Her Rapist Threatened to Make Her “Disappear.” Instead of Asylum, ICE Put Her in a Hotel and Sent Her Back.

by Lomi Kriel

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A teenage girl carrying her baby arrived at the U.S. border this summer and begged for help. She told federal agents that she feared returning to Guatemala. The man who raped her she said had threatened to make her “disappear.”

Then, advocates say, the child briefly vanished — into the custody of the U.S. government, which held her and her baby for days in a hotel with almost no outside contact before federal officers summarily expelled them from the country.

Similar actions have played out along the border for months under an emergency health order the Trump administration issued in March. Citing the threat of COVID-19, it granted federal agents sweeping powers to almost immediately return anyone at the border, including infants as young as 8 months. Children are typically entitled to special protections under the law, including the right to have their asylum claims adjudicated by a judge.

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Under this new policy, the administration is not deporting children — a proceeding based on years of established law that requires a formal hearing in immigration court.

It is instead expelling them — without a judge’s ruling and after only a cursory government screening and no access to social workers or lawyers, sometimes not even their family, while in U.S. custody. The children are not even granted the primary registration number by which the Department of Homeland Security tracks all immigrants in its care, making it “virtually impossible” to find them, Efrén C. Olivares, a lawyer with the Texas Civil Rights Project, wrote in a court declaration arguing that the practice is illegal.

Little is known about how the process works, but published government figures suggest almost all children arriving at the border are being rapidly returned.

Between April and June, Customs and Border Protection officials encountered 3,379 unaccompanied minors at or between ports of entry. Of those, just 162 were sent to federal shelters for immigrant children run by the Office of Refugee Resettlement, the Health and Human Services agency tasked with their care. CBP would not say whether the remaining minors had been expelled or explain what had happened to them.

The precise number of children who are detained or to what situations they are returned is difficult to ascertain.

“We are only reaching a tiny fraction of these kids,” said Lisa Frydman, vice president of international programs at Kids in Need of Defense, an advocacy group for migrant children with partners across Central America. “The rest are just gone.”

Lawyers have fielded frantic calls from family members whose children suddenly went missing after crossing the U.S. border. Of the thousands of unaccompanied minors expelled under the health order, advocacy organizations said that they have only found about three dozen after months of searching across the United States, Mexico and Central America.

The Guatemalan teenager is one of them. She told child protection workers in Guatemala that she was sent to an American hotel with her baby for days and allowed only a brief call with her father in the United States. Then she and her infant were flown to Guatemala, where her case so alarmed international refugee groups that they referred her for protection in another country, determining that she was in peril. Advocates would not provide her age or other personal details to protect her.

The Associated Press first reported last month that the administration has detained at least 169 children in three Hampton Inn & Suites hotels in El Paso and McAllen, Texas, as well as Phoenix, before expelling them. New government numbers show that practice grew to more than 240 children over the past three months. Children reported being held for weeks in hotel rooms by an unlicensed government contractor, with little ability to reach anyone outside.

Advocates said the administration’s expulsion policy is far more concerning than simply the practice of lengthy hotel detention, which they argue violates a long-standing court settlement protecting migrant children. Most kids who now reach U.S. soil are quickly flown back to their home countries — often to danger, forcing the intervention of international child welfare agencies to protect them from harm. Some children told advocates that they were sent to Mexico, even if they were not from there, in the middle of the night.

The U.S. government has largely declined to comment or release statistics, citing litigation that the American Civil Liberties Union and other advocacy organizations have brought against the expulsion program.

In June, a desperate father in Houston found Linda Corchado, an immigration attorney in El Paso. His 16-year-old son was detained somewhere in an American hotel, although where or by whom he did not know. He said the government was about to fly the boy back to Honduras, where he feared his son might be executed by gang members who threatened him after he saw them kill another man.

Corchado alerted the ACLU, and the boy became the first plaintiff in what lawyers hoped would be a test case as they argued that the government was illegally using an obscure provision of the federal Public Health and Welfare Code, written in 1893, to justify expelling all migrants, even children, at the border.

A father, left, holds hands with his 16-year-old son. The father alerted the American Civil Liberties Union when his son faced deportation to Honduras, where he feared certain death from gang members.
Carolina Guerrero for ProPublica and The Texas Tribune

The boy’s case spurred an emergency court hearing in June in Washington, D.C., before U.S. District Judge Carl Nichols, who ruled that the ACLU was “likely to succeed” in its arguments that the government did not have the authority to expel the boy under the health declaration, issued by the Centers for Disease Control and Prevention.

Within days, Justice Department attorneys paused the boy’s expulsion and agreed to allow him to request asylum through the immigration courts — the legal process usually required for migrant children coming here alone.

Attorneys found more children facing expulsion.

The relative of another 16-year-old Honduran boy told an advocate at the U.S. port of entry in El Paso that the teenager had disappeared in U.S. custody after they crossed the border together. Corchado called CBP and requested the protection screening allowed for the boy under the expulsion process, but federal agents said that they were moving him to a hotel to fly him back.

