Dec. 14, 2021.
America's response to the variant shows how much progress has been made over the past two years.
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Hokyoung Kim has a credit card.
The Omicron variant of the coronaviruses set off a chain of events when scientists discovered it last month.
Health experts held news conferences that raised more questions than answers. Travel bans probably came too late. The variant was reported in every country on the map. The rest of us waited to learn more about the threat we were facing.
The same sequence unfolded two years ago when the novel coronaviruses was first discovered. The United States was woefully unprepared for the challenges ahead in the early weeks of 2020.
Dr. Charles Chiu, an infectious disease specialist and microbiologist at the University of California, San Francisco, said that they had a delay of one to two months before they were able to identify the presence of the virus. It had spread widely between multiple states and from coast to coast by that time.
Omicron is a sign that the current epidemic is not over, and it is one of many failures that have been well-chronicled.
Omicron is a dress rehearsal for the next epidemic. Detection, tracking and slowing the spread of a health threat is the same work that will be required to stop a future outbreak in its tracks.
The analogy is not perfect. Scientists were on high alert when Omicron arrived because they had already developed vaccines and treatments for the virus. Less warning may be the next Pandemic.
Rick Bright, the chief executive of the Pandemic Prevention Institute at the Rockefeller Foundation, said that there are pathogens worse than the one that caused the outbreak of the coronaviruses that are emerging and re-emerging.
The emergence of Omicron gives us an opportunity to take stock of both the gains we have made and the ways in which we are still falling short. Whatever progress we have made is not enough.
It would have been unremarkable if it had been a San Francisco resident who took a Covid test. It came back positive the next day.
The resident had recently returned from South Africa, where the Omicron variant was widespread.
The traveler's test sample was flagged for prioritygenomicsequencing, which would reveal the exact genetic code of the virus that had invaded the traveler, and whether it had Omicron's telltale mutations.
The San Francisco microbiologist, Dr. Chiu, was hired to do the sequencing. The sample was hand-delivered to Dr. Chiu's lab just a few hours after he first heard about it.
Dr. Chiu and his colleagues got to work. The process of generating the full sequence takes hours, but the scientists chose to use a technique known as nanopore sequencing, which allowed them to analyze the results in real-time.
We were able to identify more and more changes in the data.
He was certain that it was Omicron, the first case in the United States. South Africa first publicly announced the existence of the variant less than a week ago.
We can't fight what we can't see, so we need to detect and track the pathogens that threaten us. Joseph Fauver, a genomic epidemiologist at the University of Nebraska Medical Center in Omaha, said that they are better off than they were last year.
The first link is being tested. Where are the people who areinfecting? It can become impossible to stop the spread of a pathogen without accurate, timely testing.
America bungled testing from the beginning. The Centers for Disease Control and Prevention distributed faulty test kits, while supply shortages and regulatory delays created an epic mismatch between demand and supply. In the summer and fall of 2020, waits at testing sites could last hours, and the wait for results could take a week or more. There was no plan for testing.
The burden on hospitals was increased and other measures were more difficult because of these mistakes. Without testing, the strategy that helped other countries break the chain of transmission stood little chance.
The testing crunch lessened as time went on. Kelly Wroblewski, director of infectious diseases at the Association of Public Health Laboratories, said that labs diversified their supply chains, purchased new equipment and hired more staff.
Rapid, at- home tests that delivered results on the spot won emergency authorization from the FDA.
Mara Aspinall, an expert in biomedical diagnostics at Arizona State University, said that they have moved from hospitals to central labs to your living room. Ms. Aspinall is on the board of directors of a company that makes Covid tests.
The C.D.C. recommended routine screening as a way to curb transmission after imposing strict requirements on who could be tested. By the time Omicron was in the news, it was no longer unusual for a 5-year-old to get a nose job before school or for a San Francisco resident who just returned from South Africa to get a P.C.R. results.
Ms. Wroblewski said it was like a night and day comparison of where we were at the beginning of the epidemic.
The United States does less testing per capita than other high-income countries, but it has a higher share of positive tests.
Dr. Emanuel was a member of the Covid-19 Advisory Board during the presidential transition.
P.C.R. testing can be difficult to find in stores and remain beyond the budget for many Americans, because they are designed to be used frequently. The new plan to have health insurers reimburse members for at- home tests may help, but it has its limitations.
Many of the problems can be traced to the nation's failure to invest in testing early in the Pandemic. The Trump administration created a program to speed up vaccine development. Experts said that the country needed a similar effort for diagnostic tests.
Diagnostic testing should be a priority from the beginning of any future Pandemic, they said.
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Hokyoung Kim has a credit card.
The next link in the chain is routine, widespreadgenomics. This kind of monitoring helps experts keep an eye on how a pathogen is changing.
This effort got off to a slow start in the United States. Duncan MacCannell, the chief science officer at the C.D.C.'s office of advanced molecular detection, said that many of the public health labs were overwhelmed by the initial testing volume and competing obligations.
