Genomic surveillance: What it is and why we need more of it to track coronavirus variants and help end the COVID-19 pandemic

“You can’t fix what you don’t measure” is a maxim in the business world. And it holds true in the world of public health as well.

Early in the pandemic, the United States struggled to meet the demand to test people for SARS-CoV-2. That failure meant officials didn’t know the true number of people who had COVID-19. They were left to respond to the pandemic without knowing how quickly it was spreading and what interventions minimized risks.

Now the U.S. faces a similar issue with a different type of test: genetic sequencing. Unlike a COVID-19 test that diagnoses infection, genetic sequencing decodes the genome of SARS-CoV-2 virus in samples from patients. Knowing the genome sequence helps researchers understand two important things – how the virus is mutating into variants and how it’s traveling from person to person.

Before the COVID-19 pandemic, this kind of genomic surveillance was reserved mainly for conducting small studies of antibiotic-resistant bacteria, investigating outbreaks and monitoring influenza strains. As genomic epidemiologists and infectious disease experts, we perform these kinds of tests every day in our labs, working to puzzle out how the coronavirus is evolving and moving through the population.

Particularly now, as new coronavirus variants of concern continue to emerge, genomic surveillance has an important role to play in helping bring the pandemic under control.

Scientists load patient sample specimens into a robotic liquid handler to prepare them for sequencing. Nate Langer/UPMC, CC BY-ND

Tracking virus’s travels and changes

Genome sequencing involves deciphering the order of the nucleotide molecules that spell out a particular virus’s genetic code. For the coronavirus, that genome contains a string of around 30,000 nucleotides. Each time the virus replicates, errors are made. These mistakes in the genetic code are called mutations.

Most mutations do not significantly change the function of the virus. Others may be important, particularly when they encode vital elements, such as the coronavirus spike protein that acts as a key to enter human cells and cause infection. Spike mutations may influence how infectious the virus is, how severe the infection may become, and how well current vaccines protect against it.

Researchers are particularly on the lookout for any mutations that distinguish virus specimens from others or match known variants.

phylogenetic tree of SARS-CoV-2 from COVID-19 patients
Researchers can build what are essentially family trees for SARS-CoV-2, called phylogenetic trees, that map out how closely related various virus samples are. The red dots here denote patients who are part of a single outbreak, while the others are COVID-19 patients with unrelated strains. Lee Harrison, CC BY-ND

Scientists can use the genetic sequences to track how the virus is being transmitted in the community and in health care facilities. For example, if two people have viral sequences with zero or very few differences between them, it suggests the virus was transmitted from one to the other, or from a common source. On the other hand, if there are a lot of differences between the sequences, these two individuals did not catch the virus from each other.

This kind of information lets public health officials tailor interventions and recommendations for the public. Genomic surveillance can also be important in health care settings. Our hospital, for example, uses genomic surveillance to detect outbreaks that otherwise are missed by traditional methods.

Surveillance can provide a warning

But how do researchers know if variants are emerging and if people should be concerned?

Take the B.1.1.7 variant, first detected in the United Kingdom, which has strong genomic surveillance in place. Public health investigators discovered that a certain sequence with multiple changes, including the spike protein, was on the rise in the U.K. Even amid a national shutdown, this version of the virus was spreading rapidly, more so than its predecessors.

Scientists looked further into this variant’s genome to determine how it was overcoming the distancing recommendations and other public health interventions. They found particular mutations in the spike protein – with names like ∆69-70 and N501Y – that made it easier for the virus to infect human cells. Preliminary research suggests these mutations translated into a higher rate of transmission, meaning that they spread much more easily from person to person than prior strains.

Vaccine developers and other scientists then used this genetic information to test whether the new variants change how well the vaccines work. Fortunately, preliminary research that has not yet been peer-reviewed found that the B.1.1.7 variant remains susceptible to current vaccines. More worrisome are other variants such as P.1. and B.1.351, first discovered in Brazil and South Africa, respectively, that can evade some antibodies produced by the vaccines.

doctor checking on a COVID-19 patient in a hospital bed
A strong surveillance system would sequence a set proportion of those tested for COVID-19. Apu Gomes/AFP via Getty Images

Setting up a genomic surveillance system

Detecting variants of concern and developing a public health response to them requires a robust genomic surveillance program. That translates to scientists sequencing virus samples from about 5% of the total number of COVID-19 patients, selected to be representative of the populations most at risk from the disease. Without this genomic information, new variants may spread rampantly and undetected through the country and globally.