Once migrants are transferred to a hotel under the care of a government contractor, it is as if they vanish into a “legal abyss” where it is unclear which federal agency retains custody, Corchado said.

“You can’t advocate for them,” she said.

She said a supervisor with Immigration and Customs Enforcement told her that after migrants are moved there, “it’s kind of off our radar.”

Under the threat of litigation by the ACLU, the administration agreed to halt the boy’s removal and transfer him to a federal shelter while he fought for asylum, his lawyers said.

Coordinating with advocates across the country, ACLU attorneys have located at least 18 children as of late July who were being expelled, court filings show. In each case, the government agreed to halt proceedings against them — a win for the child, but a concession that blocked lawyers from obtaining a judge’s ruling on the policy as a whole.

“We assumed the government would want to have a test case in court to decide the lawfulness of this highly controversial and unprecedented practice of using public health laws to effect shadow deportations of children,” said Lee Gelernt, an ACLU attorney fighting the program in court. “The government is getting away with a complete end run around all of the protections for children that Congress has painstakingly enacted.”

Alexa Vance, a Justice Department spokesperson, declined to comment. So did April Grant, a spokesperson for ICE, citing the pending lawsuits.

Grant also refused to release statistics on children expelled by the agency, including those it detained in hotels, or provide the repatriation agreements that the U.S. holds with at least eight countries — including Guatemala, El Salvador and Honduras — that would shed light on how those countries have agreed to accept expelled children and under which circumstances.

Matthew Dyman, a spokesman for CBP, similarly said the ongoing litigation meant he couldn’t answer most questions about the policy. Alexei Woltornist, a DHS spokesman, did not respond to emails.

“Nobody Can Find Them”

Advocates said the secrecy reminds them of their search two years ago for thousands of immigrant children whom the Trump administration separated from their parents at the border.

Then, government agents sent children to federal shelters under ORR, often without tracking numbers linking them to their parents in ICE detention centers. It took a federal court order and months of taxpayer-funded efforts before many could be reunited with their parents. A few never were because their parents had been deported and so they were released instead to acquaintances or other relatives in the U.S.

What’s different now is that children are not entering the U.S. system for migrant children at all.

“Nobody can find them,” said Jennifer Podkul, vice president for policy at KIND, the advocacy group.

The majority are quickly flown back to Honduras, Guatemala and El Salvador, the three main origins of unaccompanied children to the U.S.

Once in Central America, they don’t have access to protections offered before the pandemic. Strict lockdowns have made it hard for watchdogs such as the United Nations High Commissioner for Refugees to track unaccompanied children after they are sent back to government repatriation centers.

Government representatives in those three Central American nations said that they could not differentiate between children who had been returned under the health order and those who had been deported under usual proceedings. But what they could report alarmed advocates.

Since the start of the pandemic through early July, at least 476 unaccompanied children have been sent back to Honduras, about half flown from the United States and the rest largely returned from Mexico, the Honduran federal agency overseeing children reported.

Guatemala reported about 380 such children returned from the United States in roughly that same period, according to a government spokesperson. El Salvador said more than 70 unaccompanied minors had been returned, and Mexico’s government reported some 1,050 of its own children were returned between April and June, the latest data available.

The total for unaccompanied children governments said had been returned to those four countries — about 1,700 — is far less than the last official figure the U.S. government released. In early June, it said it had expelled at least 2,175 “single minors” under the health declaration. Then, citing litigation, the administration stopped providing that data.

“The number of kids who have been received doesn’t match up with the number of kids who have been expelled,” said Frydman of KIND.

She and other advocates suspect children from other countries are informally expelled to Mexico. Many in the last few months have reported that U.S. authorities returned them there — sometimes alone in the middle of the night and without being processed by Mexican immigration officials.

KIND found at least three unaccompanied minors from Central America in Mexico.

Two were siblings who said they arrived on their own at the port of entry in El Paso. CBP officers told them “the border is closed,” the children later told attorneys, who declined to reveal the siblings’ ages or other details for their safety.

Federal officials sent the siblings to Ciudad Juarez, where they were homeless until they went to a shelter, which contacted Mexico’s child welfare agency.

Dyman, the CBP spokesperson, did not respond to questions about the siblings. But he said non-Mexican children can be expelled there only if they are with adult relatives. They are not supposed to be sent there alone.

“When minors are encountered without adult family members, CBP works closely with their home countries to transfer them to the custody of government officials and reunite them with their families,” Dyman wrote in an email.

He said agents may exempt migrants from expulsion under certain circumstances, such as when they cannot be returned to their countries or if officers suspect they were victims of human trafficking. But he declined to elaborate on how CBP officials make those exceptions and conduct screenings, saying that information is “law enforcement sensitive.”