There was little coordination between the research laboratories that established their own independent programs.
In the spring of 2020, the C.D.C. created a consortium of academic, commercial and public health labs to start bootstrapping a more focused national effort. A lack of resources and a fragmented health care system slowed progress.
In 2020, a lot of the machines that were used to sequence the genomes were not being used.
The emergence of the Alpha variant and an influx of federal funding in the late 2020s kicked genomic surveillance into high gear. According to the C.D.C., the country has gone from less than 3000 samples a week to 50,000 to 60,000 since January.
When news of Omicron broke, some labs increased their efforts by adding weekend hours and night shifts. The first to detect it was Dr. Chiu's lab, but researchers in other states followed suit.
Dr. Chiu said that Omicron has shown that they have expanded their capacity to be able to identify the variant.
The research teams were looking for the variant in sewage. Wastewater analysis can provide a snapshot of the prevalence of the virus in a community, because the virus is shed in feces.
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The US has close to a million Covid deaths. The United States is on the verge of killing more people than any other country from the virus. Most of the people who have died in the US have been 65 or older. One in 100 older Americans have died from the disease.
New York has mandates. New York State has a vaccine requirement for health care workers that allows medical, but not religious, exemptions. A new statewide mandate went into effect requiring masks at all indoor public spaces that don't require proof of full vaccination.
Wastewater epidemiology has been around for a long time, but it has been turned into a mainstream strategy by the epidemic. The need to monitor the virus prompted the C.D.C., in partnership with other federal agencies, to create the National Wastewater Surveillance System, which could eventually be used to monitor antibiotic-resistantbacteria, food-borne pathogens and other microbes.
Omicron was a test of the approach. The variant was found at eight wastewater treatment plants in Houston days before the city reported its first cases.
The managing director of pathogen surveillance at the Pandemic Prevention Institute said that this is the kind of thing that allows them to get out in front of the disease.
Some experts are not sure if we have passed Omicron, a test of our readiness for the unexpected. The United States was behind in detecting the variant.
Dr. Eric Topol is the founder and director of the Scripps Research Translational Institute.
According to the international database of viral genomes, the country has had a smaller share of cases since the beginning of the Pandemic.
When the Omicron news broke on Thanksgiving, it was likely that the processing times would be even longer than usual. There was a dip in the number of virus sequences added to public databases during the week after the holiday.
Some states have more than 20 percent of their Covid cases identified, while others have less than 3 percent.
Dr. Emanuel said that it was not an effective infrastructure for genetic surveillance of viral infections. It has to be uniform nationwide.
The data was from Sept. 9 to Dec. 8.
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Scientists said that the country needs to do a better job of identifying people who are most likely to be carrying a new variant. Rather than restrict travelers from abroad, officials could make a more concerted effort to test them for the virus.
The people with breakthrough infections and those with compromised immune systems should be the priority for the next round of sequencing.
The senior associate dean for research at Florida Atlantic University's College of Medicine said that they have to sequence, but they have to make sure they are in the right communities.
In the United States, it is much more difficult to link the viral sequence to clinical data than it is in Britain. Did the sample come from someone who was in the I.C.U. or just home with a sniffle? Were they given the vaccine and when?
The Fred Hutchinson Cancer Research Center in Seattle has an expert on viral evolution and surveillance who says they can do a lot with sequence. It makes it hard to address important scientific questions.
The country has made some progress that could help us in the future. Public health laboratories can now use new equipment and expertise to track the flu, food-borne illnesses and whatever the next great global health threat turns out to be.
After the crisis has passed, funding will need to be continued. Dr. Bright said that the historical pattern was surge and then forget.
Many exhausted health officials have already left their jobs, and legislators have passed more than 100 laws limiting the public health powers of state and local authorities, according to a New York Times review.
Some of the problems highlighted by the Pandemic are not new. The United States was always going to get a heavy lift from a highly coordinated genomic program like Britain's.
The health care system is a giant mess, according to Jeremy Kamil, a researcher at the Louisiana State University Health Sciences Center Shreveport.
Pandemic preparedness is not done in a vacuum. Ensuring that every country has the resources to detect and respond to emerging pathogens will be necessary if we are to prevent the next big global outbreak.
The United States is a large and fractured country with a lot of distrust of public officials. Ensuring that labs have the capacity to detect Omicron or any new pathogen is easier than addressing these enormous problems.
Dr. Fauver said he was confident in the ability to detect the variant. I don't think we can do anything about it. Every time we sequence, we detect the Delta variant.
The surge had already begun before the Omicron news broke. The variant could soon overtake Delta, as scientists find more Omicron cases every day. What we should aim for is not clear. Should we spend the winter trying to stop infections? Is it possible to protect the highest risk people from death and disease? Ensuring that hospitals are not overrun?
Emily Gurley is an epidemiologist at the Johns Hopkins Bloomberg School of Public Health. We don't have that. We don't have that for Omicron.