So how is the U.S. performing in the area of genomic surveillance? Not very well, and well behind other developed countries, coming in 34th in the number of SARS-CoV-2 genomes sequenced per number of cases. Even within the U.S., there is large variation among states for genomes sequenced per number of cases, ranging from Tennessee at 0.09% to Wyoming at 5.82%.

But this is about to change. The Centers for Disease Control and Prevention, in conjunction with other agencies of the federal government, is partnering with private labs, state and local public health labs, academia and others to increase genomic surveillance capacity in the U.S.

Masked woman and man, pointing at computer screen, with a map of genetic relationships
Author Lee Harrison and a colleague surmise the relationship between various virus samples based on their genomic sequences. Nate Langer/UPMC, CC BY-ND

Reaching the new national goal of 5% set by the White House is not as simple as footing a hefty bill for a laboratory to perform the tests, though. Laboratories must collect the samples, often from different sources: public health labs, hospitals, clinics, private testing labs. Once the sequencing test is performed, bioinformaticians use advanced programs to identify important mutations. Next, public health professionals merge the genomic data with the epidemiological data to determine how the virus is spreading. All of this requires investment in training people to perform these tasks as a team.

Ultimately, to be useful, a successful genomic surveillance program must be fast and the data needs to be made publicly available immediately to inform real-time decision-making by public health officials and vaccine manufacturers. Such a program is one of the public health tools that will help bring the current pandemic under control and set up the U.S. to be able to respond to future pandemics.

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Germany’s strange nostalgia for the antebellum American South

Swastikas may be banned in Berlin, but Confederate flags still fly.

Alongside MAGA hats and Trump 2020 banners, Reich flags and Brandenburg eagles, the American South’s battle flag has been raised high during Germany’s anti-lockdown demonstrations – the most recent of which took place in Dresden in early March.

It’s appeared in the window of an apartment complex and in advertisements for an annual Christmas carnival. The flag has also reportedly been seen in Berlin’s bars.

Perhaps its presence in Germany simply represents how the Confederate battle flag has become an international meme of the contemporary far right. The Stars and Bars could exist as just another image decontextualized and propagated through the internet’s airless corridors like, say, Che Guevara. German Neo-Nazi websites do sell “Südstaaten” – or Southern – gear, along with Ansgar Aryan and Thor Steinar merch.

However, as a cultural historian writing on transnational fascism, I see the flag as part of a longer history of German nostalgia for the American antebellum South. Germans’ identification with the region stretches back, paradoxically, to the very book that helped bring an end to that era of slavery: Harriet Beecher Stowe’s “Uncle Tom’s Cabin.”

From Uncle Tom to … Nazism?

On the U3 Line of Berlin’s mass transit system, there’s a stop called Onkel Toms Hütte, or Uncle Tom’s Cabin.

The stop bears the name of a neighborhood tavern and beer garden that stood for almost 100 years, from 1884 until 1978. German restaurants, inns and beer gardens bore the title of the anti-slavery polemic, which became a shorthand for a type of Southern comfort – evidence of the novel’s complex, counterintuitive and, at times, disturbing reception.

When the novel was translated into German and published in 1852 – the same year as its American release – it was immensely popular. Though the melodrama about the cruelty of American slavery did much to stir German opinion against the practice, it also initiated a fascination with the seemingly simpler life of the slave depicted in Stowe’s domestic scenes.

A cottage industry sprouted up around it: plays, musical scores, even European-set reimaginings in which slavery became an increasingly elastic concept.

The Berlin tavern, built in 1884, adopted the name Onkel Toms Hütte because its proprietor liked the novel. It was just one of many leisure establishments that drew on Stowe’s novel to promise a “good ol’ time.” Heike Paul, a professor of American studies at FAU Erlängern-Nuremberg, characterizes this attitude as a “romanticization of slavery and a nostalgic, even remorseful view of its ‘pastness.’”

This hazy romanticization was undergirded by racial prejudice, which found in Stowe’s depiction of Tom as a “happy slave” a justification for racial hierarchy. Though “Uncle Tom’s Cabin” was originally cultivating sympathy for Black slaves, by the early 20th century it was invoked by both German progressives and conservatives as proof of Black inferiority and as a justification for colonization. An introduction to a 1911 German edition of “Uncle Tom’s Cabin” describes how “the Negroes are undeniably an inferior race, and, now that they have been freed, are widely perceived to be a plague in the United States.”

‘The happy slave’ trope in ‘Uncle Tom’s Cabin’ resonated in Germany. Discogs

Bettina Hofmann, a professor of American studies at Bergische Universität Wuppertal, argues that “Uncle Tom’s Cabin” introduced racial terms to the German language that foreshadow the Nazi race categories. However, as she qualifies, “it would be an anachronism to accuse Stowe of having paved the way for Hitler’s thoughts on race.”