Statistics from Mexico’s National Migration Institute show that more than 200 children from El Salvador, Guatemala and Honduras have been expelled to Mexico under the health declaration as of June. That number includes unaccompanied children and those with adults. An official at Mexico’s Secretary of Interior wrote that it does not have a formal agreement with the U.S. on how to return unaccompanied children from other countries, so it does not keep cumulative statistics.

“Shadow Operation”

Usually children coming to the U.S. alone from nations other than Mexico must be flown home — an operation delayed by logistics during a global pandemic. By law, they cannot be held for more than 72 hours in temporary CBP processing facilities before they are sent to shelters run by ORR.

That agency is currently detaining about 850 children, although it has 14,000 taxpayer-funded beds available. Before the administration’s health order, ORR in late March was holding about 3,600 unaccompanied minors.

Instead of placing children in these federally regulated and state-licensed shelters, where they would have access to counsel and social workers, the U.S. moved hundreds of minors to a clandestine network of hotels — under the custody of a contractor not licensed to care for children.

The administration provided that data to attorneys litigating a court-ordered settlement that sets specific rules on how the government is allowed to hold migrant children. That 1997 consent decree, known as the Flores Settlement, requires migrant children in detention have certain rights, including that they be released quickly and held in licensed child care facilities.

In April, May and June, the government confined at least 240 children awaiting expulsion — including more than a dozen younger than 6 — in hotel rooms, according to legal filings submitted to the court overseeing compliance with the Flores Settlement.

In April, ICE, via its contractor MVM Inc., held at least 29 unaccompanied migrant children for as long as 10 days in the three Hampton Inn & Suites hotels in Texas and Arizona before expelling them.

Vans outside a Hampton Inn where migrant children were being detained in McAllen, Texas.
Brenda Bazán for ProPublica and The Texas Tribune

In May, the contractor detained 80 children for days in those three hotels. In June, 120 were held there before being expelled, according to the government reports.

A 5-year-old was kept in a hotel room for 19 days in June before she was expelled.

An 8-month-old was held in a Hampton Inn for 12 days that month before being turned back with a 9-year-old sibling.

As of June 30, according to the administration’s most recent reports submitted under the Flores Settlement, a 2-month-old had been detained in a Hampton hotel for four days while awaiting expulsion along with 19 other children.

Neha Desai, an attorney with the National Center for Youth Law, an organization that litigates to ensure the government abides by that consent decree, called the prolonged detention of migrant children in hotels a “blatant breach” of that settlement.

“This is a shadow operation,” she said.

The U.S. has always briefly held a small number of children in hotel rooms after an immigration judge ordered them removed if there was a delay with their deportation flights.

But such widespread detention for up to three weeks involving children whose protection claims have never been adjudicated “flies in the face of the law,” said Andrew Lorenzen-Strait, a former senior ICE official who left the agency last year. He said Congress and the courts have repeatedly held that children should not be kept in hotel rooms for more than one night — and even then, only in limited circumstances.

“The government is playing cowboy with regards to children’s safety,” he said.

Bob Carey, who headed ORR under President Barack Obama, called the practice “horrific … you have vulnerable children in the care of a private contractor with little, if any, transparency or adherence to state law, federal guidelines, legislation and a court settlement.”

Not much is known about MVM, the private security contractor from Virginia that detains the children in hotel rooms. A spokesperson wrote in an email that its multimillion-dollar agreement with ICE to transport unaccompanied minors prevents it from disclosing information. It referred questions to ICE, which declined to comment and refused to release the contract.

In 2018, Reveal from the Center for Investigative Reporting found that MVM had held children for longer than a day in vacant office buildings in Phoenix. An ICE spokesperson said the agency did not permit the company to detain children for more than 24 hours in those offices, which she said were intended as “waiting areas” for same-day transport between CBP and ORR shelters. An MVM spokesperson termed it a “regrettable exception” to the company’s policy of finding a hotel when there are delays in transporting children.

Details about the company’s current contract came to light in a July court filing from Andrea Sheridan Ordin, a former U.S. attorney appointed to monitor the Flores Settlement in 2018. The federal judge overseeing that consent decree determined that was necessary because the government was not complying with it.

Ordin recommended ICE cease detaining unaccompanied minors in hotels, citing a “lack of formal oversight.” She wrote MVM’s “transportation specialists” are required to have only an associate’s degree or high school diploma and one year of relevant work experience. They separated migrant children in hotel rooms by age and gender and allowed “little to no access to recreation.” Children must be “within the line of sight” of contractors at all times.

Ordin said detention for weeks in hotel rooms can have a “harmful” impact on children, adding that MVM did not appear to have consistent requirements “regarding the special needs of young children, including hygiene, nutrition, or emotional well-being.”

Ordin wrote that what was initially a “stop-gap measure” for the government to fly back children outside of normal proceedings has transformed under its expulsion policies into an “integral component of the immigration detention system” for children.

