much capacity as the New York Genome Center, which often uses dozens of machines for research projects that may involve sequencing the genomes of many people in search of specific genes behind a disease.<\/p>\n\n\n\n

Given that the human genome is about 100,000 times longer, sequencing the coronavirus genome is a much smaller task.<\/p>\n\n\n\n

Michael Zody, a scientist at the genome center, said the center is working to overcome obstacles, such as obtaining samples and how to quickly prepare large quantities of them for sequencing machines.<\/p>\n\n\n\n

\"Right now, we're still actively trying to expand,\" he said.<\/p>\n\n\n\n

One of the first and most surprising additions to the city's surveillance efforts was a day care center that Rockefeller University opened last year to allow scientists to return to work.<\/p>\n\n\n\n

The university, a biomedical research institution on Manhattan's Upper East Side that counts five Nobel Prize winners among its faculty, was deeply involved in the response to the 1918 influenza pandemic a century ago. So it's perhaps not surprising that daycare centers play a role in scientific research.<\/p>\n\n\n\n

Scientists there have been working on a highly sensitive saliva test that would make it easier to test babies and young children who often refuse nasal swabs. Recently, the university has begun sequencing positive coronavirus cases to see if the children may have been infected with a more contagious variant.<\/p>\n\n\n\n

In a way, the babies and toddlers delivered every day have become sentinels across the city.<\/p>\n\n\n\n

\"We're just starting to do that,\" Dr. Robert Darnell of Rockefeller University said last week. \"We've sequenced about 15 so far.\"<\/p>\n\n\n\n

Joseph Goldstein leads the health care practice in New York after spending many years working on criminal justice and police reporting at the Metro Desk. He also spent a year covering Afghanistan from The Times' Kabul bureau.<\/p>\n\n\n\n

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