Still, it remains a dim possibility that “Uncle Tom’s Cabin” had at least some influence. Stowe’s novel was, after all, one of Hitler’s self-proclaimed favorite books.

‘The Lost Cause’ in the Thousand-Year Reich

Despite a general ambivalence toward the U.S., Nazi Germany did sympathize with the antebellum South. The pubs inspired by “Uncle Tom’s Cabin” fed – and fed off of – the desire for a simpler life that slaves were supposed to have enjoyed, and which Nazism, in its idea of “volksgemeinschaft,” a people’s community, also promised.

The South after the Civil War and Germany after World War I had suffered humiliating defeats, and each revised its identity and history in the face of those losses. As both had prided themselves on their military prowess, they sought to fashion narratives that would explain their losses without admitting their shortcomings. Recognizing the similarities, the German historian Wolfgang Schivelbusch brings them together in his 2000 book “The Culture of Defeat.”

However, Schivelbusch emphasizes the differences in the stories they told. The South crafted the narrative of the “Lost Cause,” in which the experience of defeat became a Christlike sacrifice.

Meanwhile, the Nazis trumpeted the “Dolchstoßlegend,” the myth of the stab in the back. The German Army had been undefeated in the field, they claimed, but lost the war because of sabotage from within. This myth focused attention on internal enemies who needed to be eliminated.

A woman looks at a movie poster of 'Gone with the Wind.'
Depictions of the South – found in films like ‘Gone with the Wind’ – found an eager audience in Germany. ullstein bild via Getty Images

But the “Lost Cause” nonetheless resonated in Nazi Germany. The success of Margaret Mitchell’s 1936 novel “Gone with the Wind” and David O. Selznick’s subsequent 1941 film adaptation points to a desire in Nazi Germany for the melodrama of sacrifice that Schivelbusch suggests the German narrative of defeat lacked. The sentimental novel went through 16 printings in Germany, selling nearly 300,000 copies. Adolf Hitler and Joseph Goebbels watched the film repeatedly, even as they eventually banned it for general viewership. Praising the film in his diary, Goebbels declared, “We will follow this example.”

The onetime Nazi functionary Hermann Rauschning writes that Hitler felt the Confederacy had been the real America.

“Since the Civil War, in which the Southern States were conquered, against all historical logic and sound sense, the Americans have been in a condition of political and popular decay,” he recalled Hitler telling him. Though perhaps apocryphal, Rauschning’s memory of the Führer’s words squares with Hitler’s enthusiasm for “Gone with the Wind”: “In that war, it was not the Southern States, but the American people themselves who were conquered.”

Danger of Stars and Bars sentimentality

It is not only the self-declared far-right that flies the Confederate flag in Germany. Civil War reenactors do mock battle under its banner, an East Berlin country music scene gathers with it hung aloft, and even some enthusiasts of German author Karl May, who set his novels in the American West, wave it proudly. These groups insist their use of the flag “has no racist meaning.” When pressed, they appeal to tradition.

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Distrust of nostalgia has been a vital part of Germany’s post-World War II national project of “working through the past.” One would expect Germans, of all people, to be wary of such justifications.

For sale at an online German neo-Nazi merchandiser is an image of the Confederate flag bearing a “Totenkopf” – a skull and crossbones. It is an embellishment of the flag. And yet it reveals what has been there, hiding behind nostalgia, all along.

4 reasons why migrant children arriving alone to the US create a ‘border crisis’

Children arriving at the southern border without their parents have presented a political and humanitarian challenge for the past three presidents.

Their numbers began rising considerably after 2009, when 19,418 children were taken into custody at the border, according to U.S. Customs and Border Protection. Unaccompanied minors peaked in 2014, with 68,000 apprehensions. Analysts say 2021 is on pace to break that record, with more than 600 children arriving daily to the U.S.-Mexico border. Most are teenagers seeking asylum.

Reports of children in warehouses or jaillike facilities have set President Joe Biden on the defensive about what critics refer to as a “crisis at the border.” In his first press conference, on March 25, 2021, Biden repeatedly stressed that his practice is different from that of former President Donald Trump, who introduced a policy of separating migrant children from their parents and detaining them in cages.

“We are not talking about people ripping babies from mothers’ arms,” Biden said.

He said his administration is “moving rapidly … to get these kids of out of the border patrol facilities.”