The administration argued she had overreached her authority. Children expelled under the health order, it contended, were not subject to protections under the Flores Settlement because they had never formally entered “immigration” custody.

Lawyers representing children under that settlement requested a judge’s ruling, writing that the government has a “penchant for unilaterally disregarding” the consent decree.

A Sense of Deja Vu

Thirty-five years ago, a 15-year-old Salvadoran girl fleeing a civil war in her homeland was also imprisoned in an American hotel under the care of unlicensed private security guards. Jenny Flores’ case forced the most significant overhaul yet of how U.S. authorities can detain migrant children. In fact, the 1997 federal settlement is named for her.

Carlos Holguín, who began litigating that case in 1985, said there is now a sense of “deja vu … but the degree of lawlessness is even beyond what was going on then.”

Since taking office, the Trump administration has tried to end the Flores Settlement, arguing that it and a 2008 trafficking law work as “loopholes” encouraging families to send children here alone. The government has attempted to undo the settlement through regulations and requested Congress curtail the Trafficking Victims Protection Reauthorization Act, which requires certain safeguards for children arriving alone at the border.

So far, both efforts have failed.

The administration tried separating parents and children at the border, but a federal judge largely ruled against the practice in 2018, allowing it only in narrow circumstances such as if the adult poses a danger.

U.S. District Judge Dolly Gee, who is in charge of the Flores Settlement, has determined the administration must quickly release children locked up with their parents in immigrant detention centers, most recently citing the risk of coronavirus spreading.

“The family residential centers are on fire and there is no more time for half measures,” she wrote in a June 26 order.

The government is now arguing it can force detained parents to choose between freeing their children or staying indefinitely imprisoned with them.

But none of the administration’s attempts to undo either the settlement or the law have been as effective as the expulsion order, which is “eviscerating every single protection mechanism outlined by Congress and the courts with one sweeping gesture,” said Podkul of KIND.

Late last month, the ACLU sued to allow its lawyers access to children detained in the McAllen Hampton Inn after a video went viral showing a Texas Civil Rights Project lawyer forcibly pushed away.

“The children are in imminent danger of unlawful removal,” the attorneys wrote.

Facing a public relations scandal, Hilton quickly announced that all three hotels had canceled reservations with MVM.

“We expect all Hilton properties to reject business that would use a hotel in this way,” a Hilton spokesperson said.

Government attorneys agreed to pause the expulsion of the migrants who they said remained in the McAllen hotel on the date of the lawsuit — once again, ACLU attorneys said, mooting litigation on the broader policy. A separate suit involving a 13-year-old Salvadoran girl who was expelled this summer is still pending in a Washington, D.C., federal court.

By the time the administration stopped the removal of the migrants detained at the Hampton Inn, most who had been held there had already been expelled or transferred elsewhere — some, advocates said, just before the ACLU filed its lawsuit. Only 17 family members, including one unaccompanied child, remained in that hotel.

What happened to the rest? No one would say.

Do you have access to information about expelled migrant children or children detained in hotels or about the contractor MVM Inc. that should be public? Email lomi.kriel@propublica.org. Here’s how to send tips and documents to ProPublica securely.

For more coverage, read ProPublica’s previous reporting on immigration.

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KL raids offices of 3 broadcasters in probe over documentary

Why punish press? So, government can claim to do best and not have to admit mistakes or graft.

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The Malaysian authorities raided the office of Al Jazeera in Kuala Lumpur and two local broadcasters yesterday, as part of a probe over a documentary by the Qatar-based company that alleged mistreatment of foreign workers during the Covid-19 pandemic.

The offices of Astro and Unifi TV were raided by the police and government watchdog Malaysian Communications and Multimedia Commission, police said.

It is believed that Astro and Unifi TV had broadcast the Al Jazeera documentary.

Al Jazeera said two computers were seized from its office.

“Conducting a raid on our office and seizing computers is a troubling escalation in the authorities’ crackdown on media freedom and shows the lengths they are prepared to take to try to intimidate journalists,” said Al Jazeera English managing director Giles Trendle.

“Al Jazeera stands by our journalists and we stand by our reporting. Our staff did their jobs and they’ve got nothing to answer for or apologise for. Journalism is not a crime,” he added.

On July 3, Al Jazeera aired Locked Up In Malaysia’s Lockdown, which focused on the plight of thousands of undocumented migrants detained during raids carried out in areas under tight coronavirus lockdowns.

The documentary, which was critical of the Malaysian government’s move, sparked backlash online, while the Malaysian government decried the report as inaccurate, misleading and unfair.

This prompted the police to launch an investigation and a manhunt for Bangladeshi national Mohamad Rayhan Kabir, who was critical of the Malaysian government in the documentary. Malaysia’s Immigration Department said Mr Rayhan, 25, was arrested on July 25 and his work permit was revoked.

“This Bangladeshi national will be deported and blacklisted from entering Malaysia forever,” Immigration Department director-general Khairul Dzaimee Daud said late last month.

There is rising anger in the country towards migrants and refugees, who are accused of spreading the coronavirus and taking jobs from locals hit hard by the pandemic. There are some 2.2 million registered foreign workers in Malaysia and an estimated two million more migrants who work in the country illegally.

Let’s block ads! (Why?)

6 states band together to secure rapid COVID testing | TheHill

The governors — from Virginia, Louisiana, Massachusetts, Michigan, Ohio and Maryland — said the goal of the compact is to show private companies that there is significant demand to scale up the production of these tests, which deliver results in 15 to 20 minutes. The states will also coordinate on policies and protocols regarding the testing technology.

Additional states, cities and local governments may join the compact in the coming days and weeks, the governors said.

The states are in discussions with Becton Dickinson and Quidel — the U.S. manufacturers of antigen tests that have already been authorized by the Food and Drug Administration — to purchase 500,000 tests per state for a total of three million tests.

Source: 6 states band together to secure rapid COVID testing | TheHill

Yes, PCR tests can detect “the COVID virus”

I was asked to write some comments for a fact check article about some of the myths going around about PCR-based testing and whether PCR tests can detect “the COVID virus”. In particular, an agglomeration of them in the form of a Facebook video by a guy in his car. I wrote a few hundred too many words – so here are most of them.

Don’t listen to a car dude

First up – the comments which generated the need for this article were from someone who appeared to have zero understanding about PCR or PCR test design or PCR use. Some of the comments were wrongly attributed to the creator of the PCR test, Kary Mullis, who, as we know, died before this pandemic began.

The speaker – who I will not specifically oxygenate here – also seemed to have no scientific experience, or any expertise in science (he was unfamiliar with routine words used by anyone in the biological sciences) and I’d guess that he hasn’t ever worked in a laboratory, designed a pair of PCR primers, constructed, optimised or validated a PCR test, regularly consumed or written scientific literature or generated or interpreted any scientific data. In sort – this guy is not an expert so please take what he said with a grain of NaCl (you know what that is, right?). These are important factors when someone is lecturing at you and using their platform to pull down or threaten experts on the topic. This sets the stage. It provides context.

The purpose of these sorts of comments seems to be disruption and the erosion of trust in expertise and science. There is possibly something here about the speaker feeling that they know something special or something different from the real experts. I’m sure there’s a much longer treatise on who this person just wanting his five minutes of fame, that his mum told him he was special and that he felt unheard or misunderstood. But during a major public health event where lives are on the line, these selfish reasons aren’t enough.

The claim that PCR tests can be contaminated

Contamination of PCR is a real issue and I’ve covered this here just recently. Labs that routinely use PCR and RT-PCR are extremely careful to consider and account for and prevent that from being an issue. These expert labs also include controls in every run which tell them if a contamination problem has occurred.

LEARN STUFF
RT = reverse transcription. This is an enzymatic step that precedes the PCR (polymerase chain reaction) cycling, still in the same tube, producing a DNA copy of an RNA target, such as a small portion of the RNA which makes up the genes and genome of SARS-CoV-2 and most other respiratory viruses that infect humans. The PCR is an enzymatic process that produces a new chain of nucleotides that are a mirror image of the original target region’s nucleotide sequence (genetic code) through a process of heating and cooling controlled by a programmable thermal cycler. It’s a cyclical process which copies (amplifies) that small piece of DNA millions of times until it reaches a level we can record using fluorescence detectors. Without the amplification, there is too little viral genetic material to detect.

The claim that PCR tests only detect a small part of the virus

Each RT-PCR test is designed to be specific to the intended virus (there are examples where that may not be the intention). So labs have a number of these tests; reference labs may have dozens!

The types of RT-PCR used to test for virus only seek out a small part of the complete genome sequence. This is to make the tests work as quickly (an hour or less) and efficiently as possible.

woman touching wallThis is not in any way related to a fluorescence producing probe.
Photo by Victoria Borodinova on Pexels.com

In particular, the “real-time” PCR method has been used widely since the 2009 fluA/H1N1 pandemic. It works best with shorter target regions. Real-time RT-PCR (RT-rPCR) includes a fluorescence-producing (the fluorogenic bit) DNA probe. The probe adds another layer of target-specificity to the test. It also generates a signal when the viral RNA is present (but not, when it isn’t). The probe doesn’t take part in the PCR amplification – it just binds to the DNA as it builds up…in real-time! When enough DNA is present, the probe will produce a detectable fluorescent signal. The signal grows a bit more during each cycle until the PCR finishes.

That small target sequence is usually – but not always – chosen to be highly specific to the target; both primers and probe bind only to the intended viral target.

PCR gleans its extreme specificity from the primers. At each and every position of a new DNA primer, we have one of four nucleotides to choose from, dATP, dCTP, dGTP and dTTP.