Child migration has long been such a vexing, bipartisan quandary for four primary reasons, based on my research as an immigration scholar and analysis in dozens of law review articles.

Children protest President Obama’s immigration policies in Washington, D.C., in 2014. Linda Davidson / The Washington Post via Getty Images

1. Children need care

Migrant children cannot simply get jobs and fend for themselves upon arrival to the U.S. They need to be housed, educated and fed. While some may have family with them or in the U.S., many do not.

By law the Department of Health and Human Services, or DHHS, must transport unaccompanied children to a facility run by the Office of Refugee Resettlement, a DHHS department, within 72 hours of the children’s being apprehended by Customs and Border Protection. While their legal status as immigrants or asylum-seekers is being resolved – which can take over two years – authorities attempt to connect the children with a parent, family member or family friend in the U.S.

A child who has no known U.S. connections is placed in a licensed shelter or foster home while the asylum application or immigration process proceeds. Nonprofit and for-profit groups operate more than 170 housing facilities in 22 states under grants from the Office of Refugee Resettlement.

The Trump administration slashed federal funding for refugee services, forcing many shelters and resettlement offices to close. Biden says his administration is “moving rapidly to try to put in place what [Trump] dismantled.” To address rising child migration and the Trump-era facilities shortage, Biden has ordered another 16,000 beds to house these children.

Boy runs across a shallow, water-filled gully
A teenage migrant crosses from Ciudad Juarez, in Mexico, to California, March 21, 2021. John Moore/Getty Images

2. Care is costly

Unlike the roughly 11 million undocumented adults in the United States – a vital labor force that, studies show, drives key sectors of the U.S. economy like agriculture and construction – undocumented children require economic resources.

In 2014, a House of Representatives subcommittee held a hearing on that year’s record-high child arrivals. As Rep. Raul Labrador of Idaho observed, “The impact has been felt across the country, imposing a variety of costs, such as for education, health care, policing and criminal justice.”

Children also need translators and legal counsel during their immigration proceedings, and they cannot pay these costs. It falls to federal, state and local governments, as well as nonprofit organizations, to provide legal pro bono services. Despite these efforts, an estimated 75% to 90% of children undergo U.S. deportation proceedings without a lawyer to represent them, though in practice they are rarely deported.

Communities where the children are ultimately placed bear the brunt of youth immigration, receiving hundreds of newcomers or more each year.

“Texas alone received nearly 5,300 children in just a seven-month period at the beginning of this year. Miami-Dade District in Florida reported that it had 300 more students in a single quarter of last year, which costs about $2,000 more per additional student,” Labrador said in 2014.

The federal government provides resources to help cover these costs. But budget planning is difficult, as city officials are not always informed when children are to arrive. DHHS has also faced criticism for not tracking children once they are placed with sponsors.

Children sit in a classroom with a teacher pointing at a whiteboard up front
Migrant children learn English in a class created for new Spanish-speaking arrivals in Worthington, Minnesota, on Sept. 5, 2019. Courtney Perry/For the Washington Post

3. Care is complicated

These last two issues combine to create an incentive for policymakers to simply demand these children be returned to their home countries.

But many of these children face violence in their home countries and are thus seeking political asylum. As President Biden suggested during his first press conference, sending them home would violate U.S. law, which requires the protection for those who face a well-founded fear of persecution.

The U.S. has human rights obligations under international law, too, including a proscription against returning refugees to a country where they would face “cruel, inhuman or degrading treatment, torture or other irreparable harm.”

Following domestic and international law, the U.S. should contact the families of unaccompanied minors to ensure parents are aware that their children are in the U.S. and consent to their residing in the country, perhaps permanently.

But finding these parents, especially in remote areas of Central America, can be difficult. Younger children may know only their parents’ names – not their address or phone number. Sometimes the contact information they have is outdated or incorrect.

4. Migrants are nobody’s constituents

These are all big problems, but the U.S. government has solved big problems before. So why is the country still struggling to effectively deal with the decade-old issue of child migrants?

The primary reason, in my analysis: politics.

Undocumented immigrants – and particularly children – are not the constituents of any Washington politician. They have no voice within the U.S. democratic system. While journalists can and do report on immigration problems, and public interest law firms can and do represent these children in immigration proceedings, unaccompanied minors are simply not part of any politician’s voting bloc or reelection strategy.

Consequently, the issue is often overlooked or mishandled without real political repercussions. There are public relations costs to a presidential administration’s being perceived as allowing children to suffer. But survey research shows American voters don’t rate immigration high on their priority list.

And undocumented immigrants and refugee children themselves cannot really hold politicians accountable for their failures at the border.