Deoxynucleotide triphosphates. 2’deoxycytidine-5′-triphosphate (dCTP; C9H16N3O13P3),2′-deoxyguanosine-5′-triphosphate (dGTP; C10H16N5O13P3),2′-deoxyadenosine-5′-triphosphate (dATP; C10H16N5O12P3) and 2′-deoxythymidine-5′-triphosphate (dTTP; C10H17N2O14P3). From https://virologydownunder.com/pcr-primers-a-primer/

If we designed a sequence-specific primer of 20nt nucleotides in length (a ’20mer’), the chance that the same exact sequence will occur randomly in nature would be (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4) x (1/4). That means there’s a 1 in 1012 chance of a 100% identical sequence occurring randomly in nature. Pretty small chance. That last bit is relevant to how incredibly specific RT-PCR tests can be.

Our test is designed to detect a particular virus. We can look at the genetic sequences of all the other known viruses and gauge, with quite a bit of confidence, that this test will not interact with their genetic material. This helps us avoid one form of false result (rarely are things absolute in biology).

A nucleotide sequence alignment comparing the sequences of a few influenza A virus genes. Whenever a sequence in the alignment differs from the highlighted (yellow) sequence, we see a black line using this computer program. Where the sequences are identical, we see a grey line. If I wanted to design a test to detect all these virus variants, I’d probably fail to detect the first one because of all the differences. But there are some grey regions in which I could design my primers to sit, and they seem to have the same sequence – a ‘conserved region’ – across all the other virus variants in this alignment.

So rather than next to impossible, it’s actually highly probable that expert primer and RT-PCR test designers do detect what we design our primers and probe (see below) to detect.

The claim that PCR tests don’t detect “the COVID virus”

RT-PCR tests in use today are extremely effective at very sensitively and specifically detecting SARS-CoV-2, the virus that causes COVID-19. Some are a bit better than others, but they very much can detect SARS-CoV-2. Some early RT-rPCR tests were designed intentionally to allow for sequence variation just in case the virus did a lot of changing early on (it didn’t).

Additionally, SARS-CoV-2 tests do not detect other coronaviruses (see that caveat above and it really only holds for other closely related SARS-like and bat CoVs), or rhinoviruses or adenoviruses, parainfluenza viruses, influenza viruses, respiratory syncytial viruses and so on, that may be found in the same patient sample.

But we test developers also check this in the real world. We test other related and unrelated viruses (like those👆) and different types of human samples (snot, saliva, sputum, swabs, liquids etc) during a process called validation. This way we know what the primers – and thus the RT-PCR test – can do and can’t do. This is all part of the expertise developed over decades of our use of PCR methods.

Of course, a badly designed RT-PCR can have problems, as can anything in science, or life. False positives and negatives can happen because of test design issues (not just because of sampling and timing issues), but professional laboratories watch for this, minimise the risk of this and can identify and rectify this. And they spend time on test design, optimisations and that validation thing.

Expertly designed and used SARS-CoV-2 tests have been well-proven to detect this virus. The leading tests have also been tested on SARS-CoV-2 RNA purified from virus isolated and grown in cells in the lab – so we know it is this virus that we’re detecting. We can also design and order viral sequences in the lab and have them made commercially, so again, we know the tests detect the viral sequences we expect them to and not other viruses.

The claim that PCR tests don’t detect the whole genome

Is correctamundo.

But that is by design, not an error or an oversight. We have only been able to quickly and relatively easily (compared to even a decade ago) detect entire viral genomes – a key part of the science of genomics – in very recent times.

It is still costly, less sensitive and slower to determine the entire sequence of a virus compared to simply detecting its presence using an RT-rPCR test though.

For cluster, outbreak, epidemic and pandemic control and for patient management – detection the presence of viral RNA (which real-time RT-PCRs do) is all that is needed. For more extensive tracking of virus change over time and to better understand where an outbreak may have come from – genomics is great, but only a small fraction of viruses usually get this treatment. That will change with time.

A positive result doesn’t mean virus is present – but we can be pretty sure it was

A positive RT-PCR result doesn’t prove that replicating (also called infectious or viable) virus is present. It proves that its genetic material – the RNA – is present.

But we have learned much about this virus in 7 months and SARS-CoV-2, like other viruses we detect with RT-rPCR, is present before and during the peak symptomatic period. These are also the times we get sampled and tested because we feel sick. We know from experience that when detectable viral RNA is present in a patient’s sample, there is often an infectious virus present as well. RNA is not so stable that it hangs around without a constant source producing more of it.

Even though it’s really sensitive, RT-rPCR has a limit of detection – as we have been seeing in the story of “false negatives” among patients being tested for SARS-CoV-2 well after they became clinically well.

So we use the RT-rPCR result as a surrogate indicator of the presence of the infectious virus.

Our other option would be to try and “grow” virus in the lab, but this has problems. It is slower, more expensive (lots of labour costs), affected by poor sample handling/storage/cold chain, needs a high level of expertise (actually a dying art) and is much less sensitive than real-time RT-PCR.

For some non-experts, including medical Doctors in some cases, this caused a big problem in the early years of PCR as it moved from a research tool to an aid for patient diagnosis.

They couldn’t understand what a PCR positive result meant because they were used to virus culture results….which were less often positive because the method was less sensitive.

Now you are more expert than you were

So now you may know a bit more about this subject than you did before. Hopefully, I’ve explained that PCR tests can detect “the COVID virus”. I feel confident in saying that you will know a lot more than a certain guy in a certain car in a certain video. Always be willing to learn a new thing. Thanks for reading.

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The post Yes, PCR tests can detect “the COVID virus” appeared first on Virology Down Under.

Beirut port destoyed by massive explosion — EUROPE DIPLOMATIC

A huge explostion has hit the Lebanese capital, Beirut, causing widespread damage and injuring many people, officials said. It is not yet clear what caused the explosion in the port area of the city. Video posted online showed a large mushroom cloud and destroyed buildings, broken glass and dust in surrounding area. Watch the scene […]

Beirut port destoyed by massive explosion — EUROPE DIPLOMATIC

Many Americans Are Convinced Crime Is Rising In The U.S. They’re Wrong. | FiveThirtyEight

People, today, base their beliefs about crime, by what they see on the news. And whether the crime is local or 1,000 miles away, it is perceived as being a “local” threat. 538 and other researchers just don’t get how people translate visual/oral exposure to news. We almost always translate danger anywhere, as danger “here.” And that s the natural thing to do. No brain smart but body smart. Research on how to help people “see” the broader picture would be helpful.

Source: Many Americans Are Convinced Crime Is Rising In The U.S. They’re Wrong. | FiveThirtyEight

COVID-19 is Tearing Through Nursing Homes. Mitch McConnell Wants to Give Their Owners Legal Immunity.

So, you messed up and many people died as a result – as pay back for past campaign donations her is a get out of responsibility card. After all, people can’t sue the Senator for his malfeasance. Only fair that people who did not take precautions should get off free – NOT!

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For months, Senate Majority Leader Mitch McConnell has upheld an ultimatum about passing new COVID-19 relief legislation this summer: No economic stabilization package will pass the Senate unless it protects businesses from coronavirus-related lawsuits. “We need to provide protection, litigation protection, for those who have been on the front lines,” McConnell said during a Fox News interview in April. “We have a red line on liability.”

Last Monday, a bill introduced by Sen. John Cornyn (R-Texas) and coauthored by McConnell clarified exactly which front lines Senate Republicans are interested in defending. The proposal, titled the Safe to Work Act, would make it harder for workers and customers to sue companies for negligently exposing them to the coronavirus and raises the bar for patients to sue healthcare providers for coronavirus-related malpractice. It also extends “front line” protections to healthcare executives, including nursing home owners, until 2024.

As negotiations over the coronavirus relief package stall, in part due to McConnell’s red line, experts on elder law and advocates for nursing home residents are alarmed that the Republicans’ proposed immunity shield could destroy what little accountability there is for nursing homes at a time when they’ve become deadly hotspots of COVID-19. According to the Centers for Medicare and Medicaid services, more than 40,000 people living in skilled-nursing facilities have died of the coronavirus—more than one quarter of all deaths from the illness. Those deaths represent around 1 in 32 of the country’s 1.3 million nursing home residents, though that is likely an undercount due to incomplete data.

Nursing home industry representatives have argued that a liability shield is necessary to protect providers’ ability to make difficult decisions in an emergency situation. “Subjecting health care workers and facilities to onerous litigation even as they have done their level best to combat a virus about which very little was known when it arrived in the United States would divert important health care resources from hospitals and providers to courtrooms,” the bill reads.

Yet by making liability lawsuits all but impossible, experts warn that corporate owners would not only be protected from claims of mismanaging their response to COVID-19, they would be free to pursue the kinds of cost-cutting that could endanger their vulnerable residents. “This act is not about responding to COVID-19,” says Nina Kohn, an elder law expert at Syracuse University. “It’s about using COVID-19 as a screen to eviscerate a system of public accountability that average individuals in this country rely on, but which certainly can limit corporate profitability.”

The pandemic has already created an unprecedented lack of oversight for nursing homes. In March, the Centers for Medicare and Medicaid Services ordered federal and state inspectors to only enter facilities deemed in need of infection control oversight, and didn’t clarify until June that facilities with COVID-19 outbreaks required state inspections. In May, the Government Accountability Office found that even before the pandemic, most nursing homes had infection control problems but faced no fines or other consequences. (Inspectors also may enter facilities where residents are considered to be in “immediate jeopardy”—emergency situations authorities are notoriously bad at identifying.) Meanwhile, family members, who often flag problems with their loved ones’ care, were banned from visiting all facilities starting in early spring, except for end-of life visits. So were volunteers and ombudsmen who resolve complaints and fight for residents’ interests.

“Essentially, the nursing home industry was given a holiday from any type of monitoring, oversight, or accountability during the COVID-19 pandemic, and most of that is still continuing to this very day,” says Richard Mollot, executive director of the Long Term Care Community Coalition, a New York-based nonprofit. “The normal systems that are there to protect residents are gone,” says Toby Edelman, senior policy attorney at the Center for Medicare Advocacy. “The last thing that exists is litigation.”

Fewer than 50 lawsuits have been filed so far against long-term care facilities for their handling of the coronavirus or treatment of residents during the pandemic, according to a database maintained by Hunton Andrews Kurth, a corporate law firm. In April, a woman filed a wrongful death suit against the Life Care Center of Kirkland, Washington, where her mother died of COVID-19 in March. (The facility has been linked to 129 cases and 37 coronavirus deaths.) Last month, a Tennessee woman sued a nursing home, claiming it did not adequately isolate patients with respiratory symptoms; her mother, a resident there, was infected and died of COVID-19 in late March. Another lawsuit against a nursing home in Southern California alleges it ignored infection control protocols, failed to hire enough staff, and downplayed the threat of COVID-19, leading to a resident’s death. 

Senate Republicans’ relief bill would provide nursing homes sweeping protections against coronavirus related-lawsuits, moving them to federal court and imposing stringent requirements on plaintiffs. Families would only have a year to pursue cases and would be required to obtain costly affidavits and certified medical records before filing. The bill would also raise the standard of proof plaintiffs must meet while narrowing the definition of gross negligence so that, Kohn says, it is “almost impossible to satisfy.” The bill also specifies that any problems at a nursing home due to a lack of staff or resources can’t be considered gross negligence—providing a ready-made defense for most facilities, which are often understaffed and have been losing money

“The nursing home industry was given a holiday from any type of monitoring, oversight, or accountability during the COVID-19 pandemic.”

“The intention is to stop all litigation,” Edelman says. The staffing exemption, she predicts, could be a defense for any nursing homes that do get sued: “‘Yeah, we didn’t feed your mother or give her her medication, but it’s not our fault, because we didn’t have the staff.’”

Even in normal times, advocates say, lawsuits against nursing homes are uncommon, both due the difficulty of bringing cases and their emotional toll on family members. “They don’t want to dwell on on how terrible the end of their loved one’s life was,” Mollot says. “They want to move on, to think of their loved one as not being in pain any longer.” Many cases are blocked by arbitration agreements, which were permitted after the nursing-home industry fiercely fought the Obama administration’s effort to ban them. Cases that do make it in front of a judge typically involve serious allegations such as severe bed sores, falls, and malnourishment. Plaintiffs must prove that their loved one would have survived if not for neglect or serious mistakes, and that their death was foreseeable, Kohn says. And families don’t stand to win much in damages, in part due to residents’ already-short life expectancy.

But advocates say lawsuits, though rare, matter because they can deter maltreatment. While few lawsuits make it to court, the “small threat of a big loss,” as Kohn puts it, can keep nursing homes from cutting corners to increase their profit margins. About 70 percent of the country’s 15,400 nursing homes are operated for profit. Those privately owned facilities are less likely to receive four or five-star ratings on the federal nursing home quality scale than nonprofit or government-operated homes, and more likely to be flagged as persistently low-performing or cited for abuse, a New York Times investigation found in May.

The nursing home industry, which Politico calls “one of the lobbying world’s quiet powerhouses,” has been arguing since early in the pandemic that long-term care companies should be granted legal immunity for their response efforts. The push began on the state level, where nursing home interest groups pressured governors to protect them from lawsuits. In an April 2 letter, the Florida Health Care Association, a trade group, asked Florida Gov. Ron DeSantis, to “extend sovereign immunity” to healthcare workers, including nursing homes. By late July, at least 28 states had enacted executive orders or laws protecting healthcare providers, sometimes including nursing homes, from liability lawsuits, according to the National Consumer Voice for Quality Long-Term Care. New York and New Jersey went further, granting providers some protection from criminal prosecution.

But those state-level successes were not enough for the nursing home industry. The American Health Care Association, which represents long-term care facilities, has spent more than $1.7 million this year lobbying the federal government on issues including coronavirus relief, according to the Center for Responsive Politics. Last month, Mark Parkinson, the organization’s president and CEO, wrote in a message to members that a federal immunity shield was a top priority for his organization, along with obtaining additional funding. (On July 22, President Donald Trump announced an additional $5 billion in nursing home funding.) “Only a reasonable federal immunity solution that will protect our operators and staff for their good faith efforts during this challenging time is what we’re asking for,” Parkinson wrote.

“Fortunately, Senate Majority Leader McConnell is strong on this issue and has said that if liability immunity is not in the next stimulus bill, he will not allow the bill to advance,” he added. “That gives us a real shot at success.”